Biology subjects

Zhang, W.

Publications and source records attributed to Zhang, W..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Probiotic Lactiplantibacillus plantarum VB165 improves metabolic disorders in Insulin-Resistant Mice

This study investigated the effects of Lactiplantibacillus plantarum VB165, a probiotic strain with intrinsic -glucosidase inhibitor (AGI) activity, on metabolic disorders in high-fat diet (HFD)-induced insulin-resistant (IR) mice. Male C57BL/6 mice were divided into four groups: normal control diet (NCD), NCD supplemented with VB165, HFD, and HFD supplemented with VB165. After 16 weeks, VB165 supplementation significantly attenuated HFD-induced weight gain and reduced epididymal and inguinal white adipose tissue indices. VB165 also improved glucose intolerance and insulin resistance (IR), as demonstrated by oral glucose tolerance tests (OGTT) and insulin tolerance tests (ITT), and lowered fasting blood glucose, fasting insulin, and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) levels. Additionally, it ameliorated dyslipidemia by reducing serum total cholesterol, triglycerides, and low-density lipoprotein cholesterol (LDL-C), while alleviating hepatic steatosis and adipocyte hypertrophy. Mechanistically, VB165 enhanced intestinal barrier function by upregulating tight junction proteins (ZO-1 and Occludin), reduced systemic inflammation by lowering LPS, IL-6, and IL-1{beta}. Gut microbiota analysis revealed that VB165 modulated community composition, suppressing HFD-enriched genera (e.g., Ileibacterium and Coriobacteriaceae_UCG_002) and promoting beneficial taxa (e.g., Faecalibaculum and Oscillibacter). These findings demonstrate that L. plantarum VB165 improves HFD-induced metabolic disorders via multi-target mechanisms, highlighting its potential as a probiotic intervention for IR and related metabolic diseases.

microbiology↗

bioRxiv2026

Beyond Acoustic Cues: Olfactory-Mediated Avoidance of Bats by Crickets

The evolutionary arms race between insectivorous bats and their insect prey is a classic paradigm of acoustic predation and evasion, with insects having evolved sophisticated auditory countermeasures. Both bats and insects also rely heavily on olfaction for key behaviors, such as social communication. Moreover, predator-derived odors are well-established as risk cues in many other predator-prey systems. However, whether olfaction plays a role in the bat-insect arms race remains unknown. Here, we unveil a previously unknown olfactory dimension to this interaction. We demonstrated that the body odor of the insectivorous bat Scotophilus kuhlii triggered robust avoidance and electrophysiological antennal responses in a common cricket prey, Loxoblemmus equestris. We identified limonene as a behaviorally active volatile in bat odor that elicited electrophysiological responses in cricket antennae and was sufficient to elicit avoidance in crickets. Field experiments confirmed that limonene exposure reduced cricket calling activity, demonstrating the ecological relevance of this cue. Our findings establish that insects can detect and initiate avoidance of phylogenetically distant vertebrate predators via olfaction, a process that could be mediated by the elemental perception of individual odor compounds. This work broadens the sensory framework of a classic predator-prey system, and highlights olfactory eavesdropping as a functional strategy in phylogenetically distant predator-prey systems.

ecology↗

bioRxiv2026

Targeting MTHFD2 disrupts mitochondrial redox homeostasis and restores venetoclax sensitivity in acute myeloid leukemia

One-carbon metabolism is frequently dysregulated in human cancer including acute myeloid leukemia. However, the mitochondrial mechanisms by which one-carbon enzymes support leukemia survival and therapeutic response remain incompletely defined. Here, we report that the one-carbon metabolism enzyme MTHFD2 is a critical regulator of acute myeloid leukemia nucleotide metabolism, redox homeostasis, and disease progression. We show that genetic ablation of MTHFD2 suppresses acute myeloid leukemia cell proliferation in vitro and significantly delays leukemia onset in a genetically engineered mouse model, while sparing healthy hematopoietic stem and progenitor cell function. Stable isotope tracing demonstrates that MTHFD2 supports de novo purine synthesis and sustains mitochondrial NADH and NADPH production. Consistent with this role, MTHFD2 inhibition increases mitochondrial superoxide levels, and combined purine supplementation and mitochondrial reactive oxygen species neutralization rescues acute myeloid leukemia cell viability. We also demonstrate that the small-molecule inhibitor DS18561882 directly inhibits mitochondrial MTHFD2 activity and phenocopies genetic deletion. DS18561882 exhibits activity across a cohort of 60 primary AML patient samples, synergizes with venetoclax in treatment-naive acute myeloid leukemia, and restores venetoclax sensitivity in resistant AML models. These findings establish mitochondrial MTHFD2 as a genetically validated, therapeutically targetable metabolic vulnerability in acute myeloid leukemia and support targeting mitochondrial one-carbon metabolism to enhance and restore venetoclax response.

