Biology subjects

Lyu, H.

Publications and source records attributed to Lyu, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Tools for genetic mapping and gene identification in Caenorhabditis briggsae

The nematode Caenorhabditis briggsae serves as an important companion species for Caenorhabditis elegans for comparative studies. Because C. briggsae exhibits androdioecious reproduction and ease of laboratory culture similar to C. elegans, it has long been used for genetic studies in cross-species comparisons of mutant phenotypes to uncover the evolution of gene function. Here, we provide an updated toolkit for C. briggsae genetic experiments, leveraging the resource of recently improved C. briggsae genome sequence assemblies with variant mapping tools and gene identification methods. We identify and validate a set of indel variants between CGC2 (AF16) and two divergent strains, HK104 and VX34. We then use these variants to genetically map 10 previously isolated mutations and identify the impacted genes using high-throughput sequencing. We combine these new genes with others curated from the literature into an updated map with 73 genes, providing an enriched resource for C. briggsae genetic studies.

genetics↗

bioRxiv2026

Direct electrochemical cortisol detection via transition-resolved interrogation at a defect-engineered graphene interface

Continuous tracking of cortisol is central to understanding human stress physiology, yet direct electrochemical detection without biological receptors remains challenging despite its promise for stable and dynamic sensing. Electrochemical reduction of cortisol typically occurs at highly negative potentials, where parasitic interfacial currents, hydrogen evolution, and substantial capacitive background overlap with the cortisol reduction signal, preventing accurate quantification. We overcome this barrier through an integrated material-measurement strategy combining a defect-engineered graphene interface with a transition-resolved interrogation (TRI) measurement strategy. First, we engineered polybenzimidazole-derived laser-induced graphene containing nitrogen-rich defects while suppressing oxygen-derived functionalities which reduced parasitic background currents within the same cathodic potential regime. Next, we designed TRI to leverage differences in the time-dependent evolution of overlapping cathodic processes to isolate a localized cortisol-associated electrochemical reduction transition. Derivative-domain projection coupled with background estimation enables its reliable quantification. This integrated sensing architecture enables sensitive, selective, and dynamic cortisol detection in both artificial and biological interstitial fluids at low nanomolar concentrations. The response remains reproducible across physiologically relevant variations in pH, ionic strength, temperature, and repeated cycling. Together, these capabilities provide a basis for continuous electrochemical cortisol monitoring for future study of stress physiology.

bioengineering↗

bioRxiv2026

Scorpion toxin peptide BMK86-P1 achieves mutation-reversible inhibition of KCNA2 at the cost of reduced efficacy in heteromers and murine neurons

The discovery of distinctive function-phenotype relationships in monogenetic channelopathies has turned out to be critical for the development of precision medicine approaches. However, the best prediction of clinical phenotypes depends on neuronal function, where existing models lack tools to isolate currents of individual voltage-gated potassium channel subunits and differentiate variant effects in complex systems. Ideally, one should be able to overexpress subunit variants with an additional mutation that confers resistance against the tool to isolate the variant effect. Therefore, we solid-phase synthesized the KV1.2 specific scorpion toxin peptide BMK86-P1 and oxidized it with modest efficacy. In mammalian cells this BMK86-P1 selectively inhibited KV1.2 homomers, but not heteromers with KV1.1. Critically, the KCNA2 p.Val381Tyr mutation, which reverses BMK86-P1's selective inhibition of KV1.2, also altered the activation of KV1.2 homomers to resemble those of KV1.1. In addition, BMK86-P1 in murine neurons did not alter passive membrane properties, single action potential properties, or action potential firing. Surprisingly, it induced only minimal changes in spontaneous excitatory postsynaptic currents. In summary, this KV1.2 subunit selective toxin peptide asserts its effects primarily on homomeric channels, while only weakly inhibiting KV1.2-heteromeric channels and consequently preventing any meaningful impact on neuronal function. This highlights the limits of peptide synthesis together with the need for testing specific compounds on complex systems.

