Biology subjects

Yang, D.

Publications and source records attributed to Yang, D..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

High-throughput protein target mapping enables accelerated bioactivity discovery for ToxCast and PFAS compounds

Chemical pollution is a global threat to human health, yet the toxicity mechanism of most contaminants remains unknown. Here, we applied an ultrahigh-throughput affinity-selection mass spectrometry (AS-MS) platform to systematically identify protein targets of prioritized chemical contaminants. After benchmarking the platform, we screened 50 human proteins against 481 prioritized chemicals, including 446 ToxCast chemicals and 35 per-and polyfluoroalkyl substances (PFAS). Among 24,050 interactions assessed, we discovered 35 novel interactions involving 14 proteins, with fatty acid-binding proteins (FABPs) emerging as the most ligandable protein family. Given this, we selected FABPs for further validation, which revealed a distinct PFAS binding pattern: legacy PFAS selectively bound to FABP1, whereas replacement compounds, PFECAs, unexpectedly interacted with all FABPs. X-ray crystallography further revealed that the ether group enhances molecular flexibility of alternative PFAS, to accommodate the binding pockets of FABPs. Our findings demonstrate that AS-MS is a robust platform for the discovery of novel protein targets beyond the scope of the ToxCast program and highlight the broader protein-binding spectrum of alternative PFAS as potential regrettable substitutes.

pharmacology and toxicology↗

bioRxiv2025

Deciphering the Pathogenic Landscape of Amyloid Light-Chain Cardiomyopathy

Amyloid light-chain cardiomyopathy (ALCA) is an infiltrative disorder marked by misfolded immunoglobulin light-chain deposition in the myocardium, ultimately leading to cardiac dysfunction. Despite its clinical severity, the underlying mechanisms remain poorly understood. Here, we integrated multi-omics analyses of human cardiac samples to construct a comprehensive cellular and spatial atlas of the ALCA heart. We observed a marked expansion of PTX3+ fibroblasts (FB), which undergo a distinct phenotypic transition into pro-fibrotic POSTN+ FB regulated by EGR1.Concurrently, SPP1+ macrophages (Mac) emerged as major drivers of fibrosis, interacting robustly with PTX3+ FB via APP-CD74, GAS6-MERTK, and TGF-{beta}1-TGF-{beta}1/2 pathways. Endothelial cell (EC) profiling revealed substantial vascular remodeling characterized by the emergence of specialized capillary-like immune endothelial cells expressing chemokines CXCL1, CXCL3, and CCL2, alongside depletion of functional capillary EC. Immunologically, elevated cytotoxic CD8+ T cells and reduced NK cells contributed to an imbalanced inflammatory milieu, with NF{kappa}B2 orchestrating both fibrotic and immune pathways across multiple cell types. These findings highlight the pivotal role of fibroblast-immune crosstalk, particularly the SPP1+ Mac-PTX3+ FB axis, in driving ALCA pathogenesis. Targeting these pathological cellular interactions may offer a promising therapeutic avenue to mitigate fibrosis, restore immune homeostasis, and improve cardiac function in ALCA.

bioinformatics↗

bioRxiv2025

A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon

The niche environment surrounding intestinal stem cells (ISCs) varies along the length of intestine and provides key cues that regulate stem cell fate. Here, we investigated the role of cellular redox balance in colonic ISC function. We show that hypoxia and Wnt signaling synergize to restrict the reactive oxygen species (ROS) generating enzyme NADPH oxidase 1 (NOX1) to the crypt base in the distal colon. NOX1 function maintains a more oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric stem cell self-renewal and directing lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1 (HIF1)-dependent signaling with regulation of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1). Our studies show that cellular redox balance is a central and niche-dependent regulator of epithelial homeostasis and regeneration and provide a basis for understanding disease propensity in the distal large intestine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/634856v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@107798aorg.highwire.dtl.DTLVardef@1bc9013org.highwire.dtl.DTLVardef@96d56aorg.highwire.dtl.DTLVardef@95268d_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIThe balance of cycling intestinal stem cells (ISCs) versus committed epithelial cells in the uniquely hypoxic niche of the distal colon is regulated by NADPH oxidase 1 (NOX1) dependent H2O2 both at homeostasis and during regeneration. C_LIO_LIPhysiological increase in cellular H2O2 favors maintenance of glycolysis in ISCs for self-renewal through regulation of isocitrate dehydrogenase 1 activity. C_LIO_LIMaintenance of the increased cellular oxidative state stabilizes HIF1 through a re-enforcing metabolic circuit. C_LIO_LIA shift from a relatively oxidative to a reductive cell environment in distal colonic ISCs leads to decreased progression through the cell cycle and altered cell fate determination. C_LI

