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Liu, H.

Publications and source records attributed to Liu, H..

At least 253 records · Page 14Linked to original sources

FASN Inactivation-induced Progranulin (GRN) Expression Promotes Lysosome-dependent Cell Death to Suppress Leukemogenesis

Cancer cells rely on lipogenesis in addition to exogenous lipid uptake, and fatty acid synthase (FASN) is aberrantly overexpressed in myeloid leukemia. However, the precise role of FASN in leukemogenesis in vivo remains elusive. Here, we demonstrated that FASN is essential for leukemogenesis. Ablation of FASN impeded leukemic cell growth, survival, clonogenicity in vitro, and the leukemic burden in vivo. Conditional knockout of FASN barely affected hematopoiesis but significantly attenuated the leukemic progression of MLL-AF9 transplants. By screening a library of platensimycin derivatives, we identified compound MS-C19 as a potent FASN inhibitor. Pharmacological targeting of FASN by MS-C19 suppressed leukemic cell growth and clonogenicity in clinical AML blasts. Mechanistically, both MS-C19 treatment and FASN deficiency triggered the activation of lysosomal and inflammatory gene expression. Loss of FASN led to lysosomal membrane permeabilization and subsequent lysosome-associated cell death, but not lysosome biogenesis. We further identified that GRN, a lysosomal and neuroinflammatory gene, was potently transcribed by TFEB upon FASN loss. Depletion of GRN significantly reversed the inhibitory effects caused by FASN knockdown. Our work demonstrates that FASN is a therapeutic target for myeloid leukemia, and inactivation of FASN by the lead compound MS-C19 provides an alternative approach for leukemic intervention. Key PointsO_LIGenetic ablation of FASN induces apoptosis, impedes leukemia cell growth, and improves the survival of leukemic xenografts. C_LIO_LITargeting FASN by the compound MS-C19, a derivative of the natural microbe antibiotic platensimycin, reduces the cell survival of leukemic cell lines, the clinical leukemic blasts, and MLL-AF9 transformed murine leukemic cells. C_LIO_LIFASN inhibition induces lysosome-dependent cell death that relies on Progranulin (GRN) expression. C_LI

cancer biology↗

Hydroxyl and Trifluoromethyl Radical Carbohydrate Footprinting for Probing Protein Binding Components of Oligosaccharides

Carbohydrates are found in various forms in living organisms, both as free-standing glycans as well as glycoconjugates including glycoproteins, glycolipids, and glycosaminoglycans. These structures play crucial roles in many biological processes, often mediated or influenced by interactions of carbohydrates with other biomolecules. However, studying these interactions is particularly challenging due to the structural complexity of carbohydrates, their dynamic conformational behavior, and the low binding affinities often involved. To address these challenges, we are developing a novel method that leverages mass spectrometry-based radical footprinting of carbohydrates (RFC). We monitored changes in the solvent accessibility of specific regions within oligosaccharides by measuring variations in the apparent rate of hydroxyl radical and trifluoromethyl radical-mediated oxidation. In our studies, a collection of trisaccharide isomers and N, N',N''-triacetylchitotriose (NAG3) shows no significant change in modification in non-binding protein solutions. However, in the presence of two proteins that bind NAG3 specifically, NAG3 oxidation is reduced. We find that the free reducing end is the primary site of hydroxyl radical oxidation under covalent labeling conditions, allowing it to distinguish interactions at the glycan reducing end. Trifluoromethyl radicals, conversely, label broadly across the trisaccharide by substitution into a C-H bond. Overall, this approach offers a powerful new approach for identifying glycan-protein interactions and mapping the binding interface of glycans.

biochemistry↗

MEK-dependent bioenergetic demand drives terminal CD8+ T cell exhaustion

Loss of mitochondrial function contributes to CD8+ T cell dysfunction during persistent antigen encounter. How chronic antigen leads to this metabolic dysfunction remains unclear. Here, we show that TCR-dependent mitochondrial NADH accumulation drives production of ROS, ultimately leading to mitochondrial dysfunction. Among TCR-dependent proximal signaling components, MEK inhibition uniquely reduced nutrient uptake and mitochondrial NADH accumulation while increasing proliferation. As a result, MEK inhibition during chronic TCR stimulation reduced terminal T cell exhaustion. Mechanistically, we found that chronic MEK activation in T cells drove ATP demand by increasing global protein synthesis rates in vitro and in vivo. MEK inhibition reversed chronic TCR stimulation-driven increases in RNA polymerase II CTD phosphorylation, reducing transcription rates at effector- and terminal-exhaustion associated genes while maintaining transcription of memory-associated genes. These findings establish MEK-dependent metabolic demand as a driver of T cell exhaustion and elucidate the role of MEK inhibition in enhancing immunotherapy efficacy.

