Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Assay concordance sets exact ceilings on what one biological score can predict

Computational models of biology are ranked by averaging one prediction against many experimental realizations of a phenotype that are treated as interchangeable. We show this imposes an exact, model-free ceiling fixed by how much those realizations agree with each other, and that the ceiling depends on the evaluation metric through a single support-function identity. Measuring assay concordance across four public registries, 2,822 MaveDB score sets, 217 ProteinGym assays, two drug screens and 1,150 CRISPR cell lines, we find that two assays of one target agree at 0.56-0.68, and that 541 domains measured twice with different proteases fix assay reliability at 0.897, so 70-90% of every ceiling is irreducible biology rather than noise. Published predictors realize 63% of the achievable on the correlation benchmarks report and 18% on the top-1% selection their users perform. We provide the estimator, the ceilings, and the measurements the field has not made.

bioinformatics↗

bioRxiv2026

An entropy-based diagnostic framework for characterizingmethylation state dynamics during preimplantation development

DNA methylation undergoes predictable changes with age, and preimplantation embryos are known to undergo global epigenetic reprogramming. However, the specific fate of age associated methylation signatures during early development has not been systematically quantified. Using published human sperm age associated differentially methylated regions (DMRs) as a feature space, we integrated single cell methylome and transcriptome data to develop the Transgenerational Reset Operator (TRO), a computational framework for profiling preimplantation stages. We found that the morula stage represents the nadir of age associated methylation entropy while retaining high developmental potency, distinguishing it from a simple demethylation endpoint. Dynamical modelling revealed that independent DMR drift fails to recapitulate the morula state, requiring a coordinated, structured correction concentrated in specific DMR subsets and modules with marked directional sensitivity. Independent chromatin accessibility data supported a stage specific methylation accessibility coupling at morula, albeit with modest effect sizes. Cross species mouse and orthogonal multiomic evidence suggested partial conservation but with weight dependence and heterogeneity. Collectively, our study defines morula as a computational "ground zero" candidate for age associated methylation features and proposes a testable hypothesis of developmental regulation, while emphasizing that matched parental offspring perturbation experiments are needed to establish causal mechanisms.

developmental biology↗

bioRxiv2026

Programmable Recruitment of RNA-Binding Proteins Enables Small Molecule-Directed Destabilization of Nuclear Pre-mRNA

Chemically induced proximity has not been systematically applied to control RNA fate. Here, a programmable platform was developed to identify RNA-binding proteins (RBPs) that can be recruited by small molecules to destabilize RNA. Using microtubule-associated protein Tau (MAPT) pre-mRNA as a model target, a heterobifunctional molecule was designed to bind both a ligandable structure in MAPT pre-mRNA and FKBP12F36V-tagged RBPs. Screening of a library of tagged RBPs identified several proteins that reduced MAPT RNA levels, including zinc finger protein 36 (ZFP36) and nanos C2HC-type zinc finger 3 (NANOS3). The approach was then extended from engineered proteins to an endogenous RBP. Using small molecule ligandability maps, a cysteine-reactive ligand for ZFP36 was identified. When this ligand was linked to the MAPT-binding small molecule, endogenous ZFP36 was recruited to MAPT mRNA, reducing its abundance in cells. Genetic and chemical controls demonstrated that activity was dependent on both RNA binding and ZFP36 recruitment, supporting an induced-proximity mechanism. These studies establish a general strategy for identifying new recruitable RBP effectors and should advance ribonuclease-targeting chimera (RiboTAC) technology by expanding the repertoire of effector proteins that can be harnessed for RNA degradation. More broadly, new effectors can be discovered through model reporter-based screens and translated to endogenous systems by mining known protein binders and ligandability maps, providing a systematic path to develop small molecules that control RNA stability, including RNAs targeted through structured regions of nuclear pre-mRNAs.

