Biology subjects

Yuan, Z.

Publications and source records attributed to Yuan, Z..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Dynamic transcriptional heterogeneity in pituitary corticotrophs

A large body of evidence has shown that corticotrophs, the anterior pituitary cells central to the generation of hormonal stress responses, exhibit heterogeneous functional behavior, suggesting the presence of functional sub-populations of corticotrophs. We investigated whether this was the case at the transcriptomic level by conducting a comprehensive analysis of scRNA-seq datasets from rodent pituitary cells. We envisaged two alternative scenarios, one where robust subtypes of corticotrophs exist, and the other where these subpopulations were only transient states, possibly transitioning into one another. Our findings suggest that corticotrophs transition between multiple transcriptional states rather than existing as rigidly defined subpopulations. We employed marker gene-based comparisons and whole transcriptome label transfer approaches to analyze transcriptional signatures across datasets. Marker-based clustering revealed strikingly low similarity in the identified subpopulations across datasets. This analysis evidenced the presence of transcriptional states with different functional relevance, related to different stages of hormonal signalling. Similarly, the label transfer approach, which considers non-linear interactions across the entire transcriptome showed that transcriptional states could be detected across independent datasets. This classification relied on broader gene expression patterns rather than conventional marker genes, reinforcing the notion of continuous rather than discrete cell states. Furthermore, trajectory analysis by RNA velocity indicated dynamic transitions between transcriptional states, suggesting the presence of transcriptional mechanisms facilitating rapid recruitment of corticotrophs in response to physiological demands. Our findings align with evidence from other endocrine cell types, such as lactotrophs and pancreatic {beta}-cells, where hormone secretion is linked to fluctuating transcriptional activity. The observed transitions in corticotroph states suggest a mechanism allowing flexible hormonal responses to unpredictable and time-varying stressful events. Additionally, this study highlights the challenges associated with scRNA-seq methodologies, including data sparsity, batch effects, and pseudoreplication, underscoring the need for rigorous experimental design and reproducibility in single-cell transcriptomics research. These insights contribute to a broader understanding of pituitary cell plasticity and endocrine adaptation mechanisms.

cell biology↗

bioRxiv2025

QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organism Genomes

Despite the increasing number of genomes, the annotation of protein-coding genes is still lacking. In some genomes where transcriptome data is not available, various tools have been developed to annotate genes based on homologous proteins, but each tool has its limitations. Here, we propose quickprot, a user-friendly command-line tool that constructs a set of redundancy-free gene models from the target genome based on the homologous protein sequences of a set of closely related species. We tested its applicability in stonefish, and the results showed that it has high accuracy and runs faster than existing tools. This low-cost, high-precision annotation method is expected to become a useful tool for genome annotation, which will contribute to the research of comparative genomics. The software is implemented in Python and licensed under the MIT License. The source code, documentation, and tutorials can be obtained at https://github.com/thecgs/quickprot.

bioinformatics↗

bioRxiv2025

Altered Interpersonal Neural Synchronization during Social Interaction After Shared Excluded Experiences in Depressed Adolescents

BackgroundMajor depressive disorder (MDD) is common in adolescents, and the special development stage, during which adolescents brain and neuroendocrine system develop intensively, makes it subtly difficult to develop prevention and treatment strategies for depressed adolescents compared with depressed adults. Meanwhile, public psychosocial stressors significantly influence adolescents mental health and social interaction, rendering it essential to explore how a shared psychosocial stressor, i.e., shared excluded experiences, influences social interaction in depressed adolescents. MethodsWe designed a 4-player cyberball game to probe adolescents responses to shared excluded experiences and explore the underlying interpersonal neural synchronization (INS) with functional near-infrared spectroscopy (fNIRS). ResultsWe found that shared excluded experiences could enhance adolescents social interaction preferences but decreased INS in each pair of excluded adolescents, which indicates a reduced willingness to interact with others after the exclusion. However, no significantly different behavioral responses to the shared excluded experiences were found in depressed adolescents compared to adolescents as healthy controls (HC). Further analyses revealed that adolescents with MDD experienced more negative feelings than HC after exclusion. Of note, adolescents with MDD demonstrated stronger INS than HC, indicating the potential empathic stress in depressed adolescents. In addition, there existed altered brain-behavioral association patterns in responses to shared excluded experiences in depressed adolescents. ConclusionsIn summary, our study gives us deeper insights into how a shared psychosocial stressor impacts the INS in depressed adolescents, and it might be demonstrated that INS could be more sensitive than behavioral responses to detect social interaction deficits in depressed adolescents.