immunology↗

Function of the auditory cortex characterized by its intrinsic dynamic coactivation patterns estimated in individuals

Determining the functional organization of the auditory cortex (AC) has been difficult with conventional task-based approaches due to the broad responsiveness of auditory subregions to various acoustic properties. Moreover, most studies have investigated functional organization of AC with static methods, although brain has shown to be organized into dynamic networks. Here, we investigated dynamically varying coactivation patterns of the local networks in the auditory cortex (AC) determined from 7T fMRI data with a novel individualized network-based algorithm. An eight-pattern solution was selected for closer examination based on its high reproducibility of the occurrence rates (r=0.86) and the spatial topography (r=0.79) between sessions. Dynamic AC patterns successfully captured interindividual variability, as indicated by significantly higher variability between than within individuals for the AC pattern occurrence rates and spatial topographies. The coactivation patterns shared similarities between resting-state and auditory-task data, as indicated by the group-level similarity of 0.84 and individual-level similarity of 0.71 in the spatial topographies. Furthermore, the occurrence rates of AC patterns identified in the task data, using pattern templates derived from resting-state data, correlated with specific task contrast regressors. Our results indicate that the AC function can be characterized by a set of dynamically varying coactivation patterns that are consistently observed during resting state and auditory stimulation, and that get synchronized with auditory input. These findings enhance our understanding of the relationship between spontaneous and stimulus-driven activity in the AC and support the development of more time-efficient paradigms for studying its functional organization.

neuroscience↗

Dimethyl fumarate reprograms cervical cancer cells to enhance antitumor immunity by activating mtDNA-cGAS-STING pathway

BackgroundCervical cancer (CC) remains a significant global health challenge for women, especially in advanced stages where effective treatments are limited. Current immunotherapies, including PD-1/PD-L1 blockades and adoptive T cell therapies, show limited response rates and durability. Dimethyl fumarate (DMF), an FDA-approved drug for autoimmune diseases, has demonstrated that it might exhibit direct antitumor activity in several cancers. However, its influence on anti-tumor immunity and its function in CC remain poorly understood. This study aims to investigate the therapeutic potential of DMF in CC models and elucidate its underlying mechanisms of action. MethodsCC cell lines and mouse models were treated with DMF. Transcriptional level changes in cervical cancer cells following DMF treatment were analyzed by RNA-seq. Mitochondrial DNA (mtDNA) release, and cGAS-STING activation were assessed via qPCR, immunofluorescence, immunoblotting and ELISA. CD8+ T cell recruitment was analyzed by flow cytometry. Combinatorial therapies (DMF + anti-PD-1/TILs) were tested in syngeneic or patient-derived xenografts (PDX) models. ResultsDMF treatment induces mitochondrial dysfunction in tumor cells, resulting in the release of mtDNA into the cytosol. The cytosolic mtDNA activates the cGAS-STING-TBK1 pathway and type I interferon response, leading to the secretion of CCL5 and CXCL10, thereby enhancing CD8 T cell infiltration. Additionally, DMF exhibits synergistic effect with PD-1 blockade in murine CC model, and can enhance the therapeutic efficacy of adoptively transferred T cells toward CC patient-derived xenografts model. ConclusionThis work elucidated that DMF reprograms CC cells to activate the mtDNA-cGAS-STING pathway, fostering a chemokine-rich microenvironment that recruits CD8+ T cells. Its synergy with PD-1 blockade or TIL therapy underscores its potential as an immunomodulatory adjuvant. These findings suggest that DMF holds promise as a novel immunotherapeutic strategy for improving clinical outcomes in CC.

immunology↗

Microengineered transplantation of human solid tumors for in vitro studies of CAR T immunotherapy

