bioRxiv Science⌕ Search

Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 415 records · Page 23Linked to original sources

Cholinergic--dopaminergic interplay underlies prediction error broadcasting

Neuromodulatory systems, notably basal forebrain cholinergic and midbrain dopaminergic pathways, critically influence reinforcement learning 1-3. However, whether and how they cooperate or compete to jointly control associative learning functions remains unresolved. Here we demonstrate that basal forebrain cholinergic and midbrain dopaminergic projection systems form a coordinated and cross-regulating architecture for encoding prediction errors. Using dual-cell-type optogenetic tagging and real-time neurotransmitter measurements in mice performing a psychometric operant learning task, we simultaneously monitored cholinergic and dopaminergic activity during learning. Dopamine and acetylcholine jointly encoded reward prediction errors synergistically following reward and reward-predicting stimuli. In contrast, aversive outcomes elicited opposite responses in cholinergic neurons and approximately half of dopaminergic neurons. Activity in these two populations exhibited negative trial-by-trial correlations, revealing antagonistic dynamics. Consistently, channelrhodopsin-assisted circuit mapping uncovered a disynaptic inhibitory pathway from cholinergic to dopaminergic neurons. Chemogenetic suppression of cholinergic activity disrupted dopaminergic prediction error signaling, reduced punishment-induced suppression of dopamine release, and impaired learning. These results demonstrate that prediction error signaling is jointly implemented by coordinated interactions between major neuromodulatory systems, challenging the prevailing view of their functional independence and revealing coordinated cross-system interactions as an organizing principle of reinforcement learning, with implications for neuropsychiatric disease 4-6.

neuroscience↗

PXL: a Nucleic Acid-Binding Module of Promyelocytic Leukemia Protein

The promyelocytic leukemia protein (PML) is a stress-response factor that assembles into PML nuclear bodies, dynamic subnuclear compartments involved in tumor suppression and antiviral defense. The most abundant isoform, PML-1, has been linked to transcriptional regulation, genome stability, and antiviral responses, yet the molecular basis of these functions remains unclear. Here, we report that PML-1 contains a unique nucleic acid- binding module, PXL, and determine its three-dimensional structure by X-ray crystallography. Further biochemical, mutational, and cellular analyses, including RNA-seq, demonstrate that this module selectively binds single-stranded G-rich RNA and DNA motifs and modulates the transcriptome. These findings reveal an unexpected molecular function of PML and provide a framework for understanding its roles in nuclear organization and gene regulation.

biochemistry↗

ProteinConformers: large-scale and energetically profiled descriptions of protein conformational landscapes

Modeling protein conformational landscapes is essential for understanding dynamics, allostery, and drug discovery, yet existing resources lack diverse conformational coverage, energetic annotations, or benchmarking standards. ProteinConformers (https://zhanggroup.org/ProteinConformers) provides 2.7 million geometry-optimized conformations generated with a multi-seed molecular dynamics strategy, paired with 13.7 million energy evaluations and 5.5 million similarity annotations. It delivers continuous landscapes from non-native to near-native states, benchmarking framework for multi-conformation generators, and an interactive analysis platform.

bioinformatics↗

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↗

Endothelial PTBP1 Deletion in Transplanted Cardiac Tissue Limits Cardiac Allograft Vasculopathy

