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Gu, P.

Publications and source records attributed to Gu, P..

11 recordsLinked to original sources

HSF1 controls transcriptional programs that establish thalamostriatal shaft synaptic architecture and preserve cognitive flexibility

Cognitive flexibility (CF) declines during aging and is further impaired in neurodegenerative diseases such as Huntingtons disease (HD), yet the molecular mechanisms underlying these deficits remain poorly understood. Thalamostriatal (T-S) synapses are critical for CF, and we previously identified Heat Shock Factor 1 (HSF1) as a regulator of T-S density in HD. However, how HSF1 regulates T-S synapses and whether it modulates cognitive flexibility (CF) remained unclear. Here, we combined HSF1 ChIP-seq, transcriptomics, synapto-proteomics, targeted genetic manipulations and behavioral analyses to study how HSF1 regulates T-S synapses and CF. We found HSF1 directly controls a transcriptional program governing postsynaptic architecture and actin cytoskeletal dynamics, which are disrupted in aging and HD. Loss of HSF1 drives selective destabilization of actin patches at T-S shaft synapses and impaired CF decline. Our results underscore a novel function for HSF1 in the regulation of striatal neural circuits with essential implications in the neurobiology of cognitive flexibility.

neuroscience↗

Targeting DNMT1 augments anti-tumor CD8⁺ T cell function

Chronic stimulation of CD8 T cells within the tumor microenvironment (TME) induces a hypofunctional state characterized by diminished cytotoxicity and functionally impaired anti-tumor function, known as exhaustion. Exhaustion is associated with epigenetic changes that remain relatively stable despite interventions like immune checkpoint inhibition (ICI). Although epigenetic changes are potentially reversible, reports of therapeutic strategies to effectively restore function in exhausted CD8 T cells remain limited. Here, we report DNA methyltransferase 1 (DNMT1) inhibition (DNMT1i) in counteracting CD8+ T cell dysfunction during the anti-tumor response. We show that DNMT1i synergizes with ICI to rescue the tumor cell killing activity of chronically stimulated CD8 T cells in a melanoma model. DNMT1i mitigates transcriptional features of exhaustion while inducing a divergent effector program. DNMT1i attenuates the global increase in chromatin accessibility associated with exhaustion and enables epigenetic remodeling of the exhausted chromatin landscape upon restimulation. Finally, DNMT1i enhances the effector function of melanoma patient-derived tumor infiltrating lymphocytes after prolonged ex vivo expansion. These studies establish DNMT1 targeting as a promising strategy to counteract CD8 T cell exhaustion and potentiate ICI efficacy.

immunology↗

Genetically Encoded Melanin as a Photostable Scattering Contrast for Whole-Brain Tomography

Large-scale brain imaging has traditionally depended on fluorescent reporters, but challenges like photobleaching and inconsistent signals hinder quantitative analysis in intact tissues. In response, we present MelaCAST (melanin-based scattering CAST imaging), a novel genetically encoded scattering method for whole-brain visualization. Using AAV to deliver tyrosinase allows for cell-type-specific melanin synthesis, providing a stable intracellular scattering contrast across the mouse brain. Combining tissue clearing with scattering tomography, MelaCAST offers non-photobleaching, high-throughput volumetric imaging of genetically targeted cell populations in intact brains. This technique establishes melanin as a genetically encoded scattering reporter and broadens whole-organ imaging capabilities beyond traditional fluorescence methods.

neuroscience↗

High-throughput whole-brain scattering imaging resolves Amyloid plaques through clearing-assisted contrast modulation

Label-free scattering imaging is widely used in pathology because it enables sensitive tissue assessment without exogenous contrast agents. Yet its limited optical penetration has prevented scattering-based methods from being applied to whole-organ pathology mapping. Here we present clearing-assisted scattering tomography (CAST), a high-throughput, label-free whole-brain mesoscope enabled by selective lipid clearance for scattering enhancement (SELiC). SELiC modulates endogenous refractive-index heterogeneity in cleared tissue, providing whole-brain optical penetration while retaining strong scattering contrast from amyloid plaques and white-matter fibre bundles. CAST enables volumetric imaging of intact mouse brains and brain-wide mapping of amyloid plaque pathology across anatomical regions. This platform establishes a scalable route for label-free, system-level analysis of amyloid pathology and tissue architecture in Alzheimers disease (AD) models.

bioengineering↗

Disrupted priming within draining lymph nodes drives immune quiescence in gastric cancer

The gastric mucosa is characterized by continuous innate immune surveillance and inflammatory signaling, yet a high proportion of gastric carcinomas (GCs) are recalcitrant to immune-directed therapies. The mechanisms by which GCs evade adaptive immune surveillance within the highly antigenic microenvironment of the gastric mucosa remains unknown. To address this, we collected patient-matched tumor tissue, distant normal tissue, metastasis, and draining lymph nodes to generate a large-scale single-cell immune profiling dataset from 64 patients (n=179 samples, >150,000 cells). From single cell analysis, we identified two distinct sources of impaired tumor surveillance within tumor draining lymph nodes. First, we observed that a significant fraction of tumor draining lymph nodes had undergone cytokine-driven reprogramming, leading to reduced dendritic cell homing and limited T cell priming. Second, T cells undergoing successful activation exhibited limited expansion and constrained differentiation, marked by expression of the quiescence-associated transcription factor Kruppel-like Factor 2 (KLF2). Overexpression of KLF2 in primary T cells limited both their differentiation and cytotoxic capacity. These findings implicate both impaired T cell priming and KLF2-dependent T cell quiescence in limiting T cell immunity in gastric adenocarcinoma. We suggest these findings represent an emerging model for immune silencing in tumors developing from tissues with chronic inflammation.