cancer biology↗

bioRxiv2026

MetaReact: A Reaction-Aware Transformer for End-to-End Prediction of Drug Metabolism

Accurate prediction of drug metabolites and enzyme selectivity is essential for rational drug design and safety assessment. However, existing computational approaches are often limited to specific enzyme families or reaction types, lacking the capacity to model enzyme-subtype specificity and prioritize major metabolites. Here, we present MetaReact, an end-to-end generalizable Transformer-based model that unifies the prediction of metabolic enzymes, metabolites, and sites of metabolism (SOM). By integrating structure-aware encoding ReactSeq, a chemistry reaction-based pretraining, MetaReact consistently outperforms state-of-the-art methods across multiple benchmarks under three settings: enzyme-agnostic, enzyme-completion, enzyme-conditioned. Notably, it achieves 60% Top-3 accuracy in identifying major metabolites and superior CYP450 enzyme-subtype prediction/SOM recognition. Case studies validate its applicability to complex natural products, synthetic cannabinoids, and clinical candidates, facilitating toxicity assessment and molecular optimization. This scalable, rule-free solution advances human metabolism modeling, with potential for computational pharmacokinetics and early drug discovery.

biochemistry↗

bioRxiv2026

Unbiased Single-Cell Transcriptome-Proteome Co-Profiling Reveals Malignant Dormancy and Post-Transcriptional Buffering of CTCs

Leptomeningeal metastasis is driven by rare cerebrospinal fluid circulating tumor cells (CSF-CTCs). However, the mechanisms underlying their adaptation to chemotherapeutic stress remain elusive, primarily because transcriptomics alone poorly predicts functional protein states. Here, we present scMAPS, a single-cell multi-omics method that employs magnetic-assisted partitioning cell lysates to enable unbiased transcriptome-proteome co-profiling without loss-prone physical splitting and precision device. By coupling scMAPS with our custom CLEAP (CTC Label-free Enrichment and Accurate Picking) system, we performed the first deep multi-omics profiling of rare clinical CSF-CTCs before and after localized chemotherapy, detecting an average of 2,547 proteins and 7,821 genes per cell. The integrated CLEAP-scMAPS pipeline reveals a coordinated prioritizing survival over proliferation malignant dormancy phenotype and identified post-transcriptional buffering as the primary driver of treatment resistance. Our platform enables the comprehensive molecular phenotyping of rare clinical specimens, providing a highly versatile framework for decoding complex post-transcriptional regulatory networks.

cell biology↗

bioRxiv2026

High-Fidelity Long-term Whole-embryo Lineage and Fate Reconstruction by Iterative Tracking with Error Correction

Reconstructing the complete cell lineages and fate maps of a living embryo has remained a central challenge in developmental biology. Here we introduce ITEC (Iterative Tracking with Error Correction), a fully unsupervised method that automatically reconstructs the lineage of every cell in the embryo with high fidelity. ITEC was validated with manually annotated lineages on four cross-species datasets including zebrafish, mouse, and Drosophila. We reconstructed the developmental lineages of a zebrafish embryo from terabyte-scale data of total 18.5 million cells with an estimated accuracy of over 99.7%. With ITEC, we revealed spatiotemporal dynamics of key morphogenetic processes such as somite boundary formation, demonstrated the various patterns of spatial sorting among adjacent organs or anatomical regions, and identified associations between cellular movement and spatial transcriptomics. ITEC provides a powerful platform for retrospective fate mapping and systematic exploration of developmental dynamics at the cellular scale and single-embryo level.

