Biology subjects

Cheng, Y.

Publications and source records attributed to Cheng, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Digital molecular kinetics enabled by large-scale nanopore arrays for multidimensional biophysical profiling

While widely used, traditional technologies like surface plasmon resonance (SPR) are limited by narrow temporal windows (transient capture and baseline drift), dynamic heterogeneity, and poor physiological temperature performance. Meanwhile, early nanopore approaches are often constrained by limited throughput and heavy reliance on customized modification schemes. Here, we present a digital molecular kinetics (DMK) platform based on large-scale nanopore arrays. By introducing a universal coupling and probe reporting system, DMK achieves broad versatility across diverse molecular pairs, including proteins, peptides, small molecules, DNA, and polymerase complexes. In addition to accurately recovering classical SPR association and dissociation rate constants, by harnessing massive single-molecule event analysis, DMK breaks traditional performance boundaries: it facilitates robust thermodynamic-kinetic profiling across a wide temperature range, resolves distinct conformations in heterogeneous samples, enables ultra-low dissociation rate quantification via maximum likelihood estimation, and reveals energy wells via voltage gradients for binding analysis against environmental perturbations. Furthermore, DMK enables the capture of rapid binding events missed by SPR, offering a new perspective on molecular interaction complexity. This platform offers an effective alternative and upgrade to SPR, opening a digital paradigm for complex molecular analysis and drug discovery.

biophysics↗

bioRxiv2026

Ratio-preserving super-resolution FLIM for quantitative live-cell lifetime imaging

Super-resolution (SR) fluorescence lifetime imaging promises nanoscale maps of molecular environment and function, but photon-limited acquisition and computational reconstruction can distort lifetime estimates, particularly for ratio-derived frequency-domain measurements under SR conditions. Here we introduce structured-illumination frequency-domain FLIM (SIM-fdFLIM), an SR lifetime imaging platform that combines commercial dual-tap fdFLIM detection with ratio-preserving reconstruction. SIM-fdFLIM uses direct-current (DC)-stabilized lifetime estimation to improve reconstruction robustness under low signal-to-noise conditions, followed by ratio-domain integrated variational estimation (RIVE) to correct channel misregistration and suppress noise amplification after SR reconstruction. The method achieves ~100 nm spatial resolution in lifetime maps and enables live-cell imaging at 2.8 Hz over a 56 x 56 {micro}m2 field of view. Across representative fluorophore standards, RIVE reduces lifetime standard deviation by approximately threefold relative to non-RIVE SIM-fdFLIM while preserving mean lifetime agreement with calibrated widefield fdFLIM. In living cells, SIM-fdFLIM resolves mitochondrial cristae-scale lifetime heterogeneity, mitochondrion-to-mitochondrion functional dynamics, nanoscale lipid-environment variations and perturbation-sensitive organelle-contact signatures. These results establish SIM-fdFLIM as a ratio-preserving platform for quantitative SR lifetime imaging, extending live-cell FLIM into a regime that combines nanoscale spatial resolution, Hz-rate acquisition, and preserved lifetime fidelity.

bioengineering↗

bioRxiv2026

Matrix stiffness shapes immunometabolic states and response to PD-1 blockade in gastric cancer

The extracellular matrix of solid tumors exhibits spatially heterogeneous stiffness, yet how matrix stiffness shapes antitumor immunity in gastric cancer (GC) remains unclear. Here, we integrated anti-PD-1 clinical cohorts, GC specimens, single-cell and spatial transcriptomic analyses, a syngeneic mouse model, and tunable-stiffness hydrogels to clarify the immunological consequences of matrix stiffness. High matrix stiffness was associated with collagen accumulation and immune exclusion, while higher stiffness-associated transcriptional scores were related to poorer response to PD-1 blockade. Matrix softening markedly reshaped the immune microenvironment and enhanced the efficacy of PD-1 blockade. Mechanistically, stiff matrices promoted F-actin remodeling and YAP nuclear enrichment, driving LDHA-dependent glycolytic reprogramming in GC cells that further impaired the effector function of CD8 T cells. Intriguingly, matrix softening was accompanied by enhanced IFN-{gamma}-responsive PD-L1 expression in GC cells, consistent with adaptive immune resistance that may contribute to the limited antitumor effects of matrix softening alone. These findings suggest that matrix remodeling alleviates spatial and metabolic constraints on antitumor immunity, providing a preclinical rationale for combining matrix softening with PD-1 blockade in GC.

