Biology subjects

Leon, J.

Publications and source records attributed to Leon, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Stealth CAR-Tregs evade CD3 antibody therapy and skew immune responses toward regulation

Organ transplantation standard of care relies on lifelong immunosuppression, increasing infection and malignancy risks. An emerging approach using Chimeric Antigen Receptor Regulatory T cells (CAR-Tregs) targeting donor antigens, allows the suppression of alloimmune responses while preserving protective immunity. However, transplant recipients harbor a substantial pool of alloreactive memory T-cells, limiting CAR-Tregs tolerance-promoting effect. To address this challenge, our strategy combines selective depletion of activated T-cells, using non-mitogenic CD3 antibody therapy, with HLA-A2-targeted-CAR-Treg therapy. We established that T-cell receptor alpha chain (TRAC) deletion does not impair CAR-Treg antigen-specific activation, expansion, or their transcriptomic, phenotypic, epigenetic, and functional profiles. TRAC-/-CAR-Tregs exhibit robust protection from CD3 antibody depletion in circulation and peripheral tissues, whereas most TRAC+/+CAR-T cells are eliminated. Importantly, TRAC+/+CAR-T cells that escape CD3 antibody mediated depletion exhibit a transcriptomic signature consistent with T-cell exhaustion. Our findings demonstrate that CD3 antibody therapy provides an in vivo survival advantage to TRAC-/-CAR-Tregs, thereby shifting the immune balance toward regulation. This approach might enhance the translational potential of CAR-Treg therapy by reducing the required cell dose needed for clinical efficacy.

immunology↗

bioRxiv2026

Integrated genomic analyses reveal hierarchical organisation of quantitative resistance to biologically distinct soil-borne pathogens in wheat

Quantitative disease resistance is essential for durable crop protection, yet how numerous small-effect loci are organised across genomic and functional scales remains poorly understood. We investigated resistance to four distinct soil-borne pathogens in bread wheat (Triticum aestivum) by integrating genome-wide association mapping, linkage disequilibrium (LD)-defined hotspot analysis, comparative genomics, epistatic network analysis, haplotype analysis, functional annotation, transcriptomics and experimental evaluation. Resistance was highly polygenic and pathogen- and environment-dependent, with associated loci distributed across all three wheat subgenomes. Approximately two-thirds of hotspot components were shared among pathosystems, although evidence for excess sharing varied among comparisons and null models. Epistatic hubs were enriched within shared components, while interaction networks were dominated by interchromosomal and cross-subgenome interactions. Haplotype effects depended on local genomic context. Despite limited sharing of individual genes, convergence increased at the putative gene-family and broader defence-related functional levels. These findings support a hierarchical model in which pathogen- and environment-dependent resistance architectures are organised through partially shared genomic regions, local haplotypes and genetic interaction networks, with increasing convergence at broader functional levels. Limited transferability of individual marker associations in the independent panel further highlights the potential of multilocus breeding strategies that integrate favourable haplotypes, recurrent genomic regions, and diverse resistance mechanisms.

plant biology↗

bioRxiv2026

Developmental prefrontal myelination shapes inhibitory interneuron function and adult social behavior

Early-life adversity and abnormal myelination are implicated in psychiatric disorders, but how developmental myelination influences adult social cognition remains unclear. Here, we tested whether disrupting developmental myelination in the medial prefrontal cortex (mPFC) impairs adult social behavior. Using complementary genetic strategies in male mice, we suppressed Myelin Regulatory Factor (Myrf)-dependent myelination locally in the juvenile mPFC or broadly in oligodendrocyte-lineage cells. Both approaches selectively impaired adult social novelty preference while sparing sociability, locomotion, and affective behaviors. Focal prefrontal dysmyelination also reduced social dominance. Spatial transcriptomics revealed coupling between myelin-related genes and parvalbumin (PV) interneuron markers in the healthy mPFC, which was disrupted by developmental hypomyelination. Consistent with this transcriptional alteration, PV interneurons showed reduced high-frequency firing despite preserved intrinsic excitability. In the human prefrontal cortex, MBP-PV expression was correlated in controls but not in individuals with schizophrenia. These findings indicate that developmental prefrontal myelination contributes to PV interneuron maturation and suggest that disrupted oligodendrocyte-interneuron coordination may contribute to impaired social recognition.