BackgroundCardiac allograft vasculopathy (CAV) is a leading cause of late graft failure and mortality following heart transplantation, with limited therapeutic options. Endothelial cells (ECs), at the interface between the donor graft and host immune system, play a central role in CAV development. However, the molecular mechanisms driving endothelial dysfunction and vascular remodeling in chronic heart transplant rejection remain poorly understood. MethodsTo characterize endothelial alterations associated with CAV, we isolated nuclei from cardiac tissues of four human donor groups: (1) early post-transplant CAV-negative surveillance biopsies, (2) CAV-negative explanted grafts with acute cellular rejection (ACR), (3) late-stage CAV-positive explanted grafts, and (4) naive non-transplanted control hearts. We applied intranuclear cellular indexing of transcriptomes and epitopes (inCITE-seq) to profile endothelial gene expression together with nuclear protein levels of splice factor polypyrimidine tract-binding protein 1 (PTBP1), a key post-transcriptional regulator of endothelial inflammatory responses. Functional relevance of PTBP1 was assessed using endothelial-specific deletion of Ptbp1 in an F1 hybrid murine model of CAV. ResultsIn human CAV, endothelial cells exhibited increased transforming growth factor-{beta} (TGF-{beta}) signaling and reduced oxidative phosphorylation (OxPhos) transcripts. Nuclear PTBP1 protein levels were markedly elevated in CAV endothelium and were associated with TGF-{beta}-responsive transcriptional programs and correlated with clinical indices of cardiac dysfunction. In murine heart transplants, endothelial-specific deletion of Ptbp1 markedly reduced hallmarks of CAV, including neointimal hyperplasia, fibrosis, and lymphocyte activation. At the molecular level, endothelial Ptbp1 deletion prevented suppression of mitochondrial transcripts and preserved mitochondrial content and integrity under hypoxic stress, attenuating interferon signaling in endothelial cells. ConclusionThese findings identify PTBP1 as a central endothelial regulator linking pro-fibrotic stress to mitochondrial dysfunction and immune activation in chronic cardiac allograft rejection. Targeting endothelial PTBP1 may represent a strategy to limit chronic graft injury while minimizing systemic immunosuppression.

immunology↗

Alternative splicing expands the functional portfolio of a plant virus to control the viral cycle

Viruses frequently have limited coding space, yet efficiently manipulate complex hosts by deploying intricate, often poorly understood strategies. Geminiviruses, devastating plant pathogens with small single-stranded (ss) DNA genomes, replicate in the nucleus aided by the viral replication-associated protein (Rep), the most conserved protein within this family and related ssDNA viruses. Rep initiates viral DNA replication and represses its own promoter to regulate the infection cycle. The molecular mechanisms enabling this dual functionality are so far unknown. Here, we show that the geminivirus tomato yellow leaf curl virus (TYLCV) exploits the host spliceosome to produce novel Rep splice variants. Splicing generates Rep isoforms lacking the central oligomerization domain that cannot initiate replication but strongly repress the Rep promoter. Conversely, Rep mutants deficient in splicing promote replication but fail to repress transcription. Reduced Rep splicing interferes with the viral gene expression hierarchy and decreases infectivity. Our findings therefore reveal a previously unrecognized viral strategy in which alternative splicing produces functionally specialized viral protein isoforms, providing a mechanistic explanation for the dual role of Rep in viral replication and gene regulation. Splicing events with potentially similar functional consequences in related viruses suggest that this strategy may have convergently evolved across diverse viral lineages infecting different domains of life.

plant biology↗

CLM-X: A multimodal single-cell foundation model with flexible multi-way Transformer for unified scRNA-seq and scATAC-seq analysis

AO_SCPLOWBSTRACTC_SCPLOWAdvances in single-cell multimodal profiling have enabled a more systematic analysis of cellular biology, yet the rapid accumulation of large-scale, heterogeneous datasets poses substantial challenges for integrative analysis. Recently, Transformer-based cell language models (CLMs) are becoming powerful foundational tools for learning transferable cell representations from unimodal single-cell datasets. However, a unified and flexible multimodal foundation model for joint modeling of scRNA-seq and scATAC-seq datasets remains underexplored. Here, we present CLM-X, a multimodal single-cell foundation model built on multiway Transformer architecture. CLM-X employs a harmonized tokenization design together with a stage-wise masked reconstruction pretraining strategy, enabling unified modeling of RNA-only, ATAC-only, and paired RNA-ATAC input within a single Transformer-based framework. We pretrain CLM-X on million-scale unimodal and multimodal datasets, and systematically evaluate its transferability on five downstream tasks including batch correction, modality integration, cross-modal translation, cell type annotation, and perturbation prediction. Across comprehensive benchmarks on 10 datasets, CLM-X consistently outperforms existing multimodal methods and unimodal foundation models, with particularly clear advantages in RNA-ATAC cross-modal translation and genetic-perturbation-response prediction. Overall, CLM-X establishes a unified and flexible multimodal foundation model for integrative analysis of scRNA-seq and scATAC-seq datasets, advancing a more robust, comprehensive, and biological interpretable single-cell analysis beyond current multimodal fusion approaches and unimodal foundation models.

