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Biology subjects

Wu, P.

Publications and source records attributed to Wu, P..

At least 37 records · Page 2Linked to original sources

Disorganization impairs cognitive maps built from visual inputs

Background and HypothesisCognitive disorganization is a core disturbance across the psychosis spectrum, characterized by difficulties integrating perceptual information into coherent representations. How such disturbances affect the construction of internal cognitive maps remains unclear. A key question is whether these maps emerge from visual input as readily as from language structure. We hypothesized that cognitive disorganization would impair cognitive maps derived from visual input while sparing performance when structure was provided linguistically. Study DesignParticipants with varying schizotypy learned food items associated with two attributes: who consumed the food (age group) and when it was consumed (time of day). These attributes were presented as images or language descriptions and organized in a two-dimensional (2D) conceptual space. Participants then completed similarity judgment and reward-learning tasks requiring inference of the underlying relational structure. Study ResultsAmong individuals with higher cognitive disorganization, 2D distances were less predictive of similarity judgments, but only when relational structure had to be inferred from visual input. In the reward-learning task, computational modeling indicated that decisions were guided by spatial representations (Gaussian process). Higher cognitive disorganization was associated with weakened spatial generalization when structure had to be inferred from visual input, but not when it was provided through language. ConclusionsCognitive disorganization disrupts the ability to build and use cognitive maps from visual input, while performance appeared preserved when structure was conveyed through language. These findings support the shallow cognitive map hypothesis and suggest that cognitive disorganization selectively disrupts the transformation of perceptual input into stable relational representations.

neuroscience↗

The Immunogenicity Database Collaborative (IDC): A Standardized, Publicly Available Database for Clinical Immunogenicity Observations and Insights

The incidence and impact of anti-drug antibodies (ADAs) against biotherapeutics remain difficult to predict, limiting efforts to mitigate immunogenicity risk prior to clinical trials. Existing data are fragmented across disparate sources with inconsistent definitions, representing a key barrier to progress in the field. Here, we present the Immunogenicity Database Collaborative (IDC) and its release of the Immunogenicity Database (DB) V1: a structured clinical immunogenicity dataset integrating therapeutic characteristics, sequence, and patient cohort-level data from publicly available sources. The dataset includes 4,146 ADA datapoints, 1,788 cohorts, 727 clinical trials and 218 therapeutics. We highlight trends in ADA incidence, evaluate sources of variability, and identify driving factors of immunogenicity risk. This work provides a foundational resource to standardize and support immunogenicity risk assessment across the industry. It also provides an initial data architecture and invites the research community to contribute towards future expansions of the database into key areas of interest to the field.

pharmacology and toxicology↗

Non-apoptotic death of the C. elegans linker cell is primed by MYRF-1 activation of pqn-41/polyQ

Linker cell-type death (LCD) is a morphologically conserved non-apoptotic cell-death process with features resembling polyglutamine-dependent neurodegeneration. In C. elegans development, LCD eliminates the male-specific linker cell following its long-range migration. Using single-cell mRNA sequencing of migrating and dying linker cells, we identify myrf-1, encoding a membrane-bound transcription factor implicated in human developmental disorders, as a key LCD regulator. MYRF-1 translocates to the linker cell nucleus during early migration and, surprisingly, its auxin-inducible degradation then, but not later, blocks LCD. MYRF-1 directly binds known LCD genes, including pqn-41, encoding an aggregation-prone polyglutamine protein. Deleting a bona fide MYRF-1-binding site within pqn-41 promotes linker cell survival. Our findings reveal that linker cell death is primed well before cell demise takes place, temporally uncoupling death commitment and execution.

cell biology↗

Tissue-specific regulation of PNPLA3 promotes lipid remodeling in response to dietary and temperature stress

