Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

SimulScan and Partial Least Squares: Visualizing swallowing through functional and dynamic imaging correlations

PurposeSwallowing is a complex function involving the precise coordination of muscles, nerves, and brain areas, and can be disrupted in a variety of neurological conditions. Current imaging studies to visualize the central control of swallowing cannot examine both the biomechanics of the swallow and the brain activity associated with swallow events. An updated version of SimulScan is introduced that provides high-quality and high-speed dynamic imaging, together with fMRI acquisitions, to enable data-driven analysis of swallowing function through a partial least squares correlation (PLSC) analysis. MethodsIntegrating updated dynamic imaging approaches, SimulScan can achieve dynamic MRI at 23.75 frames per second and BOLD fMRI at a 1.6 s TR. Five subjects were recruited and scanned with SimulScan twice and with videofluoroscopy to compare the preliminary reliability of measuring swallowing biomechanics and the test-retest relationship in correlated functional and dynamic components of PLSC. ResultsHigh reliability of biomechanical measures of swallowing were achieved across the two SimulScan runs. In addition, these showed moderate correlation with videofluorscopy measures. Correlations between dynamic and functional imaging across runs also showed high reliability indicating that SimulScan with PLSC can extract maps of linked correlations between the brain and the oropharyngeal region. ConclusionThe updated version of SimulScan with PLSC analysis enables the study of central control of swallowing, providing simultaneous biomechanical visualization of the swallow along with brain functional signals.

neuroscience↗

bioRxiv2025

TET1 non-catalytic activity shapes the chromatin landscape that directs de novo methylation establishment in the male germline

In the germline, DNA methylation is globally erased in primordial germ cells (PGCs), enabling establishment of sex-specific methylomes in prospermatogonia or oocytes. The catalytic activity of TET1 is required for complete demethylation in PGCs, yet sperm from Tet1-/- mice display methylation defects not explained by incomplete erasure. Instead, these defects arise from abnormal de novo methylation during development, coinciding with erosion of H3K4me3, a chromatin modification that blocks DNMT3A/3L. Using a catalytically inactive Tet1HxD mouse line, we demonstrate a non-catalytic role of TET1 in promoting H3K4me3 deposition and protecting a subset of sperm hypomethylated regions from aberrant methylation in prospermatogonia.

developmental biology↗

bioRxiv2025

Loss of cell cycle gatekeeping by 1 CNOT3 impairs hematopoietic stem and progenitor cell division and repopulating activity

Adult mammalian hematopoietic stem cells (HSCs) constitute a heterogeneous population responsible for generating various cell types in the blood throughout adulthood. Gene expression programs underlying regulation of self-renewal and differentiation of HSCs are tightly regulated. However, how post-transcriptional regulation of gene expression influences HSCs and hematopoiesis remains largely unexplored. Here, we report the critical role of CNOT3, a subunit of the CCR4-NOT complex, in regulating hematopoietic stem cells (HSCs) function in adult hematopoiesis. We observed that Cnot3 mRNA is highly expressed in HSCs and CNOT3 ablation in the murine Cnot3 conditional knockout mouse model resulted in anemia, reduced bone marrow cellularity and enhanced extramedullary hematopoiesis in spleen. Deletion of Cnot3 resulted in the early expansion of immunophenotypic HSCs which were then progressively lost over time. Cnot3 knockout hematopoietic stem/progenitor cells (HSPCs) failed to reconstitute hematopoietic systems of recipient animals in transplantation assays. Single-cell RNA sequencing (scRNA-seq) analysis of HSPCs revealed disruptions in lineage development and loss of HSCs. Transcriptomic profiling and cell cycle analysis demonstrated that Cnot3 deletion led to increased cycling activity in HSCs. Our results indicate that CNOT3 is critical for maintenance of homeostasis in HSCs and the hematopoietic system.

developmental biology↗

bioRxiv2025

FveOCRs - a database for open chromatin prediction in wild strawberry based on a large language model

