Biology subjects

Xing, Y.

Publications and source records attributed to Xing, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Highly Adaptive Conductive Polymer Electronics Enhance Neural Data and Learning Accuracy

Human skin, the bodys largest organ, plays a vital role in sensing and transmitting neuronal, mechanical, and biochemical signals, making it an essential non-invasive interface for health monitoring, rehabilitation, and human-machine interaction. However, aging-related changes, including thinning, increased wrinkling, dryness, and altered collagen structure, significantly impact electrical impedance, conductance, and contact stability, challenging the fidelity and consistency of bioelectronic signal acquisition. Here, we address this gap by developing "AdapSkin," an age-adaptive, skin-mimicking, bio-adhesive, and stretchable polymeric electronic skin interface that seamlessly conforms to diverse skin properties, enabling high-fidelity and high-density electrophysiological recording. The soft electrodes of AdapSkin are composed of an aqueously processed, homogeneously mixed organic nanocomposite with a conductive polymer percolation network, forming a gel-like interface that reduces modulus and enhances skin-electrode contact. The materials platform achieves extraordinary softness and electrical stretchability of up to 1200% through a double-network composite structure. AdapSkin significantly minimizes age-induced variations in interfacial impedance and signal-to-noise ratio (SNR), improving signal consistency for neuromuscular assessment, prosthetic control, and rehabilitation applications. Scalable fabrication enables the creation of large-area electrode arrays, which reduces motion artifacts, improves sEMG mapping reliability, and ensures long-term signal stability across various age groups. Machine learning analysis further demonstrates AdapSkins superior accuracy in gesture classification for elderly users, highlighting its potential to enhance prosthetic control, assistive robotics, and rehabilitation for individuals with sarcopenia and neuromuscular decline. By improving signal quality and adaptability in aging populations, AdapSkin advances fair bioelectronic interfaces, fostering more equitable and effective healthcare technologies for age-related conditions.

bioengineering↗

bioRxiv2025

Comparison of Human Melanoma Single Cell Profiles to Evolutionary Medicine Model Xiphophorus Provides Insights In Disease Control

Melanoma remains one of the deadliest forms of cancer. Despite recent therapeutic advances including immune checkpoint inhibitors and small-molecule kinase inhibitors, patients frequently develop treatment resistance. Novel models are needed to devise strategies that overcome resistance and further reduce melanoma-related mortality. Interspecies hybrid fish from the Xiphophorus lineage develop mutant Epidermal Growth Factor Receptor (EGFR)-driven melanomas that display morphology, bulk gene expression, disease initiation and progression processes mimicking those of human melanomas. These similarities have enabled their comparative use in evaluating why human melanomas exhibit cancer cell plasticity, including dynamic transitions between proliferative and invasive states. However, it remains unclear whether Xiphophorus melanomas recapitulate some or all of these features. To address this, we performed single-nucleus RNA sequencing (snRNAseq) analysis of Xiphophorus melanomas. Multiple cancer cell types mirroring the human melanoma cell populations were identified, including proliferative cancer cells, dedifferentiated neural crest-like cells, mesenchymal-like cancer cells in addition to fibroblast, endothelial, and immune cells. Employing comparative analyses with results from human melanoma studies, it is demonstrated that Xiphophorus melanomas faithfully mimic the cellular heterogeneity observed in human melanoma.

genetics↗

bioRxiv2025

Environmental Heterogeneity Altered the Growth Fitness of Antibiotic-Resistant Mutants and the Resistance Prevalence in Escherichia coli populations

Antibiotic resistance is one of the most critical issues in public health. As antibiotic-resistant bacteria emerge under certain selection pressure, their further proliferation can facilitate the prevalence and maintenance of the antibiotic resistance. Here, we investigated which environmental factors could affect the growth fitness of antibiotic-resistant Escherichia coli strains using growth competition assays. We found that when antibiotic resistance selection pressure was removed, lower temperature and nutrient limitations, especially iron (Fe) deficiency, fostered a better fitness to resistant mutants when co-cultivated with the wild type, whereas changes in pH or salinity (Na or K) did not. Moreover, the growth advantage of resistant mutants under the selection pressure was reversed by suboptimal conditions like acidic/basic pH, high K salinity, and Fe limitation. These identified key environmental factors influencing the growth fitness of antibiotic-resistant mutants provide important insights into the prediction and mitigation of antibiotic resistance in heterogeneous environments.

