Biology subjects

Cheng, S.

Publications and source records attributed to Cheng, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Vascular specification from diversified mesoderm culminates in endothelial convergence

Vasculogenesis establishes the embryonic circulatory system, yet how a common vascular program emerges across multiple embryonic and extraembryonic developmental environments remains incompletely understood. Here, we reconstruct mouse vasculogenesis through integrated single-cell, spatial, lineage and perturbation analyses. We find that vascular specification emerges from distinct sources of pre-specified mesoderm through a transient Kdr+Etv2- vascular-primed state promoted by BMP signaling. Primed cells persist until E8.0- E8.5, after which they resolve into committed derivatives. Dual blood-endothelial potential is largely restricted to early vitelline progenitors, whereas embryonic and umbilical progenitors contribute predominantly to endothelial lineages. Temporal VEGF signaling perturbations validate the inferred specification sequence, placing VEGF downstream of vascular priming and demonstrating its indispensable role in vascular and primitive blood specification. Unlike most developmental lineages, endothelial derivatives converge toward a common transcriptional state while retaining transcriptional traces of their developmental origins. Together, these findings establish a mechanistically validated developmental sequence for mammalian vasculogenesis.

developmental biology↗

bioRxiv2026

Robust and accessible in situ sequencing with an open-source automated sequencer

Targeted in situ sequencing underlies many spatial transcriptomic, barcoded connectomic, and multiplexed perturbation techniques. Each experiment requires many cycles of chemical reactions and imaging that are time-consuming and error-prone to perform manually, and few commercial platforms can sequence highly diverse RNA barcodes in situ at cellular resolution across large tissue sections. Here we present Seq-o-Matic, an open-source automated in situ sequencer built entirely from commercially available components, which integrates fluidics, heated incubation, and imaging of up to three continuous 18 mm x 50 mm areas on standard microscope slides. Relative to manual sequencing, Seq-o-Matic reduced hands-on time 6- to 17.5-fold and total run time about 2.6-fold. Across three runs spanning two mouse strains and a neonatal marmoset, sequencing quality, measured by signal retention, channel specificity, and phasing, was similar to that of four manually sequenced mouse brains. In four mouse hemispheres sequenced in separate runs (two C57BL/6J, one NOD, and one WSB), consensus cell types were present in every brain and corresponded to those of a manually sequenced C57BL/6J brain. Within cortical excitatory neurons, the two C57BL/6J brains were more similar to each other than were brains of different strains, suggesting that technical variation between runs was small relative to strain differences. Seq-o-Matic thus makes consistent, high-throughput in situ sequencing accessible to laboratories without specialized in situ sequencing expertise.

genomics↗

bioRxiv2026

PDGFRα-directed fibroblast-homing peptides for targeted delivery of nucleic acid therapeutics

Efficient and cell type-specific delivery remains a major barrier to the clinical translation of nucleic acid therapeutics (NATs), particularly for fibroblast-driven diseases in which target cells are poorly accessible in vivo. By integrating single-cell transcriptomics with cell-surface protein profiling, we identified platelet-derived growth factor receptor alpha (PDGFR) as a fibroblast-enriched surface receptor. A panel of PDGFA-derived short peptides was designed and screened across multiple human and mouse cell types, leading to the identification of two fibroblast-homing peptides, Pep3 and Pep5, which displayed rapid and preferential uptake in fibroblasts. PDGFR; knockdown reduced peptide internalisation as measured by live-cell imaging, confirming receptor-mediated uptake. To evaluate their potential as delivery vehicles for NATs, a fibroblast-based cellular model of collagen VI-related congenital muscular dystrophy (COL6-CMD) was used for further validation. Lead peptides were conjugated to a splice-switching phosphorodiamidate morpholino oligomer (PMO) targeting the recurrent COL6A1 c.930+189C>T variant. Peptide-PMO conjugates retained exon-skipping activity and Pep3-PMO enhanced collagen VI protein deposition in patient-derived fibroblasts following repeated treatment compared to unconjugated PMO. Transcriptomic profiling demonstrated no activation of inflammatory, oncogenic, or PDGFR; receptor-associated signalling pathways following peptide-PMO treatment. Collectively, these findings establish PDGFR-targeting fibroblast-peptides as a promising platform for selective delivery of NATs to fibroblasts.