neuroscience↗

bioRxiv2026

DAP12-deficient microglia adopt a TREM2-independent antigen-presenting state with a glial-to-neuronal cascade in Nasu-Hakola disease

Nasu-Hakola disease (NHD), a dementia with about 200 cases worldwide, is caused by loss-of-function mutation of TYROBP, encoding DAP12, or its receptor TREM2. TREM2-DAP12 is the switch that converts microglia from a surveillant to a reactive state; what DAP12-deficient microglia become and to what extent they reshape their microenvironment is unknown. We profiled prefrontal cortex and hippocampus from an NHD donor and control by single-nucleus RNA sequencing and mapped the glial changes in situ by spatial transcriptomics. NHD microglia adopted a CIITA-driven, MHC class II-high antigen-presenting state with complement, iron and glycolytic programs and Fc receptors but not the TREM2-dependent lipid program. Astrocytes became pan-reactive and lost metallothionein expression, oligodendrocytes lost mature cells and cholesterol synthesis, and excitatory neurons lost presynaptic and activity programs, consistently between regions and across a published cohort. DAP12 deficiency left microglia in an antigen-presenting state short of the TREM2-dependent arm, accompanied by a glial-to-neuronal cascade.

neuroscience↗

bioRxiv2026

Long-term voluntary exercise reveals limited translation of hippocampal molecular responses into neuroprotection in 5xFAD mice

Physical exercise promotes systemic and neural adaptations that support healthy brain aging and may mitigate Alzheimers disease (AD) progression. However, the capacity of the AD-afflicted brain to mount and translate exercise-responsive molecular adaptations into neuroprotection remains unclear. Here, we examined the effects of long-term voluntary wheel running (VWR) on molecular, neuropathological, and behavioral outcomes in independently studied male and female 5xFAD mice. VWR elicited expected metabolic and transcriptional remodeling of inguinal white adipose tissue, confirming engagement of exercise-responsive peripheral biology. In contrast, hippocampal transcriptional responses were modest, with few differentially expressed genes and coordinated changes emerging primarily at the pathway level. These responses involved synaptic, neuroimmune, mitochondrial, neurotrophic, and monoaminergic processes and differed qualitatively between the two groups. Several components of the canonical hippocampal exercise response also failed to converge into coordinated cellular adaptations: synaptic protein abundance changed without altering synapse density, while neurotrophic, neurogenic, and vascular responses showed little correspondence across molecular and cellular measures. VWR also produced little change in hippocampal amyloid pathology or behavioral function despite sustained exercise engagement. Together, these findings demonstrate that the 5xFAD brain retains modest molecular responsiveness to prolonged voluntary exercise but may be unable to mount a sufficiently robust or coordinated response to produce broad neuroprotective effects. These findings highlight disease context as an important determinant of the efficacy of exercise-based interventions in neurodegenerative disease.

neuroscience↗

bioRxiv2026

Genome-wide association analysis reveals new loci for leaf water status, biomass and plant architectural traits in bread wheat under rainfed conditions

Drought during reproductive development and grain filling is a major constraint to bread wheat productivity in rainfed environments. In the present study, we employed genome-wide association analysis in an untapped diversity panel of wheat genotypes relevant to natural dryland conditions. A total of 186 genotypes were evaluated for drought-related physiological, biomass, and architectural traits under terminal rainfed stress in Azerbaijan. Relative water content, plant height, fresh weight, dry weight, flag leaf length, and flag leaf width were assessed at the milk ripening stage. These data were subjected to genome-wide association analysis using 19,737 SNP markers to identify loci and epistatic interactions involved in the determination of these traits. The panel showed broad phenotypic variation and significant genotypic effects for all traits, with broad-sense heritability ranging from 0.991 for plant height to 0.385 for flag leaf width. GWAS identified a major locus for relative water content on chromosome 2D at SNP marker AX-86184518, which explained 11.94% of the genotypic variation. Candidate-gene analysis highlighted the proximal WEB-family-like gene TraesCS2D03G1001000 as the main candidate gene. Plant height showed strong additive loci, mainly on chromosomes 2A and 4A, whereas biomass and flag leaf traits showed suggestive additive loci and epistatic interactions. These findings provide candidate loci and interaction patterns in the genetic make-up of essential traits, which may facilitate indirect selection in breeding new varieties.