Treatment of solid malignancies using chimeric antigen receptor (CAR) T cells remains a significant challenge, but current efforts to advance this therapy are challenged by our limited capacity to probe and understand cancer-immune interactions in human solid tumors. Here, we present a microengineered platform for in vitro modeling of malignant solid tumors during CAR T therapy. This system makes it possible to vascularize human tumor explants and perfuse them with blood-borne immune cells in a controlled manner. We first present a microphysiological model of human lung adenocarcinomas infused with CAR-T cells and show how this system can be used to simulate, visualize, and interrogate tumor-directed trafficking and effector function of CAR T cells. We then demonstrate the proof-of-principle of testing a chemokine-directed CAR T cell engineering strategy in a model of malignant pleural mesothelioma and validating our in vitro assessment using a matching in vivo mouse model. Finally, we describe a potential therapeutic target discovered by single-cell RNA sequencing that can be pharmacologically modulated to increase the efficacy of CAR T cells for lung adenocarcinoma, for which we also present specific biomarkers identified by global metabolomics analysis. We believe that the bioengineering principle demonstrated here will make important contributions to developing new capabilities for preclinical studies of adoptive cell therapies for cancer and other complex diseases.

bioengineering↗

AI-driven computational pathology for recurrence risk assessment in early-stage breast cancer

Recurrence related to poor prognosis is a leading cause of mortality in patients with breast cancer (BC). The MammaPrint (MP) genomic assay is designed to stratify recurrence risk and evaluate chemotherapy benefits for early-stage HR+/HER2- BC patients. However, MP fails to reveal spatial tumor morphology and is limited by high costs. In this study, we establish a BC MP cohort and develop CPMP, a weakly supervised agent-attention transformer model, to predict MP recurrence risk from annotation-free BC histopathological slides. CPMP achieves an AUROC of 0.824 {+/-} 0.03 in predicting MP risk groups. We further leveraged CPMP for spatial and morphological analyses to explore histological patterns associated with MP risk groups. The model reveals tumor spatial localization at the whole-slide level and highlights distinct intercellular interaction patterns of MP groups. It also characterizes the diversity in tumor morphology and uncovers MP High-specific, Low-specific, and colocalized morphological phenotypes that differ in quantitative cellular composition. Prognostic evaluation in the external cohort exhibits significant stratification of distant metastasis risk (HR: 3.14, p-value = 0.0014), underscoring the prognostic power of CPMP. These findings demonstrate the capability of CPMP in MP risk prediction, offering a flexible supplement to genomic risk assessment in early-stage BC.

pathology↗

Maternal Immune Activation Disrupts Epigenomic and Functional Maturation of Cortical Excitatory Neurons

Elevated levels of maternal pro-inflammatory cytokines during gestation can disrupt offspring neural development, increasing the risk of neurodevelopmental disorders. We studied the effects of Poly(I:C)-induced maternal immune activation (PIC-MIA) during mid-gestation on developing cortical excitatory neurons DNA methylation and transcriptome. PIC-MIA disrupted the developmental regulation of synapse-related genes and of genes implicated in autism spectrum disorders. Genomic regions that gain or lose DNA methylation during normal development were altered following PIC-MIA, including neurodevelopmental transcription factor binding sites. The DNA methylation and transcriptional changes were consistent with a delay in excitatory neuron maturation. Whole-cell recordings showed that PIC-MIA preferentially altered the physiological development of layer 5 excitatory neurons. Taken together, present results suggest that alterations in the epigenome, through the disruption of circuit formation, may drive the long-term consequences of maternal infection during gestation.

neuroscience↗

Kinocilia of Vestibular Hair Cells: Bridging Structural and Functional Traits of Primary and Motile Cilia

Vestibular hair cells (HCs) convert gravitational and head motion cues into neural signals through mechanotransduction, mediated by the hair bundle--a mechanically integrated organelle composed of stereocilia and a kinocilium. The kinocilium, a specialized form of primary cilium, remains incompletely defined in structure, molecular composition, and function. To elucidate its characteristics, we conducted single-cell RNA sequencing of adult vestibular and cochlear HCs, uncovering a selective enrichment of primary and motile cilia-associated genes in vestibular HCs, particularly those related to the axonemal repeat complex. This enrichment of orthologous axonemal-related genes was conserved in zebrafish and human vestibular HCs, indicating a shared molecular architecture. Immunostaining validated the expression of key motile cilia markers in vestibular kinocilia. Moreover, live imaging of bullfrog and mouse HCs from crista ampullaris revealed spontaneous kinociliary motion. Together, these findings define the kinocilium as a unique organelle with molecular features of primary and motile cilia and suggest its previously unknown role as an active, force-generating element within the hair bundle.

