Biology subjects

Liu, S.

Publications and source records attributed to Liu, S..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Rapid Podocyte ablation Causes Acute Renal Tubule Cell Necrosis and Interstitial Fibrosis

It remains unclear whether podocyte loss directly causes acute renal tubular cell (RTC) damage and interstitial fibrosis, thereby leading to renal failure. Here, we applied intermedilysin (ILY)-mediated human CD59 (hCD59) cell ablation to generate an acute, specific podocyte-ablation mouse model. Cre-induced hCD59 transgenics (ihCD59) were crossed with Nphs2Cre to generate ihCD59+/-/Nphs2Cre+/- mice. The specific and rapid podocyte-ablation mediated by ILY injection directly caused RTC necrosis, leading to renal failure and even death within 2-3 days in a dose-dependent manner. Treating mice that received an ILY lethal dose with peritoneal dialysis or administering a non-lethal dose, we extended their survival beyond six weeks and found that mice developed interstitial fibrosis and glomerulosclerosis with persistent proteinuria and tubule damage. Podocyte-ablation caused massive disruption of glomerular function at week 1, and then partial recovery by week 2. Genes and pathways of TLRs and apoptosis, and mitochondrial functions were respectively upregulated and downregulated in both ablated-podocyte mouse and biopsied-glomerulonephritis patient kidney samples. Together, this rapid podocyte-ablation causes acute RTC necrosis that progresses to interstitial fibrosis in this mouse model, which is applicable for dissecting mechanisms underlying podocyte injury-mediated tubular damage and glomerular repair, with the potential to reveal novel therapeutic targets for kidney diseases.

pathology↗

bioRxiv2026

The Kifc3 Motor Protein Controls Centrosomal Factor Cep192 in Ontogenic Coordination of Megakaryocyte Development

The distinct features of neonatal megakaryocytes, high proliferation and inefficient platelet production, have clinical repercussions. A diminished capacity for stress thrombopoiesis, the response to acute drops in platelet counts, contributes to the high prevalence of thrombocytopenia in premature infants and to impaired platelet recovery after umbilical cord blood stem cell transplantation. High proliferation also promotes leukemogenesis in babies with Down Syndrome (DS). The transcriptional coactivator Mkl1/MrtfA participates in programming the ontogenic shift from fetal/neonatal to adult-type megakaryopoiesis; in this activity it is opposed by the DS-associated kinase Dyrk1a. In a screen for downstream ontogenic effectors in human progenitors, we identified the kinesin Kifc3 as a factor selectively decreased in adult megakaryocytes and whose knockdown in neonatal megakaryocytes induced adult-type morphogenesis with augmented platelet release. Kifc3 acts as a minus-end directed motor for centrosomal delivery of various cargos. Centrosomal release of Cep192 has recently been found induce cellular process extensions through actin remodeling, reminiscent of megakaryocyte platelet release. In our studies, Cep192 showed striking upregulation and dispersion in adult vs neonatal megakaryocytes, and Kifc3 knockdown recapitulated this effect in neonatal megakaryocytes. A role for Cep192 in promoting megakaryocyte morphogenesis, distinct from its role in centrosome biogenesis, was demonstrated in vitro and in vivo. In silico screening for Kifc3 inhibitors identified a small molecule that affected neonatal megakaryocytes similarly to Kifc3 knockdown, indicating feasibility for therapeutic argeting of the Kifc3-Cep192 pathway in clinical conditions associated with fetal-type megakaryopoiesis. Key PointsO_LIThe motor protein Kifc3 dictates megakaryocyte ontogeny in association with its control of the centrosomal actin-remodeling factor Cep192. C_LIO_LIKnockdown or small molecule targeting of Kifc3 enhances neonatal megakaryocyte morphogenesis and thrombopoiesis. C_LI

