Biology subjects

Li, H.

Publications and source records attributed to Li, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2026

Crystal structure and molecular dynamics simulations of rademikibart Fab-IL-4Rα complex reveal biochemical basis for next-generation potent IL-4Rα inhibition in type 2 allergic and inflammatory diseases

Rademikibart (CBP-201) is a human monoclonal antibody with higher binding affinity to IL-4R compared to dupilumab. Dupilumab is a first-generation interleukin-4 receptor alpha (IL-4R) inhibitor for treating IL-4R-dependent inflammatory disorders, including several dermatologic and respiratory conditions. Rademikibart, however, demonstrated better inhibition of STAT6 intracellular signaling in vitro and similar potency in inhibiting both IL-4 induced TARC release and IL-4 induced B cell activation. To further characterize the molecular function of rademikibart and its differentiation from dupilumab, we determined the crystal structure of the rademikibart fragment antigen binding (Fab) bound to IL-4R at 2.71 [A] resolution and compared this to the 2.82 [A] resolution structure of dupilumab Fab bound to IL-4R. The rotation angle between dupilumab and rademikibart bound to IL-4R is 54.88{degrees}. This rotation enables the binding epitopes of rademikibart, but not dupilumab, on IL-4R to overlap more closely with the conserved binding interface naturally utilized by IL-4 and IL-13 cytokines. Molecular dynamics (MD) studies on rademikibart and dupilumab bound to IL-4R examined the stability of the complexes and effects of amino acid mutations on receptor complex formation. MD simulations demonstrated that the third interface loop (residues 145 to 153 in domain 2) of IL-4R interacts directly with rademikibart, which is absent in the dupilumab/IL-4R complex. This finding is confirmed by increased hydrogen bond interactions at the interface between rademikibart and IL-4R, demonstrating superior binding energy for rademikibart. Through analysis of the x-ray crystallography structures, MD-equilibrated structures, and computational point-mutation analysis of rademikibart, we identified residue Y50 and R55 of the light chain and R97, R99, and Y101 of the heavy chain of rademikibart as key residues interacting with IL-4Rs third interface loop. Our data provides a molecular and structural rationale for the enhanced IL-4R inhibition by rademikibart over dupilumab, confirming rademikibart as an optimized second-generation IL-4R inhibitor.

biochemistry↗

bioRxiv2026

Fruit trichome density outweighs cuticle thickness as the dominant barrier to postharvest water loss in tomato

Fruit cuticle thickness and biochemical composition have traditionally been regarded as the primary determinants of postharvest water loss in fleshy fruits. However, several reports indicate that some tomato mutants with thinner fruit cuticles or less cutin and waxes do not always show increased transpiration, suggesting that additional surface features influence postharvest water loss. Here, we s how that fruit trichome density is a previously underappreciated determinant of postharvest water loss in tomatoes. Using two independent mutants, cr-slhdziv7 and cr-slhdziv9, which exhibit reduced fruit trichome density, we found that both mutants displayed reduced water loss rates and extended shelf life during postharvest storage despite having thinner cuticles and reduced levels of key cutin monomers. Further molecular analyses, including RNA-seq, yeast one-hybrid (Y1H), and dual-luciferase reporter assays, revealed that these two HD-ZIP IV proteins not only regulate fruit trichome formation but also directly or indirectly modulate the expression of multiple cutin biosynthesis genes. Collectively, our results demonstrate that the benefit of reducing trichome-associated microchannels can outweigh the negative effects of cuticle thinning on postharvest water loss. This study establishes fruit trichome density as an important and previously underestimated target for improving postharvest fruit quality and shelf life. HighlightO_LIFruit trichome density controls tomato postharvest water loss and dominates over cuticle thickness barrier. C_LIO_LILess trichomes reduce microchannels, lowering transpiration despite thin cuticles and extending tomato fruit shelf life. C_LI

plant biology↗

bioRxiv2026

TCMCard: A High-Confidence Digital Infrastructure for Traditional Chinese Medicine Quantified by Multi-Dimensional Evidence Integration