bioinformatics↗

bioRxiv2026

Improved vector toolkit for genome writing in mammalian cells

Efficient genome writing in mammalian cells requires robust methods for integrating large DNA payloads. The previously described method mammalian Switching Antibiotic resistance markers Progressively for Integration (mSwAP-In) enables iterative, biallelic genome rewriting in mammalian stem cells with DNA payloads exceeding 100 kb. However, the lack of standardized vectors and certain technical constraints have limited its broader adoption. Here we present an improved plasmid toolkit designed to streamline the implementation of mSwAP-In. The toolkit includes two core vectors. pLP-TK (pCTC174) is a landing-pad plasmid compatible with Golden Gate assembly of genomic homology arms and supports both mSwAP-In and the recombinase-mediated cassette exchange method Big-IN. mSwAP-In MC2v2 (pKBA135) is a versatile Big DNA assembly and delivery vector that supports Gibson-based assembly and incorporates positive, negative, and fluorescent selection markers, as well as a backbone counterselection cassette to minimize unwanted plasmid integration. The vector architecture also enables propagation in yeast and bacterial hosts, inducible plasmid copy-number amplification in standard E. coli strains, and CRISPR/Cas9-mediated payload release through preinstalled guide RNA target sites. We further characterize the FCU1/5-FC counterselection system in mouse embryonic stem cells and define conditions that minimize its bystander toxicity. Finally, we provide a set of Cas9-gRNA expression plasmids optimized for common mSwAP-In applications. Together, these reagents constitute a standardized and experimentally validated toolkit that simplifies large-scale genome writing using mSwAP-In.

synthetic biology↗

bioRxiv2026

Photorhabdus metabolites reshape soil microbial communities and promote plant growth and insect resistance

Photorhabdus bacteria are potent insect-killing microbes associated with entomopathogenic nematodes and offer opportunities for environmentally benign pest control. They can be applied as foliar sprays or soil drenches without their nematode vector, resulting in massive amounts of Photorhabdus cells and their (toxic) metabolites introduced into the soil. However, their effects beyond the target organisms are unknown. To fill this knowledge gap, we investigated the soil legacy effects of Photorhabdus cells and their metabolites on soil microbial communities, plant performance and resistance to herbivores. To this end, we first conditioned soils with i) mechanically killed (MK) or Photorhabdus-infected insect larvae, ii) aqueous extracts of MK or Photorhabdus-infected insect larvae, iii) cell-free Photorhabdus supernatants, iv) autoclaved soil complemented with live soil previously conditioned with MK or Photorhabdus-infected insect larvae. We then grew maize plants in these soils and measured plant biomass, profiled soil microbial communities and plant metabolites, and evaluated plant resistance against two pest insects Diabrotica balteata and Spodoptera frugiperda. We found that conditioned soils increased plant biomass by 10-26% relative to controls and significantly altered soil bacterial and nematode communities, and to a lesser extent, fungal communities. Re-inoculating conditioned soil microbiota into autoclaved soils recreated the plant growth-promoting effects, indicating microbial-mediated mechanisms. Additionally, plants grown in soils conditioned with Photorhabdus-infected insect cadavers were often more resistant to herbivorous insect attack, in a strain-specific manner. On average, D. balteata and S. frugiperda larvae gained 10-20% and 10-59% less weight, respectively, when fed on plants grown in conditioned soils than on plants grown in control soils. The plant metabolic profiles of plant leaves and roots also varied with resistance levels. We conclude that Photorhabdus metabolites modulate soil microbial communities towards a structure that enhances plant growth and triggers systemic responses against herbivores.

microbiology↗

bioRxiv2026

Multi-site MRI analysis of morphometric differences in brain regions in the presence of hearing loss and tinnitus across the adult lifespan