BackgroundWoodland strawberry (Fragaria vesca) is a widely used model system for cultivated strawberries and Rosaceae for molecular genetic studies. Nevertheless, available databases for its cis-regulatory element identification are limited. With the emergence of large language models in plant research, strawberry research could benefit significantly from applying these models. One such model derived from Plant DNA Large Language Models (PDLLMs) effectively predicts open chromatin regions (OCRs), which are nucleosome-depleted areas typically associated with cis-regulatory elements. However, improvement of the models accessibility and utility will be needed to facilitate the models application in strawberry as well as other plant species. ResultsWe developed the FveOCRs database (http://liulab.online:33838/FveOCRLiuLabTestVer25), which predicts open chromatin regions located within 5,000 bp upstream sequences, the first and second introns and exons, and the longest introns in Fragaria vesca genes. Predictions were generated using a sliding-window approach based on one of the PDLLMs. In the database, users could predict open chromatin regions for input DNA sequences from any plant species and obtain visual graphs with precise predicted regions of open chromatins. ConclusionsThe FveOCRs database is the first database for open chromatin region prediction in Fragaria vesca based on a Plant DNA Large Language Model. It can also predict OCRs in user-provided DNA sequences from any plant species. The resource and its accessible visual graphs will facilitate discovery of cis-regulatory elements and engineering of gene expression in strawberry and other plant species.

bioinformatics↗

bioRxiv2025

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems

Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture.

microbiology↗

bioRxiv2025

Ethylene receptors are functionally conserved in calcium permeability across the green lineage

The gaseous hormone ethylene plays a key role in regulating plant growth and stress responses. Although Ca{superscript 2} has long been implicated in ethylene signaling, the identity of molecules controlling Ca{superscript 2} permeability involved has remained elusive. Here we show that Arabidopsis ethylene receptors ETR1 and ERS1 are Ca2+ permeable, and that ETR1 mediates ethylene-induced cytosolic Ca2+ increase and regulates hypocotyl elongation. Homologs of ETR1 from eight land plant and algal species also exhibit Ca{superscript 2} permeability, suggesting an evolutionarily conserved function. We further demonstrate ethylene enhances the Ca2+ permeability of ETR1 and its homologue from the charophyte Klebsormidium flaccidum. These findings uncover a previously unrecognized but conserved role of ethylene receptors in Ca{superscript 2} permeability regulation in the green lineage, with broad implications for Ca{superscript 2} signaling in plant development and environmental adaptation.

plant biology↗

bioRxiv2025

Migration patterns and hybridization within the Asian stonechat complex in response to a major geographical barrier

Long-distance avian migration is thought to be under strong natural selection. Facing geographical barriers, migrants display various patterns considered to be adaptive. For example, they may detour along either side around the barrier or cross it, requiring specialized behavioral adaptations. Variations within closely related taxa are excellent sources for understanding the evolutionary background of migration and how barriers are shaping migration routes. In Asia, some species are assumed to have a migratory divide in response to the major geographical barrier, the Qinghai-Tibet Plateau (QTP), including the stonechat taxa (Siberian Stonechat Saxicola maurus maurus and Amur Stonechat S. stejnegeri). As they detour along either side of the QTP, these taxa are believed to disfavor a crossing over the highland. However, the more southernly distributed Tibetan Stonechat (S. m. przewalskii) breeds on the QTP, suggesting adaptation to high elevation. To investigate migration patterns and the potentially associated genetic differences, we studied migration routes and population genetics of four populations around the assumed migratory divide in Russia and Mongolia, and of one from the QTP in China. Our results confirmed the existence of a migratory divide between maurus and stejnegeri, albeit with extensive hybridization. We observed both the hypothesized western and eastern routes, but also found individuals employing intermediate routes crossing the QTP, of which two-thirds were clear hybrids. Meanwhile, przewalskii followed a highland-crossing route and was genetically differentiated from maurus and stejnegeri. The diverse migration routes among Asian stonechats show differential responses towards the geographical barrier. The intermediate route may be associated with hybridization, and its conditional viability may facilitate gene flow between maurus and stejnegeri. The Asian stonechat complex thus offers great opportunities for novel research of the genetics and evolution of migration. The specific evolutionary background associated with inhabiting and crossing the QTP can offer new perspectives in this field. Teaser textMigratory divides can arise in birds because alternative routes around migratory barriers would select for behaviors to restrict hybridization. Hybrids of parental types that employ alternative routes are hypothesized to embark on intermediate routes that would expose them to suboptimal conditions, resulting in post-zygotic reproductive isolation. However, this hypothesis is challenged when a sister taxon actually breeds on the geographical barrier. This is the case in the Asian stonechat complex that breeds near or on the Qinghai-Tibet Plateau (QTP), the roof of the world. We demonstrated a migratory divide in central Siberia to Mongolia for race maurus and stejnegeri, yet showed also evidence for extensive hybridization. Hybrids migrated along a newly discovered intermediate route, seemingly viable and overlaps with the migration trajectory of race przewalskii over the eastern part of the QTP. The Asian migratory divide relative to the QTP thus provided new insights to the evolution of landbird migration.