microbiology↗

bioRxiv2025

A 3D framework for delimiting a polyploid complex in Rorippa (Brassicaceae): combining trait evolution, herbarium records, and machine learning

Species delimitation in polyploid complexes remains a fundamental challenge due to pervasive morphological overlap and genomic redundancy. We examined the Rorippa dubia-indica complex (Brassicaceae), a polyploid lineage comprising tetraploid and hexaploid taxa. We developed an integrative 3D framework (Delimitation, Distribution, and Decoding) that synthesizes spatiotemporal data from field (2017-2020; n = 3,136) and herbarium (1893-2021; n = 2,015) collections to diagnose misidentification, model distributions, and reconstruct classification criteria used in polyploid complexes. Morphological traits with varying degrees of plasticity were evaluated under controlled conditions to identify stable diagnostic characters. Seed arrangement, petal number, and genome size or ploidy level exhibited clear interspecific differentiation. Phylogenomic analyses based on chloroplast genomes further defined species boundaries clarified by these taxonomic traits. We then revised herbarium specimens and applied machine learning classification models to assess the extent of specimen misidentification and to recover the trait-based rationale behind species assignments. Initial misidentification rates reached 12-50% across virtual or physical specimens, largely due to reliance on plastic traits. These errors substantially distorted spatial distribution models and future climate projections. Our findings underscore the need for secondary specimen evaluation and demonstrate the importance of integrating morphologic and phylogenetic inference with machine learning tools to resolve morphologically overlapping polyploid complexes. This approach offers direct applications for biodiversity assessment, evolutionary research, and conservation planning.

systems biology↗

bioRxiv2025

Bacterial Community Structure and Diversity of Common Mosquito Species in Chengdu: Insights from PacBio Third-Generation

Mosquitoes, as critical vectors of diseases such as Japanese encephalitis, dengue fever, and yellow fever, pose significant public health risks in Chengdu, a subtropical city in southwestern China. This study integrated ecological surveillance and PacBio third-generation sequencing to characterize the symbiotic microbiota of four dominant mosquito species (Aedes albopictus, Culex pipiens, Culex tritaeniorhynchus, and Armigeres subalbatus) across urban and rural habitats. From 2020 to 2024, mosquito density monitoring revealed spatial heterogeneity(Aedes albopictus, Culex pipiens, Culex tritaeniorhynchus, and Anopheles sinensis), with outer ring areas exhibiting the highest density (34.69 mosquitoes per trap), while central urban zones had the lowest (3.60). Sequencing identified 717 high-quality Amplicon Sequence Variants (ASVs), with Aedes albopictus harboring the most unique bacterial species (191). Beta diversity analysis demonstrated distinct microbial clustering among species, driven by Pseudomonadota dominance (54.27-93.89%) and variations in secondary phyla (Bacteroidota, Campylobacterota). Functional prediction via KEGG highlighted elevated human disease-associated pathways in Ae. albopictus, contrasting with reduced environmental adaptation activity. Notably, Wolbachia (clade B) and Klebsiella variicola exhibited species-specific abundance patterns, underscoring their roles in pathogen suppression and public health risks. Unclassified taxa (norank_d Bacteria, Candidatus_Hydrogenedentes) clustered near novel mosquito-associated spirochetes, suggesting underexplored functional microbiota. This study provides foundational data for understanding mosquito-microbe interactions and informs strategies for mitigating vector-borne disease. Author SummaryMosquito-borne diseases such as dengue fever and Japanese encephalitis pose severe public health risks in subtropical regions, yet critical gaps remain in understanding how mosquito-associated microbes influence disease transmission in under-resourced areas. Chengdu, a megacity in southwestern China, faces unique challenges due to rapid urbanization, climatic suitability for mosquito proliferation, and disparities in public health infrastructure compared to eastern coastal regions. This study integrates five years of ecological surveillance (2020-2024) and PacBio third-generation sequencing to map mosquito density patterns and characterize symbiotic bacterial communities in four dominant mosquito species (Aedes albopictus, Culex pipiens, Culex tritaeniorhynchus, and Armigeres subalbatus). Key findings reveal stark spatial heterogeneity in mosquito density, with rural outer-ring areas harboring 10-fold higher densities (34.69 mosquitoes/trap) than urban centers. Notably, Aedes albopictus exhibited the highest diversity of unique symbiotic bacteria (191 species), including Wolbachia (clade B), known to suppress arboviruses like dengue. Conversely, Armigeres subalbatus carried high abundances of Klebsiella variicola, an emerging human pathogen linked to severe infections. Functional analyses further highlighted elevated human disease-associated pathways in Ae. albopictus, underscoring its dual role as a disease vector and microbial reservoir. This work provides the first comprehensive baseline data on mosquito-microbe interactions in Chengdu, identifying actionable targets for biocontrol (e.g., leveraging Wolbachia) and early-warning systems for pathogen surveillance. By bridging ecological, molecular, and public health perspectives, our findings offer critical insights for mitigating neglected tropical diseases in subtropical regions where socioeconomic disparities intersect with high disease burdens.