neuroscience↗

Breaking the Link: Neural Dissociation of Attention and Working Memory through Inhibitory Control

Attention and working memory (WM) encoding have traditionally been considered inseparable processes with shared neural mechanisms. Here, using an innovative experimental design and a multimodal approach, we provide the first direct neural evidence that attention and WM encoding are dissociable. Functional MRI identifies the supramarginal gyrus (SMG) as the key region enabling this dissociation, while dynamic causal modeling reveals the neural circuitry through which the SMG exerts inhibitory control over attentional representations, regulating their integration into WM. Furthermore, neuromodulation via transcranial direct current stimulation (tDCS) demonstrates that enhancing SMG activity strengthens this inhibitory control, providing causal evidence for the dissociation mechanism. A second tDCS experiment with varied stimuli confirms the generalizability of this mechanism and reinforces the robustness of our results. These findings challenge the long-standing view that attention and WM encoding form a continuous process, demonstrating instead that they constitute two dissociable neural processes of information selection.

neuroscience↗

Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain

Aging is a major risk factor for neurodegenerative diseases, yet underlying epigenetic mechanisms remain unclear. Here, we generated a comprehensive single-nucleus cell atlas of brain aging across multiple brain regions, comprising 132,551 single-cell methylomes and 72,666 joint chromatin conformation-methylome nuclei. Integration with companion transcriptomic and chromatin accessibility data yielded a cross-modality taxonomy of 36 major cell types. We observed that age-related methylation changes were more pronounced in non-neuronal cells. Transposable element methylation alone distinguished age groups, showing cell-type-specific genome-wide demethylation. Chromatin conformation analysis demonstrated age-related increases in TAD boundary strength with enhanced accessibility at CTCF binding sites. Spatial transcriptomics across 895,296 cells revealed regional heterogeneity during aging within identical cell types. Finally, we developed novel deep-learning models that accurately predict age-related gene expression changes using multi-modal epigenetic features, providing mechanistic insights into gene regulation. This dataset advances our understanding of brain aging and offers potential translational applications. HighlightsO_LISingle-cell multi-omic profiling maps the epigenetic and spatial transcriptomic landscape of brain aging across multiple regions. C_LIO_LICell-type-specific genome-wide demethylation of retrotransposable elements correlates with increased chromatin accessibility and expression. C_LIO_LIElevated TAD boundary strength emerges as a unique marker of brain aging associated with CTCF gaining accessibility. C_LIO_LIA novel deep-learning model reveals the significance of epigenetic features on age-related transcriptomic changes across genes. C_LI

genomics↗

Nanobinders for Synaptotagmin 1 enable the analysis of synapticvesicle dynamics in rodent and human models.

Synaptic neurotransmission is a critical hallmark of brain activity and one of the first processes to be affected in neural diseases. Monitoring this process, and in particular synaptic vesicle recycling, in living cells has been instrumental in unraveling mechanisms responsible for neurotransmitter release. However, currently available reporters suffer from major limitations such large probe size or lack of suitability for human neurons, hampering the understanding of human synaptic pathophysiology. Here we describe the NbLumSyt1 toolkit, a panel of nanobody-based affinity probes targeting the luminal domain of the synaptic vesicle protein Synaptotagmin 1 (Syt1). These new tools enable quantitative, non-invasive imaging and functional interrogation of synaptic transmission in human neurons, with unprecedented precision, versatility and cost efficiency, in technologies ranging from fixed-and live-cell super-resolution imaging to electron microscopy and mass spectrometry. Overall, NbLumSyt1 nanobinders provide a valuable platform for human synaptic physiology and pathophysiology, benefiting fundamental neuroscience and translational efforts to study and develop treatments for brain-related disorders.