genomics↗

Quantitative mapping of nanoscale EGFR-Grb2 assemblies by DNA-PAINT

Receptor tyrosine kinase signaling is initiated by extracellular ligand binding, which drives the formation of membrane-protein assemblies that activate intracellular signal transduction. Accurately resolving the molecular composition of these assemblies in situ remains challenging due to their nanoscale dimensions and intrinsic heterogeneity. Here, we introduce a single-molecule super-resolution imaging and analysis workflow designed to resolve and quantitatively characterize individual membrane-protein assembly sites in cells. We apply this approach to the nanoscale organization of the epidermal growth factor receptor (EGFR) and its adaptor protein Grb2 following stimulation with the native ligand epidermal growth factor (EGF). As activation progresses, we observe a reduction in EGFR density at the plasma membrane, a progressive accumulation of Grb2 at EGFR assembly sites, and an increase in both dimeric and higher-order oligomeric EGFR. The experimental and analytical framework presented here is broadly applicable to the study of diverse membrane-protein assemblies.

biophysics↗

Rab32/Rab38-positive Lysosome-Related Organelle degrades lipid droplet in hepatocytes by microautophagy

Rab32 and Rab38 are paralogous small GTPases involved in the biogenesis of lysosome-related organelles (LROs), yet their roles in hepatic lipid metabolism remain poorly defined. Here, Rab32 and Rab38 double-knockout (DKO) male mice exhibited an age-dependent increase in body weight accompanied by hepatic lipid accumulation, suggesting impaired hepatic lipid processing. In AML12 hepatocytes, Rab32 and Rab38 localized to ring-like, LAMP1-positive structures characteristic of LROs, whose size increased with cell confluence. Pharmacological inhibition of lysosomal acid lipase with orlistat led to the accumulation of lipid droplets (LDs) within Rab32/38-positive LROs, indicating that LD degradation occurs in these compartments. Additional treatment with bafilomycin A1 revealed invagination-like internal membrane structures within enlarged LROs. These processes were not affected by artificial inhibition of macroautophagy, highlighting the involvement of microautophagy. Ring-like signals positive for phosphatidylinositol 3-phosphate (PI3P) or phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) were detected within or adjacent to LRO membranes, and LDs were frequently associated with these structures, suggesting a role for PI3P and PI(3,5)P2 in internal membrane formation. Vps4B was also required for efficient LD incorporation. Consistently, Rab32/38 double-knockdown (DKD) AML12 cells exhibited increased lipid accumulation, indicating impaired LD engulfment. Together, these findings identify Rab32/38-positive LROs as a structural platform for microautophagy-mediated lipid droplet degradation in hepatocytes.

cell biology↗

Unwinding of RNA G-quadruplexes induces mouse and human totipotency

Totipotent stem cells (TotiSCs) have significant application prospects in regenerative medicine and assisted reproductive technologies. The mRNAs of totipotency-related genes are rich in G-quadruplex (G4) structures, while the G4 density of pluripotency-related genes mRNAs is relatively low, suggesting a potential functional link between RNA G4s and the totipotent state. Nevertheless, how G4s are involved in the establishment or maintenance of mouse and human totipotency remains poorly understood. Here, we demonstrate that FC3, a small-molecule RNA G4 unwinder, enables efficient induction and maintenance of mouse and human TotiSCs (mG4TotiSCs and hG4TotiSCs). These FC3-induced TotiSCs closely recapitulate the molecular features of 2-cell-stage blastomeres via transcriptomic and epigenomic profiling. Functionally, both mG4TotiSCs and hG4TotiSCs exhibit totipotent capacity: they differentiate into embryonic and extraembryonic lineages in vitro and in chimeric embryos; moreover, they autonomously self-organize into blastocyst-like structures without exogenous signalling. Mechanistically, we identify that Gata2 mRNA, a G4-containing transcript, is essential for FC3-mediated reprogramming. Genetic disruption of Gata2 would abolish totipotency induction. Collectively, RNA G4 unwinding is a new regulatory axis governing totipotency acquisition and maintenance, providing insight into the functional interplay between nucleic acid secondary structures and cell fate plasticity.