cell biology↗

bioRxiv2025

Enantioselective Protein Affinity Selection Mass Spectrometry (EAS-MS)

We report an enantioselective protein affinity selection mass spectrometry screening approach (E-ASMS) that enables the detection of weak binders, informs on selectivity, and generates orthogonal confirmation of binding. After method development with control proteins, we screened 31 human proteins against a designed library of 8,210 chiral compounds. 16 binders to 12 targets, including many proteins predicted to be "challenging to ligand", were discovered and confirmed in orthogonal biophysical assays. 7 binders to 6 targets bound in an enantioselective manner, with KD values ranging from 3 to 20 {micro}M. Binders for four targets (DDB1, WDR91, WDR55, and HAT1) were selected for in-depth characterization using X-ray crystallography. In all four cases, the mechanism for enantioselectivity was readily explained. We conclude E-ASMS can be used to identify and characterize selective and weakly-binding ligands for novel protein targets with unprecedented throughput and sensitivity.

pharmacology and toxicology↗

bioRxiv2025

Mapping brain function underlying naturalistic motor observation and imitation using high-density diffuse optical tomography

BackgroundAutism spectrum disorder (ASD), a condition defined by deficits in social communication, restricted interests, and repetitive behaviors, is associated with early impairments in motor imitation that persist through childhood and into adulthood. Alterations in the mirror neuron system (MNS), crucial for interpreting and imitating actions, may underlie these ASD-associated differences in motor imitation. High-density diffuse optical tomography (HD-DOT) overcomes logistical challenges of functional magnetic resonance imaging to enable identification of neural substrates of naturalistic motor imitation. ObjectiveWe aim to investigate brain function underlying motor observation and imitation in autistic and non-autistic adults. We hypothesize that HD-DOT will reveal greater activation in regions associated with the MNS during motor imitation than motor observation, and that MNS activity will negatively correlate with autistic traits and motor fidelity. MethodsWe imaged brain function using HD-DOT in N = 100 participants as they engaged in observing or imitating a sequence of arm movements. Additionally, during imitation, participant movements were simultaneously recorded with 3D cameras for computer-vision-based assessment of motor imitation (CAMI). Cortical responses were estimated using general linear models, and multiple regression was used to test for associations with autistic traits, assessed via the Social Responsiveness Scale-2 (SRS), and imitation fidelity, assessed via CAMI. ResultsBoth observing and imitating motor movements elicited significant activations in higher-order visual and MNS regions, including the inferior parietal lobule, superior temporal gyrus, and inferior frontal gyrus. Imitation additionally exhibited greater activation in the superior parietal lobule, primary motor cortex, and supplementary motor area. Notably, the right temporal-parietal junction exhibited activation during observation but not during imitation. Higher autistic traits were associated with increased activation during motor observation in the right superior parietal lobule. No significant correlation between brain activation and CAMI scores was observed. ConclusionsOur findings provide robust evidence of shared and task-specific cortical responses underlying motor observation and imitation, emphasizing the differential engagement of MNS regions during motor observation and imitation.

neuroscience↗

bioRxiv2025

Enhanced yield and subtype identity of hPSC-derived midbrain dopamine neuron by modulation of WNT and FGF18 signaling