The impact of age and hearing loss on the brain has garnered significant attention, as both factors have been implicated in the development of cognitive impairment or dementia. In this study, we investigated the impact of hearing loss and tinnitus on gray matter in the brain, while accounting for age. We used a comprehensive secondary analysis of structural MRI data obtained from multiple research sites (256 unique individuals) using voxel-based and surface-based morphology. After harmonization of this multi-site brain data, our research replicated the previously reported finding of age-related decline in total cortical volume, but there was no significant effect of either hearing loss or tinnitus on total cortical volume. When a region of interest analysis was conducted, the hippocampus emerged as the only brain region that showed a direct impact of hearing loss, after accounting for variance associated with age. This effect on hippocampal volume was evident in our sample from age 52 years onwards; when adjusted for hearing loss, the decline began at age 56 years. For the presence of tinnitus, ventral posterior cingulate gyrus showed main effects with respect to cortical volume and surface area while medial occipito-temporal gyrus and operculum of the inferior frontal gyrus showed significant main effects only with surface area. Post-hoc analysis revealed that posterior cingulate gyrus showed significantly higher volume and larger surface area in individuals with tinnitus compared to those without tinnitus. Similarly medial occipito-temporal gyrus surface area was increased whereas surface area of the inferior frontal opercular gyrus was reduced in those with tinnitus when compared to those without tinnitus. Notably, while past studies have reported that the presence of tinnitus appeared to moderate some of these effects in certain participant groups, our results suggest a more complex relationship between sensory degradation, chronic tinnitus, and brain structure in individuals across the adult lifespan. HighlightsO_LIHearing loss and tinnitus can exacerbate regional brain atrophy in the adult lifespan. C_LIO_LIHigh-frequency hearing loss affects auditory cortex gray matter volume to a larger degree in older age. C_LIO_LIHearing loss may accelerate decline in hippocampal volume by about 4 years. C_LIO_LIChronic subjective tinnitus is associated with a larger volume of cingulate cortex, increased surface area in cingulate cortex and the lingual gyrus, and decreased surface area of frontal operculum compared to controls. C_LIO_LITinnitus-related effects on regional brain atrophy are not modified by the degree of hearing deficits. C_LI

neuroscience↗

bioRxiv2026

A Novel Glycoproteomics Platform for High-Throughput Identification of Disease-Associated Glycoforms

Glycosylation is a critical post-translational modification, and its aberrant forms are potent disease biomarkers; however, the comprehensive, site-specific identification of all glycosites and glycoforms across an entire proteome remains prohibitively slow and computationally demanding. To address this bottleneck and accelerate biomarker discovery, we introduce the Glycoproteomics Data Analysis Software (GDAS), a novel, high-throughput platform designed to provide confident, proteome-scale identification of disease-specific glycoforms. GDAS streamlines the analysis through a core, multi-step workflow: it initially employs an ultrafast open search (e.g., MSFragger-Glyco) on mass spectrometry data to rapidly screen and statistically reduce the vast proteome database to a manageable subset of significantly regulated glycoproteins, conserving computational resources for subsequent, in-depth, targeted N- and O-glycosylation analysis using specialized tools (e.g., GlycReSoft and O-Pair). Furthermore, a unique Final Analysis Module utilizes an advanced statistical and machine learning pipeline (incorporating Bootstrap/Bayesian methods, XGBoost, and Random Forest) to integrate quantitative results and generate a robust, comprehensive glycosylation score. We demonstrate GDASs power to recognize biologically relevant glycosylation changes in targeted proteins by validating it using published Alzheimers disease data. GDAS can be downloaded from https://github.com/yang-lab/GDAS. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/708406v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@189b270org.highwire.dtl.DTLVardef@1221045org.highwire.dtl.DTLVardef@15a3f50org.highwire.dtl.DTLVardef@1f2d43f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Circular RNA identification using a genomic language model and a small number of authenticated examples

Genomic language models (gLMs) hold great promise for deciphering biological sequences, yet their effectiveness is hindered by the limited number of experimentally verified examples available for model training, a ubiquitous bottleneck for supervised machine learning. To overcome this challenge, we developed circFormer, the first gLM-driven approach for circular RNA (circRNA) identification. circFormer integrates curriculum learning with gLM fine-tuning: a Nucleotide Transformer model is first trained on a small set of validated circRNAs, the resulting model is used as a teacher to score [~]2.3 million noisy candidates, and the model is then fine-tuned with the noisy candidates along with their scores to improve prediction. Operating either as a standalone predictor or as a filter for existing pipelines, circFormer consistently outperformed traditional machine-learning approaches in accuracy and robustness. Among 50 circFormer-selected candidates that were overlooked by most existing tools, experimental validation using RNase R digestion and RT-qPCR confirmed 94.1% (32/34) of the evaluable candidates as genuine circRNAs. To enhance interpretability, we introduced a model-agnostic, dual-level explainable AI strategy that reveals mechanistic signatures of circRNA formation. circFormer provides a scalable, interpretable, and generalizable framework for converting noisy high-throughput data into reliable functional annotations, highlighting a practical path forward for gLM-based genomics in data-scarce settings.

bioinformatics↗

bioRxiv2026

Membrane Curvature Activates Src kinase and Promotes Metastatic Cancer Cell Survival