microbiology↗

bioRxiv2025

Glycosylation-enabled Site-specific Growth Factor Engineering for Biomaterial Functionalization

In native tissue environments, growth factors (GFs) are often physically associated with the extracellular matrix (ECM) framework. Despite the enormous potential of the chemoselective click chemistry for GF functionalization of biomaterials to recapitulate such GF-ECM association, its application is limited by the lack of a universal strategy for reliable production of clickable GFs. Here we present a novel platform technology that leverages intrinsic post-translational protein glycosylation to enable site-specific metabolic engineering of GFs with azido tags for subsequent ECM hydrogel conjugation. Using Vascular Endothelial Growth Factor as a model, we demonstrated efficient, glycosylation-dependent azido incorporation during its recombinant expression with preserved bioactivity. We further expanded the utility of this strategy to non-glycosylated proteins through engineered N-linked glycosylation via the incorporation of a signal peptide that directs newly synthesized proteins to the secretory pathway where glycosylation takes place along with a sequon for glycan attachment. The resulting GF with site-specific azido incorporation can be effectively immobilized within dibenzocyclooctyne-bearing ECM hydrogel via the copper-free click chemistry, exhibiting sustained GF retention and delivering augmented angiogenic responses. Our approach thereby offers an unprecedented opportunity to streamline recombinant protein engineering for biomaterial functionalization in tissue engineering and regenerative medicine applications.

bioengineering↗

bioRxiv2025

Cross-species analysis of experimental PH at single cell resolution reveals prominent contributions Ednrb+ EC and Dhcr24+ macrophage populations

BackgroundAnimal models are used widely to study pulmonary hypertension (PH). The cell populations that respond to disease-inducing stimuli in these models and their relationship to human disease remain incompletely defined. Materials and methodThis study analyzed the relationship between several rodent models of PH and human disease at single-cell resolution. scRNA-seq was performed on lungs from mice exposed to hypoxia or Sugen/hypoxia, rats exposed to monocrotaline, and controls. A cross-species single-cell dataset was integrated with human lung cell atlas (HLCA) and single-cell dataset from idiopathic pulmonary arterial hypertension (IPAH) to identify overlapping cell subsets between experimental and human disease and species. ResultsHigh levels of overlap were found between species and models of PH, HLCA, and IPAH datasets. Cell subsets perturbed in rat and mouse PH were similar to those found in human disease, with macrophages and endothelial cells being most affected. A novel Dhcr24high macrophage subset harboring both tissue-remodeling and pro- inflammatory features was consistently increased across models. Several functionally diverse endothelial subtypes were found, including novel Ednrb+ and Nox2+ subpopulations, reflecting enhanced apoptosis, dysregulated angiogenesis and proliferation, and reactive oxygen species-mediated stress. These macrophage and endothelial subtypes expressed numerous PH drug target genes, and exhibited potential disease-specific intercellular interactions involving Angptl4, Cxcl12, and Sema3 signaling. Disease-associated changes in these populations were confirmed by immunofluorescence in lung tissues from animals and patients. ConclusionsWe established a comprehensive cross-species single-cell atlas of mainstream rodent PH models, highlighting several novel macrophage and endothelial subtypes and signaling motifs potentially contributing to human disease.