biochemistry↗

bioRxiv2026

Orthoflaviviruses use diverse binding modes to engage LDLR family receptors

Orthoflaviviruses are major human pathogens that cause substantial morbidity and mortality worldwide. The viral envelope (E) mediates entry of orthoflaviviruses into host cells by interacting with cellular receptors, including members of the low-density lipoprotein receptor (LDLR) family. Here, we determined cryo-electron microscopy (cryo-EM) structures of yellow fever virus (YFV) E bound to low-density lipoprotein receptor-related protein 4 (LRP4) and LRP8, and of tick-borne encephalitis virus (TBEV) E bound to LRP8. Structural and functional studies reveal that YFV engages two low-density lipoprotein receptor class A (LA) repeats of LRP4 and LRP8 primarily through domain III (DIII) and the DI-DIII linker of its E protein, with each LA repeat making distinct contacts. In contrast, TBEV relies on a distinct surface on domain II (DII) of its E protein to interact with LRP8. Despite these differences, both viruses require engagement of two sequential receptor LA repeats for binding. Our findings identify key determinants of receptor specificity for these two orthoflaviviruses, with implications for vaccine development and therapeutic antibody targeting.

microbiology↗

bioRxiv2026

DYNAMIC CONFORMATIONS IN THE ACTIVATION OF PINK1 KINASE

Under mitochondrial stress, the mitochondrial kinase PINK1 is activated to phosphorylate ubiquitin, which in turn recruits the E3 ligase Parkin, thereby initiating clearance of damaged mitochondria. Dysregulation of the PINK1-Parkin signaling pathway is associated with early-onset autosomal recessive Parkinson's disease. However, the mechanisms governing PINK1 conformational dynamics and activation in response to mitochondrial stress remain poorly understood. Here, we report that Tribolium castaneum PINK1 (TcPINK1) forms specific symmetric dimers via interactions between the kinase N-lobe and the regulatory C-terminal domain. These dimers undergo dynamic conformational transitions across distinct states, including an autoinhibited state, an inactive intermediate state, a primed-activation state and an active state. Moreover, TcPINK1 undergoes lateral trans-phosphorylation through dimer-dimer interactions. Notably, symmetric dimer formation is essential for Parkin recruitment during mitophagy. These findings provide a framework for understanding the conformational plasticity and allosteric regulation of PINK1 in mitophagy.

biophysics↗

bioRxiv2026

MOLECULAR BASIS FOR PINK1 MATURATION

Phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK1), a key regulator of mitophagy, has been linked to the pathogenesis of Parkinson's disease (PD). PINK1 recruits Parkin, an E3 ubiquitin ligase, triggering mitophagy in response to mitochondrial damage. During mitophagy, the quantity, stability, and activity of PINK1 must be strictly regulated; however, the mechanisms governing these parameters under cellular stress are still unclear. Herein, we determined the structural basis for PINK1 maturation mediated by heat shock protein 90/cell division cycle 37/FK506-binding protein 51 (HSP90/CDC37/FKBP51) chaperone complex. We identified PINK1-associated proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and determined the structures of the complexes using Cryo-Electron Microscopy (Cryo-EM). Results showed that FKBP51 potentially interacts with a conserved leucine-proline-phenylalanine (LPF) motif on the activation loop of PINK1 and negatively regulates PINK1 functions in mitophagy. A PINK1 mutation located at the FKBP51 recognition site is linked to mitophagy deficiency, which can be partially rescued by specific inhibition of FKBP51. These findings reveal a general mechanism for PINK1 recognition by the HSP90/CDC37/FKBP51 chaperone complex and suggest a potential approach for upregulating PINK1 activity, which is impaired in PD.

biophysics↗

bioRxiv2026

An intact primordial interferon antiviral signalling network in amphioxus illuminates the basal chordate origin of vertebrate IFN immunity