While clinical trials are ongoing using human pluripotent stem cell-derived midbrain dopamine (mDA) neuron precursor grafts in Parkinsons disease (PD), current protocols to derive mDA neurons remain suboptimal. In particular, the yield of TH+ mDA neurons after in vivo grafting and the expression of some mDA neuron and subtype-specific markers can be further improved. For example, characterization of mDA grafts by single cell transcriptomics has yielded only a small proportion of mDA neurons and a considerable fraction of contaminating cell populations. Here we present an optimized mDA neuron differentiation strategy that builds on our clinical grade ("Boost") protocol but includes the addition of FGF18 and IWP2 treatment ("Boost+") at the mDA neurogenesis stage. We demonstrate that Boost+ mDA neurons show higher expression of EN1, PITX3 and ALDH1A1. Improvements in both mDA neurons yield and transcriptional similarity to primary mDA neurons is observed both in vitro and in grafts. Furthermore, grafts are enriched in authentic A9 mDA neurons by single nucSeq. Functional studies in vitro demonstrate increased dopamine production and release and improved electrophysiological properties. In vivo analyses show increased percentages of TH+ mDA neurons resulting in efficient rescue of amphetamine induced rotation behavior in the 6-OHDA rat model and rescue of some motor deficits in non-drug induced assays, including the ladder rung assay that is not improved by Boost mDA neurons. The Boost+ conditions present an optimized protocol with advantages for disease modeling and mDA neuron grafting paradigms.

cell biology↗

bioRxiv2025

Synergizing Network Pharmacology and Pan-Cancer Analysis in TCM Repositioning for Tumor Therapy

BackgroundRepositioning Traditional Chinese Medicine (TCM) for cancer treatment, addressing heterogeneity through synergistic effects, aligns with the evolving trend of combination therapy. However, the complexity of TCM and the lack of methodology hinders the elucidation of TCM treatment mechanisms and potential indications. The research aims to construct develop a comprehensive method combining network pharmacology and pan-cancer analysis (NetPharm-PanCan) for TCM repositioning, exemplified by the Astragali Radix-Curcumae Rhizoma (ARCR) herb pair. MethodThe TCM-component-gene network was constructed using Cytoscape3.7.2 with gene screening based on components from TCMSP and targets predicted via the Swiss Target Prediction database. The core gene set of the ARCR (CGSARCR) was identified by analyzing network via the dual algorithm, namely Degree and MCODE followed by GO and KEGG enrichment analyses. The pan-cancer analysis encompassing Gene Set Variation Analysis (GSVA), immune infiltration correlation, cancer pathway analysis, and Gene Set Enrichment Analysis (GSEA) was unveiled to identify the potential indications. Multivariate cox regression analysis was employed for identifying prognostic genes, followed by the modeling for potential therapeutic indications using the R software. The Metescape database was harnessed to reveal similarities and differences in the mechanisms for prognostic genes associated with potential indications. The XGBoost algorithm was used to construct an indication prediction system according to the analysis results above. ResultThe CGSARCR comprises 28 genes targeting all ARCR components. The pan-cancer analysis revealed that the CGSARCR showed significantly higher tumor scores than normal tissue scores across nine different types of cancer, including THCA, KIRC, LUAD, COAD, BRCA, STAD, ESCA, and others. The CGSARCR correlated strongly with cancer-related pathways and the immune microenvironment. Prognostic models evaluate the potential of these indications as follows: THCA> KIRC> LUAD> COAD> BRCA> STAD> ESCA, with enrichment analysis suggesting KIRC and LUAD as the most potential indications of ARCR. The XGBoost-based system achieved high predictive accuracy (training AUC: 0.985, testing AUC: 0.96, training logloss: 0.21, testing logloss: 0.25). ConclusionThe NetPharm-PanCan method provides a robust, network-based pan-cancer analysis framework for TCM repositioning in cancer research. It provides theoretical foundations and practical tools for TCM-based drug development, with potential applicability to broader drug repurposing efforts.

bioinformatics↗

bioRxiv2025

Chronic Staphylococcus aureus infection of osteocytes promotes an intracellular viable-but-non-culturable phenotype