genetics↗

bioRxiv2026

Enriched-GF: A Reproducible High-Yield Autologous Blood-Derived Growth Factor Method for Regenerative Medicine

BackgroundPlatelet-derived Growth factors play key roles in tissue repair and regeneration, yet conventional platelet-rich plasma (PRP) formulations release these mediators inconsistently in vivo due to variability in platelet yield and activation dynamics. To overcome this limitation, direct administration of concentrated platelet-derived growth factor preparations has gained interest, though current manufacturing approaches for human platelet lysate (hPL), growth factor concentrates (GFC), and conditioned serum remain constrained by batch variability, incomplete platelet degranulation, and reliance on anticoagulants. Here, we examine alternative platelet activation workflows to establish a standardized, efficient, and reproducible method for high-yield growth factor recovery suitable for translational and clinical applications. MethodsNine GFC production protocols were compared, employing different combinations of freeze-thaw (FT) cycling, glass bead (GB) agitation, calcium (Ca2) activation, and a novel Enriched Growth Factor (Enriched-GF) method. The objective was to identify a protocol capable of maximizing growth factor yield within a three-hour workflow. Optimal Ca2 concentrations and GB conditions were determined from prior optimization studies and integrated into the Enriched-GF processing scheme. Platelet concentrates (n = 10 per protocol) were processed under each condition, and growth factor levels were quantified using ELISA. ResultsGrowth factor yields differed significantly across protocols. The greatest and most consistent increases in growth factor release were observed with the Enriched-GF method combining GB activation, FT cycling, and Ca2 stimulation. This approach resulted in markedly elevated concentrations of key regenerative mediators, including enhanced EGF release, a 4.5-fold increase in PDGF, maximal TGF-{beta} liberation, and a four-fold increase in FGF2 relative to conventional platelet lysate or conditioned serum preparations. These results were reproducible across independent donor pools, demonstrating robustness and batch-to-batch consistency. ConclusionWe describe a rapid and reproducible method for producing highly concentrated platelet-derived growth factors using a combined GB-FT-Ca2 activation strategy. The Enriched-GF protocol consistently outperformed existing platelet lysate, conditioned serum, and conventional GFC preparation methods, yielding a standardized product with enhanced growth factor content. This Enriched-GF approach offers a clinically practicable solution for applications in regenerative medicine requiring reliable and high-yield growth factor delivery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/712883v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@ac60c3org.highwire.dtl.DTLVardef@104d8eborg.highwire.dtl.DTLVardef@13d5afcorg.highwire.dtl.DTLVardef@120645c_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic overview of platelet concentrate preparation from whole blood and the generation of different platelet lysates and growth factor-enriched serum using freeze-thaw, calcium gluconate, and glass bead activation methods.

biochemistry↗

bioRxiv2026

Single-nuclei RNA-sequencing uncovers sexually divergent exercise signatures partially mimicked by TFEB overexpression in mouse skeletal muscle