developmental biology↗

bioRxiv2026

DNA-triggered AIM2 condensation orchestrates immune activation and regulation

The innate immune sensor AIM2 detects cytosolic DNA and initiates inflammatory responses, yet its activation mechanism remains incompletely understood. Here, we show that AIM2 undergoes liquid-liquid phase separation upon DNA binding, forming dynamic condensates both in vitro and in cells. These condensates serve as platforms for inflammasome and PANoptosome assembly, promoting immune activation across multiple pathways. Direct structural determination from condensates reveals the assembly of active-form ASC filaments. Mechanistically, liquid-phase condensation is governed by multivalent interactions involving different AIM2 domains, including previously uncharacterized regions and species-specific elements. In vitro and in vivo assays show that mutants specifically disrupting condensation impair immune complex assembly, cell death initiation, antimicrobial defense, and intestinal homeostasis. Moreover, AIM2-DNA condensates function as regulatory hubs targeted by host- and pathogen-derived factors to balance immune homeostasis or facilitate immune evasion. These findings establish liquid-phase condensation as a fundamental mechanism of AIM2 activation and a potential therapeutic target.

immunology↗

bioRxiv2026

Cross-Propagative Graph Learning Reveals Spatial Tissue Domains in Multi-Modal Spatial Transcriptomics

Spatial transcriptomics enables in situ characterization of tissue organization by jointly profiling gene expression profiles and spatial coordinates, with histological images as complementary contextual information. However, effectively integrating these heterogeneous modalities remains challenging due to differences in statistical properties and structural patterns. We propose st-Xprop, a cross-propagative graph network with dual-graph embedding coupling for spatial domain identification. st-Xprop constructs modality-specific graphs for gene expression and histological features, and performs alternating cross-modal propagation to explicitly model inter-modal heterogeneity while enabling complementary information exchange. Through dual-graph embedding coupling, the framework progressively learns a unified low-dimensional representation that integrates multimodal signals and preserves spatial coherence. Evaluations on multiple real spatial transcriptomics datasets demonstrate that st-Xprop consistently improves clustering accuracy and robustness, particularly in weak-signal or structurally complex regions, yielding spatial domains that are more stable and biologically meaningful.

bioinformatics↗

bioRxiv2026

The Epigenetic Factor PHF13 Governs Trophoblast Stemness and Differentiation

Differentiation of trophoblast stem (TS) cells or progenitor cytotrophoblasts (CTBs) into multinucleated syncytiotrophoblasts (STBs) is essential for placental development. Disruption of this process contributes to major obstetrical syndromes, including fetal growth restriction and preeclampsia, and Trisomy 21. However, the chromatin mechanisms governing trophoblast stemness and differentiation remain inadequately defined. Here we identify the chromatin-associated factor PHF13, uncovered through a high-throughput microRNA target screen, as a key regulator of trophoblast cell fate. PHF13 knockout TS cells exhibited defects that ultimately resulted in loss of cell viability, whereas PHF13 knockdown promoted expression of fusion-associated genes, including ERVFRD-1 and human chorionic gonadotropin (hCG). Consistently, PHF13 depletion in BeWo trophoblast cells increased hCG expression and secretion while reducing expression of canonical stemness-associated transcription factors ELF5 and TEAD4. Integrated genomic analyses further revealed that PHF13 target genes comprise a gene regulatory network that maintains trophoblast stemness and restrains differentiation. Notably, the pluripotency-associated transcription factor THAP11 partially co-occupies genomic sites with PHF13. Together, these findings establish PHF13 as a previously unrecognized chromatin regulator of trophoblast stemness and differentiation, providing mechanistic insight into pathways critical for placental development and function. HighlightsO_LIPHF13 preserves trophoblast stem cell identity C_LIO_LIPHF13 restrains syncytiotrophoblast differentiation C_LIO_LIPHF13 controls trophoblast chromatin programs with THAP11 C_LI