neuroscience↗

Glycosylated IgG antibodies accelerated the recovery of haemorrhagic fever with renal syndrome patients

AbstractHaemorrhagic fever with renal syndrome (HFRS) is a fatal disease caused by Hantaan virus (HTNV) infection. Humoral immunity is essential for effective viral clearance, however, the glycosylation characteristics of immunoglobulin G (IgG) in HFRS patients is not well known. Peripheral blood mononuclear cells from HFRS patients were obtained for B subset analysis using scRNA-seq and flow cytometry. HTNV specific IgG antibody titers were detected by enzyme-linked immunosorbent assay, and IgG glycosylation was analyzed by ultra-performance liquid chromatography. The proportions of the antibody-secreting memory (ASM) B cells and plasmablasts (PB) were significantly expanded among acute HFRS patients. We discovered significantly increased fucosylated IgG and decreased bisecting N-acetylglucosamine during the convalescent phase of HTNV infection. Meanwhile, positive correlations were observed between ASM subsets and galactosylation/sialylation in the IgG Fc region, and between PB subsets and sialylation. Notably, the glycosylation-related genes, such as RPN1 and RPN2, were primarily expressed differentially in the ASM and PB subclusters which were enriched in the N-glycosylation modifications of proteins through asparagine. Our findings indicated that IgG N-glycosylation may play a crucial role in combating HTNV infection and contributing to clinical recovery, which provided new insights for optimizing glycoengineered therapeutic antibodies.

immunology↗

PepPCBench is a Comprehensive Benchmark for Protein-Peptide Complex Structure Prediction with AlphaFold3

Peptides mediate up to 40% of protein-protein interactions (PPIs), offering high specificity and the ability to target binding sites inaccessible to small molecules, making them promising candidates for drug development. Accurate modeling of protein-peptide complexes is crucial for understanding fundamental biological processes and for advancing peptide-based drug design. However, due to the high conformational flexibility of peptides, predicting their interactions with proteins remains a significant challenge. Recent advancements in artificial intelligence (AI), exemplified by all-atom protein folding neural networks (PFNNs) such as AlphaFold3 (AF3), have expanded predictive capabilities beyond proteins to encompass protein-peptide complexes. Nevertheless, existing evaluations of these methods are often limited in scope and lack systematic, multi-dimensional, and fair comparisons of PFNN performance in protein-peptide complex prediction. Here, we introduce PepPCBench, a comprehensive benchmark framework specifically developed to evaluate AF3s capabilities in predicting protein-peptide complexes. This study utilizes a carefully curated dataset named PepPCSet, which is excluded from the AF3s training or validation sets. This dataset includes 261 protein-peptide complexes with peptide lengths ranging from 5 to 30 residues. Our benchmark results indicate that AF3 outperforms other PFNNs in prediction accuracy and structural validation. However, its performance remains insufficient for practical peptide drug discovery, indicating room for improvement. It is expected that PepPCBench can provide some valuable insights into the enhancement of protein-peptide complex structure prediction and the development of peptide-based therapeutics. The dataset and pipeline protocols are available at https://github.com/zhaisilong/PepPCBench.

bioinformatics↗

A Precision Gene Engineered B Cell Medicine Producing Sustained Levels of Active Factor IX for Hemophilia B Therapy

Hemophilia B gene therapy treatments currently have not addressed the need for predictable, durable, active, and redosable factor IX (FIX). Unlike conventional gene therapy, engineered B Cell Medicines (BCMs) are durable, redosable, and titratable, and thus have the potential to address significant unmet needs in the Hemophilia B treatment paradigm. BE-101 is an autologous BCM comprised of expanded and differentiated B lymphocyte lineage cells genetically engineered ex vivo to secrete FIX-Padua. CRISPR/Cas9 mediated gene editing at the C-C chemokine receptor type 5 locus was used to facilitate transgene insertion of an AAV6-encoded DNA template via homology-directed repair. Transgene insertion did not alter B cell biology, viability, or differentiation into plasma cells. Appreciable levels of BE-101-derived FIX-Padua were detected within 1 day after IV administration in mouse and steady state was reached within 2 weeks and persisted for over 184 days. Redosing produced an increase in FIX-Padua production close to linear dose proportionality. Comprehensive genotoxicity analysis found no off-target issues of concern. No safety signals were observed in animal tolerability and GLP toxicology studies. In conclusion, BE-101 produces sustained levels of active FIX-Padua with the ability to engraft without host preconditioning and with the potential for redosing and titratability.