Exercise induces extensive, cell-type-specific transcriptional remodeling in skeletal muscle to support metabolic flexibility and adaptation. However, the regulatory mechanisms underlying these transcriptional programs, and the extent to which they differ between sexes, remain poorly defined. We previously reported that lifelong, muscle-specific overexpression of human Transcription Factor E-B (cTFEB;HSACre transgenic mice) recapitulates many adaptive features of endurance training in both sexes, leading to profound geroprotective effects during aging even in the absence of exercise. Here, we profile transcriptional adaptations to voluntary wheel running (VWR) and TFEB-overexpression at single-nucleus resolution in young male and female mouse tibialis anterior muscle. This represents, to our knowledge, the first integrated analysis of exercise and TFEB signaling using sex as a biological variable. Using robust bioinformatic and single-nuclei RNA-sequencing approaches, we profiled six muscle-resident cell populations and uncover previously unrecognized, sex-dependent signaling nodes governing exercise-associated metabolic plasticity. TFEB activation and endurance training by VWR elicit strongly correlated transcriptional programs enriched for lipid metabolism, mitochondrial remodeling, and immune modulation, establishing TFEB-overexpression as a partial exercise mimetic. In general, female muscle exhibited enhanced extracellular matrix and lipid-associated responses to endurance training and TFEB overexpression, whereas males preferentially engaged in angiogenic and oxidative networks, revealing distinct sex-specific, sex-dimorphic, or sex-agnostic regulatory routes to metabolic flexibility. Integration with independent multi-omics datasets from endurance-trained rats (MoTrPAC) confirms the conservation of TFEB-exercise transcriptional convergence in skeletal muscle across species and potentially muscle types. Together, these findings define TFEB as a regulator of exercise transcriptional programs and reveal sex-specific molecular frameworks that drive metabolic adaptation in skeletal muscle. Furthermore, the resulting sex-resolved, single-nucleus transcriptional atlas provides a unique resource for the field, enabling comparative, mechanistic, and hypothesis-driven exploration of exercise-responsive skeletal muscle regulatory networks across sexes.

physiology↗

bioRxiv2026

Spatially resolved transcriptome-metabolome integration reveals region-specific glial lipid dysregulation associated with Alzheimer's pathology

Glial cells maintain the brains lipid and energy balance, and their breakdown is increasingly recognized as a causal contributor to Alzheimers disease (AD). While this concept is established, no approach has directly shown how glial homeostatic failure manifests across brain regions and microenvironments or how it links local pathology, such as plaques, to global metabolic imbalance. To address this gap, we developed iMIST, an integrated platform that combines MALDI-based metabolite imaging, histology, and spatial transcriptomics within a single tissue section to align molecular and anatomical information. Using a mouse model of late-onset AD that recapitulates both amyloid deposition and metabolic vulnerability, iMIST revealed that glial lipid dysregulation is widespread but spatially specialized. In gray matter, plaque-associated microglia were associated with upregulated glycerophospholipid-remodeling in cortico-thalamic areas indicating metabolic stress around local pathology. In contrast, white matter tracts rich in lipid-producing oligodendrocytes show plaque-independent deficits in galactosylceramide metabolism reflecting their high myelin demand. Both processes intensify with age, transforming adaptive glial responses into persistent metabolic dysfunction. Together, these findings demonstrate the spatial interplay between global glial metabolic imbalance and local microenvironmental stressors associated with AD pathology. By integrating transcriptomic and metabolomic information in situ, iMIST provides a framework for uncovering how regional glial vulnerability shapes the pathogenesis of neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Wheat diversity reveals new genomic loci and candidate genes for vegetation indices using genome-wide association analysis

Wheat (Triticum aestivum L.), a globally essential crop, exhibits high vulnerability to drought stress, particularly within rainfed agricultural systems. Enhancing resilience requires a deeper understanding of the genetic architecture underlying key physiological traits. Spectral vegetation indices provide a high-throughput, non-invasive approach to quantify these traits, but their genetic basis in wheat under drought remains largely unexplored. We conducted a genome-wide association study (GWAS) using 187 bread wheat genotypes evolved and selected across rainfed conditions. This population was phenotyped for 25 vegetation indices and genotyped using a 25K SNP array. Phenotypic data showed significant genetic variation with broad-sense heritability (H{superscript 2}) ranging from 0.19 to 0.95. Comparing phenotype and genotype data identified 812 Bonferroni-significant associations distributed across the A, B and D genomes. A prominent major QTL effect was identified as a hotspot on chromosome 2A, tagged by SNP marker wsnp_Ex_c36049_44083089, was among the strongest associations for 17 vegetation indices, explaining up to 20% of the genotypic variance for key traits like greenness and pigment indices. Candidate gene analysis at this locus identified the co-localization of a LEA_2/NDR1-like gene and a lectin receptor-like kinase with multiple genes involved in terpenoid, phenylpropanoid and primary metabolism, consistent with integrated roles in stress signaling and metabolic acclimation. These data show that vegetation indices are heritable digital phenotypes, which can be employed for the selection and genetic analysis of essential physiological growth parameters under varying and adverse climatic conditions.