neuroscience↗

bioRxiv2026

AI4Loop: an Artificial Intelligence Framework Reveals Increased 3D Chromatin Interactions and Therapeutic Vulnerabilities across 12,000 Cancer Samples

Three-dimensional chromatin interactions shape gene regulation, but their large-scale analysis remains limited by the cost and complexity of experimental assays. Here we present AI4Loop, a deep learning framework that infers genome-wide gene-centered chromatin interaction networks directly from RNA-seq data. Across multiple cell types, AI4Loop recovered interaction patterns consistent with clinical samples and orthogonal chromatin conformation datasets. Applied to 12,347 transcriptomes from 32 cancer types, AI4Loop revealed pervasive increases in gene-centered chromatin interactions in tumors, particularly at oncogene-associated loci. These inferred interaction networks outperformed gene expression alone in cancer classification. Integration with more than 50,000 drug-treated transcriptomes identified compounds predicted to reverse cancer-associated interaction gains. Hi-C experiments confirmed that the oxazolidinone antibiotics eperezolid and radezolid reduce breast cancer-gain chromatin interactions. Together, these results identify increased gene-centered chromatin interactions as a pan-cancer feature and provide a scalable strategy for linking 3D genome dysregulation to therapeutic vulnerabilities.

bioinformatics↗

bioRxiv2026

Cross-species Study of Canine and Human Peripheral Nerve Sheath Tumors: Clinical and Molecular Perspectives

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas. An obstacle to treating MPNSTs is a lack of effective systemic therapies. Although over 70% of human MPNSTs have lost or inactivated the epigenome regulator polycomb repressive complex 2 (PRC2), its activity and contribution to canine PNST progression remain unclear. This study compared canine peripheral nerve sheath tumors (PNSTs) and human MPNSTs across biological and clinical features, including PRC2 activity. Immunohistochemical analysis was performed for a human tissue microarray of 54 neurofibromas and 139 MPNSTs, and 63 canine PNSTs for H3K27me3, a repressive histone mark deposited by intact PRC2, and H3K27ac, which increases globally upon H3K27me3 loss. To understand the genomic alterations present in canine PNSTs, we analyzed tumor mutation burden, copy number alteration, and transcriptomes of eight canine PNST/normal pairs. The results suggested that H3K27me3 loss and associated gain of H3K27ac epigenetically drive human and canine tumors. These findings warrant further studies to evaluate whether these epigenetic deregulations alter similar gene signatures across species.

cancer biology↗

bioRxiv2026

A gap-free, telomere-to-telomere genome assembly for the Caenorhabditis briggsae reference strain AF16

The nematode Caenorhabditis elegans was the first metazoan to have its genome completely sequenced and assembled. Since that time, researchers have continuously updated the reference genome and manually curated its approximately 20,000 genes. The closely related species, Caenorhabditis briggsae, has served as a comparative model because of its similar morphology, mode of reproduction, and patterns of intra-species genetic variation. However, the genomic resources for C. briggsae lag behind C. elegans, hindering comparative genomics studies between the species. Decades of experimentation have been performed in the AF16 reference strain genetic background, so we obtained high-coverage long-read sequencing and high-throughput chromosome conformation capture data to create an updated reference genome for an isogenic derivative of AF16, named CGC2. The CGC2 genome is vastly improved relative to the existing AF16 assemblies, with no unplaced sequence, no gaps, and telomere-to-telomere contiguity. To provide genomic resources for CGC2, we exploited deep RNA-seq libraries from all developmental stages to predict protein-coding gene annotations comparable in accuracy and completeness to the existing AF16 gene models. We also performed lift-over of 108 validated insertion-deletion variants to the updated coordinate system of the CGC2 genome to facilitate future mappings of mutations. In summary, we present an updated reference genome for the canonical AF16 reference strain with improved genomic resources to enable high-quality intra- and inter-species comparative studies.