neuroscience↗

bioRxiv2025

A mouse model of Adams-Oliver Syndrome reveals defective Notch1 signaling in endothelial cells as a driver of pathogenesis

Adams-Oliver Syndrome (AOS) is a rare congenital disorder characterized by scalp, limb, and cardiovascular defects. While variants in the NOTCH1 receptor, DLL4 ligand, and RBPJ transcription factor have been implicated in AOS, the driving tissue types and molecular mechanisms by which these variants cause pathogenesis are unknown. Here, we used quantitative binding assays to show that AOS-associated RBPJ missense variants compromise DNA binding but not cofactor binding. These findings suggest that AOS-associated RBPJ variants do not function as loss-of-function alleles but instead act as dominant-negative proteins that sequester cofactors from DNA. Consistent with this idea, mice carrying an AOS-associated Rbpj allele develop dominant phenotypes that include lethality and cardiovascular defects in a Notch1 heterozygous background, whereas Notch1 and Rbpj compound heterozygous null alleles are well-tolerated. To facilitate studies into the key tissues driving AOS pathogenesis, we employed conditional genetics to isolate the contribution of the vasculature to the development of AOS-like phenotypes. Importantly, our studies show that expression of the Rbpj AOS allele in endothelial cells is both necessary and sufficient to cause lethality and cardiovascular defects. These data establish that defective Notch1 signaling in the vasculature is a key driver of pathogenesis in this AOS mouse model.

developmental biology↗

bioRxiv2025

Red Light-Activated Reversible Inhibition of Protein Functions by Assembled Trap

Red light offers strong tissue penetration and low phototoxicity, making it an attractive option for optogenetic applications. However, the available red light-inducible optogenetic tools are rather limited. Here, we present a novel red light-induced protein clustering system, namely R-LARIAT (Red Light-Activated Reversible Inhibition by Assembled Trap), that controls protein functions in a spatiotemporal manner. Our system capitalizes on the rapid and reversible binding of LDBs (nanobodies-based dimerization binders) to a bacterial phytochrome DrBphP, which uses a mammalian endogenous biliverdin chromophore to absorb red light. An anti-GFP nanobody fused with LDBs allows this method to quickly trap a wide variety of GFP-tagged proteins into light-induced protein clusters. Strikingly, our system exhibits an excellent performance in clustering efficiency with high light sensitivity and stability, it can function even when shielded by multiple glass plates. By utilizing the R-LARIAT system to trap and sequester tubulin, cell cycle progression can be blocked in HeLa cells. Therefore, the R-LARIAT system takes advantage of red light with greater tissue penetration and holds the potential to precisely control protein functions in living organisms.

cell biology↗

bioRxiv2025

Ultrasound Directly Activates Sparse Neurons and Modulates Visual Circuits in Deafened Mice