Osteomyelitis associated with periprosthetic joint infection (PJI) is a serious and growing complication of orthopaedic joint replacement surgery, with a failure to cure rate within 2-years of between 15-46%. PJI is a severe chronic infectious disease with a 20% recurrence rate and culture-negativity in 7-39% of cases, of which 14-27% are PCR-positive, findings that remain poorly explained. Osteocytes, the most numerous bone cell type, have been identified as potential long-term intracellular reservoirs for Staphylococcus aureus, shielding it from antimicrobial treatment. Here we demonstrate that in chronic intra-osteocytic infections, S. aureus consistently adopts a viable-but-non-culturable (VBNC) state, capable of spontaneous host cell escape and reversion to active growth. Whole-genome sequencing identified single nucleotide polymorphisms (SNPs) in gene pairs between clones. Two revertant clones exhibited SNPs in srrB and murA2, and five exhibited SNPs in garR and upstream of tatB. While the functional importance of these changes is uncertain, they suggest that diverse genetic mechanisms underly entrance into and exit from the intracellular VBNC state. These findings provide a compelling explanation for culture-negative, PCR-positive osteomyelitis and have direct implications for the diagnosis and treatment of PJI.

microbiology↗

bioRxiv2024

Single-cell analysis reveals distinct immune characteristics of hepatocellular carcinoma in HBV-positive versus HBV-negative cases

Infection with the Hepatitis B virus (HBV) is a key risk factor for Hepatocellular carcinoma (HCC) development and progression. It is widely recognized that immunopathological mechanisms are pivotal in developing HBV-related HCC. Nevertheless, the specific mechanisms by which HBV-induced modifications within the tumor microenvironment (TME) contribute to HCC pathogenesis are still not well understood. Here, we utilized single-cell RNA sequencing to analyze and compare the immune landscapes between HBV-positive and HBV-negative HCC. We discovered that HBV infection significantly modifies the immune cell makeup and state, and leads to the suppression and exhaustion of T cells within the TME. Specifically, an increase in SLC4A10+ CD8+ T cells and IFITM3+ macrophages was observed, along with the upregulation of the gene SLC35F1 in various immune cell subtypes. These findings offer valuable insights into the alteration of the immunological microenvironment in HCC associated with HBV infection, suggesting possible targets for immunotherapeutic intervention.

bioinformatics↗

bioRxiv2024

Comprehensive Analysis of Human Dendritic Spine Morphology and Density: Exploring Diversity of Human Dendritic Spines

Dendritic spines, small protrusions on neuronal dendrites, play a crucial role in brain function by changing shape and size in response to neural activity. So far, in depth analysis of dendritic spines in human brain tissue is lacking. This study presents a comprehensive analysis of human dendritic spine morphology and density using a unique dataset from human brain tissue from 27 patients (8 females, 19 males, aged 18-71) undergoing tumor or epilepsy surgery at three neurosurgery sites. We used acute slices and organotypic brain slice cultures to examine dendritic spines, classifying them into the three main morphological subtypes: Mushroom, Thin, and Stubby, via 3D reconstruction using ZEISS arivis Pro software. A deep learning model, trained on 39 diverse datasets, automated spine segmentation and 3D reconstruction, achieving a 74% F1-score and reducing processing time by over 50%. We show significant differences in spine density by sex, dendrite type, and tissue condition. Females had higher spine densities than males, and apical dendrites were denser in spines than basal ones. Acute tissue showed higher spine densities compared to cultured human brain tissue. With time in culture, Mushroom spines decreased, while Stubby and Thin spine percentages increased, particularly from 7-9 to 14 days in vitro, reflecting potential synaptic plasticity changes. Our study underscores the importance of using human brain tissue to understand unique synaptic properties and shows that integrating deep learning with traditional methods enables efficient large-scale analysis, revealing key insights into sex- and tissue-specific dendritic spine dynamics relevant to neurological diseases. New and NoteworthyThis study presents a dataset of nearly 4,000 morphologically reconstructed human dendritic spines across different ages, gender, and tissue conditions. The dataset was further used to evaluate a deep learning algorithm for three-dimensional spine reconstruction, offering a scalable method for semi-automated spine analysis across various tissues and microscopy setups. The findings enhance understanding of human neurology, indicating potential connections between spine morphology, brain function, and the mechanisms of neurological and psychiatric diseases.

neuroscience↗

bioRxiv2024

CD47 predominates over CD24 as a macrophage immune checkpoint in cancer.