molecular biology↗

bioRxiv2026

A Taxonomy-Informed Sparse DNA Foundation Model for Microbial Genomics

Microorganisms are indispensable to terrestrial ecosystems, with their genomic material underpinning critical functions and applications across agriculture, biotechnology, and human health. Although genomic language models have advanced representation learning in DNA sequences, the extensive diversity of microorganisms and imbalanced taxonomic representation in the pretraining corpora pose challenges for effective microbial genomic sequence modeling. Here we present MicroGlot, a taxonomy-informed microbial DNA foundation model pretrained on 3.70 million sequences comprising 378.3 billion nucleotides across 99{,}700 species. MicroGlot encodes the hierarchical relations among taxa through hyperbolic embeddings, incorporating microbial taxonomic knowledge into a sparse mixture-of-experts architecture. Zero-shot evaluation of MicroGlot's layer embeddings demonstrates that the model's representations encode phenotypic traits and taxonomic identity. Comparison with a taxonomy-ablated variant trained under the same pretraining scheme shows that incorporating taxonomic knowledge consistently improves representation quality across the layers of MicroGlot. MicroGlot also combines optimized training techniques with efficient architectural components from modern large language models, achieving leading zero-shot performance across layers and competitive fine-tuning performance with low computational overhead. In a 1000-species set sampled from major cellular domains and viral realms, MicroGlot's routing fingerprints show greater agreement with taxonomic groups than tetranucleotide composition, reflecting taxonomically structured expert routing in multilingual modeling of microbial genomes. Overall, we show that MicroGlot serves as an efficient and effective DNA foundation model for microbial genomic analysis.

bioinformatics↗

bioRxiv2026

Cellular code for mnemonic pattern separation in the human hippocampus is revealed by false memories

Theoretical models propose that pattern separation, a computation thought to be implemented by the hippocampus, allows us to differentiate between familiar and novel items. However, whether pattern separation operates in the human hippocampus remains contested, with no established single-cell correlate. We recorded the single neuron activity of 3506 neurons in the human brain while 97 patients performed a recognition memory task in which novel images similar to previously seen images led to false memories and associated behavioral errors. We identified two kinds of memory selective neurons distributed across the brain: those responding differently to falsely recognized novel and correctly recognized familiar images in a manner compatible with pattern separation, and the other signaling the subject's choice. At the population level, these cells predicted mnemonic ground truth in the hippocampus and the decision in the pre-supplementary motor area, illustrating the progression from mnemonic signals to decisions. Removing pattern separation-signaling cells abolished the continuous memory strength gradient present in the hippocampus, suggesting a role of these cells in separating memories of different strength. These results establish a single cell correlate for mnemonic pattern separation in the human hippocampus and show its behavioral relevance in episodic memory.

neuroscience↗

bioRxiv2026

Selective collateralization of transcriptomically distinct neurons organizes visual-stream output from the primary visual cortex

Parallel visual streams segregate information into pathways specialized for distinct computations, but how this segregation is achieved by anatomical segregation of primary visual cortex output remains unclear. This problem is complicated because individual neurons frequently send broadcasting projections to multiple cortical areas, and the target choice depends on both topographical location and molecular identity. Here we developed axonal BARseq2 to jointly map gene expression and high-resolution axonal projections from 1,448 neurons spanning the mouse primary visual cortex (VISp). Axonal BARseq2 recapitulated projection patterns observed by bulk tracing and single-neuron reconstruction, and recovered transcriptomic identities consistent with reference snRNA-seq datasets. Retinotopy strongly predicted projections to individual cortical targets, particularly for areas proximal to VISp, but explained little of which areas are frequently co-innervated. Instead, co-innervation patterns defined three preferential output pathways that largely corresponded to the ventral stream and two subdivisions of the dorsal stream. These pathways were associated with fine-grained transcriptional identities of L4/5 intra-telencephalic neurons, which were further validated with an external MERFISH dataset. Thus, VISp output is organized by two distinct rules: retinotopy constrains where neurons project, whereas cell-type-associated collateralization constrains which targets are co-innervated. This selective broadcasting, in which single neurons reach many higher visual areas in cell-type-specific combinations, could provide an anatomical substrate for visual-stream segregation at the level of VISp output in mice.

neuroscience↗

bioRxiv2026

Muscle March5 restrains an ATF4-GDF15 endocrine stress axis that modulates feeding and body composition

