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Ding, H.

Publications and source records attributed to Ding, H..

At least 19 recordsLinked to original sources

The Impact of Noise on Memorability in Minds and Machines

Some images are consistently remembered better than others, a stimulus property known as memorability, and deep neural networks (DNNs) are increasingly used to estimate it in place of human observers. A recent account proposes that memorable images are processed more efficiently. We argue that memorability can also be viewed as signal quality, and that efficient processing should therefore be robust to noise. Comparing memorability estimates from state-of-the-art (SOTA) models with human performance in continuous recognition tasks, we found that the two consistently diverged in how memorability changed as images were degraded by increasing levels of Gaussian noise and blur, such that models under-estimated high memorability images with noise, while over-estimating low memorability images with noise, a pattern resembling stochastic resonance. In contrast, noise degraded memorability estimates in humans, yet high memorability images were resistant to this effect. We discovered this divergence arose because conventional models are influenced by how noise alters their attention across images, whereas humans learn how images relate to one another. Building on these findings, we developed GraphMem, a model that estimates memorability from the relational structure among images rather than from the features of individual images. GraphMem outperformed SOTA models in estimating memorability under noise and blur and aligned most closely with human data. These findings caution against relying on conventional DNN-based memorability estimates for novel images, and suggest that modeling the relational structure in vision models yields more human-like memorability estimates.

neuroscience↗

Whole Blood Deep Immunophenotyping and Platelet-Leukocyte Aggregate Quantification by Spectral Flow Cytometry

Platelet-leukocyte aggregates (PLAs) are a proposed interface between coagulation and immune regulation, but their distribution across leukocyte subsets beyond monocytes and neutrophils, and their behavior in acute disorders of immune regulation, such as sepsis and severe trauma, remain largely undefined. The study of thromboimmune mechanisms in these acute conditions has relied heavily on murine sepsis models, whose species differences in platelet and leukocyte biology limit translation to human disease. Direct measurement in human whole blood is needed yet reported PLA frequencies vary widely because quantification is highly sensitive to sample handling. Here we present a robust, minimally manipulative 27-color spectral flow cytometry protocol that allows simultaneous deep immunophenotyping and classification of PLAs across >40 leukocyte subpopulations. In healthy donors, PLA frequency ranged from 1.7% on memory CD4 T cells to over 50% on monocyte subsets, with monocytes contributing 25% of all PLAs. We also found novel platelet-binding leukocyte populations, including Th9 and Th22 CD4+ T cells. Optimization identified anticoagulant choice, centrifugation conditions, dilution, and sample processing time as key determinants of reproducible measurement; PLA quantification was validated by imaging flow cytometry. In a small validation cohort of sepsis and trauma patients, the assay recapitulated established immunophenotypic features of critical illness, including neutrophilia and myeloid-derived suppressor cells (MDSC) expansion, and quantified PLAs within each subset. This protocol provides a reference framework for studying thromboinflammation and other dysregulated immune response diseases directly in human blood, and a foundation for further studies, defining the mechanisms and clinical relevance of platelet-leukocyte interactions in disease.

immunology↗

EvSpark: Lossless Speculative Decoding for Hybrid DNA Foundation Models

Hybrid DNA foundation models combine convolutional, recurrent, and attention layers, making speculative decoding more difficult than truncating a KV cache. We present EvSpark, a speculative decoding system for Evo2 that verifies draft blocks in parallel and restores all three classes of inference state by selecting retained intermediate states, without replay. A compact, hidden-state-conditioned drafter proposes each block in one parallel forward pass. On Evo2 7B, a 48-prompt benchmark with three training seeds yields 2.96x on 43 real-sequence prompts and 3.27x including the five synthetic controls. Acceleration persists at 262k-token context (1.84x - 2.43x on two bacterial genomes) and over 32k generated tokens. Retraining the same drafter architecture for Evo2 20B and 40B yields 2.18x - 2.46x on real sequences and 2.51x - 2.78x on the full suite. Autoregressive drafter comparisons and batch measurements show why low draft latency, rather than acceptance alone, determines the gain. The method preserves the target distribution in exact arithmetic. In bf16, greedy tests find no non-tie divergences across 48 prompts and six checkpoints; sampling tests expose residual numerical sensitivity, especially in repetitive sequences. A cost-efficient 7B drafter requires 1.06 incremental GPU-hours of training, excluding teacher-data collection, and achieves 2.82x on real sequences. In regulatory-DNA design, EvSpark achieves a median complete-workflow speedup of 1.57x over a calibrated batched native baseline.