cell biology↗

Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics

Predicting the kinetic pathways of biomolecular systems at all-atom resolution is crucial for understanding protein function and drug efficacy, yet this task is hindered by the immense computational cost of conventional molecular dynamics (MD) simulations. While deep learning has revolutionized static structure prediction and equilibrium ensemble sampling, simulating the kinetics of conformational transitions remains a critical challenge. We introduce BioKinema, a physically grounded generative model that predicts continuous-time, all-atom biomolecular trajectories at a fraction of the cost of traditional simulations. In particular, BioKinema utilizes a spatial-temporal diffusion architecture motivated by the exponential decay of correlations characteristic of Langevin dynamics, and is explicitly trained to generate trajectories with the correct kinetics and thermodynamics. It employs a hierarchical forecasting-and-interpolation strategy to overcome the error accumulation that often plagues long-horizon generation. Through extensive validation, we demonstrate that BioKinema generates physically stable and dynamically accurate trajectories suitable for rigorous downstream analysis. For protein systems, it reproduces the equilibrium thermodynamics of the conformational ensemble and the underlying kinetics. For protein-ligand complexes, it successfully elucidates mechanisms such as ligand-driven conformational changes and allosteric interactions. Furthermore, BioKinema leverages enhanced sampling data to predict rare kinetic events, emerging as a powerful tool for estimating ligand unbinding pathways. Collectively, these results establish BioKinema as a computationally efficient complement to MD simulations that bridges the gap between static structure and dynamic function, enabling high-throughput exploration of the kinetic landscape for structural biology and drug discovery.

bioinformatics↗

NRMLncR, a myocyte-enriched long non-coding RNA, enhances myogenesis in mouse

Myogenesis is a stepwise process encompassing myogenic progenitor proliferation, lineage commitment, differentiation, myocyte fusion, and myotube maturation, and it is orchestrated by myogenic regulatory factors (MRFs) together with signaling pathways that coordinate these transitions. Long noncoding RNAs (lncRNAs) have emerged as important regulators of muscle development and regeneration, yet how lncRNAs integrate with canonical signaling networks to shape myogenic progression remains incompletely defined. Here, we identify a novel myocyte-enriched, Notch-repressed myogenic lncRNA (NRMLncR, known as A930003A15Rik), as a previously uncharacterized regulator of mouse myogenesis. The expression of NRMLncR is robustly induced during primary myoblast activation and differentiation. Loss-of-function analyses show that knockdown of NRMLncR impairs myogenic differentiation, accompanied by reduced expression of key myogenic genes. In contrast, adenovirus-mediated overexpression of NRMLncR enhances myogenic differentiation in vitro and is associated with increased muscle fiber size in vivo. Mechanistically, MyoD and MyoG occupy the NRMLncR promoter and promote its transcription during myogenic differentiation. NRMLncR knockdown alerts the transcription of nearby genes, suggesting its function through a cis-regulatory mechanism. RNA pull-down assays further identify an interaction between NRMLncR and the RNA-binding protein CELF1. Together, these findings establish NRMLncR as a novel Notch-associated lncRNA that promotes myogenic differentiation and provide insight into lncRNA-dependent regulation of the myogenic program.

genetics↗

Disentangled multimodal evolutionary representations for cross-virus predictive modeling of antigenic change