immunology↗

B7-H3 as a Dual Clinically Relevant Checkpoint and Antibody Drug Conjugate Target Expressed Across Adenocarcinoma and Neuroendocrine Prostate Cancers

Background and ObjectivesCD276 (B7-H3) has recently emerged as a promising presumptive immune checkpoint inhibitor (ICI) and a potential antibody-drug conjugate (ADC) target for prostate cancer (PCa). We evaluated B7-H3 and 15 other clinically relevant ADC and ICI targets for expression at the RNA and protein level across the PCa continuum--hormone-sensitive, castration-resistant, and neuroendocrine. MethodsCCLE data analysis and western blot experiments were performed for quantifying RNA and protein expression variability across PCa cell lines. Inter- and intratumoral heterogeneity was evaluated by integrating single-cell RNA sequencing data across 595k cells and 102 patients, spanning the disease continuum. AR and B7-H3 knockouts of PCa cell lines were developed and investigated using R1881 and Enzalutamide to elucidate the AR-CD276 signaling pathway through qRT-PCR and flow cytometry. Key FindingsB7-H3 showed high expression in tumor and myeloid cells (tumor microenvironment - TME), lowest heterogeneity across all ADC and ICI targets, and was negatively regulated by androgen signaling. LimitationsFurther validation of ADC and ICI target protein expression in human samples and more exhaustive exploration of the AR-CD276 signaling cascade is required. ConclusionB7-H3 demonstrates the least susceptibility to selective pressure due to its stable expression across PCa disease states. Clinical ImplicationsB7-H3 represents an important ADC target for PCa due to its potential to minimize drug resistance and likely ability to be a valid target across the prostate cancer continuum. Additionally, its expression in myeloid cells supports a dual role as an ICI, further enhancing its therapeutic relevance. Graphical AbstractDiscovery of optimal checkpoints and antibody drug conjugates (ADCs) in Prostate Cancer (PCa). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/632253v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1af1115org.highwire.dtl.DTLVardef@8a9d70org.highwire.dtl.DTLVardef@6659aeorg.highwire.dtl.DTLVardef@189e200_HPS_FORMAT_FIGEXP M_FIG C_FIG Patient SummaryIn this study, we demonstrate that prostate cancer expresses high amounts of a cell surface protein called B7-H3 both when first diagnosed and throughout various stages of metastatic disease. Furthermore, we demonstrate a clear and yet to be fully resolved cross-talk between B7-H3 and the androgen signaling pathway central to prostate cancer development. We conclude that B7-H3 is therefore a highly promising therapeutic cell surface protein expressed by prostate cancer due to its stable expression potentially leading to low selective pressure and reduced drug resistance--thereby having significant implications for clinical trial design and patient inclusion considerations. Advancing PracticePCa is a highly heterogeneous disease with an increasingly wide treatment landscape, governed by various factors including clinical covariates, histopathological features, and molecular factors. B7-H3 has recently emerged as a promising clinical target for immunotherapy in the localized setting and antibody drug targeting in the metastatic setting. Despite the clinical significance, B7-H3 expression has not yet been thoroughly evaluated against other clinically relevant immune checkpoint and antibody drug targets, especially along the continuum of PCa treatment stages--hormone sensitive, castration resistant, and neuroendocrine. To our knowledge, this is the first study to characterize B7-H3 in this continuum using representative cell lines and the largest collection of PCa patient single cell sequencing data yet assembled in the literature, thus accounting for the substantial heterogeneity across PCa disease states as well as between datasets. Take Home MessageThis article explores the therapeutic relevance of clinical stage ADC targets and immune checkpoints for Prostate Cancer (PCa). We show that B7-H3 is a highly promising therapeutic candidate for PCa due to its stable expression across various disease states.

cancer biology↗

Instantaneous Frequency: A New Functional Biomarker for Dynamic Brain Causal Networks