Skeletal muscle can release endocrine stress signals during aging and wasting, but the upstream mechanisms that restrain this response remain incompletely defined. Here we identify March5 as a muscle proteostatic checkpoint that limits ATF4-dependent GDF15 production. March5 expression declined in aged and atrophic muscle, whereas muscle-specific March5 deletion induced ATF4 accumulation, marked GDF15 elevation, reduced food intake and progressive loss of body, muscle and bone mass. Restoration of feeding, GDF15 neutralization or muscle Atf4 deletion substantially attenuated the wasting phenotype. Mechanistically, March5 interacted with ATF4 and promoted its ubiquitination at K92, thereby limiting ATF4 stability and Gdf15 expression. Conversely, muscle March5 gain-of-function or pharmacological attenuation of ATF4 signaling improved feeding, body composition and physical performance in aged mice. These findings define a March5-ATF4-GDF15 endocrine stress axis linking muscle proteostatic control to feeding suppression and systemic body-composition remodeling.

physiology↗

bioRxiv2026

Spinal injury induces a stem cell-like progenitor state that promotes regenerative neurogenesis via clcf1 in zebrafish.

After spinal injury, zebrafish, in contrast to mammals, show regenerative neurogenesis, characterized by enhanced injury-induced proliferation of ependymo-radial glial cells (ERGs) and an increase in injury-induced generation of neurons from these progenitors. It is unclear whether regenerative neurogenesis simply recapitulates development or uses regeneration-specific mechanisms. Using scRNA-seq and in vivo validation we find a spinal injury-induced state in ERGs (iiERGs) in larval zebrafish. This cell state emerges mostly without proliferation and has stem cell characteristics, including weak expression of neurogenic genes and strong expression of stemness factors, such as lin28a. Expression of lin28a is not detectable during ongoing developmental neurogenesis. Following spinal cord lesion, lin28a disruption increases the numbers of ERGs undergoing neuronal differentiation and of newly-generated neurons, at the expense of proliferating ERGs and iiERGs. This supports a stemness-preserving role of lin28a in iiERGs. Importantly, iiERGs secrete growth factors, including the regeneration-specific cytokine clcf1, which depends in part on lin28a expression. Disruption of clcf1 signalling impairs spinal progenitor proliferation and injury-induced generation of new neurons, but does not affect the emergence of iiERGs. Over-expression of clcf1 is sufficient to augment neurogenesis in unlesioned animals without inducing the iiERG state, indicating that clcf1 acts as a generic growth factor. Hence, we describe an injury-specific stem cell-like ERG population that regulates regenerative neurogenesis by attenuating neuronal differentiation via lin28a and promoting progenitor proliferation via clcf1.

neuroscience↗

bioRxiv2026

High-speed volumetric single-molecule imaging using dual-wavelength light sheets and PSF-engineered enhanced biplane detection

Single-molecule localization microscopy (SMLM) enables nanoscale imaging but remains limited in three-dimensional (3D), high-speed, and high-density applications due to background fluorescence, photon inefficiency, and large point-spread function (PSF) footprints. Here, we present single-objective light-sheet microscopy with PSF-engineering enhanced biplane detection (SoLiD-3D), a versatile imaging platform that integrates dual-wavelength light-sheet illumination with dual-color, multi-configuration biplane imaging for parallel acquisition with PSF engineered detection for high-speed volumetric SMLM. Parallelized single-objective light-sheet excitation combined with PSF engineering overcomes key limitations of conventional wide-field and biplane approaches. Independent control of two excitation wavelengths for optical sectioning enables simultaneous dual-target imaging and single-target dual-color imaging with improved contrast and temporal resolution utilizing dynamically displaced light sheets for volumetric coverage. Using SoLiD-3D, we demonstrate high-speed single- and dual-target dual-color imaging that doubles localization density without sacrificing photon efficiency and continuous volumetric imaging via PSF-engineering enhanced biplane detection for whole-cell 3D imaging with improved axial localization performance over extended depth ranges. We further demonstrate improved speed by utilizing the Hummus PSF, a compact engineered PSF that enables high-precision 3D localization with a substantially reduced spatial footprint, for the first time for super-resolution imaging applications. Taken together, SoLiD-3D mitigates the trade-off between axial range and localization precision and offers improved speed compared to conventional 3D SMLM approaches.

biophysics↗

bioRxiv2026

Microstimulation of the human dopaminergic midbrain causally reshapes value-based decision-making and happiness