Macrophages hold tremendous promise as effectors of cancer immunotherapy, but the best strategies to provoke these cells to attack tumors remain unknown. Here, we evaluated the therapeutic potential of targeting two distinct macrophage immune checkpoints: CD47 and CD24. We found that antibodies targeting these antigens could elicit maximal levels of phagocytosis when combined together in vitro. However, to our surprise, via unbiased genome-wide CRISPR screens, we found that CD24 primarily acts as a target of opsonization rather than an immune checkpoint. In a series of in vitro and in vivo genetic validation studies, we found that CD24 was neither necessary nor sufficient to protect cancer cells from macrophage phagocytosis in most mouse and human tumor models. Instead, anti-CD24 antibodies exhibit robust Fc-dependent activity, and as a consequence, they cause significant on-target hematologic toxicity in mice. To overcome these challenges and leverage our findings for therapeutic purposes, we engineered a collection of 77 novel bispecific antibodies that bind to a tumor antigen with one arm and engage macrophages with the second arm. We discovered multiple novel bispecifics that maximally activate macrophage-mediated cytotoxicity and reduce binding to healthy blood cells, including bispecifics targeting macrophage immune checkpoint molecules in combination with EGFR, TROP2, and CD71. Overall, our findings indicate that CD47 predominates over CD24 as a macrophage immune checkpoint in cancer, and that the novel bispecifics we created may be optimal immunotherapies to direct myeloid cells to eradicate solid tumors.

cancer biology↗

bioRxiv2024

Phospholipid Scramblase 1 (PLSCR1) Regulates Interferon-Lambda Receptor 1 (IFN-lambdaR1) and IFN-lambda Signaling in Influenza A Virus (IAV) Infection

Phospholipid scramblase 1 (PLSCR1) is an antiviral interferon-stimulated gene (ISG) that has several known anti-influenza functions. However, the mechanisms in relation to its expression compartment and enzymatic activity have not been completely explored. Moreover, only limited animal models have been studied to delineate its role at the tissue level in influenza infections. Our results showed that Plscr1 expression was highly induced by influenza A virus (IAV) infection in vivo and in airway epithelial cells treated with IFN-{lambda}. We found that infected Plscr1-/-mice exhibited exacerbated body weight loss, decreased survival rates, heightened viral replication, and increased lung damage. Interestingly, transcriptomic analyses demonstrated that Plscr1 was required for the expression of type 3 interferon receptor (Ifn-{lambda}r1) and a large subset of ISGs upon IAV infection. The impaired expression of Ifn-{lambda}r1 and downstream ISGs may be responsible for delayed viral clearance and worse lung inflammation in Plscr1-/- mice. PLSCR1 acts as a transcriptional activator of IFN-{lambda}R1 by directly binding to its promotor after IAV infection. In addition, PLSCR1 interacted with IFN-{lambda}R1 on the cell surface of pulmonary epithelial cells following IAV infection, suggesting it also modulated IFN-{lambda} signaling via protein-protein interactions. The lipid scramblase activity of PLSCR1 was found to be dispensable for its anti-flu activity. Finally, single-cell RNA sequencing data indicated that Plscr1 expression was significantly upregulated in ciliated airway epithelial cells in mice following IAV infection. Consistently, Plscr1floxStopFoxj1-Cre+ mice with ciliated epithelial cell-specific Plscr1 overexpression showed reduced susceptibility to IAV infection, less inflammation and enhanced Ifn-{lambda}r1 expression, suggesting that Plscr1 primarily regulates type 3 IFN signaling as a cell intrinsic defense factor against IAV in ciliated airway epithelial cells. Our research will elucidate virus-host interactions and pave the way for the development of novel anti-influenza drugs that target human elements like PLSCR1, thereby mitigating the emergence of drug-resistant IAV strains.