Focused ultrasound neuromodulation (FUN) is widely regarded as a next-generation technology for neural modulation, with applications spanning rodents, non-human primates, and humans. While mechanistic studies are advancing, a persistent confound--auditory interference--casts doubt on whether ultrasound exerts direct mechanical effects or merely indirect auditory responses. To resolve this, we engineered a circular ultrasound transducer compatible with two-photon calcium imaging and examined its effects on the primary visual cortex (V1) of surgically deafened mice, eliminating auditory contributions. Our results reveal that ultrasound directly activates a sparse subset of ultrasound-sensitive neurons (USSN) (response rate >30%) in V1, comprising only a small fraction of the total population and exhibiting a spatially sparse distribution. The proportion of USSN scale with ultrasound pressure, confirming a direct neuromodulatory effect independent of audition. Intriguingly, despite this sparse activation, ultrasound significantly modulates V1 circuitry: it alters the dynamics of light-sensitive neurons (LSN), with subsets showing excitation, inhibition, or no change in response to visual stimuli. These findings provide the first rigorous in-vivo evidence that FUN induces direct mechanical effects on neural activity, disentangling them from auditory confounds. By demonstrating both the specificity and broader circuit-level impact of ultrasound in deafened mice, this study reframes our understanding of FUNs mechanisms and strengthens its potential as a precise neuromodulatory tool. HighlightsO_LIUltrasound directly activates sparse neurons in deafened mice, demonstrating auditory-independent effects. C_LIO_LISparse ultrasound-sensitive neurons in V1 show pressure-dependent responses. C_LIO_LIUltrasound modulates visual circuitry, with diverse excitatory and inhibitory effects. C_LI

neuroscience↗

bioRxiv2025

High-Parameter Spatial Multi-Omics through Histology-Anchored Integration

Spatial omics face challenges in achieving high-parameter, multi-omics co-profiling. Serial-section profiling of complementary panels mitigates technical trade-offs but introduces the spatial diagonal integration problem. To address this, we present SpatialEx and its extension SpatialEx+, computational frameworks leveraging histology as a universal anchor to integrate spatial molecular data across tissue sections. SpatialEx combines a pre-trained H&E foundation model with hypergraph and contrastive learning to predict single-cell omics from histology, encoding multi-neighborhood spatial dependencies and global tissue context. SpatialEx+ further introduces an omics cycle module that encourages cross-omics consistency via slice-invariant mappings, enabling seamless integration without co-measured training data. Extensive validations show superior H&E-to-omics prediction, panel diagonal integration, and omics diagonal integration across various biological scenarios. The frameworks scale to datasets exceeding one million cells, maintain robustness with non-overlapping or heterogeneous sections, and support unlimited omics layers in principle. Our work makes multi-modal spatial profiling broadly accessible.

bioinformatics↗

bioRxiv2025

DAZAP2 functions as a pan-coronavirus restriction factor by inhibiting viral entry and genomic replication

The SARS-CoV-2 pandemic and the emergence of novel variants underscore the need to understand host-virus interactions and identify host factors that restrict viral infection. Here, we perform a genome-wide CRISPR knockout screen to identify host restriction factors for SARS-CoV-2, revealing DAZAP2 as a potent antiviral gene. DAZAP2, previously implicated in SARS-CoV-2 restriction, is found to inhibit viral entry by blocking virion fusion with both endolysosomal and plasma membranes. Additionally, DAZAP2 suppresses genomic RNA replication without affecting the primary translation of viral replicases. We demonstrate that DAZAP2 functions as a pan-coronavirus restriction factor across four genera of coronaviruses. Importantly, knockout of DAZAP2 enhances SARS-CoV-2 infection in mouse models and in human primary airway epithelial cells, confirming its physiological relevance. Mechanistically, antiviral activity of DAZAP2 appears to be indirect, potentially through the regulation of host gene expression, as it primarily localizes to the nucleus. Our findings provide new insights into the host defense system against coronaviruses and highlight DAZAP2 as a potential target for host-directed antiviral therapies. IMPORTANCEDuring viral infection, the host defense response is mediated by a variety of host factors through distinct mechanisms that have yet to be fully elucidated. Although DAZAP2 was previously implicated in SARS-CoV-2 restriction, its mechanisms of action and in vivo relevance remain unclear. In this study, we identify the DAZAP2 as a potent pan-coronavirus restriction factor that inhibits viral infection through dual mechanisms: blocking virion fusion with both endolysosomal and plasma membranes, and suppressing genomic RNA replication. We confirm its physiological relevance in host defense using mouse models and primary cell cultures. This study advances our understanding of host-pathogen interactions. Targeting DAZAP2 or its regulatory pathways could provide a new approach to enhance host defense against current and future coronavirus threats.

