Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 163 records · Page 9Linked to original sources

bioRxiv2026

Gliomas preferentially develop within the action-mode network

Gliomas tend to arise in specific brain regions and may integrate into functional circuits, suggesting they could be regulated by brain activity. However, it remains unclear whether glioma growth is related to system-level brain networks. Analyzing neuroimaging data from three datasets including 1,310 patients with cerebral gliomas, we identified and replicated a functionally connected glioma network, which overlaps with the action-mode network (AMN), somatomotor network (SMN), and action-related subcortical regions. Resting-state functional connectivity (RSFC) of the AMN successfully predicted the location of glioma occurrence in two independent datasets with complex tumor distributions. Remarkably, no patient had a glioma entirely outside the AMN, and over 89% of patients exhibited gliomas with at least 50% overlap with the network. Moreover, the spatial overlap between glioma location and the AMN demonstrated significant prognostic value in survival analyses, with higher AMN-tumor overlap associated with poorer overall survival. Notably, the acetylcholine transporter, a key player in glioma pathogenesis that drives transcriptional reprogramming, showed an expression pattern overlapping with the AMN. Meta-analytic annotations further linked the glioma network to processes of action initiation, execution, and feedback. These findings indicate that gliomas preferentially arise in circuits involved in action and highlight the central role of the AMN in glioma pathophysiology and growth.

neuroscience↗

bioRxiv2026

A targeted mutational strategy aiding generating antisense RNA to knockdown the Ehrlichia chaffeensis p28-outer membrane protein 19 expression

Obligate intracellular pathogenic bacteria belonging to the order Rickettsiales include several important emerging pathogens causing major health and economic impact to people, companion animals, and agricultural animals. Despite some recent progress, the lack of well-established genetic manipulation methods for diverse research applications remains a challenge. We recently reported the establishment of targeted mutagenesis methods to disrupt genes in Ehrlichia and Anaplasma species. Many essential genes in Ehrlichia chaffeensis are likely refractory to targeted mutagenesis, thus we developed a novel targeted mutational approach leading to the expression of antisense RNA to facilitate the knockdown of p28-Omp19 protein expression from ECH_1143. This gene was selected as its encoded protein is among the highly immunogenic proteins of E. chaffeensis and is likely essential for the pathogen. This method involved introducing a mutation at a distal genomic location within the E. chaffeensis genome to allow for generation of a 209 nucleotide-long antisense RNA segment complementary to ECH_1143 coding mRNA from the same gene promoter which was duplicated as part of the mutagenesis. The mutational strategy was designed to retain the surrounding genomic regions unaltered. The antisense knockdown version of E. chaffeensis resulted in a reduction of p28-Omp19 expression when compared to wild-type E. chaffeensis during its replication in a macrophage cell line, where the gene expression is known to occur. We anticipate that the antisense mutational strategy will be broadly applicable to facilitate investigating essential genes of obligate intracellular bacterial pathogens.

molecular biology↗

bioRxiv2026

Phenotype-Guided In Silico Molecular Generation Using Large Language Models

Complex diseases often emerge from coordinated, system-level cellular state changes that are difficult to address with target centric drug discovery. Phenotypic drug discovery offers a principled alternative but remains constrained by the cost and scalability of pathologically relevant assays. Here we present GEMGen, a large language model-based framework that performs in silico phenotypic drug discovery by generating small molecules directly from transcriptomic representations of cellular states. GEMGen encodes desired phenotypic transitions as text-based representations of up- and down-regulated gene sets, enabling transferable modeling across experimental platforms and data modalities. Trained on large scale chemical perturbation data, GEMGen robustly identifies phenotype-oriented compounds and mechanistically related but structurally distinct candidates across multiple benchmarks. Applied to signatures induced by genetic perturbations, GEMGen produces small molecules that phenocopy gene knockdown effects and identifies chemically novel inhibitors, including previously unreported KEAP1 inhibitors that activate NRF2 signaling. Extending this approach to a disease relevant model of fibrosis, GEMGen generates compounds that reverse profibrotic transcriptional programs and cellular phenotypes. These results establish a scalable framework for translating transcriptomic phenotypes into candidate therapeutic molecules, enabling systems-level exploration of vast chemical space and offering a complementary in silico counterpart to physical phenotypic drug screens.