molecular biology↗

bioRxiv2026

Mechanistic insight into the phosphorylation of ERK by MEK

The RAS-RAF-MEK-ERK cascade regulates critical cellular processes such as cell proliferation and differentiation, with its dysregulation driving over 30% of human cancers. However, the active state of MEK and molecular mechanisms of ERK phosphorylation remain unclear. Here, we report the cryo-EM structures of phosphorylated MEK1 (pMEK1) bound to unphosphorylated and monophosphorylated ERK1. These structures reveal that pMEK1 interacts with ERK1 via three interfaces: first between MEK1 N-terminal peptide and ERK1 D-site recruitment site (DRS), second between MEK1 C-lobe and ERK1 F-site recruitment site (FRS), and third between MEK1 activation loop and ERK1 activation loop. Notably, we identify an unexpected phosphorylation mechanism: pMEK1 catalyzes ERK1 T202 phosphorylation through phosphate transfer from ERK1 Y204. In addition, pMEK1 exhibits phosphatase activity, catalyzing the dephosphorylation of ERK1 Y204. These findings allow us to delineate the catalytic cycle of MEK-catalyzed ERK phosphorylation and provide insights for targeting this oncogenic pathway.

molecular biology↗

bioRxiv2026

Synergistic Inhibition of Notch Signaling and Forced Cell Cycle Re-entry Drive Müller Glia Reprogramming in Uninjured Mouse Retina

In regenerative species, such as teleost fish, Muller glia (MG) autonomously re-enter the cell cycle after injury and give rise to functional retinal neurons. In contrast, the loss of retinal neurons in mammals is irreversible due to the limited proliferative and regenerative ability of MG. Various strategies have been developed to induce proliferation of mature mouse MG with or without injury, yet most MG daughter cells retain glial cell fate. Here, we found that MG progenies maintain high Notch signaling, which may constrain their neurogenic potential. Conditional deletion of Rbpj, the central transcriptional effector of Notch, induced limited MG-to-neuron conversion in mature MG without proliferation. However, Rbpj deletion, combined with forced MG proliferation by overexpressing cyclin D1 and suppressing p27Kip1, significantly promoted MG dedifferentiation and ectopic expression of the neuronal marker Otx2 in MG daughter cells in uninjured mouse retina. Combining Notch inhibition with MG cell cycle re-activation not only increased the numbers of bipolar- and amacrine-like cells generated from MG but also promoted the further differentiation toward ON-cone, OFF-cone, and rod-bipolar subtypes. Single-nucleus RNA and ATAC sequencing data revealed that Notch inhibition facilitated the formation of MG-derived progenitor-like cells while MG proliferation increased chromatin accessibility of neurogenic genes. Notably, most MG-derived cells survived long term despite incomplete maturation. Together, our findings delineate how Notch inhibition and MG proliferation, alone or in combination, influence the regenerative potential of MG in the mammalian retina.

cell biology↗

bioRxiv2026

Ancestral secretory programs underlie the evolution of morphological innovations across Spiralia

Understanding how morphological innovation arise from ancestral genetic and cellular systems remains a major challenge in evolutionary biology. Molluscan shells represent one of the most diverse morphological novelties within Spiralia and have been central to the ecological and evolutionary diversification of molluscs. However, the cellular basis of shell formation and the evolutionary origin of shell-forming cell types remain poorly understood. Here, we present a single-cell transcriptomic atlas of the Pacific oyster (Crassostrea gigas) mantle and show that molluscan shell-forming cell types are evolutionarily recent innovations built upon ancestral epithelial secretory systems of spiralians. We identify five spatially segregated shell-forming epithelial cell types, and demonstrate that larval and adult shell-forming cells are developmentally independent and characterized by transcriptomes enriched for evolutionarily young genes. Cross-species cell-type comparisons further reveal that oyster shell-related genes are embedded within conserved epithelial and secretory programs across spiralians. Together, we propose that a substantial genetic foundation for shell formation was already present in the last common ancestor of Spiralia, and that molluscan shell diversity arose through repeated co-option of ancestral genetic programs coupled with novel genes. Our study provides a framework for understanding how ancient cellular architectures can be repeatedly reconfigured to generate morphological novelty during evolution.

evolutionary biology↗

bioRxiv2026

Effects and Mechanisms of Aerobic Exercise on Myocardial AGEs/RAGE-p38 MAPK-NF-κB Pathway in SHR Rats