bioinformatics↗

bioRxiv2025

Gastrointestinal colonization as a source of Staphylococcus aureus in atopic dermatitis

Atopic dermatitis (AD) is a prevalent inflammatory skin disease with complex pathogenesis. Both skin and gut microbiota influence AD, with Staphylococcus aureus, in particular, exacerbating the disease. However, the relationship between S. aureus colonization in the gut and skin, and whether it affects AD, remains unclear. Using a combination of culture-based methods, microbiome analysis, and genome sequencing of S. aureus from multiple body sites of children with and without AD, we found that the gut represents a major reservoir of genetically diverse S. aureus that is transmitted to the skin, including mutants associated with worse disease. We validated this association between S. aureus gastrointestinal colonization and AD in an independent human cohort and demonstrated its direct effect on disease in an infantile AD mouse model, wherein S. aureus gastrointestinal colonization worsened skin inflammation. Overall, this study identifies a previously unrecognized S. aureus reservoir, with implications for microbiota-targeting therapies in AD.

microbiology↗

bioRxiv2025

Nonenzymatic RNA copying with a potentially primordial genetic alphabet

Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U, because of the stronger G:C vs. A:U base pair, and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s2U) and inosine (I) form by deamination of 2-thiocytidine (s2C) and A respectively. We used thermodynamic and crystallographic analyses to compare the I:s2C and A:s2U base pairs. We find that the I:s2C base pair is isomorphic and isoenergetic with the A:s2U base pair. The I:s2C base pair is weaker than a canonical G:C base pair, while the A:s2U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s2U, s2C, I and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s2C and s2U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s2U, s2C, I and A, and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying. Significance StatementA long-standing challenge in primordial nonenzymatic RNA copying chemistry is the biased incorporation of C and G over A and U due to differences in base pair strength. We hypothesized that 2-thiopyrimidine substitution could help overcome this bias since A:s2U is a stronger version of the A:U base pair, and I:s2C is a weaker version of the G:C base pair. This study explores the efficacy of a potentially primordial genetic alphabet consisting of s2U, s2C, A and I. Our results show that A:s2U and I:s2C pairs are isoenergetic and isomorphic. Our findings highlight the potential of this alternative genetic alphabet to yield a more balanced incorporation of all nucleotides, facilitating information propagation by nonenzymatic RNA copying during the origin of life.

biochemistry↗

bioRxiv2025

A SNP Foundation Model: Application in Whole-Genome Haplotype Phasing and Genotype Imputation

Millions of human genomes have been genotyped by national biobanks worldwide. Training large language models (LLM) with this data may lead to a universal model of human genome with tremendous potential. Yet the quadrillions (1015) of nucleotides-- resulting from genome length multiplied by population size--pose formidable challenges for modeling. In this study, we propose a novel AI framework designed to scale with this data and support diverse analytical tasks. To demonstrate this scheme, we developed SNPBag--a foundation model focusing on single nucleotide polymorphism (SNP). With 0.8 billion parameters, it is trained on one million synthesized human genomes, corresponding to a total of 6 trillion SNP tokens. SNPBag showed superior performance in benchmarking of multiple tasks. In genotype imputation, it achieves state-of-the-art (SOTA) accuracy. In haplotype phasing, it rivals the best method with a 72-fold speedup. By encoding 6 million SNPs per genome into a 0.75 MB embedding, SNPBag enables efficient storage, transfer and downstream applications. In particular, the genome embeddings facilitate rapid ancestry inference across global populations and detection of genetic relationships up to 12th-degree relatives. Collectively, SNPBag introduces a new paradigm for scalable, unified and multitask analysis of the ever-growing human variation data.