cell biology↗

bioRxiv2026

Senescence-inhibitory Δ133p53α counteracts accelerated ageing and mortality

Research on progeria not only contributes to treatments for the disease but also enhances our understanding of physiological ageing1. Mouse models of progeria recapitulate pathological ageing phenotypes seen in patients, including cardiovascular defects, increased cellular senescence, systemic inflammation, DNA damage accumulation, and shortened lifespan2. In cultured cells from Hutchinson-Gilford progeria syndrome (HGPS) patients, the human p53 isoform {Delta}133p53 was previously shown to inhibit p53-mediated cellular senescence, proinflammatory IL-6 production, and DNA damage accumulation, and to extend cellular replicative lifespan3. Here we show that, in a heterozygous HGPS mouse model4, transgenic expression of {Delta}133p53 reproduces these in vitro-observed effects across multiple organs in vivo and extends median lifespan by 11% (387 versus 349 days, P = 0.0379). In the aorta and skin, {Delta}133p53 abrogates progeria-characteristic pathological changes and preserves tissue integrity. Our data further suggest that {Delta}133p53 may promote a broad spectrum of ageing-counteracting mechanisms, including bone homeostasis, metabolic fitness, antioxidant defense, youthful epigenome, and tissue stemness. Together with the anti-inflammatory and tissue-preserving effects of {Delta}133p53 in naturally aged mice and its age-associated downregulation in human tissues, this study suggests that {Delta}133p53-based therapeutic strategies may be applicable not only to HGPS but also as broader interventions for preventing or delaying ageing.

physiology↗

bioRxiv2025

Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq

Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information. As a proof of concept, we used this model to predict projections of fear recall engram neurons. This study facilitates our understanding of brain multi-modal network and neural computation.

neuroscience↗

bioRxiv2025

A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics

Spatial transcriptomics (ST) platforms are limited by spatial resolution, sensitivity to low expression levels, alignment with tissue structures, and the balance across tissue complexity. Computational enhancement typically targets a single challenge, e.g., super-resolution using hematoxylin and eosin (H&E) images or sensitivity enhancement with single-cell RNA sequencing (scRNA-seq). However, most ignore the interdependence across challenges, yielding biologically inconsistent enhancement. Here we introduce FOCUS, a foundational generative model for unified ST enhancement, conditioned on H&E images, scRNA-seq references, and spatial co-expression priors. With large-scale pretrained encoders, FOCUS uses a modular design for multimodal integration and a cross-challenge coordination strategy to target co-occurring challenges, enabling joint optimization. FOCUS was trained and comprehensively benchmarked on >1.7 million H&E-ST pairs and >5.8 million single-cell profiles, demonstrating state-of-the-art performance across ten ST platforms, on both individual and coupled challenges. The real-world utility and generalizability were validated on a rare suprasellar tumor, papillary craniopharyngioma, and an unseen ST platform (Open-ST) for primary and metastatic head and neck squamous cell carcinoma.

bioengineering↗

bioRxiv2025

Characterizing the Effects of Protein Glycosylation Perturbation on Phosphorylation Signaling

Protein glycosylation and phosphorylation constitute two pervasive regulatory layers in mammalian cells, yet the effects that protein glycosylation play in phosphorylation signaling remain poorly understood. Here we show that controlled perturbation of N-linked glycan biosynthesis through glycoengineering fundamentally rewires phosphorylation signaling networks in human cells. Using comprehensive proteomics approaches, we simultaneously profiled the global proteome, glycoproteome, and phosphoproteome in engineered HEK293 cells designed to eliminate core fucosylation while enhancing sialylation and reducing GlcNAc branching complexity. Glycoengineering emerged as the dominant source of molecular variation across all datasets, with over 9,800 intact glycopeptides identified of which 3,400 are significantly altered, establishing a remodeled baseline cellular state. Upon serum stimulation, engineered cells not only exhibited markedly decreased phosphorylation responses compared to wild-type cells, but comprehensively re-wired to prefer signaling away from canonical EGFR/mTOR growth pathways. These findings establish a systematic framework for targeting glycosylation-phosphorylation regulation and nominate glycan-dependent signaling nodes as potential therapeutic vulnerabilities in glycosylation-remodeled disease states.

cell biology↗

bioRxiv2025

TRIO-AI: Hybrid temporal graph, ODE, and VAE modeling for high-resolution cellular trajectory inference in liver injury