immunology↗

bioRxiv2024

Aberrant expression of collagen type X in solid tumor stroma is associated with EMT, immunosuppressive and pro-metastatic pathways, bone marrow stromal cell signatures, and poor survival prognosis

BackgroundCollagen type X (ColX1, encoded by COL10A1) is expressed specifically in the cartilage-to-bone transition, in bone marrow cells, and in osteoarthritic (OA) cartilage. We have previously shown that ColX1 is expressed in breast tumor stroma, correlates with tumor-infiltrating lymphocytes, and predicts poor adjuvant therapy outcomes in ER+/HER2+ breast cancer. However, the underlying molecular mechanisms for these effects are unknown. In this study, we performed bioinformatic analysis of COL10A1-associated gene modules in breast and pancreatic cancer as well as in cells from bone marrow and OA cartilage. These findings provide important insights into the mechanisms of transcriptional and extracellular matrix changes which impact the local stromal microenvironment and tumor progression. MethodsImmunohistochemistry was performed to examine collagen type X expression in solid tumors. WGCNA was used to generate COL10A1-associated gene networks in breast and pancreatic tumor cohorts using RNA-Seq data from The Cancer Genome Atlas. Computational analysis was employed to assess the impact of these gene networks on development and progression of cancer and OA. Data processing and statistical analysis was performed using R and various publicly-available computational tools. ResultsExpression of COL10A1 and its associated gene networks highlights inflammatory and immunosuppressive microenvironments, which identify aggressive breast and pancreatic tumors and contribute to metastatic potential in a sex-dependent manner. Both cancer types are enriched in stroma, and COL10A1 implicates bone marrow-derived fibroblasts as drivers of the epithelial-to-mesenchymal transition (EMT) in these tumors. Heightened expression of COL10A1 and its associated gene networks is correlated with poorer patient outcomes in both breast and pancreatic cancer. Common transcriptional changes and chondrogenic activity are shared between cancer and OA cartilage, suggesting that similar microenvironmental alterations may underlie both diseases. ConclusionsCOL10A1-associated gene networks may hold substantial value as regulators and biomarkers of aggressive tumor phenotypes with implications for therapy development and clinical outcomes. Identification of tumors which exhibit high expression of COL10A1 and its associated genes may reveal the presence of bone marrow-derived stromal microenvironments with heightened EMT capacity and metastatic potential. Our analysis may enable more effective risk assessment and more precise treatment of patients with breast and pancreatic cancer. Research HighlightsO_LIColX highlights features of EMT in breast and pancreatic cancer C_LIO_LIColX gene modules are immunosuppressive and pro-metastatic C_LIO_LIColX-associated gene networks contribute to sex differences in pancreatic cancer C_LIO_LIColX-positive fibroblasts define more aggressive tumors with poorer survival C_LIO_LIColX is emerging as a biomarker for bone marrow-derived cells in cancer C_LI