evolutionary biology↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

In Vitro Fertilization Accelerates Female Reproductive Aging Through Early Ovarian Failure

Reproductive aging is characterized by the progressive decline of reproductive function, with broad implications for overall health and longevity. Environmental factors, including assisted reproductive technologies (ART), can accelerate reproductive aging by promoting premature ovarian failure in females. In vitro fertilization (IVF), though widely used and generally considered safe, is associated with lasting effects on offspring health. Using a mouse model that closely approximates human IVF, we demonstrate that IVF accelerates reproductive aging in female offspring by inducing premature ovarian failure. IVF-conceived females exhibit altered ovarian function, disrupted endocrine profiles, and transcriptomic and epigenetic changes consistent with premature reproductive decline. These findings reveal long-term consequences of IVF on female reproductive health and highlight the need to understand how early-life interventions influence reproductive longevity.

developmental biology↗

bioRxiv2025

CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies

Causal mediation analysis investigates whether the effect of an exposure on an outcome operates through intermediate variables known as mediators. Although progress has been made in high-dimensional mediation analysis, current methods do not reliably control the false discovery rate (FDR) in finite samples, especially when mediators are moderately to highly correlated or follow non-Gaussian distributions. These challenges frequently arise in DNA methylation studies. We introduce CoxMDS, a multiple data splitting method that uses Cox proportional hazards models to identify putative causal mediators for survival outcomes. CoxMDS ensures finite-sample FDR control even in the presence of correlated or non-Gaussian mediators. Through simulations, CoxMDS is shown to maintain FDR control and achieve higher statistical power compared with existing approaches. In applications to DNA methylation data with survival outcomes, CoxMDS identified eight CpG sites in The Cancer Genome Atlas (TCGA) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on lung cancer survival, and two CpG sites in the Alzheimers Disease Neuroimaging Initiative (ADNI) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on time to Alzheimers disease conversion.

bioinformatics↗

bioRxiv2025

Stage-resolved Spatial Multi-omics Reveals Myeloid Niches in Human Atherosclerotic Plaques

BackgroundAtherosclerosis, a leading cause of heart attack and stroke, involves intricate immune cell dynamics within arterial plaques, yet their spatial organization and functional roles remain elusive. MethodsWe combined Visium HD spatial transcriptomics, imaging mass cytometry, and single-cell RNA-seq across fatty-streak, advanced, and restenotic plaques to map myeloid architectures and relate them to lesion geography and extracellular matrix features. Slingshot trajectory analysis resolved macrophages differentiation path. In vitro, we tested microenvironmental and lipid cues separately: fibronectin (FN) exposure during PMA-driven THP-1 differentiation and oxidized LDL (oxLDL)-induced foam cell formation in murine bone-marrow derived macrophages (BMDMs). ResultsOur analysis identified seven macrophage subsets and two neutrophil populations with distinct spatial distribution and functional roles. In early lesions, neutrophils expressing MMP9, MPO, p47phox, TGF-{beta}1 and arachidonate 5-lipoxygenase (ALOX5), aligned with proteolysis, inflammatory processes, and endothelial-mesenchymal transition features. In advanced plaques, macrophage subsets exhibit specialized functions: Ki67+ proliferative macrophages localized near necrotic cores, sustaining local population; SPP1+ macrophages, enriched in lipid handling and tissue remodeling, are prone to apoptosis/ferroptosis, potentially promoting necrotic core expansion; and C3aR+ macrophages form antigen-presenting niches with elevated HLA-DR and CD74, engaging T cells possibly through CXCL12-CXCR4 signaling. Slingshot trajectories indicated progression from C3aR toward SPP1 remodeling states concentrated at fibronectin-rich rims. In vitro, FN increased MMP9 and TIMP1 in THP-1-derived macrophages, consistent with FN imprinting remodeling features characteristic of SPP1 macrophages in situ. Concurrently, oxLDL-treated BMDMs showed enhanced lipid-handling and remodeling modules consistent with the SPP1 program. ConclusionsThese findings define conserved myeloid niches and support a microenvironment-imprinting model that links ECM composition and lipid loading to macrophage state transitions, providing a framework for microenvironment-targeted therapies to stabilize plaques and mitigate cardiovascular risk.