Network pharmacology has become a widely used approach for deciphering multi-component, multi-target mechanisms of traditional Chinese medicine (TCM). Here we introduce TCMCard, a high-confidence digital infrastructure built on a Multi-Dimensional Evidence Integration (MDEI) framework. The framework integrates experimental activity data from authoritative chemical databases, literature-derived evidence, and structure-based similarity inference. Preprocessing steps include chemical structure normalization, species-specific filtering, and target quality scoring. Applied to conventional interaction datasets, this pipeline leads to the removal of over 60% of low-confidence noise. TCMCard supports network pharmacology exploration through an interactive visualization platform, and module analysis identifies functionally relevant communities that offer insights into the synergistic actions of TCM formulas. Overall, TCMCard may help move the field beyond simple data aggregation toward evidence-informed curation and quality-driven analysis. As an interactive and publicly accessible platform, it reveals an organized backbone within complex interaction networks, offering a more reliable basis for understanding multi-component synergy in TCM.

bioinformatics↗

bioRxiv2026

A PTM Regulatory Enzyme Co expression Code Defines Microglial Functional Heterogeneity in Cerebral Ischemia Reperfusion Injury

BackgroundCerebral ischemia-reperfusion injury (CIRI) is a major determinant of poor outcome after recanalization therapy in acute ischemic stroke. Microglial functional heterogeneity underpins neuroinflammation, yet the molecular mechanisms governing microglial phenotypic transitions remain incompletely understood. Metabolite-driven post-translational modifications (PTMs) have emerged as key regulators of microglial metabolism and inflammation, but whether PTM regulatory enzymes form co-expression modules that define microglial states is unknown. MethodsWe analyzed single-cell RNA-seq datasets from five GEO studies (GSE174574, GSE227651, GSE245386, GSE267240, GSE319237) covering tMCAO reperfusion and permanent ischemia models. Microglia were purified using double filtration (P2ry12/Tmem119/Cx3cr1+, Cd68/Adgre1/Ly6c-). PTM enzyme co-expression modules were identified by non-negative matrix factorization (NMF). Spatiotemporal dynamics were assessed by module projection across timepoints (Sham, 1d, 3d, 7d) and pseudotime analysis. Independent validation was performed in an additional tMCAO dataset (GSE245386). Sex differences were explored in a mixed-sex permanent ischemia dataset (GSE267240). ResultsThree robust PTM enzyme co-expression modules were identified: Metabolic stress-associated (M1), Pro-inflammatory-associated (M2), and Reparative-associated (M3). M1 was enriched in TCA cycle enzymes, M2 in inflammatory pathways (leukocyte activation, chemotaxis), and M3 in vascular development and translation. Module proportions and scores showed dynamic transitions: M1 decreased after reperfusion, M2 peaked at day 1-3, and M3 slightly increased at day 7. Independent validation in GSE245386 yielded high module conservation (cosine similarity = 0.874). Sex-specific differences in module distribution were observed in permanent ischemia ({chi}2 = 14.98, p = 0.00056). ConclusionsPTM enzyme co-expression modules delineate metabolic, pro-inflammatory, and reparative microglial states in CIRI with distinct spatiotemporal dynamics. This transcriptional framework supports the "PTM enzyme code" hypothesis and provides stage-specific targets for stroke therapy.

neuroscience↗

bioRxiv2026

IMPAIRED BRIDGING OF TEMPORAL DISCONTINUITIES IN OLDER ADULT HIV-1 TG RATS

The advent and widespread uptake of combination antiretroviral therapy dramatically changed the epidemiological features of human immunodeficiency virus type 1 (HIV-1), whereby older individuals (>50 years of age) account for approximately 50% of HIV-1 seropositive individuals in the United States. Nevertheless, to date, there is no extant in vivo biological system to model the unique age-related neurocognitive impairments observed in HIV-1 seropositive individuals. Herein, the utility of the HIV-1 transgenic (Tg) rat as a biological system to model age-related neurocognitive impairments and neuroanatomical alterations was evaluated. Older adult HIV-1 Tg rodents (i.e., >12 months of age upon testing initiation), relative to their control counterparts, exhibited profound neurocognitive alterations characterized by impairments in stimulus-reinforcement learning, sustained attention, and selective attention; neurocognitive deficits which support a fundamental distortion of temporal processing. Neuronal dysfunction in older adult HIV-1 Tg animals was characterized by structural alterations in pyramidal neurons, and their associated dendritic spines, in the medial prefrontal cortex and abnormal accumulation of amyloid beta (A{beta}). Interestingly, the abnormal accumulation of A{beta} mechanistically underlies, at least in part, the profound dendritic spine dysmorphology in male, but not female, HIV-1 Tg rats. More critically, however, neuronal dysfunction mechanistically underlies neurocognitive impairments in both male and female HIV-1 Tg rodents, whereby neuronal dysfunction accounts for 65.4% and 60.8% of the variance in neurocognitive function, respectively. Establishing the utility of the HIV-1 Tg rat for age-related neurocognitive impairments is fundamental to disentangling the role of HIV-1 viral proteins and comorbidities in neurocognitive function.