Midbrain circuits are thought to govern reward-guided behavior and momentary happiness, yet causal evidence in humans remains scarce. Here, we show that focal microstimulation of the substantia nigra pars compacta alters both decision making and momentary happiness in patients undergoing awake deep-brain stimulation surgery for Parkinsons disease. During a gambling task with interleaved momentary happiness ratings, stimulation delivered at outcome reduced risk-seeking in the loss domain without increasing overall gambling probability. Stimulation improved choice efficiency, guiding behavior toward gambles with higher expected value and thereby increasing cumulative earnings. Computational modeling revealed selective changes in loss processing, with reduced loss weighting and more linear loss utility, while gain processing remained unchanged. In parallel, stimulation did not tonically elevate happiness but selectively amplified outcome-related happiness changes, scaling with decision value and reward prediction errors. These results provide causal evidence that localized perturbation of human midbrain circuits reshapes valuation, choice, and momentary well-being.

neuroscience↗

bioRxiv2026

Context-Dependent Modulation of Duration Encoding in the Supplementary Motor Area

Duration judgments are calibrated by the statistics of recent temporal experience, but how this contextual influence is expressed across human timing-related brain regions remains unclear. We used functional MRI while 24 participants performed a visual temporal bisection task under two distributional contexts: one biased toward longer durations and one biased toward shorter durations. Behaviorally, distributional context shifted subjective duration judgments without changing in temporal precision, consistent with a prior-related bias. Neurally, duration-related BOLD responses varied across a priori timing regions as a function of context. The clearest region-specific evidence was stronger left-insula duration modulation in the short-biased context. SMA/pre-SMA contributed to the broader timing-network pattern, and its context-specific asymmetry was sensitive to the alignment of the duration regressor. Exploratory SMA-seeded connectivity analyses provided converging evidence that context also modulated duration-related coupling with timing- and attention-related regions. Together, these findings indicate that distributional context impacts the relative weighting of established timing-related regions during duration judgments, rather than recruiting anatomically separate timing systems.

neuroscience↗

bioRxiv2026

Neural Substrates of Duration Serial Dependence: Opposing Modulation in Basal Ganglia and Posterior Medial Cortex

Perceptual judgments are systematically biased toward recent experience, a phenomenon called serial dependence. The brain circuits underlying this effect in time perception remain unknown. Using fMRI, we identified the neural substrates of duration serial dependence and tested whether they overlap with those for motion direction. Twenty-seven participants reproduced either the duration or direction of a visual stimulus; a retro-cue revealed which feature to report 3-s after stimulus onset, separating memory-trace signals from task-switching signals. Duration serial dependence was robust and roughly four times stronger on task-repeat than task-switch trials; direction serial dependence was near zero. The previous duration produced opposing responses in the bilateral putamen (suppression) and in the posterior cingulate cortex and precuneus (reinstatement); no analogous signal emerged for direction. Task switching from direction to time task engaged the inferior frontal junction and the dorsolateral prefrontal cortex, which carried no serial dependence signal. The anatomical dissociation resolves the behavioral pattern: the duration trace is encoded in the putamen and posterior medial cortex on every trial, but task-set reconfiguration by the frontoparietal network gates its read-out into behavior, explaining the task repetition effect. These results reveal a dissociation between two functionally distinct circuits: the putamen and posterior cingulate/precuneus carry signals from the previous trial, whereas frontoparietal regions support task switching but carry little serial dependence information.

neuroscience↗

bioRxiv2026

A weak-interaction model defines the cell-autonomous function of DNA methylation in gastrulation

DNA methylation is essential for mammalian embryonic development, yet its functional implications remain debated. Here, we introduce a quantitative model that reconciles conflicting perspectives on the roles of methylation in genome regulation and cell specification. Using single-cell multiome analysis in chimeric and whole embryo mutants during mouse gastrulation and organogenesis, we separate cell-autonomous from indirect effects of methylation and demethylation machinery. We show that while the transcriptional and chromatin programs defining basic lineages can be established independently of methylation, the fidelity of differentiated states is severely impaired in its absence. Specifically, we identify hundreds of genes and thousands of cis-regulatory elements (CREs) dependent on methylation for precise regulation. CRE accessibility alterations in methylation mutants are linked with CpG dinucleotide content, and correlate with multiple transcription factor binding motifs. Our data support a weak-interaction model in which DNA methylation moderates, but does not block or instruct the potency of trans-acting regulatory machineries genome-wide.