pathology↗

bioRxiv2025

Comprehensive gene heritability estimation reveals the genetic architecture of rare coding variants underlying complex traits

Whole-exome sequencing (WES) enables high-resolution interrogation of the contribution of rare coding variants to complex trait variation. However, existing methods for heritability estimation attributed to rare-coding variants are often limited by the effects of linkage disequilibrium (LD) and by the sparse nature of rare variant data. We introduce FLEX (Fast, LD-aware Estimation of eXome-wide and gene-level heritability), a scalable and flexible framework for estimating and partitioning heritability across genes or sets of genes using WES data. FLEX integrates all coding variants- from common to ultra-rare - within a unifled model and corrects for LD-induced effects to improve the accuracy of heritability estimates. In addition, FLEX supports both individual-level and summary statistic data and is computationally efflcient for biobank-scale datasets. Through extensive simulations, we show that FLEX is well-calibrated while providing accurate heritability estimates. We applied FLEX to WES data across N = 153, 351 unrelated European ancestry individuals and 20 quantitative traits in the UK Biobank. We identifled 64 gene-trait pairs with signiflcant gene-level heritability (p < 0.05/18, 624 accounting for the number of protein-coding genes tested), among which rare coding variants explained 38% of gene-level heritability, on average. Compared to heritability estimates from genome-wide imputed SNPs, incorporation of rare and ultra-rare coding variants led to a 24.8% increase in heritability on average, while effect sizes at rare and ultra-rare variants are substantially larger ({approx} 18x on average). Partitioning across variant effect annotations, we flnd that predicted loss-of-function variants had stronger individual effects than missense variants (24% on average) while missense variants accounted for a greater share of rare coding heritability. Together, FLEX provides an adaptable and accurate approach for quantifying gene-level heritability, advancing our understanding of the genetic architecture of complex traits, and facilitating the discovery of trait-relevant genes.

genetics↗

bioRxiv2025

Atg16l1 promotes lung transplant tolerance by regulating glycolysis in macrophages

Lung transplant survival is limited by the development of chronic lung allograft dysfunction (CLAD), a type of graft rejection that lacks effective treatments. Autophagy plays a crucial role in maintaining cellular homeostasis. In a single-nucleotide polymorphism screen, we found that lung recipients with two copies of a common hypofunctional genetic variant of autophagy-related 16-like 1 rs2241880 (ATG16L1T300A/T300A), known to deplete this protein from macrophages, were more likely to develop early CLAD. To understand this, we used a mouse orthotopic lung transplant model. Recipients encoding myeloid cell-specific deletion of Atg16l1 (Atg16l1{Delta}/{Delta}) or who harbor an engineered orthologous mutation (Atg16l1T316A/T316A) showed similar susceptibility to CLAD. Transcript profiling and mitochondrial tracking studies indicated that increased mitochondrial damage and decreased autophagic removal of mitochondria in Atg16l1-deficient macrophages were associated with heightened activation of the hypoxia-inducible factor 1 (Hif1) pathway and accumulation of glycolytic transcripts. Metabolic analysis revealed reduced oxidative phosphorylation, increased glycolytic activity, and higher IL-1{beta} expression in Atg16l1-deficient macrophages. Notably, the development of CLAD in Atg16l1{Delta}/{Delta} lung recipients could be significantly prevented by additionally deleting Hif1 in myeloid cells or by treating with the glycolysis inhibitor 2-deoxyglucose. Our results show how a common autophagy-related genetic variant disrupts macrophage metabolism and impairs lung transplant tolerance, pointing toward potential therapeutic strategies to combat CLAD.