Src family kinases (SFKs) play key roles in cancer metastasis. While SFKs are classically regulated by cell adhesions and transmembrane receptors, how they become activated following tumor cell detachment remains unclear. Here, we report curvature-induced kinase activation (CIKA), a distinct mechanism through which plasma membrane curvature directly promotes Src activation. Mechanistically, membrane curvature promotes the oligomerization of TOCA-family curvature-sensing proteins, inducing local biomolecular condensation. These condensates recruit Src, stabilize its open conformation, and exclude the negative regulator Csk, converting curved membrane domains into discrete kinase activation hubs. Disruption of CIKA using TOCA mutants inhibits curvature-induced Src activation and selectively impairs the viability of detached but not adherent cells. Functionally, curvature-induced Src activation promotes anchorage-independent survival, and its disruption suppresses metastatic colonization in xenograft mouse models. These findings reveal membrane curvature as a biophysical activator of Src and suggest CIKA inhibition as a potential therapeutic strategy to target metastatic cancer cells.

cell biology↗

bioRxiv2026

Spinal cord regeneration deploys adult molecular programs that do not recapitulate embryonic development

Adult zebrafish reverse paralysis after spinal cord injury. Their regenerative capacity is stem cell-dependent and often attributed to potent progenitors that retain embryonic radial glial features and reenact developmental programs after injury. To explore the extents to which regeneration recapitulates development, we integrated single-cell RNA-sequencing datasets spanning development, adult homeostasis and adult regeneration. We found immune cell maturation and neuronal differentiation extend into the juvenile stages, while only 25% of injury-responsive adult progenitors recapitulate larval progenitor identities. By annotating larval progenitors based on their dorso-ventral identities and chronological age, we inferred the spatio-temporal features of adult sox2+ progenitors. This analysis showed the dorso-ventral progenitor identities that guide spinal cord development are not faithfully maintained in homeostatic or regenerating adults. This study reports a genome-wide, single-cell examination of similarities and differences between development and regeneration and indicates adult tissue regeneration repurposes developmental pathways into newly acquired regenerative functions rather than recapitulating development.

developmental biology↗

bioRxiv2026

FDXR Upregulation by p63/p73 is a Prognostic and Therapeutic Marker of HTLV-1-Associated Adult T Cell Leukemia/Lymphoma

Infection with human T-lymphotropic virus 1 (HTLV-1) can lead to severe diseases, including adult T-cell leukemia/lymphoma (ATL), for which current therapies are inadequate. HTLV-1 persists chronically through integration of its genome into host DNA and expansion of infected clones via cellular proliferation. Selective elimination of infected cells is the ideal treatment goal but requires identifying cellular markers dysregulated by HTLV-1 that can be exploited therapeutically. Combining metabolomics and proteomics analyses, we identified increased expression of the mitochondrial enzyme ferredoxin reductase (FDXR) as a hallmark of HTLV-1-infected cells. In patient cells, FDXR upregulation mirrored disease severity, was enriched in proliferating tumour cells and predicted worse ATL prognosis. Mechanistically, FDXR upregulation was directly driven by the transactivating isoforms of two p53 family members, TAp63 and TAp73. In silico drug susceptibility predictions, followed by targeted cytotoxicity, proliferation and Drug-Seq assays demonstrated that FDXR upregulation is associated with increased sensitivity of ATL cells to repurposed chemotherapeutic agents, particularly fluorouracil. Overall, our findings establish FDXR as a novel biomarker of HTLV-1-associated disease progression and ATL prognosis, elucidate its upstream molecular regulation, and highlight its predictive potential for chemotherapeutic sensitivity of ATL cells.

microbiology↗

bioRxiv2026

NRF2 pathway activation and SPP1⁺TREM2⁺ macrophages drive chemoradiotherapy resistance in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is among the most aggressive cancers, with low rates of durable response to chemoradiotherapy and limited therapeutic options for relapsed disease. To uncover mechanisms of treatment resistance and relapse, we performed comprehensive multi-omics profiling of >100 pre-treatment and post-relapse ESCC tumors from a prospective clinical trial (NCT04694391), integrating whole-exome/genome sequencing, bulk RNA-sequencing, single-cell RNA sequencing, and spatial transcriptomics. We identify somatic alterations in NFE2L2/KEAP1 in nearly 40% of relapsed patients, which are associated with upregulation of NRF2 signaling targets in resistant tumors and cell line models. At single-cell and spatial resolution, relapsed tumors are enriched for NRF2-activated epithelial cells that physically co-localize with immunosuppressive SPP1TREM2 macrophages. This co-localization suggests a synergistic interaction between NRF2-driven tumor programs and macrophage-mediated immune suppression that promotes relapse after chemoradiotherapy. Our findings nominate NFE2L2/KEAP1 mutations as predictive biomarkers for patient stratification and highlight therapeutic targeting of NRF2 signaling and SPP1TREM2 macrophages as rational strategies to overcome resistance in ESCC.