Resolving dynamic cellular transitions at single-cell resolution is essential for understanding complex biological processes in development, disease, and regeneration. However, existing trajectory inference methods struggle to capture heterogeneous temporal dynamics, particularly for rare or transitional cell populations critical to injury and repair responses. Here, we present TRIO-AI, a hybrid computational framework that synergistically integrates three complementary approaches: Temporal Graph Neural Networks (Temporal GNN) for branching detection, Neural Ordinary Differential Equations (Neural ODEs) for continuous state flow modeling, and Time-Variational Autoencoders (Time-VAE) for density-based transitional state identification. We applied TRIO-AI to single-cell RNA sequencing data from mouse liver ischemia-reperfusion (IR) injury across multiple timepoints (days 0, 1, 3, and 5 post-injury), comprehensively characterizing major hepatic macrophage populations. TRIO-AI identified a distinct transitional macrophage population (MPs_3) that peaks at 48 hours post-injury and exhibits coordinated signatures for lipid handling (LRP1, LRP6, ABCA1, LDLR, SCARB1), efferocytosis (MARCO, MERTK, MSR1), and extracellular matrix engagement (ITGA9, ITGB1, SDC2). This population serves as a critical integrator of multicellular pro-reparative signals through APOE-LRP1 and FN1-ITGA9 signaling axes. Spatial transcriptomics validation confirmed MPs_3 localization to peri-necrotic borders with dramatic enrichment of APOE-LRP1 co-localization at 48 hours (19 pairs) compared to 24 hours (3 pairs). Comparative analysis against five state-of-the-art methods demonstrated TRIO-AIs superior performance in detecting transitional states, accurately reconstructing branching trajectories, and identifying off-path populations missed by conventional approaches. This framework provides a powerful platform for dissecting cellular dynamics in complex biological systems and reveals new insights into macrophage-mediated tissue repair mechanisms.

bioinformatics↗

bioRxiv2025

Interleukin-17 directly triggers Epstein-Barr virus lytic reactivation in latently infected human B cells

Epstein-Barr virus (EBV) is a ubiquitous human gammaherpesvirus implicated in a wide spectrum of inflammatory and malignant diseases. Although EBV toggles between latent and lytic states, the host cues that control this switch remain incompletely defined. Interleukin-17A (IL-17A; hereafter IL-17), a signature Th17 cytokine, is abundant in EBV-associated tissues, and EBV products can augment IL-17 responses. Whether IL-17 directly modulates the EBV life cycle has remained unknown. Here we show that IL-17 alone is sufficient to induce EBV lytic reactivation in latently infected human B cells. Across RT-qPCR, immunoblotting, and RNA-seq, IL-17 increased the immediate-early regulator BZLF1 (Zta) and upregulated downstream early and late viral genes, consistent with activation of a transcriptome-wide lytic program. Culture supernatants from IL-17-treated cells contained elevated DNase-resistant extracellular EBV DNA, indicating productive replication with encapsidated genomes. Transcriptomic pathway analyses confirmed engagement of IL-17-linked signaling and highlighted inflammatory modules, including NF-{kappa}B and JAK-STAT. Gene Ontology analysis further enriched for regulation of B-cell receptor signaling and B-cell activation, situating IL-17 within B-cell inflammatory circuitry. Together, these findings identify IL-17 as a cytokine cue for EBV lytic entry and provide a mechanistic link between Th17-skewed inflammation and episodic EBV reactivation. This cytokine-driven pathway complements existing models centered on B-cell receptor signaling, hypoxia/HIF-1, COX-2/PGE2, and TGF-{beta} and motivates testing whether modulation of the IL-17/IL-17R axis can alter EBV reactivation in IL-17-rich settings. To our knowledge, this is the first demonstration that IL-17 alone directly triggers EBV lytic reactivation in human cells. IMPORTANCEEpstein-Barr virus (EBV) persists for life by maintaining latency with intermittent lytic reactivation, yet the physiological cues that initiate the latency-lytic switch remain poorly defined. Here we identify the Th17 cytokine interleukin-17A (IL-17) as a direct host trigger of EBV lytic reactivation in latently infected human B cells. IL-17 alone induced the immediate-early transactivator Zta, activated a transcriptome-wide lytic program, and promoted release of DNase-resistant extracellular EBV DNA consistent with encapsidated virions. Transcriptomic analyses confirmed engagement of IL-17-linked inflammatory modules and implicated convergence on signaling nodes shared with canonical B-cell receptor pathways. These findings establish a mechanistic link between Th17-skewed inflammation and EBV reactivation burden, providing a framework to interrogate how IL-17-rich microenvironments influence EBV dissemination and immunopathology and to evaluate whether targeting the IL-17/IL-17R axis can modulate EBV reactivation in disease settings.

microbiology↗

bioRxiv2025

Comparative vector competence of post-2015 St. Louis encephalitis virus in Culex tarsalis and Culex quinquefasciatus mosquitoes