microbiology↗

bioRxiv2025

Decoding the Molecular Language of Proteins with Evola

Proteins, natures intricate molecular machines, are the products of billions of years of evolution and play fundamental roles in sustaining life. Yet, deciphering their molecular language--understanding how sequences and structures encode biological functions--remains a cornerstone challenge. Here, we introduce Evolla, an interactive protein-language model designed to transcend static classification by interpreting protein function through natural language queries. Trained on 546 million protein-text pairs and refined via Direct Preference Optimization, Evolla couples high-dimensional molecular representations with generative semantic decoding. Benchmarking establishes Evollas superiority over general large language models in functional inference, demonstrates zero-shot performance parity with the state-of-the-art supervised model, and exposes remote functional relationships invisible to conventional alignment. We validate Evolla through two distinct applications: identifying candidate eukaryotic signature proteins in Asgard archaea, with functional Vps4 homologs validated via yeast complementation; and interactively discovering a novel deep-sea polyethylene terephthalate (PET) hydrolase, PsPETase, confirmed to degrade plastic films. These results position Evolla not merely as a predictor, but as a generative engine capable of complex hypothesis formulation, shifting the paradigm from static annotation to interactive, actionable discovery. The Evolla online service is available at http://www.chat-protein.com/.

bioinformatics↗

bioRxiv2024

Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases

Spatial transcriptomics (ST) has revolutionized our understanding of tissue architecture, yet constructing comprehensive three-dimensional (3D) cell atlases remains challenging due to technical limitations and high cost. Current approaches typically capture only sparsely sampled two-dimensional sections, leaving substantial gaps that limit our understanding of continuous organ organization. Here, we present SpatialZ, a computational framework that bridges these gaps by generating virtual slices between experimentally measured sections, enabling the construction of dense 3D cell atlases from planar ST data. SpatialZ is designed to operate at single-cell resolution and function independently of gene coverage limitations inherent to specific spatial technologies. Comprehensive validation using real 3D ST and independent serial sectioning datasets demonstrates that SpatialZ accurately reconstructs virtual slices while preserving cell identities, gene expression patterns, and spatial relationships. Leveraging the BRAIN Initiative Cell Census Network data, we constructed a 3D hemisphere atlas comprising over 38 million cells, a scale not feasible experimentally. This dense atlas enables unprecedented capabilities, including in silico sectioning at arbitrary angles, explorations of gene expression across both 3D volumes and surfaces, and 3D mapping of query tissue sections. While currently validated for spatial transcriptomics, the underlying principles of SpatialZ could potentially be adapted for spatial proteomics, spatial metabolomics, and even spatial multi-omics. Validated through internal and external testing, our computationally generated atlas maintains biological accuracy, providing unprecedented resolution of spatial molecular landscapes and demonstrating the potential of computational approaches in advancing 3D ST.

bioinformatics↗

bioRxiv2024

NicheTrans: Spatial-aware Cross-omics Translation

Spatial omics technologies have revolutionized our studies on tissue architecture and cellular interactions at single-cell resolution. While spatial multi-omics approaches offer unprecedented insights into complex biological systems, their widespread adoption is hindered by technical challenges, specialized requirements, and limited accessibility. To address these limitations, we present NicheTrans, the first spatially-aware cross-omics translation method and a flexible Transformer-based multi-modal deep learning framework. Unlike existing single-cell (non-spatial) translation methods, NicheTrans uniquely incorporates both cellular microenvironment information and flexible integration of multi-modal data, such as morphology and prior knowledge. We validated NicheTrans across diverse biological cases: Parkinsons Disease (PD), Alzheimers Disease (AD), breast cancer, and lymph nodes. Our approach demonstrated superior performance compared to existing single-cell methods, highlighting the crucial role of spatial and multi-modal information in cross-omics translation. Through NicheTrans, we uncovered spatial multi-omics domains that were not detectable through single-omics analysis alone. Model interpretation revealed key molecular relationships, including gene programs associated with dopamine metabolism and amyloid {beta}-associated cell states. Additionally, using translated protein markers as spatial landmarks, we quantified the spatial organization of key glial cell subtypes in the AD brain. NicheTrans represents a powerful tool for generating comprehensive spatial multi-omics insights from more accessible single-omics measurements, making multi-omics analysis more feasible for the broader research community.