immunology↗

bioRxiv2025

Integrative multiomic analysis links TDP-43-driven splicing defects to cascading proteomic disruption of ALS/FTD pathways

Loss of nuclear TDP-43 is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although TDP-43 is known to regulate RNA processing, including repression of cryptic exons, we currently lack a systems-level understanding of the consequences of TDP-43 loss. To address this, we generated multiomic datasets, including RNA-seq and proteomics, from human iPSC-derived neurons depleted of TDP-43. We found that differentially spliced genes, many expressing cryptic exons, had the greatest protein reductions. Surprisingly, nearly half of differentially expressed proteins were neither mis-spliced, nor differentially expressed genes; most of these also had no reported mis-splicing in seven additional post-mortem and iPSC-derived neuron datasets. Integrative network analysis identified a high-confidence disease-specific subnetwork of over 700 interacting proteins, enriched for mRNA processing, synaptic function, and autophagy. Comparison with post-mortem ALS and FTD samples revealed convergent protein and pathway disruptions. We experimentally validated network-predicted effects of cryptic splicing in ATG4B, STMN2, and DAPK1. Our analyses reveal new TDP-43-dependent molecular cascades and nominate central genes as potential ALS/FTD therapeutic targets.

neuroscience↗

bioRxiv2025

Pocket-based molecule generation with an SE(3)-equivariant language model leads to a potent and selective HPK1 inhibitor with in vivo efficacy

Deep learning shows promise in structure-based drug discovery, yet challenges persist in generating pharmacologically plausible molecules with valid 3D conformation and decent binding mode in the pocket. We introduce SE3-BiLingoMol, an SE(3)-equivariant Transformer for pocket-based 3D molecule generation, addressing two key limitations of existing language-model approaches. First, it uses Geometric Algebra Transformers for SE(3)-equivariant handling of continuous 3D coordinates. Second, a bidirectional attention mechanism mitigates conformational errors accumulated during autoregressive sampling. These innovations enable SE3-BiLingoMol to generate 2D drug-like, 3D geometrically valid molecules with superior binding modes. Validated on DUD-E dataset containing over 100 targets, the model achieved state-of-the-art performance in de novo design and optimization. We applied SE3-BiLingoMol to design potent and selective inhibitors for HPK1, a promising immunotherapy target. Through an iterative human-AI workflow, integrating AI generation with experimental validations (X-ray crystallography, bioassays), we identified Cmpd. 6. This novel tetracyclic compound demonstrates potent HPK1 inhibition, excellent cellular activity, favorable pharmacokinetics, and robust anti-tumor in vivo efficacy as monotherapy and with PD-1 blockade. Our work establishes a sophisticated generative AI framework for 3D molecule design and demonstrates its application in developing cancer immunotherapy. Highlights[bullet] SE(3)-Equivariant Language Model for Molecule Generation: We introduce a dual-channel SE(3)-equivariant language model that supports de novo molecule design and optimization, addressing key challenges in prior language model-based 3D molecule generation approaches. [bullet]Discovery of Potent HPK1 Inhibitors: Application of this model led to the discovery of highly selective HPK1 inhibitors with robust in vivo efficacy, resulting in a promising lead compound. [bullet]AI-Guided Rational Drug Development Paradigm: This work establishes a paradigm for AI-guided rational drug development, showcasing AI as a "co-pilot" that inspires drug designers with novel ideas in an "evidence-based context".