Antigenic evolution drives immune escape and complicates early assessment of emerging pathogens, especially when genomic surveillance is sparse and functional measurements lag behind real-world spread. Early prediction and generalization to unknown viruses require faithful and information-rich representations of viral evolution, a need that is not fully addressed by existing protein language model-based approaches. Here we introduce DERIVE, a flow-based generative framework that learns a disentangled latent representation of multimodal evolutionary history by integrating sequence homology with physicochemical and structural features. Using only pre-pandemic SARS-CoV-2 sequences, DERIVE prioritizes high-risk mutations, reconstructs strain-level evolutionary trajectories, forecasts immune escape and prevalence trends, and produces mutation-level effect maps. The learned representation transfers robustly across viral families, with strong concordance to functional data for influenza virus, HIV, rabies lyssavirus and chikungunya virus. Together, these results position DERIVE as a generalizable and interpretable framework for anticipating antigenic evolution and supporting early, actionable assessment of future "Disease X" threats.

bioinformatics↗

Harnessing Tumor-Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is refractory to immunotherapy due to its immunologically cold microenvironment and the scarcity of mutation-derived neoantigens. Here, we introduce NeoAPP, a computational tool designed to systematically decode neoantigens arising from tumor-specific transcripts (TSTs) generated by transcriptional dysregulation. Multi-cohort transcriptomic profiling of 413 PDAC samples using NeoAPP reveal a median of 351 neoantigens per sample derived from 56 neoantigen-encoding TSTs (neoTSTs), surpassing mutation-derived counterparts in both abundance and patient coverage. Mechanistic analyses show that non-canonical splicing junction and transposable element activation drive neoantigen generation, while FOXA2-regulated promoter usage constitutes a potential major source of neoTSTs. Tumor-derived neoTSTs are also detected in extracellular vesicles and cancer-associated fibroblasts, implicating stromal crosstalk in immune modulation. Vaccination with neoTSTs induce CD8+ T cell responses in HLA-A*02:01/A*11:01 transgenic mice and suppressed tumor growth in syngeneic PDAC models. Collectively, this work establishes TST-derived neoantigens as a dominant and therapeutically actionable antigen reservoir in PDAC, advancing a transcriptome-guided framework for neoantigen discovery with potential to overcome immune resistance in low-mutation cancers. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/705024v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@82ff31org.highwire.dtl.DTLVardef@401342org.highwire.dtl.DTLVardef@b0771corg.highwire.dtl.DTLVardef@15c03ef_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Functional activation reveals a repressor-gated fourth type VI secretion system in clinical Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major opportunistic pathogen in which the type VI secretion system (T6SS) contributes to interbacterial competition and virulence. While most strains encode three T6SSs, we here functionally characterize a fourth system (H4-T6SS) in a clinical P. aeruginosa isolate. The H4-T6SS gene cluster is transcriptionally silent under laboratory conditions. By promoter rewiring, we demonstrate that the H4-T6SS assembles a contractile machine and mediates effector secretion and robust inter- and intraspecific antagonism. We identify a dominant pore-forming effector and its secretion pathway and a silent yet conserved nuclease effector. Genetic and biochemical analyses show that H4-T6SS expression is activated by an H4-encoded transcriptional regulator and repressed by H-NS family proteins. Analysis of over 1,200 clinical isolates reveals that the H4-T6SS is distributed across lineages and geographic regions. Finally, we observe functional crosstalk between H4- and H2-T6SSs. Together, these findings establish H4-T6SS as a functional and repressor-gated secretion system that expands the competitive arsenal of clinical P. aeruginosa.

microbiology↗

Lipid monounsaturation confers cold tolerance and improves tissue viability during hypothermic storage