bioinformatics↗

A multi-agent workflow converts CAR-T patient evidence into experimentally testable hypotheses

Clinical studies of chimeric antigen receptor (CAR)-T therapy generate diverse molecular and clinical evidence that remains fragmented across publications, public repositories and patient-derived datasets, limiting systematic therapeutic discovery. Here we present BioPathfinder, an evidence-guided multi-agent workflow for closed-loop biomedical discovery. BioPathfinder constructs a provenance-aware knowledge resource linking publications with patient single-cell RNA sequencing (scRNA-seq) datasets and clinical metadata, and uses role-specialized large language model agents to generate, review and prioritize diverse, falsifiable and dataset-aware mechanistic hypotheses for computational and experimental validation. Applied to a curated corpus of CAR-T-treated patient studies and matched scRNA-seq datasets, BioPathfinder identified candidate mechanisms underlying CAR-T persistence, dysfunction and therapeutic resistance. The workflow prioritized the hypothesis that genes associated with an NK-like transition programme could be targeted to reduce CAR-T exhaustion and improve persistence. Analysis of patient scRNA-seq datasets showed enrichment of this programme in exhausted post-infusion CAR-T cells. Virtual perturbation prioritized transition-associated receptor genes, including KLRC1, KLRD1 and KLRG1, and expert review selected KLRC1, encoding NKG2A, for experimental validation. In vitro and in vivo chronic-stimulation models showed that NKG2A marked activated, exhaustion-associated CD8 CAR-T cells, whereas NKG2A blockade enhanced antitumour activity and persistence-associated functional readouts in vivo. BioPathfinder establishes a generalizable framework that transforms fragmented clinical single-cell evidence into experimentally validated therapeutic hypotheses, providing a scalable strategy for AI-guided biomedical discovery. HIGHLIGHTSO_LIBioPathfinder integrates fragmented CAR-T clinical studies, patient scRNA-seq datasets and metadata into a provenance-aware evidence resource for AI-guided hypothesis discovery. C_LIO_LIA multi-agent workflow generates, critiques and prioritizes diverse, falsifiable, dataset-aware mechanisms underlying CAR-T persistence, dysfunction and therapeutic resistance. C_LIO_LIBioPathfinder prioritizes KLRC1/NKG2A as a therapeutic target, and experimental validation demonstrates that NKG2A blockade enhances CAR-T persistence and antitumour function. C_LI

bioengineering↗

AI-enabled Spatial Profiling of Circulating Tumor-Immune Ecosystems Predicts Patient Outcomes Across Cancers

Circulating tumor cells (CTCs) and immune cells form dynamic multicellular ecosystems in blood, but their spatial organization and clinical relevance have not been systematically characterized. We developed the Cell and Cluster Identification Program (CCIP), an artificial intelligence-based framework that analyzes routine multiplex immunofluorescence blood scans to segment cells, identify CTCs and five immune lineages with high accuracy, and quantify multicellular clusters and tumor-immune interactions. Applying CCIP to 2,693 blood scans from 1,399 patients, we profiled over 60 million cells (>7 million multi-cell clusters) and linked imaging-derived features to patient outcomes. Correlated with circulating-tumor DNA mutation burdens, a 14-feature image model predicted overall survival in breast cancer, outperformed clinicopathologic variables and CTC enumeration, and generalized to prostate cancer. Prognostic imaging signatures were also associated with therapy response-related progression-free survival as well as with single-cell RNA sequencing-derived immune suppression states, connecting circulating tumor-immune architecture with systemic immune dysfunction.

cancer biology↗

Tyrosine hydroxylase–mediated neuroimmune crosstalk regulates antitumor immunity in glioblastoma during oncolytic herpes virotherapy