genomics↗

bioRxiv2025

A Recessive oca2 Mutation Underlies Albinism in Xiphophorus fish

Oculocutaneous albinism (OCA) is a group of genetic disorders characterized by impaired melanin production, leading to reduced pigmentation in the skin, hair, and eyes. Xiphophorus, a genus of small freshwater fish, has been a pivotal model organism in pigmentation disorder research, providing key findings in the genetic pathways governing physiological and pathological pigment cell biology. Leveraging the well-established research framework provided by Xiphophorus, we have identified a spontaneously occurring albinism phenotype in swordtail fish Xiphophorus hellerii. Genetic mapping of albino fish showed that albinism is associated with a recessive mutation in the oca2 gene. This discovery provides a novel opportunity to explore functions of oca2 gene in pigment cell differentiation, pigment synthesis, melanosome assembly and transportation function and amelanotic melanoma development.

genetics↗

bioRxiv2025

Single-cell spatial transcriptome reveals pathological features of human hippocampus with sclerosis

More than half of epileptic patients ultimately turned to intractable epilepsy. Mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS), the most common type of intractable epilepsies, whose pathological mechanism remains elusive. Here, using 42 human hippocampal samples from surgical donors of MTLE (32 with and 10 without HS) through single-cell resolution Stereo-seq and histologcial experiments, we revealed spatially pathological changes of gene expression and cell type composition with HS systematically. After precise parcellation of hippocampal subregions and differentially expressed gene (DEG) analysis between each region with and without sclerosis, we found Cornu Ammonis (CA) subregions with higher number of DEGs were vulnerable to sclerosis, especially CA1 and CA3. Within CA1, we found that CA1-superficial and proximal areas were more vulnerable than CA1-deep and distal areas in sclerosis. Meanwhile, after analyzing 350,795 segmented cells from Stereo-seq, we found dramatically increasing density of astrocyte accompanied with significantly decreasing density of excitatory neurons in CA1, especially superficial and proximal CA1, and CA3 in sclerosis. In these two vulnerable subregions, proliferative astrocyte (P_astrocyte) and reactive astrocyte (R_astrocyte) were found to be enriched whereas apoptotic subtype of astrocyte (A_astrocyte), related with apoptotic pathway, was mainly located in alveus, which strengthened cell communication with reactive microglia (R_microglia) in HS, revealing the novel pathological feature in our work. The pseudotime analysis indicated that CA excitatory neurons underwent synaptic impairment, energy dysfunction, aging, and finally losing cell identity until death through autophagy or apoptosis. Besides, we also found a resilient subtype, EX_CA2-4.3, highly expressed extracellular matrix related genes including PDYN, and was increasing the interaction of BDNF-NTRK, NFASC-CNTN1 to withstand the damage from sclerosis. Together, our study provided a reference of human hippocampus with and without HS caused by MTLE, and highlighted the potential pathological mechanism on molecular and cellular level of MTLE-HS.

neuroscience↗

bioRxiv2025

Pathogen and pest communities in food security crops across climate gradients: Anticipating future challenges in the Great Lakes region of Africa

CONTEXTTropical cropping systems must adapt to the current and future geographic distribution of pathogen and pest communities. An important research gap is how climate change may shift the distribution of pathogens and pests in tropical lowlands and highlands. OBJECTIVEWe evaluated the current geographic risk of 27 pathogens and pests in the production of four food security crops (banana, cassava, potato, and sweetpotato) in the Great Lakes region of Africa, and the potential future risk under climate change. Models for each pathogen and pest indicate the potential for changes in geographic distribution, with model fit indicating the potential for decision support systems to facilitate management. METHODSFirst, cropland connectivity analysis identified locations likely important in the spread of crop-specific pathogens and pests, such as locations in Rwanda and Burundi. Second, we surveyed the 27 economically important pathogens and pests in Rwanda and Burundi, mapping the distribution of each across climate gradients and quantifying patterns of association. Third, we used machine learning to develop models of each species as a function of environmental variables, including host landscape variables. We also evaluated the increase in temperature across altitudes under future climate change scenarios in this region. RESULTS AND CONCLUSIONSAmong the ten machine-learning algorithms evaluated, random forests and support vector machines generally performed best for predicting severity and infestation. Host landscape variables were useful predictors for some species. Based on climate matching, 44% of the pathogens and pests could become more common with warmer temperatures at higher altitudes, while 17% may become less common. SIGNIFICANCEThis study indicates adaptation priorities for crop health in a region with multiple challenges to agricultural sustainability. The models developed here also indicate which species may have more potential and relevance for future development of pathogen and pest forecasts.