cancer biology↗

bioRxiv2026

X-SPEAR: An Extensible Framework for Spatial Panel Evaluation and Refinement

Targeted spatial transcriptomics platforms such as Xenium require a predefined gene panel, and the genes in that panel are detected less efficiently, and to gene-specific degrees, in the spatial assay than in the single-cell reference used to choose them. We present X-SPEAR, a framework that couples DART marker selection with probe-level off-target assessment. DART learns short, interpretable Boolean gene rules and assembles several gene-disjoint rules per cell type. Its detection-aware training thins the reference to per-gene detection rates measured in a different, already completed experiment, so no Xenium data from the target tissue are needed before the panel is ordered. On held-out Xenium data from ovarian cancer, mouse brain and cervical cancer, DART substantially outperformed existing marker-selection methods at matched panel size, by 0.04-0.11 macro-F1 over Wilcoxon rank-sum, 0.04-0.08 over COSG and 0.10-0.18 over NS-Forest, and it reached Wilcoxon's best accuracy with 42-69% fewer genes. Ablations show that most of this gain comes from detection-aware training, which also improves other rank-based selectors and requires a detection profile measured with the same assay chemistry. At similar accuracy, DART's rule structure adds rules that faithfully summarise the downstream classifier, robustness to single-probe loss across 45 retinal ganglion cell subtypes, and better resolution of closely related cell states. We are applying X-SPEAR to design a Xenium panel for mouse retinal ganglion cell subtypes, and its in situ evaluation is in progress. X-SPEAR is available as an open-source Python package.

genomics↗

bioRxiv2026

Self-extending DNA recording with stochastic and programmed writing

Recording cellular histories requires new information to accumulate without erasing earlier records. Here we introduce Infinite Printer, a CRISPR recording architecture that couples self-extension to regeneration of a writable terminal context. A self-targeting prime-editing guide RNA (stpegRNA) directs repeat extension, while base editing generates diversity in situ without a separate insertion template for each character state. Earlier sequence remains upstream of the renewed terminus, linking substrate growth with record retention. Auxiliary pegRNAs specify payloads within a write-renew-write architecture. After three rounds of payload input, 4,436 distinct complete CCA-based records contained identities from all three pools. Longer AC/AT records retained shared upstream marks, and full-length sequence analysis resolved additional endpoint distinctions. Joint single-cell readout recovered 1,549 distinct records and 7,669 combinations across 12,302 transcriptome-linked cell labels from a single stpegRNA design. Spatial-transcriptomic readout recovered spacer records at 11,330 capture spots, linking record content to tissue coordinates and gene-expression profiles. Infinite Printer unites substrate renewal, sequence diversification and programmed writing with cell- and tissue-linked readout, providing a foundation for future lineage recording across large cell populations during mammalian development.

synthetic biology↗

bioRxiv2026

High-throughput affinity profiling of antibodies against soluble and native membrane targets by digital flow cytometry

Binding affinity measurements are essential for optimizing and validating therapeutic and research antibodies, yet no high-throughput platform supports quantitative affinity measurements for both soluble and native membrane targets. Here we present a suite of digital flow cytometry (dFC) assays that determine equilibrium binding affinities by directly counting free and bound molecules in homogeneous mixtures without immobilization. The assays enable titration-free absolute KD measurements for fluorescent binding partners, affinity measurements for unlabeled antibodies against membrane receptors on cell-derived extracellular vesicles (EVs), and multiplexed assays for rapid ranking or screening of antibody variants. We demonstrate applications by quantifying the effects of degree-of-labeling on the affinity of antibody-dye conjugates, and of drug conjugation on therapeutic antibody binding to receptors on human cancer EVs. By combining single-molecule quantitation, adaptable assay designs, and high-throughput analysis, dFC provides a versatile platform for therapeutic antibody optimization and research antibody validation.