The evolutionary origin of the complete interferon (IFN) antiviral signalling cascade across chordates has long remained elusive, as fully functional IFN machinery had not been biochemically reconstituted in basal cephalochordates. Here we combine phylogenetics, AlphaFold3 structural prediction, multi-omic profiling and a full panel of in vitro and in vivo functional assays to characterize an intact primordial IFN network in amphioxus Branchiostoma japonicum, the extant sister group of all vertebrates. Amphioxus encodes a pair of undifferentiated BjTBK1/IKK{varepsilon} paralogs that form cytoplasmic heterodimers, whose conserved kinase-domain phosphorylation residues are mandatory for downstream IRF-driven IFN promoter activation. Despite minimal primary sequence homology with vertebrate IFNs, BjIFN1/2 possess compact -helical core folds that hint at potential structural analogy to vertebrate mucosal type III IFN-{lambda}. We identify two primitive class II cytokine receptors BjCRFB1 and BjCRFB2 that act as functional IFN sensors. Phylogenetic and tertiary structural validations confirm these undiversified ancestral receptor prototypes arose before vertebrate IFN receptor subfunctionalization, and their distinct temporal induction profiles upon viral challenge closely mirror the mucosal immune surveillance orchestrated by vertebrate IFN-{lambda}-IFNLR signalling. AlphaFold3 ligand-receptor docking identifies BjIFN2-BjCRFB2 as the optimal binding pair among all tested combinations, yet all modelled complexes yield low interface scores indicative of weak ancestral intermolecular interactions. Downstream signal transduction relies on two STAT paralogs, BjSTATa and BjSTATb, which jointly mediate transcriptional activation of core antiviral effector genes. The conserved GTPase BjMx serves as a central IFN-stimulated effector to suppress viral replication and maintain tissue immune homeostasis. Collectively, our structural and functional evidence demonstrates that the full hierarchical IFN signalling apparatus was fully assembled in basal cephalochordates prior to vertebrate radiation. The amphioxus IFN cascade preserves core ancestral molecular traits including structure-dependent ligand conservation and primitive low-affinity ligand-receptor interactions. This study resolves a long-standing evolutionary gap and provides definitive functional evidence demonstrating that IFN-mediated innate immunity constitutes an ancestral chordate trait, rather than a vertebrate-specific evolutionary innovation. It also puts forward the hypothesis that mucosal surveillance may represent the ancestral mode of chordate IFN defence.

evolutionary biology↗

bioRxiv2026

A Centimeter-Scale, Peristaltic Human Intestinal Organoid with Integrated Neuro-Immune-Vascular Systems Recapitulates Enteritis and Orthotopic Colorectal Cancer

Human pluripotent stem cell-derived intestinal organoids hold great promise for disease modeling, drug screening, and regenerative medicine. However, conventional intestinal organoids are predominantly epithelial, small in scale, and lack the multicellular complexity required to recapitulate the pathophysiology of intestinal disorders such as inflammatory bowel disease (IBD) and colorectal cancer (CRC). Here, we report the development of Centimeter-Scale, purely 3D self-organized human intestinal organoids (IOs) from induced pluripotent stem cells (iPSCs) that encompass multiple tissue lineages, including epithelium, mesenchyme, smooth muscle, neurons, immune cells, and vasculature. These organoids achieve functional maturation by day 100+, exhibiting rhythmic peristaltic-like contractions, and by day 147 they display histological structures including lumens, crypt-like architecture, goblet cells, and smooth muscle. Importantly, for the first time, the neuro-muscle lineages arise spontaneously and autonomously in a purely 3D culture system, without any external stimulation (e.g., electrical, chemical, or mechanical), and mature to form functional neuromuscular junctions, driving macroscopically visible peristaltic-like contractions that mimic intestinal motility entirely through in vitro culture, without any xenotransplantation. Single-cell RNA sequencing at day 115 identified 12 cell subtypes across four major lineages, recapitulating the cellular diversity of the developing human intestine. Using this platform, we established an LPS/IFN-{gamma}-induced IBD model that recapitulated key pathological features, including epithelial disruption, immune cell infiltration, and IL-6 elevation. Transcriptomic analysis confirmed activation of the NF-{kappa}B and JAK2-STAT3 pathways, multi-modal cell death, and immune recruitment machinery, all consistent with clinical IBD pathology. Furthermore, we developed intestinal cancer models at 7 and 21 days showing abnormal hyperplasia, and a probiotic co-culture system demonstrating anti-inflammatory efficacy. Together, these results establish Centimeter-Scale intestinal organoids as a physiologically relevant, multicellular platform for modeling intestinal diseases and evaluating therapeutic interventions.

cell biology↗

bioRxiv2026

In situ Discovery of Immune Repertoire Reveals Antitumor Immunity and Therapeutic Antibodies

Spatial transcriptomics offers a glimpse into the immunology of tissues. However, limitations in spatial transcriptomics preclude the detection of highly diverse, low-abundance, and previously unknown sequences, including immune repertoires and microbiota. Here, we introduce Archimap, a spatial transcriptomic platform that simultaneously profiles spatial transcriptomes, immune repertoires, and microbiota from formalin-fixed paraffin-embedded (FFPE) tissues. Using Archimap, we profile the spatial localization of TCRs, BCRs, and the microbiota landscape in archived clinical tissues at single-cell resolution. Through comprehensive benchmarking, we validate Archimaps performance and fidelity. Archimap in situ assembles the immune complex and reconstructs the clonal evolution of antibodies. Together, Archimap shows the power of in situ discovery of functional immune repertoires for their antitumor immunity.