ObjectiveTo investigate the effects of aerobic swimming exercise on blood pressure, cardiac function, and the myocardial AGEs/RAGE-p38 MAPK-NF-{kappa}B signaling pathway in spontaneously hypertensive rats (SHR). MethodsTwenty-four male Wistar-Kyoto (WKY) rats were randomly assigned to three control subgroups (C-0, C-4, C-8; n=8 each). Fifty-six SHRs were allocated into seven subgroups (S-0, S-4, S-8, SE-4, LE-4, SE-8, and LE-8; n=8each) to receive different swimming intervention protocols. Systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured via the tail-cuff method. Cardiac parameters, including ejection fraction (EF), fractional shortening (FS), left ventricular end-diastolic volume (LVEDV), left ventricular end-systolic volume (LVESV), and stroke volume (SV), were assessed using echocardiography. Myocardial morphological alterations were observed through hematoxylin-eosin (HE) staining, and myocardial hydroxyproline content was quantified using the alkaline hydrolysis method. Furthermore, the myocardial expressions of advanced glycation end products (AGEs), receptor for AGEs (RAGE), phosphorylated p38 mitogen-activated protein kinase (p-p38 MAPK), and nuclear factor-kappa B (NF-{kappa}) were detected by immunohistochemistry (IHC). ResultsAerobic exercise significantly reduced blood pressure in SHRs, partially improved cardiac function and myocardial architecture, and decreased hydroxyproline content (except in the SE-4 group). Furthermore, the exercise intervention downregulated the expressions of AGEs, RAGE (except in the SE-4 group), p-p38 MAPK, and NF-{kappa}, with efficacy varying according to exercise duration and intervention cycles. ConclusionAerobic exercise alleviates the progression of hypertension and mitigates the risk of cardiac dysfunction in SHRs by inhibiting myocardial glycation. This cardioprotective effect may be mediated by the suppression of p38 MAPK activation and the subsequent reduction of NF-{kappa} nuclear translocation.

physiology↗

bioRxiv2026

Genetic insights on the mechanisms of human cortical folding

The unique and intricate pattern of human cortical folding is rooted in fetal neurodevelopmental processes and can now be comprehensively quantified by new neuroimaging-derived measures of sulcal complexity. Here, we provide the first genetic maps of human sulcal complexity. Beginning with large effects of rare variants, we survey nine different neurogenetic syndromes (n=615), detecting visible changes in sulcal complexity on a shared axis of sulcal change coupled to the prenatal timing of sulcation. Turning to common genetic variants, we use genome-wide association studies of complexity scores for 40 sulci in the UK Biobank (n[~]29,000) to (i) resolve variable heritability across sulci, (ii) reveal both local and remote shared genetic effects with cortical morphology, and (iii) identify complexity-associated genes and their embedding in brain maps of prenatal gene expression. These reference genetic maps uncover multiple new mechanistic pathways for cortical morphogenesis in health and disease.

neuroscience↗

bioRxiv2026

A Resolution-Agnostic Geometric Transformer for Chromosome Modeling Using Inertial Frame

AO_SCPLOWBSTRACTC_SCPLOWChromosomes are the carriers of genetic information. Further understanding their 3D structure can help reveal gene-regulatory mechanisms and cellular functions. However, high-resolution 3D structures are often missing due to the high cost and inherent noise of experimental screening. A standard pipeline for reconstructing the chromosome 3D structure first applies the single-cell Hi-C high-throughput screening method to measure pairwise interactions between DNA fragments at different resolutions; then it adopts computational methods to reconstruct the 3D structures from these contacts. These include traditional numerical methods and deep learning models, which struggle with limited model expressiveness and poor generalization across resolutions. To handle this issue, we propose InertialGenome, a novel transformer-based framework for robust and resolution-agnostic chromosome reconstruction. InertialGenome first adopts the inertial frame for the pose canonicalization. Then, based on such an invariant pose, it proposes a Transformer with geometry-aware positional encoding, leveraging Nystrom estimation. To verify the effectiveness of InertialGenome, we conduct experiments on two single-cell 3D reconstruction datasets with four resolutions, reaching superior performance over all four computational baselines. Additionally, we observe that the 3D structure reconstructed by InertialGenome is more in line with the results of real experimental results on two functional verification tasks. Finally, we leverage InertialGenome for cross-resolution transfer learning, yielding up to a 5% improvement from low to high resolution. The source code is available at https://github.com/yize1203/InertialGenome.