genomics↗

bioRxiv2026

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication

Accurate genome assemblies are essential for comparative genomics, yet Hi-C-guided scaffolding can introduce structural errors that misrepresent chromosome architecture and bias evolutionary inferences. Here, we identified pervasive scaffolding errors - including artificial fusions, internal inversions, and incomplete contig mounting - in two previously published Lupinus genomes (L. cosentinii and L. digitatus) using a segmentation method based on LTR retrotransposon density. We re-assembled both genomes, producing chromosome-level references of 472.7 Mb (16 chromosomes) and 427.2 Mb (21 chromosomes), with BUSCO completeness >98.5%. Synteny validation and re-application of LTR profiling confirmed that all prior errors were resolved. Using these corrected genomes together with four additional Lupinus species and two outgroup legumes, we investigated post-polyploid evolution. Synonymous substitution rate (Ks) analysis revealed a genus-specific whole-genome duplication (WGD) event (Ks = 0.17) shared by all six Lupinus species. The proportion of WGD-derived genes varied markedly, from 60% in L. digitatus to only 36% in L. mutabilis, indicating differential diploidization. While all species retained a core set of WGD duplicates enriched in cytoskeleton organization, ion transport, and defense responses, each exhibited lineage-specific functional trajectories: cell wall modification in L. cosentinii and L. digitatus, nitrogen metabolism in L. albus and L. angustifolius, flower development in L. luteus, and stress/lipid metabolism in L. mutabilis. Our corrected assemblies provide optimal references for Lupinus comparative genomics, and our findings demonstrate that a shared WGD event can lead to both conserved and highly divergent post-polyploid fates, likely underpinning adaptive diversification within the genus.

genomics↗

bioRxiv2026

Peptide-to-protein data aggregation using Fisher's method improves target identification in chemical proteomics

Protein-level statistical tests in proteomics aimed at obtaining p-value are conventionally made on protein abundances aggregated from peptide data. This integral approach overlooks peptide-level heterogeneity and ignores important information coded in individual peptide data, while protein p-value can also be obtained by Fishers method of combining peptide p-values using chi-square statistics. Here we test this latter approach across diverse chemical proteomics datasets based on assessments of protein expression, solubility and protease accessibility. Using the top four peptides ranked by their p-values consistently outperformed protein-level analysis and avoided biases introduced by inclusion of deviant peptides or imputation of missing peptide values. Fishers method provides a simple and robust strategy, improving identification of regulated/shifted proteins in diverse proteomics assays.

bioinformatics↗

bioRxiv2026

Selective Immune Silencing by Targeted TGF-β Agonists

Depletion of pathogenic T and B cells is a pillar of therapies for autoimmune, inflammatory, and transplantation-related immunological diseases. However, adverse events, safety concerns in immunocompromised patients, and disease relapse limit clinical utility. Here, we exploit the immunosuppressive properties of a transforming growth factor beta (TGF-{beta}) mimic repurposed from helminths for cell type-specific therapeutic silencing, as a new approach to complement existing therapies. Mouse CD4 and CD8 T cell-targeted TGF-{beta} agonists selectively and potently silence antigen-specific T cell responses in OVA-immunized mice by suppressing pro-inflammatory effector, cytotoxic, and T follicular helper programs, while skewing cells toward a quiescent state biased toward regulatory and type 17 T cell phenotypes. Similarly, human CD4 and CD8 T cell-targeted TGF-{beta} agonists precisely and effectively suppress live-attenuated influenza vaccine (LAIV)-induced T cell activation and expansion in human spleen organoids. Correspondingly, CD4 T cell-targeted TGF-{beta} agonist effectively ameliorated disease activity and promoted disease remission in CD4 T cell-driven models of autoimmune neuroinflammation and allergic airway inflammation, demonstrating efficacy in both prophylactic and established inflammatory settings. Moreover, both CD4 and CD8 T cell-targeted TGF-{beta} agonists ameliorated disease activity in graft-versus-host disease. Additionally, a human CD19 B cell-targeted TGF-{beta} agonist robustly inhibits germinal center B cell-to-plasmablast maturation and antibody responses in LAIV-stimulated human spleen organoids. These early-stage results suggest that cell-selective TGF-{beta} agonism merits further investigation as a versatile therapeutic approach for the precise silencing of pathogenic adaptive immune responses.