biophysics↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

Benchmarked sequencing methods reveal hidden mosaic variation in the human brain

Mosaic variants (MVs) record cellular lineages, but their recovery is strongly method-dependent. Here, we benchmarked four duplex sequencing methods alongside bulk and single-neuron genome sequencing in matched human brain tissue. The methods differed in genome representation, MV yield and mutational profiles, with limited caller-level concordance. However, read-level interrogation revealed substantially greater cross-method molecular support. To systematically recover this evidence, we developed Read-level Integration for Variant Evidence Recovery (RIVER), expanding the pool of cross-method-supported candidates by approximately two orders of magnitude relative to caller-level overlap. Orthogonal sequencing at ~10,000x across brain and peripheral tissues validated approximately half of the tested RIVER-rescued candidates. MVs recovered from a single brain region resolved broadly distributed and regionally restricted clones and provided lineage information among individual neurons. These findings show that RIVER substantially expands the pool of endogenous lineage markers available to investigate human development, aging, disease-associated mosaicism and clonal evolution.

genomics↗

bioRxiv2026

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

Localized evolutionary changes can distort ancestral state reconstruction (ASR) because conventional continuous-trait methods generally treat branchwise changes as draws from a shared background process. A disproportionately large change confined to a single branch therefore creates localized model misspecification, but how the resulting errors vary among reconstruction paradigms and phylogenetic positions remains poorly understood. Using controlled simulations on idealized and empirical mammalian phylogenies, we characterized the error patterns produced by single-branch large changes (SBLCs) across five Brownian-motion-based ASR implementations. On intact trees, errors were highly structured and method dependent: the recursive local method propagated distortion mainly upstream, whereas global methods produced multidirectional effects involving both SBLC boundary nodes, neighboring lineages, and descendants of the affected branch. We then evaluated patching, a conditional robustness procedure that partitions the phylogeny at a candidate branch, applies the same ASR method independently to the resulting subtrees, and estimates the upstream boundary node state by branch-length-weighted interpolation. Patching reduced errors near and away from the affected branch and lowered tree-wide error across trait-increasing and trait-decreasing SBLCs, a broad range of sensitivity analyses, and configurations with two co-occurring SBLCs, while introducing little additional error when no SBLC was present. Under the reference upsizing SBLC, for instance, it cut the maximum-likelihood reconstruction error at the upstream boundary node from 56.20 to 0.03 (mean true state, 4.98), matching the stable-process benchmark. In cetacean body-length evolution, patching candidate branches identified by a Levy-process model generally shifted conventional estimates toward stable-process estimates and nearby fossil references. Under an Ornstein-Uhlenbeck process with strong post-SBLC mean reversion, however, neither patching nor stable-process reconstruction recovered downstream ancestral states once the phenotypic signature of the SBLC had largely disappeared from descendant tip values, revealing an identifiability limit of terminal-only inference. Localized evolutionary change therefore creates structured, method-dependent reconstruction errors, and tree partitioning provides a complementary diagnostic of the robustness of ancestral inferences to candidate branch-localized changes.

evolutionary biology↗

bioRxiv2026

One-Entry Golden Seamless Cloning with a Reusable Donor Streamlines Plant Gene Functional Analysis