Neuroimmune crosstalk is increasingly recognized as a key regulator of tumor progression and therapeutic response, yet its role in central nervous system (CNS) tumors remains poorly understood. Here, we investigate tyrosine hydroxylase (TH)-mediated neuronal signaling in glioblastoma (GBM) and its impact on antitumor immunity and response to oncolytic virotherapy (OV). We show that TH cells are widely distributed within the GBM microenvironment, including neurons, astrocytes, and immune cells, and are enriched at the tumor margin. In addition, TH cells are present in the tumor-draining lymph nodes (TDLNs) of GBM, where they localize near lymphatic vessels and are associated with lymphangiogenesis. Notably, a subset of CD3TH T cells is detected within lymphatic structures of TDLNs, suggesting immune-intrinsic catecholamine signaling. Single-cell RNA sequencing reveals that noradrenergic signaling, particularly via {beta}2-adrenergic receptors (ADRB2), predominates in tumor-infiltrating myeloid cells and is dynamically regulated by therapy. Intratumoral administration of oncolytic herpes simplex virus (oHSV) upregulates ADRB2 expression in macrophages, whereas systemic chemo-immunotherapy induces distinct receptor modulation patterns in tumors and TDLNs. Functionally, pharmacologic {beta}-adrenergic blockade significantly enhances the efficacy of oHSV therapy in orthotopic GBM and subcutaneous melanoma models, resulting in reduced tumor growth, increased tumor cell death, and enhanced CD8 T cell infiltration. Similarly, direct inhibition of TH enzymatic activity suppresses tumor progression and further potentiates OV. Mechanistically, TH inhibition not only promotes tumor-infiltrated cytotoxic immune cells CD8, NK and {gamma}{delta} T cells, but also suppresses the activity of immunosuppressive myeloid cells, including transcriptional (Fos), and metabolism (Arg) modification in M2 macrophages and other immune cells. Collectively, these findings identify TH-mediated neuroimmune signaling as a critical regulator of tumor immunity in GBM and demonstrate that targeting catecholaminergic pathways or downstream neuroimmune crosstalk pathways can enhance the efficacy of OV. This study provides a rationale for integrating neural modulation into immunotherapeutic strategies for CNS malignancies.

Cancer Biology↗

Ciz1 safeguards Drosophila wing development by suppressing oxidative stress

Cell proliferation and fate specification are fundamental processes that ensure the generation of organs with proper size and patterning. Oxidative stress caused by accumulation of reactive oxygen species (ROS) can lead to cell cycle arrest, senescence, cell death and cell fate misspecification, thereby impairing normal development and contributing to many pathological processes. In this study, we identify Drosophila Ciz1 as a critical factor that safeguards epithelial homeostasis and development by preventing oxidative stress. Knockdown of Ciz1 in the Drosophila wing imaginal disc, an epithelial tissue that serves as the larval precursor of the adult wing, results in a small wing phenotype accompanied by thickened and ectopic veins. We further demonstrate that reduced Ciz1 expression leads to accumulation of donut-shaped mitochondria and elevated ROS levels. The increased oxidative stress subsequently suppresses proliferation via activation of JNK and promotes excessive vein formation by upregulating Rhomboid, a positive regulator of EGFR signaling. Interestingly, although Ciz1 is a zinc finger protein that predominantly localizes to the nucleus, neither its zinc finger motifs nor its nuclear localization is required for suppression of oxidative stress. Instead, the prion-like domain in its N-terminal part is essential for this activity. Our work identifies Ciz1 as an important factor in preventing oxidative stress and maintaining epithelial homeostasis.

Developmental Biology↗

BTK inhibition enhances immunovirotherapy in glioblastoma via tertiary lymphoid structure modulation