ecology↗

bioRxiv2024

Preclinical Proof of Concept for SNAPTM-TIL: a personalized, next-generation tumor-infiltrating lymphocyte therapy platform

Tumor-infiltrating lymphocyte (TIL) therapy, which involves extracting, expanding, and reinfusing immune cells to target cancer cells, has shown promise in melanoma treatment, but requires optimization for broader efficacy. The success of TIL therapy depends on the recognition of tumor-associated antigens, but neoantigen-reactive T-cells are often rare and exhausted in less immunogenic malignancies. Isolating T cells enriched in neoantigen reactivity prior to in vitro expansion and reinfusion may improve the response rates. To this end, our proprietary Specific Neo-Antigen Peptides (SNAP) technology platform improves the accuracy of neoantigen prediction and validation by combining advanced computational modeling and PepSeq, a high-throughput screen for the physical credentialing of putative neoantigens based on their affinity to bind patient-specific HLA class II proteins. This approach allows for the education and enrichment of TILs (SNAP-TILs) with personalized, predefined, highly immunogenic neoantigens prior to expansion. Using the SNAP platform, we consistently achieved, on average, an SNAP-TIL product comprising 96% CD3+ cells, with a mixture of 75% effector and 23% central memory cells. SNAP-TILs exhibited greater efficacy and selectivity in immune infiltration than TIL, which was expanded by the rapid expansion protocol alone using ex vivo models. SNAP-TIL was also reactive in highly and poorly immunogenic tumors, with 70% and 50% tumor growth inhibition in melanoma and pancreatic patient-derived xenograft models, respectively. This study demonstrates the novel benefit of our Personalized Neoantigen Pipeline approach, potentially providing a durable antitumor immune response for a larger proportion of cancer patients.

immunology↗

bioRxiv2024

Origins and Implications of Intron Retention Quantitative Trait Loci in Human Tissues

Intron retention is a type of alternative splicing in which introns remain unspliced in mature RNA transcripts. In order to explore the landscape and consequences of genetically regulated intron retention, we perform an intron retention quantitative trait loci (irQTL) analysis in 49 human tissues across 838 individuals. We identify 8,624 unique intron retention events associated with genetic polymorphisms. 1,369 irQTLs (16%) are also associated with genome-wide association study (GWAS) traits, suggesting that genetically regulated intron retention may play a causal role in the regulation of these GWAS traits. 1,999 irQTLs (23%) colocalize with eQTLs to their respective gene, suggesting that intron retention and steady-state gene expression levels are regulated by shared sets of genetic variants. Through a colocalization analysis of irQTL:eQTL events, we demonstrate that irQTLs are sufficient to generate eQTLs when one of the alternatively spliced transcripts is preferentially targeted by the nonsense mediated decay (NMD) pathway. Surprisingly, for intron retention events whose potential NMD effects can be confidently predicted based on their positions within known gene annotations, we find that 58.8% (923/1570) of the colocalized irQTL and eQTL pairs show effect size directions that are discordant with the NMD model. Moreover, we find that irQTLs are significantly more likely to occur in the same gene with the same effect size direction as compared to exon skipping QTLs. Through mathematical modeling and analysis of experimental perturbation data, we provide evidence that eQTLs are able to generate irQTLs by altering the steady state ratios of spliced and unspliced transcripts, and we postulate that this mechanism may partially underlie the widespread intron retention observed previously in various biological conditions. Taken together, these results show that intron retention and steady state gene expression levels are closely intertwined to regulate phenotypic traits.