pharmacology and toxicology↗

Multiple evolutionary events in host plant adaptation in Lepidoptera

The evolution of insect host adaptation is a key component of insect-plant coevolution, a complex process often shaped by multiple evolutionary events. In this study, we identified two UDP-glycosyltransferase (UGT) genes, SfruUGT33T10 and SfruUGT33F32, in the fall armyworm Spodoptera frugiperda, which play critical roles in the tolerance of benzoxazinoids (BXs), secondary metabolites in maize. These two detoxification enzymes exhibited distinct glycosylation patterns for BXs and varying detoxification efficiencies, reflecting independent evolutionary trajectories. Phylogenetic analyses revealed that SfruUGT33T10 originated independently within Noctuidae, while SfruUGT33F32 resulted from tandem duplication within the UGT33F gene family and may have undergone neofunctionalization within the Spodoptera genus. Our findings provide evidence that the evolution of these two UGT paralogs contributed to the variation in the tolerance to maize BXs among different Lepidopteran species. This research underscores the significance of multiple independent evolutionary routes in host plant adaptation and offer new insights into the complex evolutionary processes underlying insect-plant interactions.

evolutionary biology↗

Enhancing variant detection in complex genomes: leveraging linked reads for robust SNP, Indel, and structural variant analysis

Accurate detection of genetic variants, including single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), and structural variants (SVs), is essential for comprehensive genomic analysis. While short-read sequencing performs well for SNP and INDEL detection, it remains limited in resolving SVs, particularly in complex genomic regions, due to its short read length. Linked-read sequencing technologies, such as single-tube Long Fragment Read (stLFR), partially address this limitation by incorporating molecular barcodes to provide long-range information. In this study, we evaluate conventional paired-end linked reads (PE100_stLFR) and explore a conceptual extension: long single-end barcoded reads of 500 bp (SE500_stLFR) and 1000 bp (SE1000_stLFR). We developed_stLFR-sim, a Python-based simulator that reproduces the_stLFR workflow and enables realistic benchmarking. Using a high-quality T2T assembly of HG002, we generated multiple datasets across 12 sequencing configurations. SVs were called using Aquila_stLFR (v2) and benchmarked against the Genome in a Bottle (GIAB) HG002 SV truth set with Truvari. We show that simulated PE100_stLFR closely matches real data, validating the simulation framework. Increasing read length consistently improves SV detection accuracy, with SE1000_stLFR achieving the best performance and approaching long-read methods while outperforming short-read and pangenome-based approaches. Collectively, our results highlight the strong potential of long single-end barcoded reads for improving SV detection, and suggest that even modest increases in read length, when combined with barcode information, can provide a cost-effective and practical strategy for enhancing future sequencing technologies and SV discovery.

bioinformatics↗

DNA2 and MSH2 activity collectively mediate chemically stabilized G4 for efficient telomere replication

G-quadruplexes (G4s) are widely existing stable DNA secondary structures in mammalian cells. A long-standing hypothesis is that timely resolution of G4s is needed for efficient and faithful DNA replication. In vitro, G4s may be unwound by helicases or alternatively resolved via DNA2 nuclease mediated G4 cleavage. However, little is known about the biological significance and regulatory mechanism of the DNA2-mediated G4 removal pathway. Here, we report that DNA2 deficiency or its chemical inhibition leads to a significant accumulation of G4s and stalled replication forks at telomeres, which is demonstrated by a high-resolution technology: Single molecular analysis of replicating DNA (SMARD). We further identify that the DNA repair complex MutS (MSH2-MSH6) binds G4s and stimulates G4 resolution via DNA2-mediated G4 excision. MSH2 deficiency, like DNA2 deficiency or inhibition, causes G4 accumulation and defective telomere replication. Meanwhile, G4-stabilizing environmental compounds block G4 unwinding by helicases but not G4 cleavage by DNA2. Consequently, G4 stabilizers impair telomere replication and cause telomere instabilities, especially in cells deficient in DNA2 or MSH2.

molecular biology↗