neuroscience↗

bioRxiv2026

Precision DNA Impurity Reduction Approaches for Ultra-Pure rAAV Manufacturing

Recombinant adeno-associated virus (rAAV) vectors are a leading platform for gene delivery in basic and clinical research, yet large-scale manufacturing remains constrained by residual nucleic-acid impurities that compromise safety. In this study, we profiled the DNA species packaged within rAAV capsids and identified plasmid backbone sequences and host cell genomic DNA (hcDNA) as predominant contaminants. To mitigate this critical quality attribute, we implemented upstream strategies designed to fragment or excise backbone DNA, including TelN/TelROL excision, I-SceI meganuclease digestion, CRISPR/Cas9 cleavage, and Cre/LoxP recombination. Quantitatively, TelN/TelROL and I-SceI reduced encapsidated plasmid backbone DNA to approximately 20-30% and 20-40% of baseline levels, respectively, while CRISPR/Cas9 lowered it to about 10-20%. Notably, the Cre/LoxP system eliminated detectable plasmid backbone DNA without compromising vector-genome titers, indicating preserved genomic integrity. Additionlly, supplementating cell culture with a caspase inhibitor significantly reduced hcDNA contamination in rAAV particles to 1-5% of the baseline level. Collectively, these interventions provide practical bioprocess frameworks that markedly enhance rAAV purity via targeted DNA minimization and prevention of hcDNA fragmentation, thereby strengthening the safety profile of rAAV therapeutics in alignment with current Good Manufacturing Practice (cGMP) expectations.

molecular biology↗

bioRxiv2026

Decoupling Detection and Classification to Improve Morphological Phenotype Analysis of Sickle Red Blood Cells in Full-Scope Microscopy

Microscopy-based analysis of red blood cell (RBC) morphology is widely used to study phenotypes in sickle cell disease (SCD). Although AI models have been developed to automate classification, most are trained on pre-cropped single-cell images and thus struggle with full-scope microscopic images containing densely packed cells and diverse morphologies, which require both accurate detection and fine-grained classification. We propose an end-to-end computational framework to identify individual RBCs in full-scope microscopy images and classify them into five morphological categories: discocytes (DO), echinocytes (E), elongated and sickle-shaped cells (ES), granular cells (G), and reticulocytes (R). We first evaluate advanced detection-classification models, including You Only Look Once (YOLO) and Detection Transformers (DETR), and demonstrate that while these models effectively detect cells, their classification performance falls short of specialized classifiers trained on single-cell images, particularly for minority phenotypes. To address this limitation, we introduce a two-step framework in which a YOLO-based detector localizes and crops individual cells from full-scope images, followed by a fine-tuned DenseNet121 ensemble classifier that assigns each cell to one of the five morphological categories. The proposed framework achieves a detection-level F1-score of 0.9661 and a weighted-average classification F1-score of 0.9708, with an overall classification accuracy of 97.06%. Compared with the single-step YOLO26n baseline, the two-step pipeline yields a macro-average F1-score improvement of +0.1675, with particularly substantial gains for minority classes (E: +0.1623; G: +0.2774; R: +0.2603). Overall, this hybrid framework demonstrates a practical strategy for adapting fast, general-purpose detection models to domain-specific biomedical tasks by combining them with specialized classifiers, delivering both efficiency and high accuracy for scientific and clinical image analysis.

bioengineering↗

bioRxiv2026

Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches

Immunosenescence, the age-associated decline in immune function, is a key feature of human aging. In human lymphoid organs, however, the specific immune cell populations that acquire senescence-associated phenotypes during aging and how they influence the surrounding tissue microenvironment remain poorly understood. A spatially resolved map of these senescence-associated immune states in human lymphoid tissues could help clarify their relationship with aging and their potential contributions to the progressive decline of immune function. Here, we integrated single-cell and spatial multi-omics to systematically characterize age-related senescence in human lymph nodes (LNs). Single-cell transcriptomics of lymphoid tissues from donors aged 18 to 100 years old identified 34 immune and stromal cell types and revealed age-associated upregulation of senescence signatures in specific populations. Spatial proteomic profiling of 99 LN sections from 51 donors (18-86 years) using high-plex immunofluorescence ([~]20 million cells) mapped senescence markers (p16, p21, HMGB1, -H2AX) at single-cell resolution, revealing diverse senescent-like cell types ("senotypes") and a stepwise shift from extrafollicular to germinal center (GC) localization with age. Notably, we observed focal clonal-like senescence in GC B cells in older donor LNs. Spatial transcriptomics, epigenomics, and metabolic imaging of selected samples further elucidate the multi-omics signatures and underlying mechanisms of functional impairment, metabolic remodeling, and distinct regulatory programs in senescent-like GC B cells. This study presents a comprehensive spatial atlas of senescence-associated immune states in human lymph nodes, revealing cell-type-specific and spatial heterogeneity that may contribute to immunosenescence and the decline of immune function during aging.