immunology↗

bioRxiv2026

Joint Segmental Duplication Co-option Drives Human-specific Transcriptional Readthrough and Expression Fine-tuning of NPEPPS-TBC1D3

Segmental duplication (SD) is a major driver of functional changes in evolution and disease. Many genes embedded within SDs, such as NPEPPS and TBC1D3, display substantial copy number variation (CNV) across individuals. Yet, the precise identification of the functional copies and their transcriptional outputs remains largely unstudied. Focusing on NPEPPS and TBC1D3, we illustrate human-specific expression fine-tuning mechanisms associated with readthrough transcripts. We identified a human-specific NPEPPS-TBC1D3 digenic genomic structure that originated from a joint SD pair and became fixed across populations. Experiments demonstrate that this structure generates NPEPPS-TBC1D3 readthrough transcripts, which are the predominant isoforms of TBC1D3 expression in various cell types, fine-tuning its protein level. Furthermore, a human-specific hypomethylation signal within an upstream CpG island of NPEPPS precisely pinpoints the expressed TBC1D3 paralog. Moreover, we reveal transcriptional readthrough events are [~]3-fold enriched for joint-SD-associated transcriptional readthrough (JSDTR) and identify 109 JSDTR gene pairs, including neurodevelopmentally important pairs and clinically interesting SERF1A/B-SMN1/2. Taken together, our findings comprehensively describe an example of how a joint SD event shaped evolution and suggest that JSDTR is a broad mechanism for the emergence of new functions.

genetics↗

bioRxiv2026

Dual Inhibition of MYRF Cleavage by Its JM Region and PAN-1 CCT Gates Developmental Timing in C. elegans

Post-embryonic development proceeds through discrete stages, yet the mechanisms that coordinate transitions between stages remain incompletely defined. The transmembrane transcription factor MYRF undergoes intramolecular cleavage to release a nuclear-localized fragment essential for developmental progression in C. elegans. Previously, we showed that PAN-1 as a key partner required for MYRF activity during development. PAN-1 promotes MYRF trafficking to the cell membrane--an essential step for MYRF cleavage--through interactions between their extracellular domains (Xia et al., 2021). Here, we show that MYRF-1 cleavage and nuclear translocation oscillate with larval stage transitions in C. elegans, peaking mid-to-late stage and being suppressed during molts. Using endogenous gene editing and mutant reporters, we identify an uncharacterized juxtamembrane (JM) region in MYRF-1 that self-inhibits cleavage. JM deletion triggers premature MYRF-1 nuclear entry, early lin-4 activation, growth defects, and adult lethality. We further demonstrate that the cytoplasmic tail (CCT) of the transmembrane protein PAN-1 acts as a predominant trans-inhibitor of MYRF-1 cleavage, coupling extracellular association with cytoplasmic inhibition. PAN-1 CCT deletion causes near-constitutive MYRF-1 nuclear accumulation, leading to premature lin-4 activation, accelerated M-cell division, and larval lethality. Removing these inhibitory mechanisms on MYRF-1 cleavage overrides nutrient-responsive developmental checkpoints. These findings uncover dual inhibitory mechanisms governing MYRF-1 cleavage and establish MYRF-1 cleavage as a key gatekeeper of developmental timing.

developmental biology↗

bioRxiv2025

Developmental changes in the morphology and three-dimensional arrangement of antennal hair plates in crickets