Glioblastoma (GBM) is a highly aggressive type of glioma that is resistant to immunotherapy and is associated with poor prognosis, largely due to its immunosuppressive tumor microenvironment. Brutons tyrosine kinase (BTK) is a non-receptor kinase that not only plays an important role in oncogenic signaling, particularly in tumor growth, but also regulates the activity of tumor-infiltrating myeloid cells, including dendritic cells, macrophages, and microglia in brain tumors. High BTK expression is associated with poor survival in patients with glioma. Oncolytic herpes simplex virus type 1 (oHSV)-derived virotherapy, a novel treatment strategy, has demonstrated effectiveness against GBM; however, its efficacy is limited by the tumor microenvironment. In this study, we found that BTK is predominantly expressed in GBM-infiltrating myeloid cells. Intratumoral injection of oHSV not only promotes infiltration of myeloid cells and T cells but also activates BTK in these myeloid cells, thereby limiting oHSV infection and replication in tumor cells. Combination treatment with BTK inhibitor ibrutinib improves anti-tumor efficacy of oHSV in both human GBM12 xenograft and syngeneic murine GSC005 models. Mechanistically, BTK inhibition increases oHSV-mediated tumor cell death (cleaved caspase-3) and cytotoxic CD8 T cell infiltration, while decreasing tumor cell proliferation (Ki-67). BTK inhibition not only suppresses oHSV clearance by tumor-infiltrating microglia and macrophages but also reduces their pro-invasive effects on tumor cells. Addition of IDO inhibitor, an immune modulator, further prolongs survival in tumor-bearing mice in a syngeneic GBM model. Single-cell mRNA sequencing (scRNA-seq) analysis indicates that combination treatment modifies key signaling pathways in both tumor-infiltrating myeloid cells (macrophages and microglia) and CD8 T cells. Further analysis shows that BTK inhibition, with or without IDO inhibition, promotes the formation of tumor-infiltrating tertiary lymphoid structures (TLS) during intratumoral oHSV treatment, subsequently remodeling T cell, NKT cell, and monocyte-macrophage populations. These results indicate that BTK inhibition exerts multifaceted effects in enhancing the anti-tumor efficacy of oHSV therapy.

cancer biology↗

Harnessing Human Immune Organoid model for Systemic and Comparative Analysis of Clinically Vaccine Adjuvants

Effective vaccine adjuvants are crucial for eliciting strong, specific, and long-lasting adaptive immune responses. However, traditional vaccine and adjuvant development is often hindered by prolonged animal testing, reliance on singular evaluation metrics, and batch variability, limiting the comparative analysis of immune responses induced by different adjuvants. To our knowledge, systematic adjuvant-focused analysis in human immune organoids remains limited, particularly across distinct antigen-conditioned immune baselines. Here, we established a matrix supported human tonsil immune organoid (M-hTIO) platform, derived from tonsil tissue for systemic adjuvant evaluation. Within 2 days, the platform replicated key germinal center (GC) features, with the potential for antigen-specific antibody production and plasmablast differentiation. Dynamic GC formation and T-B cell interactions were tracked using light-field imaging. Notably, IL-21 significantly accelerates GC-like remodeling and enhanced immune responses. Employing bulk cell transcriptomics we systematically analyzed early immune signatures and prolonged adaptive responses induced by five clinical-grade adjuvants (Alum, MnJ{beta}, AddaSO3, R848, ODN 1018) paired with influenza HA and SARS-CoV-2 RBD antigens across only adjuvant, weak and strong memory backgrounds. By integrating early and prolonged response phases, M-hTIO captured complementary dimensions of adjuvant activity, distinguishing rapid immune activation from sustained adaptive remodeling. Importantly, early activation signatures and prolonged adaptive remodeling provided complementary information, highlighting the value of temporally resolved adjuvant evaluation. AddaSO3 showed a consistent activity pattern across early and prolonged response phases, supporting both rapid immune activation and sustained adaptive remodeling. Moreover, our findings reveal shared/exclusive signaling pathways and gene networks. These results represent systematic and comparative analysis of clinically tested vaccine adjuvants in a human model, paving the way for high-throughput systems vaccinology research.

immunology↗

Sex stratified analyses enable new genetic insights into brain imaging phenotypes

Sex differences are commonly observed in neuroimaging phenotypes and in the risk of brain diseases, yet the underlying genetic mechanisms remain poorly understood. We investigated sex differences in the genetic architecture of 805 neuroimaging phenotypes in 22,950 males and 22,950 females matched for sample size and covariates, and systematically compared sex-stratified with sex-combined genetic analyses. We found eight variant-trait associations with significant sex differences, 235 fine-mapped sex-dominant causal associations, 457 sex-dominant colocalizations with sex hormones, and 96 sex-dominant colocalizations with schizophrenia. Compared with sex-combined analysis, sex-stratified analysis identified 47 new genetic associations, 170 new fine-mapped causal associations, 1,019 new colocalizations with sex hormones, and 191 new colocalizations with schizophrenia. Additionally, sex-stratified analysis improved global heritability and genetic-correlation estimates and enhanced polygenic prediction for certain phenotypes. This work highlights the need to routinely perform sex-stratified genetic association analyses to elucidate sex-specific and sex-shared genetic control of neuroimaging phenotypes and related disorders.