The human pathogenic orthoflavivirus St. Louis encephalitis virus (SLEV) reemerged in the western United States in 2015 after more than a decade of absence and has since expanded throughout California with sustained interannual transmission. This shift from the historically sporadic pattern of SLEV activity before 2003 raises the question of whether contemporary strains differ in fitness from earlier strains. To assess whether reemerging SLEV possess enhanced infectivity or transmissibility, we compared five contemporary genotype III strains from California (2016-2023) with a historical genotype V strain from 2003. Growth kinetics were evaluated in mammalian, duck, and mosquito cells; vector competence was assessed in laboratory colonies of Culex tarsalis and Culex quinquefasciatus vectors; and viremia profiles were measured in Collaborative Cross recombinant intercross mice. Some genotype III strains produced higher titers than the historical genotype V strain in avian and mosquito but not mammalian cells. Several genotype III strains infected and transmitted SLEV RNA more efficiently than the historical strain in both mosquito species, although no temporal trend in fitness was observed. SLEV fitness was comparable or greater in Culex quinquefasciatus than in Culex tarsalis. Sequencing identified no shared amino acid substitutions associated with vector infection phenotypes. Although genotype III strains exhibited a delayed peak relative to the historical strain, murine viremia levels were comparable across strains. These findings show some contemporary strains exhibit equal or greater fitness than the historical strain, which may contribute to SLEV persistence and spread in California, underscoring the need for continued surveillance and targeted vector control. IMPORTANCESt. Louis encephalitis virus (SLEV) reemerged in California in 2015 after more than a decade of absence and has since established sustained transmission and expanded geographically. The factors underlying this reemergence remain poorly understood. By comparing contemporary genotype III SLEV strains with a historical genotype V strain, we found that several contemporary strains exhibit equal or greater fitness compared to the historical strain in avian and mosquito cells and are transmitted more efficiently by the two principal California vector species, Cx. tarsalis and Cx. quinquefasciatus. We also demonstrate that Cx. quinquefasciatus can transmit infectious genotype III SLEV, supporting its role in SLEV maintenance and spread. Despite differences in mosquito infection and transmission, we found no evidence that fitness in mosquito vectors or mice has continued to rise among strains detected more recently, suggesting that enhanced transmission is not driven by ongoing directional adaptation. These findings indicate that contemporary genotype III SLEV strains possess transmission competence in mosquito vectors that may have contributed successful reestablishment and persistence of SLEV California. Improved understanding of the characteristics of reemerging SLEV strains can inform surveillance, risk assessment, and vector control efforts aimed at reducing human exposure to prevent disease caused by SLEV.

microbiology↗

bioRxiv2025

Trehalose 6-phosphate activates Target of Rapamycin in plants

Coordinating carbon availability with growth is a fundamental challenge in plants. Target of Rapamycin (TOR) promotes cell growth and is activated by sugars, but the underlying molecular mechanism has remained elusive. Here, we identify trehalose 6-phosphate (T6P), a sucrose-derived metabolite, as the key signal linking carbon to TOR activity. In Arabidopsis and Brassica napus, T6P stimulates cell growth via TOR and is required for sucrose-induced TOR activation. We show immunoprecipitates using anti-TOR antibodies contain catalytically active TOR in addition to the catalytically active SnRK1 energy sensor kinase. In vitro experiments show that, SnRK11, the catalytic subunit of SnRK1 suppresses TOR activity, and T6P reverses this inhibition in a dose-dependent manner, providing biochemical evidence that T6P activates TOR by suppressing SnRK1. This work thus establishes a direct sucrose-T6P-SnRK1-TOR signaling axis that couples carbon availability to plant growth.

plant biology↗

bioRxiv2025

Immunotherapy with Pro-regenerative Macrophages from Embryonic Stem Cells Ameliorate Osteoarthritis via TNFAIP3-Mediated Chondroprotection