Antennae of insects are essential mechanosensory organs that facilitate active tactile exploration and spatial navigation. Hair-plate sensilla at the base of the antenna flagellum provide proprioceptive inputs to detect their position. In hemimetabolous insects, such as crickets, the first instar immediately after hatching also possesses antennae, but the developmental dynamics and spatial organization of antennal hair plates remain poorly understood. Here, we present a comprehensive three-dimensional analysis of the antennal hair plates in crickets across developmental stages, from the first instar to adulthood. Using scanning electron microscopy and confocal laser scanning microscopy, we demonstrated that hair plate sensilla were present from the first instars and maintained a highly stereotyped spatial arrangement throughout development. Three-dimensional quantification revealed that new sensilla added during molting were formed at specific sites within the hair plate clusters that had existed at the previous stage, maintaining the spatial pattern despite the substantial growth of the antenna. Multidimensional analyses indicated that the spatial arrangement of sensilla was consistent across individuals, suggesting that organization was genetically determined. Retrograde labeling of sensory afferents showed that sensory neurons in the hair plates converged their axons, extended axon collaterals into the ipsilateral region of the antennal mechanosensory and motor center, and ultimately projected to the subesophageal ganglion. There was no apparent difference in their projection site among hair plates, suggesting no evidence of topographic organization. Our findings highlight the conserved spatial organization of hair-plate sensilla in crickets, suggesting a robust proprioceptive system that provides reliable feedback of antennal position throughout development.

neuroscience↗

bioRxiv2025

Screening of Cellular Senescence Related Genes as Biomarkers and Therapeutic Targets for Glioblastoma by Integrated Machine Learning

Glioblastoma (GBM) is an aggressive brain tumor with limited prognostic biomarkers and therapeutic targets. This study applied an integrated machine learning (IML) framework to discover cellular senescence (CS)-related gene biomarkers and candidate therapeutic targets in GBM. Using Gene Expression Omnibus (GEO) training and validation cohorts, 113 machine learning models across 11 algorithms were integrated to pinpoint CS-associated gene signatures. Differential expression analysis combined with overlap of a CellAge senescence gene set yielded 129 CS-related differentially expressed genes (DEGs). Functional enrichment of these DEGs highlighted pathways related to cellular senescence and cell cycle regulation (Gene Ontology and KEGG). A multivariate classifier constructed via stepwise generalized linear modeling (GLM) and LASSO achieved high diagnostic performance (area under the ROC curve 0.92 in training, each independent validation set is over 0.85). Seven top-ranked genes from this model were validated, with TGF{beta}I emerging as the most robust biomarker (AUC > 0.85) and its elevated expression was associated with significantly shorter overall survival. Spatial transcriptomics and single-cell RNA sequencing localized TGF{beta}I expression to tumor cell clusters harboring high copy number variation (CNV) burdens. Immune microenvironment profiling linked TGF{beta}I expression with increased macrophage infiltration. Finally, single-cell gene set enrichment (scGSEA) and AUCell analyses indicated enrichment of ECM-receptor interaction signaling in TGF{beta}I-expressing cells. In summary, IML combined with spatial and single-cell transcriptomics identified TGF{beta}I as a potent CS-related biomarker and a promising therapeutic target in GBM.

cancer biology↗

bioRxiv2025

Receptor-tethered orthogonal IL-2 enhances regulatory T cell therapy

Regulatory T cell (Treg) therapy is an emerging platform for controlling immune overactivation. Efficacy of Treg therapy is limited by the poor persistence of infused Tregs due to insufficient IL-2, which is essential for Treg survival and function. IL-2 activates many immune cells besides Tregs, imposing a challenge for the selective provision of IL-2 to infused Tregs. In this study, we found infusions of orthogonal (ortho) IL-2 failed to enhance Tregs engineered with a corresponding orthoIL-2 receptor (IL-2R) in a mouse model of autoimmune diabetes. We then developed a receptor-tethered orthoIL-2 by optimizing the combination of IL-2, IL-2R, and the linker connecting them to achieve autocrine signaling selectively in engineered Tregs. Tregs expressing the tethered orthoIL-2 showed autocrine IL-2 signaling in vitro, enhanced CD25, CTLA-4, and Foxp3 expression, persisted without exogenous IL-2 in vivo, and prevented autoimmune diabetes using as few as 2,000 Tregs. Knocking the tethered orthoIL-2 construct into the Foxp3 locus enabled Treg-specific expression, with the additional benefit of positively reinforcing tethered orthoIL-2 expression through the activation of the Foxp3 gene by enhanced IL-2 signaling. Together, these results illustrate a safe and effective cell-engineering solution for overcoming Tregs dependency on exogenous IL-2, thereby achieving superior therapeutic efficacy.