immunology↗

bioRxiv2026

Alzheimers Disease Brain Phenotypes are Age-dependent

A widespread view of neurodegenerative disorders, including Alzheimers Disease (AD), frames their effects as accelerated aging, with the brain-age gap (BAG, the deviation of predicted brain age from chronological age) as a staple biomarker. However, BAG relies on a fundamental, untested assumption: that AD can be identified via age-invariant brain phenotypes. Using invariant representation learning on brain MRI from 44,178 individuals, we created neural representations that optimally convey age information (age-aware) or conversely remove it (age-invariant) while minimizing reconstruction distortion. We provide the first causal evidence that age information is necessary in brain biomarkers for AD detection: age-aware representations achieve competitive state-of-the-art performance and significantly outperform age-invariant ones (0.84 vs. 0.77 AUC, p < 0.001, with external validation). This necessity reveals a conceptual flaw in BAG: by subtracting chronological age, it discards the very information essential for accurate detection. Using conditional decoders to simulate aging trajectories, we found that healthy aging and AD operate along multiple independent anatomical dimensions (deep gray matter, frontoparietal, temporal). AD patients diverge from rather than accelerate healthy aging, showing pathological temporal shifts alongside, remarkably, relative frontoparietal preservation. Furthermore, representational similarity analysis suggests that even models pretrained on non-age tasks (e.g., sex or BMI) implicitly converge toward age-related features when optimized for AD. Given that the AD phenotype cannot be decoupled from age, our results establish a hard limit for age-independent biomarkers and favor multidimensional models that preserve aging structure over unidimensional summaries like BAG.

neuroscience↗

bioRxiv2026

Novel Engineered AAV Variants Demonstrate Superior Blood-Brain Barrier Penetration and Safety in Non-Human Primates

Systemic delivery of adeno-associated virus (AAV) for gene therapy of central nervous system (CNS) disorders is limited by inefficient blood-brain barrier (BBB) penetration and dose-limiting toxicity in peripheral organs, notably the liver and dorsal root ganglia (DRG)1-5. Here, we report the development of novel AAV variants via a proprietary capsid engineering platform (REACH). In non-human primates (NHPs), intravenous administration of lead variants resulted in transgene expression levels in the brain that were 600-2000 fold higher than AAV9 at the RNA level, concomitant with a 10-50 fold reduction in liver tropism and minimal off-target exposure in the heart and DRG. These engineered capsids achieve unprecedented, pan-CNS transduction with a markedly improved safety profile, representing a transformative platform for treating a broad spectrum of neurological diseases.

neuroscience↗

bioRxiv2026

Integrated single-cell and bulk transcriptomic analysis leverages liver metastasis-related genes to develop a prognostic model for colorectal cancer patients

PurposeDifferentially expressed genes (DEGs) between colorectal cancer liver metastasis (CRLM) epithelium and primary colorectal cancer (CRC) epithelium (LMR DEGs) identified based on single-cell RNA sequencing (scRNA-seq) data may become new biomarkers for CRC prognosis. MethodsAn scRNA-seq dataset was used to describe the cellular landscape of primary CRC and CRLM and identify LMR DEGs. Prognostic LMR DEGs were identified in the bulk RNA-seq dataset. Based on the prognostic LMR DEGs, multiple machine learning algorithm combinations were compared in terms of their C-index, and the best model was selected for the construction of the LMR score. ResultsAmong the 2070 LMR DEGs, 426 prognostic LMR DEGs were ultimately obtained. The combination of the randomized survival forest (RSF) model and ridge regression had the highest C-index and was therefore used to construct a 15-gene scoring system (LMR score). In the external validation set, the 1- and 5-year AUCs of the LMR score were greater than those of the AJCC stage and other scoring systems constructed with a similar dataset. In addition, the LMR score was closely associated with factors that influence CRC outcomes, such as immune infiltration. ConclusionThe LMR score may be a reliable new biomarker for predicting the prognosis of patients with CRC.