bioinformatics↗

bioRxiv2026

Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

AO_SCPLOWBSTRACTC_SCPLOWGenerative models have recently advanced de novo protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce RigidSSL (Rigidity-Aware Self-Supervised Learning), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available on this repository.

bioinformatics↗

bioRxiv2026

Spin-State Modulation by Atom-Cluster Synergy Steers H2O2 Conversion toward a Catalase-like Decomposition Pathway for Anti-Inflammatory Therapy

Nanozymes have emerged as promising enzyme mimics for anti-inflammatory therapy. However, their catalytic efficiency and substrate selectivity generally remain inferior to those of natural enzymes. Single-atom nanozymes (SAzymes), with isolated metal centers resembling enzymatic active sites, represent an important advance toward rational design of nanozyme, but achieving enzyme-like selectivity remains challenging. Herein, we reported a spin-state modulation strategy to prepare Fe-N-C nanozyme with coexisting single atoms and nanoclusters (FeSA+NC) via reductive-gas pyrolysis. Experimental analyses and density functional theory calculations revealed that Fe nanoclusters induced local symmetry breaking and charge redistribution around FeN4 sites, shifting the Fe centers toward a higher spin configuration and thereby modulating the free energy changes of the H2O2 conversion pathway. As a result, FeSA+NC showed dramatically enhanced catalase (CAT)-like activity (333.79 U mg-1) and suppressed peroxidase (POD)-like activity (38.49 U mg-1), achieving superior selectivity compared to Fe SAzymes (FeSA), which showed comparable CAT- and POD-like activities (62.39 and 60.39 U mg-1, respectively). Moreover, FeSA+NC achieved a higher superoxide dismutase (SOD)-like activity (929.27 U mg-1) than FeSA (249.68 U mg-1), enabling efficient SOD-CAT cascade. FeSA+NC effectively scavenged excessive intracellular reactive oxygen species, suppressed M1 macrophage polarization, and enhanced the therapeutic efficacy of intra-articular stem cell injection in a rat model of rheumatoid arthritis, a representative chronic inflammatory disease. This work highlights an atom-cluster synergy strategy for steering H2O2 conversion towards antioxidant pathway, offering a general design principle for safer, more controllable and more efficient nanozyme-based anti-inflammatory therapeutics.

bioengineering↗

bioRxiv2026

Functional Type I and Type II interferon crosstalk restricts progenitor exhausted CD8 T cells through spatial exclusion and checkpoint enforcement

Type I interferon (IFN-I) and interferon-{gamma} (IFN{gamma}) are central regulators of antiviral immunity, yet how they cooperatively govern CD8 T cell fate during chronic infection remains unresolved. Here, we uncover a previously unrecognized, spatially encoded interferon circuit that actively constrains progenitor exhausted CD8 T cells (Tpex) during chronic LCMV infection. Persistent IFN-I signaling indirectly restricts Tpex expansion by enforcing their sequestration within PDL1-rich B cell niches of lymphoid tissue and by suppressing T cell-derived IFN{gamma}. Blockade of IFN-I signaling enables Tpex migration into T cell zones of splenic follicles driving IFN{gamma} production, which in turn sustains PDL1 expression on myeloid cells to re-impose local inhibitory pressure. Combined IFN-I and IFN{gamma} blockade disrupts this feedback, promoting coordinated niche redistribution of Tpex and checkpoint remodeling that drives robust Tpex expansion. Single-cell transcriptomics reveal that this layered IFN-I-IFN{gamma} interplay establishes a regulatory balance that constrains Tpex proliferation while preserving effector-like transcriptional programs in their progeny effector CD8 T cells, ultimately preventing premature terminal differentiation. Thus, interferons orchestrate the coordinated T cell-myeloid regulatory circuit that integrates tissue organization, cytokine feedback, and checkpoint control to regulate CD8 T cell exhaustion during chronic infection.