The rapid loss of tissue viability during hypothermic storage frequently results in organ failure and high discard rates in transplantation. In contrast, ectothermic animals can tolerate prolonged exposure to low temperatures in their natural environments. Elucidating the mechanisms underlying this cold tolerance may therefore inform improved strategies for tissue preservation. Here, we investigate proteomic and metabolomic responses to cold exposure in the livers of two frog species from distinct habitats: the cold-sensitive African clawed frog (Xenopus laevis) and the cold-tolerant Northeastern Asian brown frog (Rana dybowskii). Cold exposure induced lipid mobilization in X. laevis, whereas it promoted phospholipid mono-unsaturation in R. dybowskii. Notably, treatment with monounsaturated fatty acids (MUFAs) or overexpression of stearoyl-CoA desaturase (SCD) reduced cell death during cold storage. Moreover, MUFA infusion significantly improved cell viability in mouse liver tissue under hypothermic conditions. Together, these findings suggest that lipid mono-unsaturation, an adaptive feature of cold-tolerant frogs, can be leveraged to enhance tissue preservation during cold storage.

biochemistry↗

Chronic Paraventricular OX1R Overexpression Induces Oxidative Stress and Hypertension in Rats

BackgroundHyperactivity of the orexin system has been implicated in hypertension, yet the long-term impact of orexin 1 receptor (OX1R) overexpression in the paraventricular nucleus (PVN), a key brain region involved in arterial blood pressure (ABP) regulation, remains unclear. This study examined whether chronic OX1R overexpression in the PVN alters cardiovascular, neuroendocrine, and oxidative functions. MethodsAdult male Sprague-Dawley rats received bilateral PVN injections of AAV2-OX1R or control virus AAV2-GFP. Their ABP and heart rate (HR) were monitored for eight weeks via radiotelemetry. Renal sympathetic nerve activity (RSNA) and ABP responses to PVN orexin A administration were assessed using in vivo recordings. Reactive oxygen species (ROS) were quantified using MitoProbe, and gene expression was analyzed by qPCR. Primary neuronal cultures were used to explore underlying mechanism involved in increased ROS production and neuronal activity. ResultsPVN OX1R overexpression increased mean ABP ([~]10 mmHg), water intake, and ROS levels in both the PVN and peripheral organs. In addition, orexin A evoked exaggerated RSNA (155% vs. 73%) and pressor responses (27 vs. 16 mmHg) in PVN OX1R overexpression rats compared to control rats, these effects were attenuated by the OX1R antagonist SB408124. Plasma vasopressin levels were elevated, and brain sections confirmed increased ROS in OX1R-positive neurons. In vitro experiments further demonstrated that orexin A upregulated ROS-generating enzymes, suppressed antioxidant genes, and enhanced neuronal excitability. ConclusionChronic PVN OX1R overexpression induces oxidative stress, sympathetic overactivity, and increased plasma vasopressin, contributing to hypertension development. Targeting PVN OX1R signaling may provide therapeutic benefit for hypertension.

physiology↗

Base-resolution DNA methylome of human MDS hematopoietic stem cell reveals TET2-GFI1 epigenetic axis repressing MDS

Dysfunctional hematopoietic stem cells (HSCs) drive the initiation of myelodysplastic syndromes (MDS), yet the genome-wide DNA methylation landscape in MDS primitive HSCs and its mechanistic contribution to disease pathogenesis remain poorly defined. Here, we establish single-base resolution DNA methylomes of bone marrow HSCs from MDS patients and healthy donors. We uncover widespread hypermethylation within CpG islands, alongside hypomethylation in repetitive elements such as Alu. Differentially methylated regions (DMRs) are enriched for genes involved in cancer-related pathways, as well as extrinsic signaling pathways and intrinsic transcriptional networks essential for HSC function. Among these, we identify GFI1 and BMI1 as key targets of DNA methylation dysregulation in MDS. Notably, using either MDS or Tet2-deficient mouse model, we demonstrate that loss of Tet2, a frequently mutated epigenetic regulator in MDS, induces promoter hypermethylation and transcriptional repression of Gfi1, contributing to expansion of the MDS or aged hematopoietic stem and progenitor cell pool. Our study not only charts the base-resolution DNA methylome of human MDS HSCs but also reveals a TET2-GFI1 axis that safeguards HSC homeostasis. These findings provide mechanistic insight into how aberrant DNA methylation drives HSC dysfunction in MDS and offer an epigenomic resource for discovering novel regulators and therapeutic targets at the stem cell level.

immunology↗