bioinformatics↗

bioRxiv2024

RNAi-mediated HBV antigen shutdown enhances the antiviral immune effects of PEGIFNalpha via altering T and B cell crosstalk

PEGylated interferon- (PEGIFN) demonstrates promising therapeutic outcomes against chronic hepatitis B (CHB), whereas patient response to PEGIFN therapy remains unsatisfied. Shutdown of hepatitis B virus (HBV) antigens by RNA interference (RNAi) could enhance PEGIFN efficacy in CHB patients, whereas the underlying immunological mechanisms remain obscure. We performed studies by utilizing our newly established extracellular humanized IFNAR (IFNAR-hEC) mice. An in-house constructed small interfering RNAs (GalNac-siHBV) was administrated to mice either alone or in combination with PEGIFN. The phenotypic and functional characteristics of peripheral and organ-specific immune cells were assessed by flow cytometry, ELISpot, RNA sequencing (RNA-seq), and single-cell RNA-seq (scRNA-seq) analysis. Our results demonstrated that combined treatment with PEGIFN and RNAi exerted a synergistic and prolonged inhibition of HBsAg ([~]4log10 IU/mL, vs PBS) and induced a higher incidence of HBsAg seroconversion ([~]30%), comparing with either monotreatment. Mechanistically, combined therapy improved the functionality of global T and B cells, triggered increased anti-HBs producing B cells, and enhanced IFN{gamma}-producing T cells. scRNA-seq analysis revealed that the combined therapy reduced inhibitory B cell-B cell interaction, enhanced MHC-I signaling mediated T cell-T cell communication, and improved T cell-B cell crosstalk, thus improving the functionality of T and B cells. Enhanced MHC-II signaling networks across B cells and hepatocytes/Cd8+ T cells further promoted HBsAg seroconversion in the combined treatment groups. These results together provided scientific rationale and lessons for the combination of the two towards better therapeutic efficacy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/626539v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@84785aorg.highwire.dtl.DTLVardef@f984fborg.highwire.dtl.DTLVardef@189a966org.highwire.dtl.DTLVardef@d081f9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIShutting down HBsAg through RNA interference augmented the antiviral immune effects of PEGIFN in chronic HBV-carrier IFNAR-hEC mice. C_LIO_LICombined RNAi plus PEGIFN augmented the functionality of T cells, promoted B cell activation and class switch, but also exerted some suppressive effects on B cells. C_LIO_LIReduced inhibitory B cell-B cell interaction, enhanced MHC-I signaling between T cells and T cells, and improved T cell-B cell crosstalk, improved the functionality of T cells and B cells. C_LIO_LIEnhanced MHC-II signaling networks across B cells and hepatocytes/ Cd8+ T cells further promoted HBsAg seroconversion in RNAi plus PEGIFN combined treatment groups. C_LI

microbiology↗

bioRxiv2024

Deep generative model for protein subcellular localization prediction

Protein sequence determines not only its structure but also its subcellular localization. Although a series of artificial intelligence models have been reported to predict protein subcellular localization, most of them provide only textual outputs. Here, we present deepGPS, a deep generative model for protein subcellular localization prediction. After trained with both protein primary sequences and protein subcellular localization fluorescence images, deepGPS shows the ability to predict cytoplasmic and nuclear localizations by reporting both textual labels and generative images as outputs. In addition, deepGPS shows potential to be further extended for other types of subcellular localization prediction, even with limited input data volumes for training. Finally, an openGPS website (https://bits.fudan.edu.cn/opengps) is constructed to provide a public and convenient platform for protein subcellular localization prediction with the scientific community.