immunology↗

bioRxiv2026

Behavioral hierarchy without a hierarchical brain

Behavior is inherently hierarchical. The prevailing view holds that hierarchical behavior arises from the brains hierarchical organization. However, this view is primarily derived from experiments in highly controlled laboratory settings, and it remains unknown whether the same principles apply during natural, freely moving behavior. Here, we show that, under naturalistic and freely moving conditions, hierarchical mouse behavior can emerge from localized cortical dynamics alone, independent of anatomical or functional brain hierarchies. We first established a naturalistic neuroethological platform that enables quantitative characterization of hierarchical behavior alongside its corresponding neural activity. Using this platform, we find that localized cortical dynamics encode multiple levels of behavioral hierarchy. Specifically, low-dimensional neural dynamics encode high-level behavioral composites, whereas higher-dimensional neural dynamics encode low-level behavioral kinematics. Finally, by selectively perturbing high-dimensional components of cortical dynamics using optogenetics, we observe a selective reduction in low-level kinematic behaviors, providing causal evidence for this relationship. Together, these findings challenge a central assumption in systems neuroscience by demonstrating that hierarchical behavior does not require a hierarchically organized brain. Instead, hierarchy emerges from the dimensional organization of localized cortical dynamics, revealing a previously unrecognized principle by which complex behavior can arise from relatively simple neural substrates. This dynamic principle offers a unifying framework for understanding how biological systems achieve behavioral flexibility under natural conditions and suggests new directions for artificial intelligence that rely on adaptive local dynamics rather than increasingly deep architectures.

neuroscience↗

bioRxiv2026

Bottom-up and generative computations both uniquely explain social brain responses

Making social evaluations from visual input is a core human ability that engages brain regions involved in social perception, including portions of the superior temporal sulcus (STS), as well as higher-level mentalizing regions, such as the temporoparietal junction (TPJ). One common hypothesis proposes that these regions operate hierarchically: social perception regions like posterior STS (pSTS) implement bottom-up computations to generate fast, stimulus-derived representations of social interactions, while mentalizing regions like TPJ perform inverse-planning computations to infer the underlying goals and motivations driving agents behavior. However, this computational-neural mapping has never been formally tested, in large part due to the lack of successful computational models of social processing. We developed computational models aligned with these two frameworks: a graph-neural-network (GNN) model that recognizes social interactions by relying on relational visual information, and a generative inverse-planning model that does so by inverting a model of agents goals and the physical world. In this preregistered study, we collected fMRI responses while participants watched videos of agentive animated shapes depicting social interactions and compared neural responses to both computational models. Surprisingly, we found that both the GNN and inverse-planning model explained neural responses in pSTS and TPJ, even after controlling for variance explained by the other model. Exploratory analyses, however, revealed a shift from early perceptual processing towards later higher-order reasoning in both regions, suggesting a temporal rather than spatial hierarchy. Overall, this study provides the first evidence that both social perception and mentalizing regions carry out a combination of relational bottom-up and higher-level inferential computations, perhaps on distinct timescales. This work also provides the first comparison of an inverse-planning model to neural activity and demonstrates that theory-driven cognitive models can successfully predict fMRI responses to social scenes. Significance StatementThe ability to recognize social interactions between others is central to humans daily lives and engages brain regions supporting social perception and mental state inference. The neural computations underlying this ability, however, are poorly understood. Here we leveraged new models of bottom-up social perception and generative social inference to test the hypothesis that these complementary computations are carried out in separate brain regions. We compared both models to brain responses from subjects viewing procedurally generated videos of social interactions. Surprisingly, we found that both models explained neural activity in both perceptual and mentalizing regions, even when controlling for effects of the other model. These findings challenge the idea of a strict division of labor in the social brain and refine our understanding of the computations supporting human social inference.

animal behavior and cognition↗

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↗