cancer biology↗

bioRxiv2026

Homozygosity for rare or common hypomorphic IL23R variants confers a predisposition to tuberculosis in humans

Homozygosity for rare loss-of-function IL23R variants abolishes IL-23-dependent IFN-{gamma} production by lymphocytes, including NK and innate-like T cells, thereby underlying clinical disease due to weakly virulent mycobacterial species. We report selective enrichment in homozygosity for four hypomorphic IL23R variants in our cohort of patients with tuberculosis. Three of these IL23R alleles are rare (G300V, G149R, and L372F), with a minor allele frequency (MAF) under 1%, but the fourth (R381Q) is surprisingly common, with an MAF as high as 10.2% in certain populations. The other 15 missense alleles found in the homozygous state in public databases are isomorphic. The four hypomorphic IL-23R variants identified dimerize with IL-12R{beta}1 and bind IL-23. However, their function is impaired by low levels of cell surface expression (R381Q, G300V) and/or as a consequence of conformational changes altering agonist efficacy. IFN-{gamma} production in response to IL-23 is impaired in innate-like T cells and NK cells. These data suggest that recessive partial IL-23R deficiency, whether due to rare or common variants, confers a predisposition to tuberculosis while preserving immunity to less virulent mycobacteria. One sentence summaryHomozygous hypomorphic IL23R variants impair IL-23-dependent IFN-{gamma} production and underlie tuberculosis.

genetics↗

bioRxiv2026

A cerebellar cognitive rheostat bidirectionally controls attention

Attention requires filtering distractors and amplifying signals, processes classically attributed to cortico-thalamic networks. Here, we reveal that the cerebellum operates as a bidirectional "cognitive rheostat" to optimize attentional states. In mice, the anterior and posterior cerebellar vermis exert opposing control over attention. Granule cells in the anterior vermis are functionally suppressed to gate sensorimotor noise via reticular nucleus-driven feedforward inhibition. Conversely, posterior granule cells are recruited by pontine inputs to amplify cognitive signals, a process relying on Grin1-mediated NMDA receptor plasticity. Circuit-specific manipulations targeting this push-pull mechanism, or localized pharmacological modulation, successfully rescued attentional deficits in an ADHD mouse model. These findings fundamentally expand the cerebellums role beyond motor coordination, identifying a topographic circuit algorithm essential for cognitive control.

animal behavior and cognition↗

bioRxiv2026

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads

Long-read sequencing is a powerful technique capturing multiple variants within single continuous reads. This length allows individual reads to bridge small and structural variants while carrying crucial phasing information. However, current computational tools treat small variant calling, structural variant (SV) detection and phasing as largely disconnected problems, failing to unleash the full potential of long reads. Here, we present longcallD, a unified framework utilizing local multiple-sequence alignment to simultaneously call and phase small and structural variants. By integrating germline phasing and retrotransposition hallmarks, longcallD also identifies low-fraction mosaic variants and detects mobile element insertions supported by a single read. Compared to existing methods, our unified approach substantially improves SV discovery and mosaic variants accuracy while maintaining competitive small variant calling. We anticipate that longcallD will provide a robust foundation for resolving complex genetic architectures in clinical and evolutionary applications.

genomics↗

bioRxiv2026

The enhanced multi-tissue atlas of regulatory effects in cattle

Cattle are integral to global food security, yet the molecular architecture of their complex traits remains poorly understood. Here, we present the Cattle Genotype-Tissue Expression (CattleGTEx) Phase 1 resource (https://cattlegtex.farmgtex.org/), a substantial expansion of the pilot study. By leveraging 12,422 RNA-seq profiles across 43 tissues and 82 breeds, we characterized 433,972 primary and 161,428 non-primary regulatory effects spanning seven molecular phenotypes. This high-resolution atlas resolves 75% of GWAS signals for 44 complex traits, significantly addressing the "missing regulation" in livestock. We propose a genetic regulatory model demonstrating how variants across multiple biological layers interact with specific biological contexts to shape phenotypic variation. Furthermore, CattleGTEx elucidates mechanisms underlying adaptive evolution between Bos taurus and Bos indicus, as well as artificial selection in dairy and beef breeds. Finally, by mapping evolutionary constraints on these regulatory effects, we demonstrate the translational value of this resource for prioritizing causal variants in human complex diseases. Together, Phase 1 of CattleGTEx provides a transformative framework for functional genomics, precision breeding, and comparative genetics.