Molecular cloning underpins functional genomics, yet current toolboxes force a trade-off. Golden Gate frameworks handle one-pot multi-fragment assembly but overcomplicate routine single-gene cloning, whereas Gibson, In-Fusion, and Gateway systems need backbone linearization, resequencing, or proprietary recombinases that leave scars. Here we present Golden Seamless (GS), a one-entry, many-destination system in which a single PCR captures a gene once into a reusable Entry-and-Expression Clone that is never re-cloned. Circle-to-circle Golden Gate moves the same validated clone into plant, yeast, or bacterial vectors without linearization, and a ccdB counter-selection with orthogonal antibiotic markers drives background near zero. Bacterial destinations embed superfolder GFP, enabling naked-eye monitoring of recombinant proteins and an antibody-free dual-modality EMSA that resolves protein and DNA channels across a >150-nm spectral gap. GS thus consolidates capture, distribution, and validation into one low-background workflow with built-in quality control, cutting the time and cost of screening many candidates across functional assays.

molecular biology↗

bioRxiv2026

Metagenomic insights into dose-dependent alterations in the tobacco rhizosphere microbiome by pyrroloquinoline quinone

Pyrroloquinoline quinone (PQQ) is known to promote plant growth, yet how the rhizosphere microbiome varies with PQQ concentration remains poorly understood. We applied metagenomic sequencing to characterize the taxonomic composition and functional potential of the tobacco rhizosphere microbiome across PQQ treatments at 0.5, 1 and 2 mol/L plus an untreated control. The rhizosphere microbiome was dominated by Pseudomonadota and Actinomycetota and differed among treatments in a concentration-associated, non-monotonic manner. The most pronounced differences were observed at 1 mol/L, where alpha diversity showed dimension-specific variation and beta-diversity analysis resolved the most distinct community profile. Taxonomic and functional profiles varied concurrently, with Streptomyces, Sphingomonas, Rhodanobacter and Lysobacter, together with functions related to biosynthesis, energy metabolism, colonization and environmental sensing, showing higher relative abundance at this concentration. No broad-spectrum antimicrobial effect was detected at the community level, and antibiotic resistance gene abundance showed no significant differences among treatments after correction for multiple testing. These findings provide a basis for further evaluation of PQQ in modulating the rhizosphere microbiome in continuous cropping systems.

microbiology↗

bioRxiv2026

Glucocorticoid receptor activation reorganizes Wnt/LEF1 regulatory circuitry associated with therapeutic response in B-cell acute lymphoblastic leukemia

Glucocorticoids (GCs) are foundational to B-cell acute lymphoblastic leukemia (B-ALL) therapy, yet how glucocorticoid receptor (GR) activation interacts with lineage regulatory circuitry to shape therapeutic response remains incompletely understood. Using LEF1 to interrogate canonical Wnt regulatory circuitry, we show that GR activation reorganizes GR+LEF1 elements into recruitment, retention, and dissociation states. LEF1 dissociates from Wnt-responsive regulatory elements while being recruited to GRE-rich GR-associated elements that progressively acquire chromatin accessibility, H3K27ac, BRD4 and BRG1. RUNX1 and AP-1 show class-dependent redistribution across LEF1-defined states, extending organization beyond LEF1. GR+LEF1 reorganization is observed in patient-derived B-ALL. GR+LEF1 elements lose accessibility in GC-resistant B-ALL and during diagnosis-to-relapse evolution, with recruitment elements enriched for remodeling. Perturbation of resistance-associated GR+LEF1 elements at BIM and BMF alters GC-induced apoptotic signaling. Together, these findings identify Wnt/LEF1 circuitry as an interface through which therapeutic GR activation reorganizes the B-ALL regulatory landscape into states associated with glucocorticoid response and resistance.

cancer biology↗

bioRxiv2026

Structural Adaptability in HIV-2 Vif Drives Broad Antagonism of APOBEC3G

APOBEC3G (A3G), a restriction factor, is a barrier for zoonosis and targeted for degradation by the lentiviral protein Vif. Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2 arose from transmissions of lentiviruses from Old World monkeys to hominid primates. While HIV-1 Vif needed to adapt to specific residues in the arms race interface with A3G, HIV-2 Vif has greater tolerance for diversity there. Here, our cryo-EM structure of HIV-2 Vif and human A3G allows us to explore the mechanism underlying HIV-2 Vif broad specificity. While HIV-2 Vif does bind the arms race interface on A3G, HIV-2 Vif encodes tryptophans with low backbone stability to engage another interface on A3G. We propose a model where flexible loops in HIV-2 Vif undergo conformational selection to recognize diverse A3Gs, whereas the equivalent loops in HIV-1 Vif are preorganized to bind hA3G.