bioinformatics↗

bioRxiv2026

Ablation and Seed-driven Restoration of an Alpha-Satellite Devoid Human Centromere Reveals Size Homeostasis Mechanisms

Human centromeres are epigenetically defined chromatin domains marked by nucleosomes containing the histone H3 variant CENP-A, which recruit the constitutive centromere-associated network (CCAN) to assemble functional kinetochores. Maintaining centromere function, including chromatin domain size and the ability to assemble the kinetochore, is essential for proper mitotic division across eukaryotes. In humans however, mechanistic studies of centromere establishment, maintenance, and size regulation have been hindered by the highly repetitive nature of canonical alphoid centromeres. Here, we develop a genetically tractable human neocentromere system which is devoid of repetitive DNA sequences. Using targeted genetic manipulation of a monoallelic naturally occurring neocentromere, we show that partial loss of centromeric chromatin triggers restoration of the residual CENP-A domain through seed-driven, sequence-independent expansion into adjacent naive chromatin. In contrast, creation of new domain boundaries without loss of centromeric chromatin mass results only in local boundary remodeling, without substantial domain expansion. These findings indicate that centromere formation proceeds through two mechanistically distinct steps, beginning with acquisition of a CENP-A seed and followed by regulated domain expansion to generate a mature centromere. More broadly, our results support a model in which centromeres transition between a maintenance state that preserves domain size and a restoration state that rebuilds centromeric chromatin following perturbation. Together, this study establishes a genetically tractable platform for dissecting the mechanisms governing human centromere formation, chromatin domain dynamics, and size homeostasis.

cell biology↗

bioRxiv2026

SpatialMOC: Accurate reconstruction of spatial multi-omics landscapes through cross-modality prediction

Spatial multi-omics technologies provide unprecedented opportunities to characterize tissue organization by measuring complementary molecular layers within their native spatial context. However, simultaneous profiling of multiple molecular modalities remains technically challenging, limiting the widespread application of spatial multi-omics and leaving most studies reliant on single-modality measurements. Here, we present Spatial Multi-Omics Cross-prediction (Spatial-MOC), a computational framework that reconstructs missing spatial molecular modalities by integrating spatial context with cross-modality representation learning. Across multiple tissues, molecular modalities, developmental stages, sequencing platforms, and degraded datasets, SpatialMOC consistently outper-formed existing computational approaches in bidirectional molecular prediction. Beyond accurate prediction, SpatialMOC faithfully reconstructed tissue architecture, preserved dynamic molecular and regulatory heterogeneity, and recovered biologically meaningful spatial landscapes from technically compromised measurements. Together, these results establish SpatialMOC as a general framework for spatial multi-omics reconstruction, extending the analytical value of existing spatial omics datasets and facilitating comprehensive investigations of tissue organization, development, and disease.

bioinformatics↗

bioRxiv2026

Niche-specific microbial community structure of subgingival plaque in periodontitis

Subgingival biofilms in periodontitis exhibit spatial heterogeneity, yet the organization of microbial communities across periodontal niches remains incompletely defined. Using paired sampling and 16S rRNA gene sequencing, we characterized non-attached and attached subgingival plaque from patients with periodontitis, together with non-attached plaque from periodontally healthy individuals. Across diversity metrics and ordination analyses, non-attached plaque from periodontitis patients occupied positions between healthy-associated and attached-plaque communities. Taxonomically, these communities contained both health-associated commensals and anaerobic genera commonly enriched in periodontitis. Network analysis identified differences in association-network topology among niches, with the non-attached periodontitis network containing more retained associations than the healthy network. These cross-sectional results describe niche-associated patterns of subgingival community composition and association structure. They do not establish temporal progression, direct microbial interactions, or clinical utility.

microbiology↗

bioRxiv2026

Ecological trajectories and microbial network reorganization across caries-associated oral niches