genomics↗

bioRxiv2026

Mannosylated nanoparticle immunogens enhance the circumsporozoite protein-specific B cell response and improve protection against sporozoite challenge

Underprocessed oligomannose glycans on protein nanoparticle immunogens engage the innate immune system through mannose-binding lectin and complement, enhancing immunogen trafficking and B cell responses. However, the extent to which oligomannose glycans directly improve protective immunity has remained unclear. Here we generate a series of CSP-bearing I53-50 nanoparticle malaria vaccine candidates with defined numbers and types of engineered N-linked glycans and systematically evaluate their immunogenicity and protective efficacy. Oligomannose display enhanced early plasmablast and germinal center B cell responses, leading to increased CSP-specific memory B cells, long-lived plasma cells, and durable serum antibody titers. Furthermore, nanoparticles bearing oligomannose glycans conferred the strongest protection against sporozoite challenge. By comparing immunogens with defined glycoforms, we attribute improved immune responses and protection specifically to oligomannose rather than complex or truncated glycans. These results will help guide the development of general strategies for glycan engineering aimed at enhancing the protective efficacy of nanoparticle vaccines.

immunology↗

bioRxiv2026

De novo design of a macrocycle induced dimerization system for cellular control

Investigating and manipulating cellular events requires precise control of protein function. To enable control over cellular processes, we set out to design a chemically induced dimerization (CID) system consisting of a de novo designed ligand and protein pair. Here we describe the design of a C2 symmetric membrane permeable macrocyclic peptide and a cognate protein homodimer which binds the macrocycle through a large interface with both chains. The designed homodimer binds the macrocycle with a KD of 36 nM, and the x-ray crystal structure of the protein homodimer-macrocycle complex is very close to the computational design model, with the C2 axis of the macrocycle aligned with the homodimer C2 axis. Transcriptional and split luciferase assays in mammalian cells demonstrates conditional control over both a reporter gene expression and luciferase reconstitution.

biochemistry↗

bioRxiv2026

BioEngine: scalable execution and adaptation of bioimage AI through agent-readable interfaces

Foundation models and curated repositories have transformed bioimage AI, yet most biologists cannot readily run, adapt, or extend them on available hardware. BioEngine lls this gap as the execution and adaptation layer between curated AI and scalable compute, deployable on a laptop, workstation, or cluster. Scientists then screen models, ne-tune from the browser, enable real-time smart microscopy, and deploy analysis applications, all by describing their goal to an AI agent.

bioinformatics↗

bioRxiv2026

Versatile and scalable reflective micromirrors for single-objective light sheet microscopy

We present a tunable microfabrication pipeline for creating robust, reflective inserts that adapt conventional commercial imaging chambers for single-objective light sheet (LS) illumination. This system reduces the complexity associated with dual-objective LS setups and specialized LS chambers while retaining the native functionality and biocompatibility of the original chambers. The fabricated insert features a metalized, 3D nanoprinted micromirror with an angled reflective surface, enabling alignment of a thin LS for sectioning and imaging throughout mammalian cells. Using this pipeline, we demonstrate that single-objective LS illumination achieves an over 4X improvement in the signal-to-background ratio compared with conventional widefield epi-illumination in both fixed and live cell samples. Furthermore, we show substantial resolution enhancement for single-molecule localization microscopy compared to epi-illumination for improved imaging at the nanoscale. The versatile and scalable design offers an easily implemented approach to bring the benefits of single-objective LS microscopy to a wide array of biological studies.

biophysics↗

bioRxiv2026

Natural and breeding selection converge on overlapping haplotypes with divergent directions and outcomes in wheat

Understanding how natural and breeding selection interact to shape crop genomes is essential for improving resilience under climate change. Here, we applied a k-mer-based, alignment-free haplotype assignment approach to whole-genome resequencing data from 827 wheat landraces representing seven geographic groups and 208 modern cultivars. We identified haplotypes associated with local adaptation that were enriched in specific agroecological regions, many of which were derived from wild-relative introgressions. Comparative analyses revealed that natural and breeding selection largely targeted overlapping haplotype sets, but often drove them in opposite directions. Notably, haplotypes conferring adaptive advantages were frequently associated with negative regulation of agronomic traits, explaining their reduced prevalence among breeding-selected haplotypes. These results reveal the genomic basis of trade-offs between environmental adaptation and productivity and offer a framework for exploiting adaptive diversity in wheat improvement.

plant biology↗