genetics↗

Ferritin Nanoparticle-Based Indirect ELISA for Immunodominant Region Screening and B-cell Epitope Validation of African Swine Fever Virus

African swine fever virus (ASFV) poses a severe threat to the global pig industry, creating an urgent need for effective vaccines and reliable diagnostic tools. While numerous ASFV B-cell epitopes have been reported based on murine-derived monoclonal antibodies (mAbs), such epitopes may not fully represent the antibody targets recognized in naturally infected pigs. Therefore, we need an approach to screen immunodominant regions by evaluating the reactivity of pre-defined epitopes with ASFV-infected pigs sera. In this study, we developed an indirect enzyme-linked immunosorbent assay (iELISA) based on recombinant epitope-ferritin nanoparticles (EFNs), as a platform for immunodominant region screening and epitope validation. This assay, hereafter referred to as EFNs-iELISA, shows an approximately twofold improvement in sensitivity compared with synthetic peptide-based ELISA for linear B-cell epitopes, and improved discrimination over GST-His-peptide and BSA-conjugated peptide formats. Using EFNs-iELISA, we evaluated 22 known murine-derived B-cell epitopes and 17 predicted epitopes from ASFV proteins CD2v, P30, P54, and P72 with ASFV-positive and negative porcine sera. According to the calculated cut-off threshold, tested epitopes were classified into different groups with positive or negative reactivity. Our analysis confirmed that among 22 known murine-derived ASFV B-cell epitopes, 16 (72%) also showed positive reactions with porcine-derived sera. Whats more, we also screened 7 new porcine-specific immunoreactive regions on these proteins. The EFNs-iELISA method provides a practical tool for screening immunodominant regions of ASFV, with potential applications in vaccine and diagnostic research.

immunology↗

Mapping Core Components of Membrane-less Organelles in Living Cells by Phase-APEX2 Proximity Labeling

Membrane-less organelles (MLOs), formed via liquid-liquid phase separation, are crucial for organization of biomacromolecules and cellular processes, yet their dynamic nature challenges compositional analysis. Conventional proximity labeling methods lack the specificity to overcome high background and systematic biases inherent in studying these condensates. Here we introduce Phase-APEX2, a three-input AND-gate strategy that dramatically enhances labeling specificity. By integrating a split-APEX2 system with a light-controlled H2O2 generator, we developed Phase-APEX2 platforms for two application contexts: Phase-APEX2-MS for proteomics and Phase-APEX2-seq for genomics. Our analyses revealed not only the core interactomes of the nucleolus and stress granules with high accuracy but also uncovered distinct "molecular grammars" governing their assembly and a surprising link between nucleolar dynamics and the transcriptional regulation of mitosis-related genes. This highly specific and adaptable platform opens new avenues for exploring the composition and function of diverse biomolecular condensates.

cell biology↗

Transcontinental Spread of HPAI H5N1 from South America to Antarctica via Avian Vectors

Our study has for the first time identified H5N1 strains (clade 2.3.4.4b, genotype B3.2) in brown skuas from the Fildes Peninsula, South Shetland Islands, Antarctica. These findings indicate that highly pathogenic avian influenza H5N1 viruses is now actively circulating in Antarctic ecosystems, representing a significant expansion of its geographic range.

genomics↗

Loss of Regulator of telomere elongation helicase (Rtel1) impairs alveolar epithelial cell progenitor function but does not exacerbate experimental fibrosis