This study introduces instantaneous frequency (IF) analysis as a novel method for characterizing dynamic brain causal networks from fMRI blood-oxygen-level-dependent (BOLD) signals. Effective connectivity, estimated using dynamic causal modeling (DCM), is analyzed to derive IF sequences, with the average IF across brain regions serving as a potential biomarker for global network oscillatory behavior. Analysis of data from the Alzheimers Disease Neuroimaging Initiative (ADNI), Open Access Series of Imaging Studies (OASIS), and Human Connectome Project (HCP) demonstrates the methods efficacy in distinguishing between clinical and demographic groups, such as cognitive decline stages, sex differences, and sleep quality levels. Statistical analyses reveal significant group differences in IF metrics, highlighting its potential as a sensitive indicator for early diagnosis and monitoring of neurodegenerative and cognitive conditions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/628965v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@10da58org.highwire.dtl.DTLVardef@6eee6borg.highwire.dtl.DTLVardef@e6e756org.highwire.dtl.DTLVardef@15dff2a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe study introduces instantaneous frequency (IF) as a novel biomarker derived from dynamic brain effective connectivity, capturing temporal fluctuations in brain networks. C_LIO_LIThe proposed IF biomarker effectively differentiates between various clinical stages, such as Mild Cognitive Impairment (MCI) and Alzheimers Disease (AD), and demographic factors, including sex and sleep quality. C_LIO_LIThe robustness and clinical relevance of the IF biomarker are validated using three independent datasets: ADNI, OASIS, and HCP, demonstrating its potential in cognitive and neurological research. C_LI

neuroscience↗

The Hidden Diversity of Vascular Patterns in Flower Heads

O_LIVascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flowers heads. C_LIO_LIWe imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism. C_LIO_LIThe vascular system in the head of the model plant Gerbera hybrida is qualitatively different from those of Bellis perennis and Helianthus annuus, characterized previously. Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, and Tanacetum vulgare represent variants of the Bellis and Helianthus systems. In each species the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values. C_LIO_LIIn spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature. C_LI

plant biology↗

Organs-on-a-Chip Database (OOCDB): A Comprehensive, Systematic and Real-time Organs-on-a-chip Database

Organs-on-a-Chip is a microfluidic microphysiological system that uses microfluidic technology to make high-resolution and real-time imaging analysis on the structure and function of living human cells at the level of tissue and organ in vitro. Compared with the traditional two-dimensional cell culture model and animal model, organs-on-a-chip technology can simulate the pathological and toxicological interactions between different organs or tissues more closely and reflect the collaborative response of multiple organs to drugs. Although lots of organs-on-a-chip-related literature have been published, none of current databases have achieved all the following functionalities yet: searching, downloading and analyzing data and results from literature of organs-on-a-chip. To address this need, we established a database named organs-on-a-chip database (OOCDB), as a platform to integrate information related to organs-on-a-chip from various sources: literature, patents, microarray and transcriptome sequencing raw data, many open access data of organs-on-a-chip and organoids, as well as the data generated in our lab. OOCDB comprises dozens of sub databases and analysis tools and each sub database contains a number of data related to organs-on-a-chip, aiming to provide a comprehensive, systematic and convenient search engine for researchers. In addition, it provides functions such as mathematical modeling, three-dimensional model and citation map to meet the needs of researchers and to promote the development of organs-on-a-chip. The organs-on-a-chip database can be visited at http://www.organchip.cn.

bioinformatics↗

TrpA1 is a shear stress mechanosensing channel regulating intestinal homeostasis in Drosophila

Adult stem cells are essential for maintaining normal tissue homeostasis and supporting tissue repair. Although genetic and biochemical programs controlling adult stem cell behavior have been extensively investigated, how mechanosensing regulates stem cells and tissue homeostasis is not well understood. Here, we show that shear stress can activate enteroendocrine cells, but not other gut epithelial cell types, to regulate intestine stem cell-mediated gut homeostasis. This shear stress sensing is mediated by transient receptor potential A1 (TrpA1), a Ca2+-permeable ion channel that expressed only in enteroendocrine cells among all gut epithelial cells. Genetic depletion of TrpA1 or modification of its shear stress sensing function causes reduced intestine stem cell proliferation and intestine growth. We further show that among the TrpA1 splice variants, only select isoforms are activated by shear stress. Altogether, our results suggest the naturally occurring mechanical force such as fluid passing generated shear stress regulates intestinal stem cell-mediated tissue growth by activating enteroendocrine cells, and Drosophila TrpA1 as a new shear stress sensor.

developmental biology↗

Continuous Theta Burst Stimulation to the Secondary Visual Cortex Does Not Impair Central Vision in Humans

Continuous theta burst stimulation (cTBS) is a powerful form of repetitive transcranial magnetic stimulation capable of suppressing cortical excitability for up to 50 min. A growing number of studies have applied cTBS to the visual cortex in human subjects to investigate the neural dynamics of visual processing, but few have specifically examined its effects on central vision, which has crucial implications for safety and inference on downstream cognitive effects. The present study assessed the safety of offline, neuronavigated cTBS to V2 by examining its effects on central vision performance. In this single-blind, randomized sham-controlled, crossover study, 17 healthy adults received cTBS (at 80% active motor threshold) and sham to V2 1-2 weeks apart. Their central vision ([≤]8{degrees}) was tested at 1-min (T1) and again at 50-min (T50) post-stimulation. Effects of condition (cTBS vs. sham) and time (T1 vs. T50) on accuracy and reaction time were examined using Bayes factor. Bayes factor results suggested that cTBS did not impair stimulus detection over the entire central visual field nor subfields at T1 or T50. Our results offer the first explicit evidence supporting that cTBS applied to V2 does not create blind spots in the central visual field in humans during a simple detection task. Any subtler changes to vision and downstream visual perception should be investigated in future studies.

neuroscience↗