cancer biology↗

bioRxiv2026

Cell Type Architecture and Positional Gene Gradients in an Adult Animal at Subcellular Resolution

The spatial organization of cell types and gene expression underlies tissue architecture and organismal physiology. However, resolving complete cellular and molecular landscapes within a three-dimensional context remains challenging, particularly in organisms with high cellular heterogeneity and complex geometry. Here, we developed a semi-supervised workflow to reconstruct high-resolution three-dimensional spatial transcriptomic models of the planarian Schmidtea mediterranea at single-cell resolution. Planarians are basal bilaterians capable of regenerating body structures after injury. Our reconstruction maps the distribution of cell types and spatially patterned gene expression across the intact organism and identifies 119 candidate positional control genes (PCGs). These genes are expressed across muscle, neural, and epidermal populations. Functional perturbation of selected candidates, including pitx3, ptpn11, pi4ka, upf3b, and cul1, revealed roles in regeneration following injury. In addition, we identify intestinal cells as prominent components of the microenvironment surrounding adult tgs1 pluripotent stem cells (neoblasts). Together, these results demonstrate the utility of three-dimensional spatial transcriptomic reconstruction for mapping cellular architecture and positional gene regulation in complex adult organisms.

developmental biology↗

bioRxiv2026

Geoclimatic oscillations and ancient reciprocal adaptive introgression shape the evolutionary trajectories of threatened Coilia

Geoclimatic oscillations have repeatedly reshaped biodiversity, yet how ancient lineages persist and diversify through profound environmental upheavals remains a central question in evolutionary genomics. By integrating chromosome-level genome assemblies, population genomics, and transcriptomic data across the Coilia species complex, we reconstruct deep evolutionary histories of Coilia along the dynamic East Asian margins. Our analyses reveal divergences dating to the Miocene, coinciding with major tectonic and climatic transitions, including Tibetan Plateau uplift-linked reorganization of the Yangtze drainage toward the East China Sea, and the Middle Miocene Climatic Optimum. Despite long-term separation, we uncover evidence for ancient, reciprocal introgression among Coilia lineages, with gene flow confined to discrete genomic regions rather than distributed genome-wide. These introgressed regions are enriched for loci associated with immune function, vascular development, and osmoregulatory processes, and exhibit population genetic signatures consistent with positive selection. Temporal modelling indicates that this window of adaptive exchange preceded Pleistocene glacial intensification, after which gene flow became effectively restricted. Together, our results suggest that transiently permeable species boundaries historically acted as reservoirs of adaptive variation, shaping evolutionary trajectories and facilitating niche differentiation under repeated geoclimatic oscillations. This study highlights ancient adaptive introgression as an important evolutionary process contributing to the long-term persistence of threatened coastal fishes.

evolutionary biology↗

bioRxiv2026

4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

Regeneration relies on precise spatiotemporal gene expression and cellular responses to establish tissue identity and body patterning. Using high-resolution Stereo-seq (715 nm) on 353 sections from 16 whole animals at 8 regeneration timepoints, we constructed a 4D spatiotemporal transcriptomic map of planarian regeneration. Our analysis captured 36 refined cell types from 3,508,004 segmented cells, enabling genome-wide transcriptional imputation of gene expression dynamics across body axes at cellular, tissue, and organismal scales. We identified dynamic positional gradients and distinct spatially distributed cell types during regeneration, including an injury-induced Anterior Regenerative Zone (ARZ). The ARZ exhibited enriched positional signals in epidermal, muscle, and neural cells and was regulated by Mediator 8, which is crucial for polarity remodeling and blastema formation. This study provides a comprehensive spatial molecular and cellular map of regenerative processes, highlighting injury-induced spatial domains and key regulatory factors in planarian regeneration. We also provide an interactive web portal, offering a valuable resource for exploring and analyzing regeneration mechanisms in a spatiotemporal context.

developmental biology↗