Inherited loss-of-function mutations in the replication-associated helicase Regulator of telomere elongation helicase (RTEL1) are among the most frequent monogenic causes of familial pulmonary fibrosis (FPF), but the specific functional role of RTEL1 in lung development, homeostasis, and injury-repair has not been determined. Using single-cell RNA-sequencing to define the cellular diversity and molecular programs following intratracheal bleomycin injury in mice, we observed that Rtel1 was most highly expressed in the lung epithelium, and its expression was reduced in PF epithelial cells compared to nonfibrotic controls. While global deletion of Rtel1 leads to embryonic lethality, constitutive deletion of Rtel1 in the lung epithelium (Rtel{Delta}epi) led to normal lung structure and architecture. Rtel1{Delta}epi mice exhibited accelerated telomere attrition and impaired AEC progenitor potential ex-vivo. Despite decreased AEC progenitor function, no differences in lung fibrosis were observed in Rtel{Delta}epi mice compared to controls following single-dose or repetitive intratracheal bleomycin. Together, these data implicate RTEL1 as a regulator of AEC progenitor function but this level of progenitor dysfunction is not alone sufficient to cause or exacerbate experimental lung fibrosis.

cell biology↗

Neutrophil-microglia interaction drives reversible motor dysfunction in neuromyelitis optica model induced by subarachnoid AQP4-IgG

Neutrophils and neutrophil extracellular traps (NETs) contribute to early neuromyelitis optica (NMO) histopathology initiated by IgG targeting astrocytic aquaporin-4 water (AQP4) channels. Yet, the mechanisms recruiting neutrophils and their pathogenic roles in disease progression remain unclear. To investigate molecular-cellular events preceding classical complement cascade activation in a mouse NMO model, we continuously infused, via spinal subarachnoid route, a non-complement-activating monoclonal AQP4-IgG. Parenchymal infiltration of netting neutrophils containing C5a ensued with microglial activation and motor impairment, but no blood-brain barrier leakage. Motor impairment and neuronal dysfunction both reversed when AQP4-IgG infusion stopped. Two-photon microscopy and electron-microscopy-based reconstructions revealed physical interaction of infiltrating neutrophils with microglia. Ablation of either peripheral neutrophils or microglia attenuated the motor deficit, highlighting their synergistic pathogenic roles. Of note, mice lacking complement receptor C5aR1 exhibited reduction in neutrophil infiltration, microglial lysosomal activation, neuronal lipid-droplet burden and motor impairment. Pharmacological inhibition of C5aR1 recapitulated this protection. Immunohistochemical analysis of an NMO patients early spinal cord lesions revealed analogous pathological findings. Our study identifies neutrophil-derived C5a signaling through microglial C5aR1 as a key early driver of reversible motor neuron dysfunction in the precytolytic phase of NMO. One Sentence SummaryNeutrophil-derived C5a coactivates microglia to drive reversible motor paresis initiated by a non-complement-activating aquaporin-4-IgG binding to astrocytes in a mouse model of neuromyelitis optica.

neuroscience↗

Characterization of full-length and cytoplasmic tail-truncated envelope glycoproteins incorporated into human immunodeficiency virus (HIV-1) virions and virus-like particles

During transport to the surface of infected cells, the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer is cleaved to produce the mature functional Env trimer ((gp120/gp41)3). Env cleavage stabilizes the pretriggered Env conformation (PTC), the major target for broadly neutralizing antibodies. Although the mature Env is relatively enriched in virions and virus-like particles (VLPs), conformationally flexible uncleaved Envs typically contaminate preparations of these particles. In non-permissive cells, the long [~]149-residue gp41 cytoplasmic tail (CT) is necessary for Env incorporation into virions. In a minority of HIV-1 strains, the gp41 CT is clipped in virions by the viral protease. Here, we compare Envs with CT truncations and CT alterations that increase or decrease protease clipping in permissive cells. Changes in protease clipping affected amphotericin B sensitivity, but did not alter other viral phenotypes. By contrast, a corresponding CT truncation (L748STOP) increased cell-surface and virion Env levels, cell-cell fusion, and virus infectivity and cytotoxicity. Notably, in diverse HIV-1 strains, the ratio of cleaved/uncleaved Envs in preparations of virions and extracellular vesicles was increased by this CT truncation. ESCRT and ALIX-binding region (EABR) vesicles incorporated significantly more uncleaved CT-truncated Env than HIV-1 VLPs. Env CT deletion/truncation did not qualitatively alter the viral neutralization profile; however, increased antibody concentrations were required to neutralize viruses with the higher levels of cleaved Env that resulted from CT truncation. Specific CT truncations provide a means of enriching the PTC and limiting the incorporation of nonfunctional and conformationally heterogeneous uncleaved Envs into preparations of virions and VLPs. IMPORTANCEThe human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer mediates entry of the virus into host cells. The pretriggered conformation (PTC) of Env is the major target for protective broadly neutralizing antibodies, but the PTC is unstable and therefore difficult to study. The cleavage of the flexible Env precursor stabilizes the PTC. Therefore, the presence of uncleaved Env compromises the purity of the PTC in Env preparations. We found that certain truncations of the Env cytoplasmic tail resulted in improved ratios of cleaved:uncleaved Env in preparations of HIV-1 viruses or virus-like particles. In some contexts, cytoplasmic tail truncation increased the level of Env in virus preparations. Although higher concentrations of antibodies were required to neutralize these viruses, Envs with specific truncations of the cytoplasmic tail retained the PTC. Thus, cytoplasmic tail truncation could assist efforts to purify and characterize the Env PTC on the viral membrane.