cancer biology↗

bioRxiv2024

Unanchored ubiquitin chains promote the non-canonical inflammasome via UBXN1

Ubiquitination is a major posttranslational covalent modification that regulates numerous cellular processes including inflammasome signaling. Cells also contain unanchored ubiquitin chains (polyUb) that bind protein targets non-covalently, but their physiological functions in immunity have been appreciated only recently. Here, we report that ubiquitin regulatory x domain-containing protein 1 (UBXN1) activates the noncanonical inflammasome via unanchored Lysin (K) 48- or 63-linked polyUb. UBXN1 deficiency impairs the activation of caspase-4/11, secretion of inflammasome-dependent cytokines and pyroptosis in response to intracellular lipopolysaccharide (LPS). UBXN1-deficient mice are protected from LPS- and cecal-ligation-and-puncture-induced sepsis, evidenced by reduced mortality and systemic inflammation, compared to UBXN1-sufficient littermates. Mechanistically, UBXN1 together with unanchored K48/63-linked polyUb bind caspase-4/11, the intracellular sensors of LPS, and promote their assembly and activation. Depleting cellular unanchored polyUb with recombinant ubiquitin-specific proteinase 5 (USP5) reduces UBXN1 binding to caspase-4/11 and inflammasome signaling, while USP5 inhibitors enhance pyroptosis in an UBXN1-dependent manner. Thus, this study identifies a critical UBXN1-dependent posttranslational mechanism involved in noncanonical inflammasome activation and UBXN1 as a potential therapeutic target for sepsis and advances a fundamental understanding of unanchored polyUb biology.

immunology↗

bioRxiv2024

Prenatal stress increases corticosterone levels in offspring by impairing placental glucocorticoid barrier function

To investigate the association between prenatal stress (PS) and corticosterone, and its influence on DNA methylation of genes related to the placental glucocorticoid (GC) barrier, including 11{beta}-HSD2, P-gp, NR3C1, and FKBP5. The PS model was established through chronic unpredictable mild stress (CUMS). DNA methylation of GC-related genes was analyzed using reduced representation bisulfite sequencing (RRBS), and the results were confirmed using MethylTarget sequencing. The mRNA and protein expression levels of these genes were detected through qRT-PCR and Western blotting, respectively. Plasma corticosterone levels are elevated in pregnant female rats exposed to PS conditions and their offspring. Compared to the offspring of the prenatal control (OPC) group, the offspring of the prenatal stress (OPS) group showed down-regulation in both mRNA and protein expression of DNMT 3A and DNMT 3B, while up-regulation was observed in the expression of DNMT1. RRBS analyses identified P-gp and FKBP5 as hypermethylated genes, including a total of 43 differentially methylated sites (DMS) and 2 differentially methylated regions (DMR). MethylTarget sequencing revealed that both genes had 15 differentially methylated CpG sites. This study provides preliminary evidence that PS disrupts the placental GC barrier through abnormal gene expression caused by hypermethylation of GC-related genes, resulting in elevated corticosterone levels in offspring and affecting their growth and development.

developmental biology↗

bioRxiv2024

Transport-Related Effects on Intrinsic and Synaptic Properties of Human Cortical Neurons: A Comparative Study

Transporting human brain tissue from the operating theater to an off-site laboratory may affect sample integrity for electrophysiological studies. This study investigated how a 30-40 minute transport influenced the intrinsic, synaptic, and morphological properties of human cortical neurons. Electrophysiological recordings were performed on Layer 2/3 (L2/3 pyramidal cells and fast-spiking (FS) interneurons from human cortical slices (n = 200 neurons from 32 surgeries), comparing on-site recordings at RWTH Aachen University Hospital and off-site at Research Centre Juelich. Action potential firing patterns remained largely preserved across both recording sites, but several differences were observed. Off-site recorded pyramidal cells showed a slightly depolarized resting membrane potential and a significantly lower rheobase current. In off-site recorded FS interneurons, we found a narrower action potential half-width and an increased amplitude, suggesting altered ion channel kinetics and/or neuromodulatory environment. Additionally, a significant reduction in large rhythmic depolarizations (LRDs) and the amplitudes of excitatory postsynaptic potentials (EPSPs) in off-site recorded FS interneurons indicated an impaired synaptic efficacy. The dendritic spine densities in apical oblique and apical tuft dendrites of off-site recorded pyramidal cells were also reduced. These findings emphasize the need for optimized transport conditions to preserve synaptic integrity, network properties, and neuronal morphology. Standardized protocols are crucial for ensuring reliable and reproducible results in studies of human cortical microcircuits. Significance StatementThis study demonstrates that transporting live human brain tissue for neuronal recordings significantly impacts the intrinsic, synaptic, and network properties of cortical neurons. By comparing on-site and off-site recordings, we found that even a brief transportation (30-40 minutes) induces increased neuronal excitability, reduced synaptic efficacy, and diminished network events such as LRDs. These alterations are likely due to the mechanical stress and washout of critical neuromodulators, which compromise tissue integrity and neuronal function. The findings underscore the necessity for optimizing transport protocols to preserve synaptic and network integrity, ensuring reliable and reproducible results in human brain research. Ultimately, this work advances our understanding of cortical microcircuitry and informs best practices for handling human brain tissue in experimental settings.