Immune cell-based therapies for osteoarthritis (OA) remains underexplored. Macrophages coordinate tissue repair, yet their functional heterogeneity and therapeutic applicability, particularly for designed stem cell-derived populations with tailored reparative properties are not fully delineated. Inspired by embryonic skeletal development as a paradigm of scarless regeneration, we identified a pro-regenerative macrophage population through a single-cell RNA atlas of developing skeletal tissues. We subsequently established a mechanically dynamic induction approach to efficiently generate pro-regenerative macrophages from human embryonic stem cells (hESCs), mimicking this developmental phenotype. In vitro, these macrophages mitigate cartilage degradation in OA explants and suppress pro-inflammatory, catabolic signaling in chondrocytes. Injection into murine OA joints robustly attenuates disease progression, reduces extracellular matrix breakdown, and resolves synovial inflammation, representing the first demonstration of immune cell-based therapy for OA. Mechanistically, these macrophages orchestrate chondroprotection not through broad immunosuppression, but by activating a TNFAIP3-dependent signaling hub that restrains inflammatory and catabolic responses in chondrocytes. This TNFAIP3 activation precisely reversed the OA-associated gene signature, suppressing catabolic mediators while enhancing reparative factors, thereby restoring the anabolic-catabolic balance. Our findings uncover a developmental blueprint for engineering pro-regenerative macrophages from stem cells and establish a pioneering targeted immune cell therapy that engages an intrinsic chondroprotective program, offering a transformative and translationally relevant strategy for OA treatment.

immunology↗

bioRxiv2025

High-throughput in silico screen uncovers key regulators of 3D genome architecture

The vertebrate genome is spatially organized into topologically associating domains (TADs), primarily via cohesin-mediated loop extrusion which typically halts at convergent CTCF binding sites to establish domain boundaries. However, despite the essential roles of CTCF and cohesin in establishing TADs, a long-standing paradox persists: CTCF and cohesin binding sites dramatically outnumber observed TAD boundaries, suggesting the existence of undiscovered architectural factors. To identify such missing factors, we conducted high-resolution in silico screens using C.Origami, a multi-modal AI model for predicting chromatin interactions. Remarkably, we identified ZNF654 and JMJD6 as novel factors uniquely defining TAD boundaries. Experimental validation confirmed that ZNF654, an uncharacterized vertebrate-specific zinc-finger protein, interacts with CTCF to form an architectural protein complex that demarcates chromatin domains. Genetic knockout of ZNF654 weakens TAD boundary strength without influencing other CTCF or cohesin binding sites. JMJD6, a deeply conserved jmjC-family dioxygenase, marks the anchors of the strongest chromatin stripes at both TAD boundaries and enhancer-promoter sites, while deleting JMJD6 weakens or diminishes such interaction signature. These results revealed the long-sought factors that uniquely mark TAD boundary and chromatin interaction anchors which, together with CTCF and cohesin, demarcate chromatin domains during 3D genome organization. Last, the evolutionary trajectory of ZNF654 and JMJD6 offers key insight into the evolutionary origins of 3D genome organization across metazoan species.

genomics↗

bioRxiv2025

Enhancer/Enhanceosome/Super-enhancer and the promoter-proximate RNA Polymerase II (Pol II) pausing are coupled

Virus infection triggers the expression of IFN-x{beta}, which requires at least four groups of transcription factors and p300/CBP to form an enhanceosome. The promoter-proximal Pol II pausing regulation in metazoans includes the recruitment of CDK9 by JMJD6 and BRD4, the generation of a unique phosphorylation pattern of CTD of Pol II, the recruitment of JMJD5, and the cleavage of arginine methylated histone tails on the +1 nucleosome. We find that both BRD4 and p300/CBP control the activity of CDK9. It is likely that the BRD4 docking site on nucleosomes is generated by p300/CBP. We conclude that enhancer/enhanceosome/super-enhancer and Pol II pausing regulation are coupled and could be the unique universal mechanism that differentiates animals from unicellular organisms.

biochemistry↗

bioRxiv2025

SCAF1 driven polyadenylation site usage regulates mRNA isoform expression and neuronal differentiation

Accurate co-transcriptional processing is required for correct gene expression of mRNA transcript isoforms under unperturbed conditions, but particularly during development, to ensure tissue-specific mRNA isoform expression. Here we show that the poorly studied SR-related CTD-associated factors SCAF1 protein regulates polyadenylation site usage towards the end of genes. SCAF1 interacts directly with the phosphorylated C-terminal domain (CTD) of RNA polymerase II (RNAPII), in a complex enriched with elongation and 3 end processing factors. While SCAF1 knockout in HEK293 cells is innocuous, it leads to a shift towards expression of shorter mRNA transcripts by co-transcriptional usage of early polyadenylation sites. SCAF1 deficiency induced via auxin-dependent degradation in neuron differentiating mouse embryonic stem cells (mESCs) results in neuronal commitment defects, mediated by altered mRNA isoform usage that impacts expression of key neuronal genes. These findings highlight the importance of mRNA isoform usage and underscores the key role for SCAF proteins in its regulation though polyadenylation site selection.