microbiology↗

Regulation of essential hepatocyte functions and identity by super-enhancers in health and disease

Physiologically, hepatocytes perform an estimated 500 essential liver functions to ensure systemic homeostasis. The mechanisms how hepatocytes maintain these numerous crucial functions in response to physiological and pathophysiological challenges are largely unknown. In this study, we found that vital liver function genes (e.g., HNF4A, ALB, coagulation factors, and SLC2A2) in hepatocytes possess super-enhancers. Interfering with the super-enhancers by dCas9-sgRNA remarkably decreases the expression of these genes. Quiescent liver progenitor cells (LPCs) do not have active super-enhancers in vital liver function genes. In acute liver failure (ALF) caused by massive hepatic necrosis, activated LPCs perform liver function and differentiate into hepatocytes to rescue patients lives. We show that activated LPCs gradually form super-enhancers in liver function genes (e.g., HNF4A, ALB, and coagulation factors) during proliferation and differentiation. These super-enhancers are regulated by FOXA2 through the recruitment of HNF4 a, p300 and Mediators in most liver function genes, such as ALB and coagulation factors. However, super-enhancers in some genes (e.g., SLC2A2) are FOXA2-indenpendent. Hepatic FOXA2 expression is closely associated with the clinical outcome of ALF. In a cohort of ALF patients, robust FOXA2 is observed only in the surviving patients. Collectively, super-enhancers represent a critical epigenetic regulatory mechanism that enables rapidly enhanced transcription of liver function genes in response to pathophysiological challenges. In urgent clinical syndrome such as ALF, LPCs rescue liver function by rapid formation of super-enhancers in vital genes.

molecular biology↗

TGF-β serves as a critical signaling determinant of liver progenitor cell fate and function

Liver progenitor cells (LPCs) are the smallest cholangiocytes that perform hepatocyte functions to rescue the lives of patients suffering from acute liver failure (ALF) caused by massive hepatic necrosis (MHN). To date, it remains largely unknown how LPCs remain quiescent and become activated following MHN. This study elucidates the essential role of TGF-{beta} in regulating LPC quiescence and activation. Spatial transcriptomics analysis of liver tissues from four MHN-ALF patients revealed that LPCs receive multiple active signals from surrounding macrophages and hepatic stellate cells, including TGF-{beta}, HGF, and EGF. Physiologically, TGF-{beta} inhibits LPC proliferation by impeding G1-S phase transition. Ectopic Smad7 expression remarkably increased LPC proliferation in 3,5-diethoxycarbonyl-1,4-dihydrocollidine-fed mice. Intriguingly, extensive LPC proliferation was observed in ALF patients despite robust TGF-{beta}-p-SMAD2 signaling in activated LPCs. Immunohistochemistry and immunofluorescence revealed significantly elevated expression of p-MET, p-STAT3, p-EGFR, and p-ERK in LPCs, indicating active HGF and EGF signaling. In vitro, either HGF or EGF promoted LPC proliferation despite the presence of TGF-{beta}. Beyond acting as mitogens, HGF and EGF regulate master hepatocyte genes (e.g., HNF4) and cholangiocyte genes (e.g., SOX9) in LPCs. Notably, HGF-dependent HNF4 required TGF-{beta}-activated SMADs. Collectively, TGF-{beta} serves as a critical signaling determinant of LPC fate and function.

cell biology↗