biophysics↗

bioRxiv2026

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

Anti-tuberculosis (TB) immunity typically emphasizes CD4+ T and CD8+ T cells that only provide limited protection against Mycobacterium tuberculosis (Mtb) infection. The anti-TB function of CD4+CD8+ T cells remains unexplored, mostly due to the dogma that ThPOK and Runx3 antagonize each other to block their development and their scarcity. Here, we show that immunization of BCG (Bacillus Calmette-Gu&eacuterin) with Complete Freund's Adjuvant (CFA) markedly induced CD4+CD8+ T cells through the gut microbiota Clostridium butyricum or its metabolite maleic acid. Mtb-specific CD4+CD8+ T cells exhibited a broad T-cell receptor repertoire and sterilized Mtb infection by inducing SLAMF1 and neutrophil responses. Mechanistically, maleic acid interacted with PAK2 to promote STAT5 phosphorylation at Ser127, thus upregulating Ets1 expression. Direct binding of Ets1 to the Runx3 and ThPOK promoters orchestrated their expression to redirect the CD8+ T cell differentiation towards the CD4+CD8+ lineage. Moreover, immunization of BCG plus Clostridium butyricum or maleic acid sterilized Mtb infection in mouse models. These findings establish CD4+CD8+ T cells as superior immune effectors against Mtb, a concept that could fundamentally redirect the current paradigm for anti-TB vaccine development.

microbiology↗

bioRxiv2026

Multiomics Reveals IGF-1 c.258A > G Reduces Triacylglycerol Containing Medium-Chain Fatty Acid in Milk

Fatty acid composition of milk triacylglycerol (TAG) is important for neonatal growth. We previously identified a synonymous mutation widely distributed in human populations, IGF-1 c.258A > G, which decreased milk TAG content in gene-edited mice. So far, the acyl chain composition of affected TAGs, underlying molecular mechanism, and cross-species conservation remain unclear. Here, integrated transcriptomic and metabolomic analyses of mouse mammary glands revealed that this mutation downregulates IGF-1 expression and elevates lipoprotein lipase (LPL) activity, and potential associations between IGF-1 and peroxisome proliferator-activated receptor {gamma} (PPARG), fatty acid synthase (FASN) and lipin 1 (LPIN1). Association analysis in 295 Bama pigs carrying this gene polymorphism showed reduced milk lipid content in sows; further, correspondingly lower litter weight was significantly associated with the genotype. Integrated metabolomic profiling of mouse mammary glands and porcine milk demonstrated insufficient production of lauric and myristic acids. Accordingly, supplementing these two fatty acids restored TAG content. Mechanistically, IGF-1 promotes triacylglycerol-containing medium-chain fatty acid (MCFA-TAG) synthesis by activating the PPARG-FASN/LPIN1 axis, whereas increased LPL activity indirectly suppresses this axis through long-chain fatty acid accumulation. Together, our results reveal the molecular mechanism whereby this mutation affects milk lipid synthesis, providing insights into the regulation of MCFA-TAG synthesis.

molecular biology↗

bioRxiv2026

An entropy-based diagnostic framework for characterizingmethylation state dynamics during preimplantation development