neuroscience↗

bioRxiv2024

Stoichiometry of HIV-1 Envelope Glycoprotein Protomers with Changes That Stabilize or Destabilize the Pretriggered Conformation

During human immunodeficiency virus (HIV-1) entry into host cells, binding to the receptors, CD4 and CCR5/CXCR4, triggers conformational changes in the metastable envelope glycoprotein (Env) trimer ((gp120-gp41)3). CD4 binding induces Env to make transitions from its pretriggered conformation (PTC) to more "open" conformations that are sensitive to inhibition by antibodies, CD4-mimetic compounds (CD4mcs) and exposure to cold. Changes in functional membrane Envs have been identified that either stabilize or destabilize the PTC. Here, we investigate the stoichiometric requirements for the PTC-stabilizing and -destabilizing changes in the Env protomers. To this end, we generated viruses bearing Envs with mixed protomers exhibiting different degrees of PTC stability and determined the sensitivity of the viruses to cold (0{degrees}C) and, in some cases, to a CD4mc. The number of stabilized Env protomers required to achieve stabilization of the PTC was inversely related to the degree of PTC stabilization that resulted from the introduced Env change. For strongly stabilizing Env changes, modification of a single protomer was sufficient to achieve PTC stabilization; given adequate stability, the modified protomer can apparently constrain the conformation of the other two protomers to maintain the PTC. Weakly stabilizing Env changes needed to be present in all three protomers to achieve efficient stabilization of the PTC. In many cases, the PTC was disrupted when destabilizing changes were present in only a single protomer. These complementary results suggest that conformational symmetry among the protomers of the functional Env trimer is conducive to the integrity of the PTC. IMPORTANCEThe human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer consists of three protomers. In response to receptor binding, the flexible Env changes its conformation to mediate virus entry into host cells. The shape-shifting ability of Env also contributes to HIV-1s capacity to evade the host immune system. The pretriggered (State-1) conformation (PTC) of Env is an important target for virus entry inhibitors and host antibodies, but is unstable and therefore incompletely characterized. Changes in Env amino acids that either stabilize or destabilize the PTC have been identified. Here, we define how many Env protomers need to be modified by these changes to achieve stabilization or destabilization of the PTC. These results can guide the placement of changes in the HIV-1 Env protomers to control the movement of the Env trimer from the PTC, allowing better characterization of this elusive conformation and testing of its utility in vaccines.

microbiology↗

bioRxiv2024

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis

Tumour progression is driven by dynamic interactions between cancer cells and their surrounding microenvironment. Investigating the spatiotemporal evolution of tumours can provide crucial insights into how intrinsic changes within cancer cells and extrinsic alterations in the microenvironment cooperate to drive different stages of tumour progression. Here, we integrate high-resolution spatial transcriptomics and evolving lineage tracing technologies to elucidate how tumour expansion, plasticity, and metastasis co-evolve with microenvironmental remodelling in a Kras;p53-driven mouse model of lung adenocarcinoma. We find that rapid subclonal expansion contributes to a hypoxic, immunosuppressive, and fibrotic microenvironment that is associated with the emergence of pro-metastatic cancer cell states. Furthermore, metastases arise from spatially-confined subclones of primary tumours and remodel the distant metastatic niche into a fibrotic, collagen-rich microenvironment. Together, we present a comprehensive dataset integrating spatial assays and lineage tracing to elucidate how sequential changes in cancer cell state and microenvironmental structures cooperate to promote tumour progression.

cancer biology↗