plant biology↗

bioRxiv2026

HvbZIP33 and HvbZIP76 have overlapping roles in foliar transpiration in drought-stressed barley

Basic leucine zippers (bZIP) constitute one of the biggest protein families and evolutionarily conserved transcription factors (TFs) in plants. We obtained mutant lines for two bZIP TFs, HvbZIP33 and HvbZIP76, in the genetic background of the barley cultivar Golden Promise (GP) via targeted gene-specific mutagenesis using an RNA-guided Cas9 endonuclease. A comprehensive morphological, physiological and transcriptomic analysis was performed in wild-type GP compared with hvbzip33 and hvbzip76 mutants under drought stress. The morphological and physiological changes were similar in both mutants and in the wild-type GP. Most strikingly, the mutants exhibited accelerated wilting and increased water loss. This effect was primarily caused by higher stomatal conductance (gs) and transpiration rate (E) in mutants compared to wild-type GP under both control and drought conditions, which in turn had a detrimental effect on the mutants intrinsic water use efficiency (iWUE). Likewise, the transcriptome profiles of hvbzip33 and hvbzip76 were more similar to each other than those of wild-type GP. We found that the number of differentially regulated genes under control versus drought-stress conditions was higher in the mutants than in wild-type GP, suggesting that the mutants try to compensate for accelerated foliar water loss. The study highlights the essential roles of HvbZIP33 and HvbZIP76 in balancing water loss in barley. These findings provide a foundation for engineering enhanced drought tolerance in barley through targeted manipulation of these genes to optimize transpiration rates.

genetics↗

bioRxiv2025

Toward passive acoustic occupancy surveys of rare red uakari monkeys (Cacajao ucayalii): using automatic signal recognition and cluster analysis to organize signals?

We tested a workflow using a cluster analysis to develop a classifier to detect red uakari monkey calls using clustering and Hidden Markov Models, and Kaleidoscope viewer to review and discount false positives. We used recordings collected in a series of behavioral studies on a habituated group of red uakari monkeys on the Yavari-Miri River in the Peruvian Amazon as training data to develop the classifier and tested it on a passive acoustic survey at the same site where uakari distributions were known to us. We estimated detection probabilities for red uakaris and used an occupancy model to estimate habitat use to compare with use determined by behavioral research. We assessed a workflow for processing passive acoustic primate surveys that would eliminate false positives and demand minimal time and coding expertise from those implementing the analyses and reviewing audio recordings. These are key considerations in the design of landscape-scale PAM surveys for rare species.

ecology↗

bioRxiv2024

Integrative Transcriptomics Reveals Layer 1 Astrocytes Altered in Schizophrenia

Schizophrenia is one of the most prevalent psychiatric disorders with unclear pathophysiology despite a century-long history of intense research. Schizophrenia affects multiple networks across different brain regions. The anterior cingulate cortex (ACC) is the region that connects the limbic system to cognitive areas such as the prefrontal cortex and represents a pivotal region for the etiology of schizophrenia; however, the molecular pathology, considering its cellular and anatomical complexity, is not well understood. Here, we performed an integrative analysis of spatial and single-nucleus transcriptomics of the postmortem ACC of people with schizophrenia, together with a thorough histological analysis. The data revealed major transcriptomics signatures altered in schizophrenia, pointing at the dysregulation of glial cells, primarily in astrocytes. We further discovered a decrease in the cellular density and abundance of processes of interlaminar astrocytes, a subpopulation of astrocytes specific to primates that localize in the layer 1 and influence the superficial cortical microenvironment across layer 1 and layers 2/3 of the cortex. Our study suggests that aberrant changes in interlaminar astrocytes could explain the cell-to-cell circuit alterations found in schizophrenia and represent novel therapeutic targets to ameliorate schizophrenia-associated dysfunction.