genetics↗

bioRxiv2026

LRP6-Guided Engineering of AAV9 Variants with Enhanced Blood-Brain Barrier Penetration and Reduced Liver Tropism in Non-Human Primates

The blood-brain barrier (BBB) severely restricts the delivery of systemically administered adeno-associated virus (AAV) vectors for central nervous system (CNS) gene therapy. To overcome this limitation, we engineered a library of AAV9 capsid variants through rational design focused on the low-density lipoprotein receptor-related protein 6 (LRP6), a conserved mediator of transcytosis. A multi-tiered screening strategy, encompassing human BBB endothelial cells followed by neuronal and glial target cells in vitro, identified three lead variants (QL9-21, QL9-22, and QL9-25) with markedly enhanced transduction potential. In mice, these variants achieved a 5-28 fold increase in brain-wide gene delivery compared to AAV9, without elevating hepatic tropism. Crucially, evaluation in non-human primates (NHPs) revealed that the lead variant, QL9-21, mediated a striking 3-40 fold enhancement in viral genome delivery across all examined brain regions versus AAV9, while concurrently reducing liver accumulation by 2.6 fold. Our study establishes an LRP6-guided engineering platform that yields novel AAV9 vectors capable of efficient, species-conserved BBB penetration coupled with a favorable safety profile, representing a significant advance toward clinically translatable CNS gene therapies.

neuroscience↗

bioRxiv2026

Unbiased Single-Cell Transcriptome-Proteome Co-Profiling Reveals Malignant Dormancy and Post-Transcriptional Buffering of CTCs

Leptomeningeal metastasis is driven by rare cerebrospinal fluid circulating tumor cells (CSF-CTCs). However, the mechanisms underlying their adaptation to chemotherapeutic stress remain elusive, primarily because transcriptomics alone poorly predicts functional protein states. Here, we present scMAPS, a single-cell multi-omics method that employs magnetic-assisted partitioning cell lysates to enable unbiased transcriptome-proteome co-profiling without loss-prone physical splitting and precision device. By coupling scMAPS with our custom CLEAP (CTC Label-free Enrichment and Accurate Picking) system, we performed the first deep multi-omics profiling of rare clinical CSF-CTCs before and after localized chemotherapy, detecting an average of 2,547 proteins and 7,821 genes per cell. The integrated CLEAP-scMAPS pipeline reveals a coordinated prioritizing survival over proliferation malignant dormancy phenotype and identified post-transcriptional buffering as the primary driver of treatment resistance. Our platform enables the comprehensive molecular phenotyping of rare clinical specimens, providing a highly versatile framework for decoding complex post-transcriptional regulatory networks.

cell biology↗

bioRxiv2026

Quinone reductase 2 reads H3 serotonylation to support neuronal maturation

Histone H3 Gln5 serotonylation (H3Q5ser) is a recently described posttranslational modification1 that plays important roles in guiding transcriptional permissiveness in brain and peripheral systems2-5. H3Q5ser has been implicated in diverse physiological and pathological processes ranging from neural differentiation1 to sensory processing6, circadian rhythmicity7, stress responsivity8, placental gene regulation9, and tumorigenesis10-19. Since H3Q5ser can occur in combination with H3 Lys4 trimethylation (H3K4me3), most mechanistic studies to date have focused on H3Q5sers roles in modulating H3K4me3 reader interactions, where it has been shown to potentiate TAF3/TFIID binding to H3K4me31,20,21 and inhibit the recruitment of K4me3 demethylases21; however, whether H3 serotonylation functions as an autonomous chromatin signaling mark through dedicated reader proteins has remained unknown. Here, using a combination of proteomic-, structural-, molecular-, epigenomic-, and cellular-based approaches, we demonstrate that the Quinone reductase 2 (QR2) enzyme reads H3Q5ser independently of H3K4me3. CRISPR-Cas9-mediated disruption of H3 serotonylation or QR2s binding to the mark in human induced pluripotent stem cell-derived neurons impairs the establishment of neuronal transcriptional programs, alters synaptic connectivity, and disrupts electrophysiological maturation. These findings thus uncover an H3 serotonylation-dependent chromatin signaling axis that is essential for human neurodevelopment.

molecular biology↗