Dental caries is a biofilm-mediated disease associated with ecological changes in the oral microbiome. How microbial community organization differs among healthy plaque, caries-associated plaque, and carious dentin remains incompletely defined. We used 16S rRNA gene sequencing to profile paired supragingival plaque and carious dentin samples from patients with caries, together with supragingival plaque from healthy controls. Caries-associated plaque showed higher diversity than healthy plaque, whereas diversity was lower in carious dentin. Ecological ordering placed the three sample types along a health-plaque-dentin continuum. Association-network analysis showed distinct network structures in caries-associated plaque and carious dentin, with the dentin network displaying greater density and lower modularity. By integrating differential-abundance and network centrality results, we identified taxa associated with the dentin niche. A sparse logistic regression model using three genera distinguished plaque from dentin in patient-grouped cross-validation (AUROC, 0.780; AUPRC, 0.718). These cross-sectional findings describe niche-associated microbiome organization in dental caries and provide candidate features for future validation in independent, clinically relevant cohorts.

microbiology↗

bioRxiv2026

LncRNA-mediated organization of oncogenic chromatin state is a targetable vulnerability in leukemia

Long non-coding RNAs (lncRNAs) are increasingly recognized as critical regulators of gene expression underlying various cellular functions, however, the functional and mechanistic contributions of most lncRNAs to tumorigenesis remain poorly defined, and targeting of lncRNAs is challenging with conventional therapeutic approaches. Here, we uncover human PAN3-AS1 and its murine ortholog Lnc35682, previously uncharacterized lncRNAs embedded within a conserved syntenic genomic locus, as highly expressed in acute myeloid leukemia (AML). Using genetic mouse models, human cell lines and primary patient samples, we show that PAN3-AS1 is essential for leukemia maintenance but dispensable for normal hematopoiesis. Mechanistically, we find that elevated PAN3-AS1 influences chromatin accessibility, thus promoting leukemia gene expression programs. This is mediated, at least in part, by PAN3-AS1s association with the nuclear lamina through a defined functional region that is required for its leukemogenic function. We further characterize a feed-forward regulatory circuit between PAN3-AS1 and its neighboring gene FLT3 that directly links the aberrant lncRNA functions to the FLT3-mutant AML subtype. To therapeutically exploit the regulatory node, we engineer a myeloid leukemia-preferentially targeted lipid nanoparticle (LNP) formulation and demonstrate effective delivery of siRNAs against endogenous targets into leukemia cells in experimental animals. LNP-siPAN3-AS1 alone or in combination with a clinically used FLT3 inhibitor, Gilteritinib, reduces leukemia burden and significantly delay leukemogenesis in vivo. Overall, our study uncovers a therapeutic vulnerable lncRNA-centric circuitry and provides compelling preclinical evidence for the development and application of a novel RNA targeting-LNP based therapy for treatment of myeloid leukemia. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/744058v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@10c9d42org.highwire.dtl.DTLVardef@12864e7org.highwire.dtl.DTLVardef@f87f6aorg.highwire.dtl.DTLVardef@750cbf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

MMMAS: A Mendelian Mismatch Matrix Analysis System for Deterministic Pre-Screening of Germplasm Collections

Pedigree errors, duplicate accessions, and undocumented kinship limit the effective use of large genebank collections. Existing tools such as CERVUS and COLONY require allele-frequency estimates and return relationship-level assignments, providing no collection-wide view of Mendelian consistency. We developed the Mendelian Mismatch Matrix (MMM) framework and its open-source implementation, MMMAS (Mendelian Mismatch Matrix Analysis System). We applied MMM to apple (Malus x domestica; 1,085 accessions, 15 SSRs) and sweet cherry (Prunus avium; 383 accessions, 13 SSRs) datasets from the German Fruit Genebank. MMM converts pairwise Mendelian mismatch numbers (Mmn) into an N x N symmetric matrix, from which we derive four collection-scale indices (Mmin, the Mendelian minimum mismatch number; Mavg, the Mendelian average mismatch number; Mzmp, the Mendelian zero-mismatch partner number; Mmmd, the Mendelian mismatch-mode duplication index) and the Mendelian Exhaustive Stratification (MES) grading system. Apple showed a gradient-type structure (Mendelian Grade-gap Index, MGI = 0.125), sweet cherry a broken-type structure (MGI = 0.545). The Mmin-Mavg strategy identified 20 and 10 distinct accessions in apple and sweet cherry, including the scab-resistance donor Malus x floribunda 821 (Rvi6) and the fire-blight donor M. x robusta 5. The Mmmd index flagged one literature-confirmed pair of duplicate genotypes in sweet cherry. Of CERVUS-confirmed parent-offspring pairs, 97.31% in apple and 100% of high-confidence pairs in sweet cherry fell within Mmn <= 1. Mzmp rankings matched documented breeding history, with 'Cox Orange' (Mzmp = 57) and 'Luebecker Bunte' (Mzmp = 49) ranking first in each species. The complete end-to-end analysis of all 588,070 apple pairwise comparisons took 7.24 s on an ordinary workstation. This deterministic pre-screening framework, with a parameter-free core, supports routine quality assessment in germplasm collections.