neuroscience↗

bioRxiv2024

Activation of the muscle-to-brain axis ameliorates neurocognitive deficits in an Alzheimer disease mouse model via enhancing neurotrophic and synaptic signaling

INTRODUCTIONSkeletal muscle regulates central nervous system (CNS) function and health, activating the muscle-to-brain axis through the secretion of skeletal muscle originating factors ( myokines) with neuroprotective properties. However, the precise mechanisms underlying these benefits in the context of Alzheimers disease (AD) remain poorly understood. METHODSTo investigate muscle-to-brain axis signaling in response to amyloid {beta} (A{beta})- induced toxicity, we generated 5xFAD transgenic female mice with enhanced skeletal muscle function (5xFAD;cTFEB;HSACre) at prodromal (4-months old) and late (8-months old) symptomatic stages. RESULTSSkeletal muscle TFEB overexpression reduced A{beta} plaque accumulation in the cortex and hippocampus at both ages and rescued behavioral neurocognitive deficits in 8- months-old 5xFAD mice. These changes were associated with transcriptional and protein remodeling of neurotrophic signaling and synaptic integrity, partially due to the CNS-targeting myokine prosaposin (PSAP). DISCUSSIONOur findings implicate the muscle-to-brain axis as a novel neuroprotective pathway against amyloid pathogenesis in AD.

neuroscience↗

bioRxiv2024

Same data, different results? Evaluating machine learning approaches for individual identification in animal vocalisations

Automated acoustic analysis is increasingly used in behavioural ecology, and determining caller identity is a key element for many investigations. However, variability in feature extraction and classification methods limits the comparability of results across species and studies, constraining conclusions we can draw about the ecology and evolution of the groups under study. We investigated the impact of using different feature extraction (spectro-temporal measurements, linear and Mel-frequency cepstral coefficients, as well as highly comparative time-series analysis) and classification methods (discriminant function analysis, neural networks, random forests, and support vector machines) on the consistency of caller identity classification accuracy across 16 mammalian datasets. We found that Mel-frequency cepstral coefficients and random forests yield consistently reliable results across datasets, facilitating a standardised approach across species that generates directly comparable data. These findings remained consistent across vocalisation sample sizes and number of individuals considered. We offer guidelines for processing and analysing mammalian vocalisations, fostering greater comparability, and advancing our understanding of the evolutionary significance of acoustic communication in diverse mammalian species.

animal behavior and cognition↗

bioRxiv2024

Expression interplay of calcium-binding genes and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca2+ signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding genes was found to be specific for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of EF-hand genes, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding genes, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3-UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability. Key messageThe fine-tuned expression of calcium-binding genes and transcription factors during the osmotic phase underlies the susceptibility and tolerance to salt stress responses of contrasting bread wheat genotypes.

molecular biology↗

bioRxiv2023

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.

genomics↗

bioRxiv2023

An interwoven network of transcription factors, with divergent influences from FoxP3, underlies Treg diversity

FoxP3+CD4+ regulatory T cells (Tregs), essential for immunologic and organismal homeostasis, have diverse functions and corresponding gene expression programs. How the many controlling transcription factors (TFs) organize to determine Treg identity and diversity remains unclear. We combined single-cell chromatin accessibility profiling, machine learning, and high-density natural genetic variation, validated with TF knockout, CRISPR-editing, and binding data, to define the Treg regulatory network. Distal enhancers proved driven by imbricated multi-TF inputs, employing strategies different from promoter regions. Topic modelling resolved a framework of chromatin programs shaped by distinct TF motifs. This framework anchored surprisingly heterogenous responses to IL2. It identified an unrecognized role for the Smarcc1 remodeler. FoxP3 impacted only some segments of this framework, either activating or repressing programs, amplifying a core Treg identity defined independently. Its absence in Treg-like cells unleashed cytokine expression, but not Th de-differentiation. This work provides a unifying scaffold to understand and manipulate Treg states.

immunology↗