genetics↗

bioRxiv2024

BMP4 is sufficient to induce a caudal organizer

The caudal part of a vertebrate embryo consists of somites, neural tube, lateral plate mesoderm derivatives and the tailbud. However, the minimal conditions and factors sufficient to induce the caudal region, particularly in humans, remain unresolved. Here, we show that BMP4 alone, when administered at appropriate dosage, is sufficient to induce the formation of an organizer for caudal induction. This organizer induces caudal cell fate specification and morphogenesis in zebrafish embryos. In 3D human pluripotent stem cells (hPSCs) aggregates, BMP4 can induce an elongated embryonic structure characterized by caudal fates. Importantly, hPSCs instructed by BMP4 are sufficient to induce a secondary caudal region when grafted into the animal pole of the zebrafish embryo. Our study thus uncovers BMP4 as the inducer in the formation of a caudal organizer in the vertebrate embryo. Significance statementWe demonstrate that BMP4 alone can induce the formation of a caudal organizer, a critical structure that guides the development of the caudal region in vertebrates. Using zebrafish embryos, embryonic explants, human pluripotent stem cell xenografts, and 3D human stem cell aggregates, we show that this organizer replicates morphogenesis and key differentiation pathways seen in natural development. Our findings uncover a novel role for BMP4 and define the minimal requirements for inducing this organizer, offering new insights into vertebrate development and potential applications in regenerative medicine.

developmental biology↗

bioRxiv2024

Screening macrocyclic peptide libraries by yeast display allows control of selection process and affinity ranking

Macrocyclic peptides provide an attractive modality for drug development due to their ability to bind challenging targes, their small size, and amenability to powerful in vitro evolution techniques such as phage or mRNA display. While these technologies proved capable of generating and screening extremely large libraries and yielded ligands to already many targets, they often do not identify the best binders within a library due to the difficulty of monitoring performance and controlling selection pressure. Furthermore, only a small number of enriched ligands can typically be characterised due to the need of chemical peptide synthesis and purification prior to characterisation. In this work, we address these limitations by developing a yeast display-based strategy for the generation, screening and characterisation of structurally highly diverse disulfide-cyclised peptides. Analysis and sorting by quantitative flow cytometry enabled monitoring the performance of millions of individual macrocyclic peptides during the screening process and allowed us identifying macrocyclic peptide ligands with affinities in the low micromolar to high picomolar range against five highly diverse protein targets. X-ray analysis of a selected ligand in complex with its target revealed optimal shape complementarity, large interaction surface, constrained peptide backbones and multiple inter- and intra-molecular interactions, rationalising the high affinity and exquisite selectivity. The novel technology described here offers a facile, quantitative and cost-effective alternative to rapidly and efficiently generate and characterise fully genetically encoded macrocycle peptide ligands with sufficiently good binding properties to even therapeutically relevant targets.

biochemistry↗

bioRxiv2024

Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis

Orofacial cleft (OFC) is a common human congenital anomaly. Epithelial-specific RNA splicing regulators ESRP1 and ESRP2 regulate craniofacial morphogenesis and their disruption result in OFC in zebrafish, mouse and humans. Using esrp1/2 mutant zebrafish and murine Py2T cell line models, we functionally tested the pathogenicity of human ESRP1/2 gene variants. We found that many variants predicted by in silico methods to be pathogenic were functionally benign. Esrp1 also regulates the alternative splicing of Ctnnd1 and these genes are co-expressed in the embryonic and oral epithelium. In fact, over-expression of ctnnd1 is sufficient to rescue morphogenesis of epithelial-derived structures in esrp1/2 zebrafish mutants. Additionally, we identified 13 CTNND1 variants from genome sequencing of OFC cohorts, confirming CTNND1 as a key gene in human OFC. This work highlights the importance of functional assessment of human gene variants and demonstrates the critical requirement of Esrp-Ctnnd1 acting in the embryonic epithelium to regulate palatogenesis.

genetics↗