DNA methylation undergoes predictable changes with age, and preimplantation embryos are known to undergo global epigenetic reprogramming. However, the specific fate of age associated methylation signatures during early development has not been systematically quantified. Using published human sperm age associated differentially methylated regions (DMRs) as a feature space, we integrated single cell methylome and transcriptome data to develop the Transgenerational Reset Operator (TRO), a computational framework for profiling preimplantation stages. We found that the morula stage represents the nadir of age associated methylation entropy while retaining high developmental potency, distinguishing it from a simple demethylation endpoint. Dynamical modelling revealed that independent DMR drift fails to recapitulate the morula state, requiring a coordinated, structured correction concentrated in specific DMR subsets and modules with marked directional sensitivity. Independent chromatin accessibility data supported a stage specific methylation accessibility coupling at morula, albeit with modest effect sizes. Cross species mouse and orthogonal multiomic evidence suggested partial conservation but with weight dependence and heterogeneity. Collectively, our study defines morula as a computational "ground zero" candidate for age associated methylation features and proposes a testable hypothesis of developmental regulation, while emphasizing that matched parental offspring perturbation experiments are needed to establish causal mechanisms.

developmental biology↗

bioRxiv2026

Chromosomal instability shapes spatial and temporal phenotypic diversity in a malignant peripheral nerve sheath tumour

Understanding the spatial and temporal dynamics of tumour evolution is crucial for determining the drivers of cancer progression. Linking genotype to phenotype across a tumour remains challenging, however. Here, we use single-cell and spatial multi-omics to comprehensively profile a primary malignant peripheral nerve sheath tumour (MPNST) and its multifocal recurrence. Combining the native barcoding system from extensive heterogeneity in copy number alterations with mutation data, we resolve the evolutionary tree of this tumour, revealing a branching structure suggestive of ongoing chromosomal instability. We show that gene dosage effects contribute to phenotypic diversity and scale predominantly linearly with copy number. Using spatial genomics assisted by laser capture microdissection and spatial transcriptomics, we performed in situ lineage tracing in this human tumour, elucidating the relationship between local expansions and interactions between tumour cells and the microenvironment. These findings demonstrate the potential of combined bulk, single-cell and spatial techniques to dissect cancer evolution in time and space and link genotype to phenotype in detail.

genomics↗

bioRxiv2026

When are Biomedical Postdocs Ready for the Faculty Job Market? A Mixed-Methods Analysis of Metrics and Resilience Among Faculty Job Seekers

PurposeDiscussions surrounding the biomedical faculty job market often focus on applicant competitiveness and external metrics such as number of publications and funding records. Consequently, there is typically less discussion about applicant readiness, the point at which applicants perceive themselves as prepared to enter the market. Since 2018 our group, the Faculty Job Market Collaboration (FJMC), has conducted annual end-of-cycle surveys of biomedical faculty job applicants, producing the largest longitudinal dataset on this process to date. MethodsWe employed a mixed-methods design examining faculty applicants in biological science fields in North America. Regression analyses were conducted on a longitudinal dataset of 729 respondents across multiple hiring cycles. To determine how applicants evaluated their own preparation, qualitative interviews were conducted with a separate cohort of biomedical postdoctoral applicants during the 2024-2026 job cycles. ResultsOur findings demonstrate that rather than depending on a single quantitative threshold, readiness is a multifaceted construct shaped by actionable and interpersonal drivers. Key factors influencing an applicants perceived readiness include taking agency to submit applications, receiving explicit support from a mentor, incorporating strategic use of artificial intelligence tools into application preparation, and their career stage. ConclusionBy distinguishing individual readiness from systemic assumptions of market competitiveness, this study highlights a blind spot in academic workforce development. Our results suggest that applicants can achieve readiness and successful outcomes through different combinations of support, strategy, and timing rather than a uniform metric profile. By integrating quantitative and qualitative data, our study provides an evidence-based framework for understanding applicant readiness and offers practical guidance to help trainees navigate the increasingly competitive academic job market. Teaser TextOur mixed-model analysis of the biomedical faculty job market is designed to help prospective faculty candidates assess their readiness to enter the job market. By integrating multiple indicators of academic productivity, funding success, and professional experience, our study provides evidence-based benchmarks that can guide applicants in evaluating their competitiveness and identifying areas for further development before pursuing faculty positions.

scientific communication and education↗