genetics↗

bioRxiv2026

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

Epigenetic aberrations are a hallmark of cancer; however, systematic chromatin state maps of cancer cells are unavailable. We generated and analyzed 803 histone mark profiles in 142 cancer cell lines and 114 human tumors belonging to 9 solid tumor types. Irrespective of their cell-of-origin, cancer cells segregate from normal tissues based on their enhancer patterns, suggesting enhancer deregulation is a fundamental epigenetic feature in cancer. Enhancer based clustering defined 5 distinct subgroups of cancer cells (EpiC1-5) with unique developmental trajectories, molecular features and dependencies. Importantly, we define a set of core TFs that are critical for EpiC-specific enhancer patterns and survival. Notably, EpiC4 represented a predominantly epigenetic, pan-cancer subtype that displays poor survival, activation and dependence on a FN1-CAV1-SRC-PI3K-AKT signaling network. Together, these data uncover enhancer heterogeneity in pan-cancer systems with identification of a novel enhancer-based subtype and identify potential new therapeutic targets associated with unique epigenetic features.

cancer biology↗

bioRxiv2026

Enhancing Recombinant Vector Assembly Efficiency: A Novel Methodological Approach

With the rapid development of modern biotechnology, DNA vectors have become fundamental tools for inserting, transferring, and expressing specific gene sequences in various fields such as gene cloning, gene expression, gene editing, and gene therapy. However, when dealing with complex structured DNA sequences, traditional vector construction methods face challenges with low connection efficiency. This study proposes a new method for constructing recombinant vectors by employing a strategy of high-temperature treatment followed immediately by placement on ice, effectively reducing the complexity of DNA structures and enhancing the efficiency of PCR product-vector connection, thereby improving the construction efficiency of recombinant vectors. This paper describes the technical details of the method, experimental validation, and applications in gene cloning, gene recombination editing, and the preparation of gene therapy drugs, providing a new efficient tool for molecular biology experiments.

biochemistry↗

bioRxiv2026

The Capillary endothelial cell-governed niche sustains angiogenesis in proliferating infantile hemangioma via multilayer stromal support

Infantile hemangioma (IH), the most common benign vascular tumor in infants, is characterized by the aberrant proliferation of hemangioma endothelial cells (HemECs) and excessive angiogenesis. However, it is unclear how the tumor microenvironment sustains these active angiogenic signals. We performed single-cell RNA sequencing and spatial transcriptomic to profile 30 samples from proliferating IH, involuting IH, and normal skin. The results indicated that HemECs comprised distinct subpopulations. Among them, capillary endothelial cells (Cap.ECs) had an immature phenotype and functioned as the core drivers of IH. The endothelial-to-mesenchymal transition endothelial cells (endoMT-ECs) secreted collagen and engaged in CD44-mediated crosstalk with Cap.ECs to construct the angiogenesis-active niche in the tumor microenvironment (TME) of proliferating IH. Blockade of CD44-mediated intercellular communication effectively suppresses the angiogenesis of HemECs and promotes tumor regression. Beyond the endothelial layer, pericytes tightly enveloped Cap.ECs, with SERPINE2+ subtypes sustaining their angiogenic activity via ANGPT signaling. Pseudotime trajectory analysis revealed that the mesenchymal stem cells (MSCs)-enriched niche serves as a progenitor pool for Cap.ECs in proliferating IH. Our findings thus revealed that IH progression relies on CD44-mediated endoMT-EC-Cap.EC crosstalk and on both pericyte and MSC niches to sustain angiogenesis. HIGHLIGHTSO_LICapillary endothelial cells drive infantile hemangioma progression, with pericytes tightly ensheathing them. C_LIO_LICD44-mediated capillary and endoMT-derived endothelial cells crosstalk construct the angiogenic-active niche in the tumor microenvironment of proliferating infantile hemangioma. C_LIO_LIThe MSC-enriched niche provides a progenitor pool for the capillary endothelial cells in proliferating infantile hemangioma. C_LI

cancer biology↗