bioinformatics↗

bioRxiv2025

Effector loss and gain drives pathogen host range at a fitness cost

Epidemic preparedness depends on tracking microbial evolution that drives shifts in ecological behaviors such as disease emergence. However, the genetic constraints for microbial host adaptation to emerge for generalist and specialist behaviors remain poorly described. Here, we show that generalist cereal pathogen Xanthomonas translucens arose from a specialist ancestor via the loss of a single effector gene, xopAL1. Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineage. However, this niche expansion via XopAL1 loss incurs a significant pathogenic fitness cost to colonize barley. Moreover, the specialist lineage gained an additional effector gene, xopAJ, which enhanced virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further identified key host pathways mediating resistance to the specialist lineage of X. translucens, opening avenues for potentially identifying targets for crop improvement. Our work provides an experimentally validated evolutionary framework to understand mechanisms of intergenera host jump. Overall, we demonstrate that single events of gene loss and gain shape ecological behaviors of pathogens by creating a dynamic trade-off between niche breadth and specialization.

microbiology↗

bioRxiv2025

Dual-patterned pluripotent stem cells self-organize into a human embryo model with extended anterior-posterior patterning

Human gastruloids are a powerful class of stem cell-derived models that recapitulate key features of early embryonic development, including symmetry breaking and the emergence of three germ layers1-3. However, they lack anterior embryonic structures and coordinated axial organization4-6. To address this limitation, we pre-patterned human pluripotent stem cells (hPSCs) by exposing them to either anterior (FGF2) or posterior (CHIR99021 [CHIR] & retinoic acid [RA]) cues. Upon mixing, these dual-patterned hPSCs interacted and self-organized into elongated structures with both anterior and posterior features--which we term anterior-posterior (AP) human gastruloids. Anteriorly pre-treated cells robustly intercalated into posteriorly pre-treated cells, collectively giving rise to a continuum of neural tissues--including a brain-like domain, a neural tube-like structure, and neuro-mesodermal progenitors (NMPs)--with segmented somites arrayed bilaterally. Single cell RNA sequencing (scRNA-seq) revealed that human AP gastruloids contain cell types resembling the midbrain-hindbrain boundary (MHB), regionalized hindbrain structures (i.e. rhombomeres 1-8), regionalized neural crest (i.e. cranial, vagal, trunk)7,8 and head mesoderm. Transcriptomic comparisons to primate embryos revealed that human AP gastruloids most closely resemble Carnegie stage 11 (CS11) embryos. While they lack a notochord and full dorsal-ventral polarity, human AP gastruloids recapitulate key spatial and temporal features of early neurulation and somitogenesis. Perturbation of folic acid metabolism or rho-associated kinase (ROCK) signaling induced spinal cord defects, phenocopying aspects of spina bifida and other neural tube defects, highlighting this models potential for studying congenital disorders9. AP gastruloids may serve as a simple, robust, scalable platform for modeling coordinated human AP body axis development. More broadly, our results suggest that controlled interactions between differentially prepatterned progenitors can initiate self-organization of complex body axis features. The "pattern-and-mix" strategy may serve as a generalizable framework for assembling spatially organized stem cell models of mammalian development.

developmental biology↗

bioRxiv2025

Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice

Targeted protein degradation is a favorable strategy for studying the immediate downstream effects of protein loss-of-function. An appealing platform among these technologies is the auxin-inducible degron (AID) system. Although this system has been applied extensively to cell and animal models, degradation resistance to long-term auxin treatment has not been studied. With the advent of the new AID2 system, cellular toxicity due to the high concentrations of auxin required in the original AID1 system is no longer a concern, making it possible to study protein degradation over extended periods. In this study, we derived multiple miniAID-tagged knock-in human cell lines and a Ctcf-miniAID knock-in mouse strain to investigate mechanisms of degradation resistance. We revealed four independent resistance mechanisms, including a nonsense mutation in the CTCF coding sequence that removed the miniAID peptide, a missense point mutation in the miniAID coding region that disrupted ubiquitin complex targeting, and silencing of the OsTIR1 adaptor protein. Resistance to auxin degradation was also acquired in mouse primary CtcfminiAID/miniAID knock-in B-ALL cells through missense mutations of the OsTIR1(F74G) protein in vivo and ex vivo. In summary, our innovative study expands our understanding of the AID system and cautions careful consideration of design for future applications in mammalian system.

cell biology↗