molecular biology↗

bioRxiv2025

Integration of single-cell transcriptome and genetic profiles reveals critical cell types and genes in inflammatory bowel disease

The progression of inflammatory bowel disease (IBD), grouped into Crohns disease (CD) and ulcerative colitis (UC), involves multiple cell types and genes, but the identification of critical cell types and genes that contribute to intestinal inflammation remains challenging. By integrating human intestinal single-cell transcriptomic data from approximately 200 donors, we revealed the stromal cell-derived network in CD, enrichments of immune cells such as Th1 in CD, atypical B cells and Tfh in UC, AXL+SIGLEC6+ DCs and IgG+ Plasma B cells in both, and the association between SPP1+ Macrophages, FAP+ Fibroblasts and anti-TNF treatment resistance. We also investigated the gene expression characterization of enteric neurons. Additionally, by linking cell-type-specific transcriptional alterations with genetic profiles of disease risk and intestinal gene expression, we proposed B cells and cycling epithelial cells as critical cell types, and identified epithelial genes, such as GPX4, as associated with CD pathology. In summary, our study comprehensively characterized the single-cell landscape of human intestines in IBD and provided insights into cell types and genes highly involved in genetically determined CD pathology, thereby informing CD prediction, diagnosis, and the development of new therapeutic targets.

immunology↗

bioRxiv2025

Harmine Selectively Drives Human Beta Cell Differentiation and Function Via Protein Kinase A Pathways

Harmine and other small molecule inhibitors of the kinase DYRK1A induce human beta cells to replicate and regenerate in vitro and in vivo, and are effective at reversing diabetes in animal models. In addition to its beta cell proliferative and regenerative effects, harmine also induces expression of transcription factors and other genes involved in beta cell differentiation and function, exemplified by PDX1, MAFA, NKX6.1, GLP1R, PCSK1 and many others. Harmine also rapidly enhances glucose-stimulated insulin secretion in vitro and in vivo, reversing diabetes within days in diabetic mice transplanted with a marginal mass of human islets. We had assumed that this pro-differentiation or pro-function effect was a common feature of all DYRK1A inhibitors, and was mediated by DYRK1A inhibition. Thus, DYRK1A is a primary target (we refer to it as Target 1) for harmine. Here, to our surprise, we report that the pro-differentiation effect is not a generalized action for all small molecule DYRK1A inhibitors and does not result from DYRK1A interference or genetic silencing. Instead, the prodifferentiation effect is restricted to a small select subset of DYRK1A inhibitors (harmine, 2-2c and 5-IT). Remarkably, the pro-differentiation effect results from the unique ability of these drugs to activate protein kinase A (PKA), a dual mechanism that distinguishes this class from other DYRK1A inhibitors. The beneficial effects of harmine on PKA appear to be indirect, driven by an as yet unidentified, Target 2 in the PKA pathway. These findings make it clear that all DYRK1A inhibitors are not interchangeable, and that those that drive both proliferation and differentiation/function will likely be preferable in human clinical therapeutic settings. They also provide a novel target or roadmap for enhancing human beta cell differentiation in Type 1 and Type 2 diabetes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/692818v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@bd015corg.highwire.dtl.DTLVardef@a46f9borg.highwire.dtl.DTLVardef@19b4f65org.highwire.dtl.DTLVardef@179aa28_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

ERAD Activity Distinguishes the Functional Heterogeneity of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) rely on precisely controlled proteostasis to sustain lifelong self-renewal, yet whether intrinsic proteostatic characteristics can prospectively define functional diversity within the HSC pool remains unknown. In this study, we developed a dual-fluorescence reporter system to visualize endoplasmic reticulum-associated degradation (ERAD) activity in vivo and discovered that ERAD activity can prospectively predicts the long-term reconstitution potential of HSCs. Remarkably, ERAD states were maintained through self-renewal, revealing an inheritable "proteostatic memory" within the HSC pool. Transcriptomic and functional analyses identified SOCS2 as a key regulator of this process: SOCS2 inhibits JAK2 signaling to sustain ERAD activity, whereas hyperactive JAK2 interacts with the ERAD E3 ligase Hrd1 and suppresses VCP-mediated misfolded substrate. These findings define a SOCS2-JAK2-ERAD axis that connects cytokine signaling to intrinsic proteostasis remodeling, establishing ERAD activity as a predictive and heritable marker of HSC function and providing a conceptual framework for understanding hematopoietic stem cell heterogeneity.

cell biology↗