immunology↗

bioRxiv2025

A global P-Process map to avoid P-value abuse

P-abuse is serious in difference identification analysis of data. How to avoid P-abuse is a huge challenge. Here, we evolve P-value (a single value) to P-Process (a global landscape of P-values under different sample size) to help researchers correctly recognize and use p-value. We observed -ln(P-Process) after rotation has very similar morphology with Wiener Process (or Brownian motion). Based on this property, for any sample size, we estimated the 95% fluctuation range of P-value and further estimated how many samples (N95()) could make sure 95% of P-values less than the given significant level . Tests proved that the estimation obtains a good performance with only a small number of samples in each group. For broader accessibility, a free web-service, P-Process Map, is available online to show the whole landscape of P-Process. At the end of the article, we explained 10 of the most typical P-abuse problems which can be easily voided by using P-Process. This "rethinking" of P-value from a higher position, which is profoundly different from the way we have seen this for the past century, would yield a new era - 2P era in which hypothesis testing is strongly required to evolve from P-value to P-Process.

bioinformatics↗

bioRxiv2025

Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data

DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, we introduce a first approximation of the species search engine (SSE). Our SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. We discuss the advantages and limitations of the proposed approach and the possibility of extending it to other tissues.

zoology↗

bioRxiv2025

Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site

While a number of efficient chemical proteomics methods are available for determining protein targets of pharmaceutical drugs, each approach exhibits its own "blind spot" and development of complementary techniques is needed. Here, we introduce the Above-Filter Digestion Proteomics (AFDIP) approach based on the monitoring of the rate of trypsin digestion. Digestion rate is decreased at the site of ligand binding to its target protein, while other sites may simultaneously experience an increase the digestion rate. Molecular dynamics (MD) simulations revealed that this increase may be due to allosteric structural changes related to backbone flexibility. We showcase the utility of AFDIP for deconvoluting the targets of versatile drugs and metabolites. Like other techniques, AFDIP allows for a two-dimensional analysis, with the second dimension based on drug concentration. AFDIP exhibits structural resolution, identifying drug target binding sites within [≤]10 [A], and for larger proteins often [≤]5 [A] of the crystallography-determined binding sites. Compared to earlier introduced limited proteolysis approaches, AFDIP provides easier sample preparation, deeper proteome analysis and broader sequence coverage. AFDIP is expected to find its place among the most efficient chemical proteomics methods currently available.

biochemistry↗

bioRxiv2025

IQI: Individualized Quantitative trait loci (QTL) Index

There is currently no standard efficient method to precisely detecting and characterizing the difference of quantitative trait loci (QTL) effect among groups and/or populations at individual level. The main reason is that the traditional global regression based QTL analyses can only derive an overall effect of genetic variants on the quantitative trait in a specific group. It is a big challenge to obtain the individual-level QTL effect, which is necessary for accurate testing and precise characterization. Here, we first proposed an individualized QTL index (IQI) that represents the degree of regulation between genetic variants and the trait for each individual. Based on IQI, Differential QTL (DQ) analysis framework was presented to accurately detect the case-control differences in more detail. In addition, IQI can be a new feature/biomarker applied to various accurate bioinformatics analysis, such as differential analysis, disease prediction, and survival analysis. Overall, IQI affords a new perspective on pathogenic mechanisms and will facilitate the study of genetic regulation more detailedly and precisely.

bioinformatics↗