bioinformatics↗

bioRxiv2024

Type-I IFNs induce GBPs and lysosomal defense in hepatocytes to control malaria

Plasmodium parasites undergo development and replication within the hepatocytes before infecting the erythrocytes and initiating clinical malaria. Although type-I interferons (IFNs) are known to hinder Plasmodium infection within the liver, the underlying mechanisms remain unclear. Here, we describe two IFN-I-driven hepatocyte antimicrobial programs controlling liver-stage malaria. First, oxidative defense by NADPH oxidases 2 and 4 triggers a pathway of lysosomal fusion with the parasitophorous vacuole (PV) to help clear Plasmodium. Second, guanylate-binding protein (GBP) 1 disruption of the PV activates caspase-1 inflammasome, inducing pyroptosis to remove the infected host cells. Remarkably, both human and mouse hepatocytes enlist these cell-autonomous immune programs to eliminate Plasmodium; their pharmacologic or genetic inhibition led to profound malarial susceptibility, and are essential in vivo. In addition to identifying the IFN-I-mediated cell-autonomous immune circuits controlling Plasmodium infection in the hepatocytes, this study extends our understanding of how non-immune cells are integral to protective immunity against malaria.

immunology↗

bioRxiv2024

Disruption of the Novel Nested Gene Aff3ir Mediates Disturbed Flow-Induced Atherosclerosis in Mice

Disturbed shear stress-induced endothelial atherogenic responses are pivotal in the initiation and progression of atherosclerosis, contributing to the uneven distribution of atherosclerotic lesions. This study investigates the role of Aff3ir-ORF2, a novel nested gene variant, in disturbed flow-induced endothelial cell activation and atherosclerosis. We demonstrate that disturbed shear stress significantly reduces Aff3ir-ORF2 expression in athero-prone regions. Using three distinct mouse models with manipulated AFF3ir-ORF2 expression, we demonstrate that AFF3ir-ORF2 exerts potent anti-inflammatory and anti-atherosclerotic effects in ApoE-/- mice. RNA sequencing revealed that interferon regulatory factor 5 (IRF5), a key regulator of inflammatory processes, mediates inflammatory responses associated with AFF3ir-ORF2 deficiency. AFF3ir-ORF2 interacts with IRF5, promoting its retention in the cytoplasm, thereby inhibiting the IRF5-dependent inflammatory pathways. Notably, IRF5 knockdown in AFF3ir-ORF2 deficient mice almost completely rescues the aggravated atherosclerotic phenotype. Moreover, endothelial-specific AFF3ir-ORF2 supplementation using the CRISPR/Cas9 system significantly ameliorated endothelial activation and atherosclerosis. These findings elucidate a novel role for AFF3ir-ORF2 in mitigating endothelial inflammation and atherosclerosis by acting as an inhibitor of IRF5, highlighting its potential as a valuable therapeutic approach for treating atherosclerosis.

cell biology↗

bioRxiv2024

Pexidartinib plus FLT3-directed CAR-Macrophage for the treatment of FLT3-ITD-mutated acute myeloid leukemia in preclinical model

Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. Internal tandem duplication of FMS-like tyrosine kinase 3 (FLT3-ITD) mutations occur in about 25%-30% of AML cases and are associated with adverse prognosis. Recent advances indicate that M2-like leukemia-associated macrophages (M2-LAM) are highly infiltrated in the bone marrow of FLT3-ITD+ AML patients; however, the underlying mechanisms and therapeutic implications are still elusive. Herein, we reveal that conditioned medium from FLT3-ITD+ MOLM-13 AML cells polarized M2-LAM and impaired their phagocytic activities. Unexpectedly, co-culture of M2-LAM protected MOLM-13 cells from the treatment of FLT3 inhibitor quizartinib by activating their FLT3 signaling pathway. Pharmaceutically, FLT3/CSF1R dual inhibitor pexidartinb effectively suppressed M2-LAM, reduced leukemic burden, and prolonged the survival of MOLM-13-xenografted mice. To enhance the phagocytic activities of macrophages, FLT3-directed chimeric antigen receptor-engineered macrophages (FLT3L-CAR-Macrophage) were generated using FLT3 ligand (FLT3L) as the recognizing domain of CAR. Transfection of THP-1 monocytic cells-or umbilical cord blood mononuclear cells-derived macrophages with FLT3L-CAR-encoding mRNA enhanced their phagocytic activities to MOLM-13 cells in vitro. Consistently, FLT3L-CAR-Macrophage differentiated from FLT3L-CAR-expressing THP-1 cells effectively phagocytosed MOLM-13 cells in vitro, reduced leukemic burden and prolonged the survival of MOLM-13-xenografted mice. Importantly, treatment of pexidartinib resulted in upregulation and surface localization of FLT3-ITD protein in MOLM-13 cells, sensitized MOLM-13 cells to the treatment of FLT3L-CAR-Macrophage in vitro, and synergized with FLT3L-CAR-Macrophage to further reduce leukemic burden in MOLM-13-xenografted mice. Together, our data indicate that pexidartinib plus FLT3L-CAR-Macrophage could be a promising therapeutic strategy for the treatment of FLT3-ITD+ AML in preclinical model which warrants further investigation. Graphical AbstractPexidartinib plus FLT3L-CAR-M{varphi} for the treatment of FLT3-ITD+ AML in preclinical model. Pexidartinib suppressed AML growth, reduced M2-LAM, increased FLT3 surface expression and synergized with FLT3L-CAR-M{varphi} to target FLT3-ITD+ AML in vitro and in vivo. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/615313v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1e7c0f4org.highwire.dtl.DTLVardef@2cdf6eorg.highwire.dtl.DTLVardef@e84borg.highwire.dtl.DTLVardef@1929d28_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Ex vivo and in vivo HIV-1 latency reversal by Mukungulu, a protein kinase C-activating African medicinal plant extract

Current HIV latency reversing agents (LRAs) have had limited success in clinic, indicating the need for new strategies that can reactivate and/or eliminate HIV reservoirs. "Mukungulu," prepared from the bark of Croton megalobotrys Mull. Arg., is traditionally used for HIV/AIDS management in Northern Botswana despite containing an abundance of protein kinase C (PKC)-activating phorbol esters ("namushens"). Here we show that Mukungulu is tolerated in mice at up to 12.5 mg/kg while potently reversing latency in antiretroviral therapy (ART)-suppressed HIV-infected humanized mice at 5 mg/kg. In peripheral blood mononuclear cells (PBMC) and isolated CD4+ T-cells from ART-suppressed people living with HIV-1, 1 {micro}g/mL Mukungulu reverses latency on par with or superior to anti-CD3/CD28 positive control, as measured by HIV gag-p24 protein expression, where the magnitude of HIV reactivation in PBMC corresponds to intact proviral burden levels in CD4+ T-cells. Bioassay-guided fractionation identifies 5 namushen phorbol ester compounds that reactivate HIV expression, yet namushens alone do not match Mukungulus activity, suggesting additional enhancing factors. Together, these results identify Mukungulu as a robust natural LRA which may warrant inclusion in future LRA-based HIV cure and ART-free remission efforts.

microbiology↗

bioRxiv2024

Structural and biochemical characterization of the ALX4 dimer reveals novel insights into how disease alleles impact ALX4 function

1.How homeodomain proteins gain sufficient DNA binding specificity to regulate diverse processes has been a long-standing question. Here, we determine how the ALX4 Paired-like protein achieves DNA binding specificity for a TAAT - NNN - ATTA dimer site. We first show that ALX4 binds this motif independently of its co-factor, TWIST1, in cranial neural crest cells. Structural analysis identified seven ALX4 residues that participate in dimer binding, many of which are conserved across the Paired-like family, but not other homeodomain proteins. Unexpectedly, the two ALX4 proteins within the dimer use distinct residues to form asymmetric protein-protein and protein-DNA interactions to mediate cooperativity. Moreover, we found that ALX4 cooperativity is required for transcriptional activation and that ALX4 disease variants cause distinct molecular defects that include loss of cooperativity. These findings provide new insights into how Paired-like factors gain DNA specificity and show how disease variants can be stratified based on their molecular defects.

molecular biology↗