Background & AimsPNPLA3(I148M) is the strongest genetic risk factor for steatotic liver disease (SLD), but its functional role and tissue-specific regulation remain unclear. In mice, PNPLA3 is abundant in liver, yet undetectable in adipose depots. Here, we characterize the molecular mechanisms underlying these tissue-specific differences in PNPLA3 expression in mice to clarify its functional role and link to SLD risk. MethodsPnpla3 mRNA and PNPLA3 protein levels were quantified in liver and adipose depots of fasted and refed mice at 30{degrees}C and 6{degrees}C. Signaling pathways regulating PNPLA3 expression in adipocytes were examined using adrenergic agonists and pathway-specific modulators. Translation and proteasomal inhibitors were used during adrenergic stimulation to investigate the discordance between Pnpla3 mRNA and protein levels. Relationship between PNPLA3 levels and triglyceride (TG) fatty acid composition was also assessed. ResultsAt thermoneutrality, feeding strongly increased PNPLA3 levels in liver but it remained undetectable in adipose tissue of mice. Conversely, cold exposure or {beta}3-adrenergic stimulation had no effect on hepatic PNPLA3, but increased PNPLA3 >19-fold in brown adipose tissue (BAT), despite causing a >75% reduction in Pnpla3 mRNA, indicating robust post-translational regulation. In BAT, adrenergic signaling via cAMP/PKA and PI3K/AKT elevated PNPLA3 by reducing proteasomal degradation. PNPLA3 expression correlated with depletion of TG-long-chain polyunsaturated fatty acids (TG-LCPUFAs) in both liver and BAT, consistent with a role in lipid remodeling. ConclusionsThese findings reveal striking tissue- and context-specific regulation of PNPLA3, but a conserved association between its expression and TG-LCPUFAs levels, suggesting that PNPLA3 modulates lipid remodeling in response to metabolic stress and that disrupting this function may contribute to SLD susceptibility. Impact and implicationsDespite being the strongest genetic risk factor for SLD, PNPLA3s physiological role remains unclear. Using mouse models, this study reveals that PNPLA3 is regulated in a tissue-specific manner in response to feeding and cold exposure, thereby promoting remodeling of cellular lipids to adapt to dietary and environmental challenges. The localization of PNPLA3 action and its tissue-specific regulation are directly relevant to hepatologists and metabolic researchers aiming to understand its influence on intracellular lipid composition and its effects on disease susceptibility. Moreover, modulation of PNPLA3 turnover--and its impact on LCPUFAs remodeling--emerges as a potential therapeutic strategy for regulating lipid homeostasis in SLD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/684800v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ee6ac7org.highwire.dtl.DTLVardef@a45d74org.highwire.dtl.DTLVardef@f39929org.highwire.dtl.DTLVardef@cc826b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPNPLA3 is regulated in a highly tissue-specific manner in mice. C_LIO_LIIn liver, feeding-but not cold exposure-induces PNPLA3 primarily through transcriptional mechanisms. C_LIO_LIIn adipose tissue, cold exposure-but not feeding-induces PNPLA3 through post-transcriptional mechanisms. C_LIO_LIIn adipose tissue, cold exposure increases PNPLA3 despite a reduction in Pnpla3 mRNA. C_LIO_LIPNPLA3 remodels lipids in liver and adipose tissue to maintain lipid homeostasis, a process disrupted in SLD. C_LI

physiology↗

Rapid adipose tissue expansion triggers proliferation of memory adipose tissue T cells and accumulation of novel T helper 2 (Th2) regulatory cells

Obesity generates a pro-inflammatory state contributing to immune dysregulation and metabolic disease. In response to overnutrition, adipose tissue immune cells undergo dynamic changes featuring a shift from a type 2 anti-inflammatory phenotype in lean adipose tissue to a pro-inflammatory phenotype in obese adipose tissue, contributing to obesity associated adipose tissue inflammation featuring an accumulation of macrophages and T cells. Adipose tissue T cells (ATTs) from mice and humans with obesity have an exhausted phenotype, suggesting chronic activation. However, the mechanism(s) that regulate the balance between anti-inflammatory and pro-inflammatory ATT phenotypes with obesity are not understood. We sought to investigate how and if ATT cells respond to early obesity. We characterized the temporal and phenotypic changes in ATTs in response to initial adipose tissue remodeling, using short-term high fat diet (stHFD) as a model. We observed the accumulation of ATTs in the visceral adipose tissue (VAT) due to the induction of proliferation in memory, and not naive, ATTs with 7 days of HFD. Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) demonstrated a decrease in Tregs and {gamma}{delta} T cells with an increase in a novel Th2 cell population with immune regulatory capacities featuring expression of the immunoregulatory cytokine Tgfb1, and an activated gene expression profile featuring an increase in Nr4a1 and Itk, in VAT with 14 days of HFD. This study represents the first description of a Th2 regulatory cell population in adipose tissue, and its increase with short-term HFD suggests underexplored mechanisms of ATT subpopulation activation and regulation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/683711v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1e48080org.highwire.dtl.DTLVardef@b067f6org.highwire.dtl.DTLVardef@1794cf5org.highwire.dtl.DTLVardef@ab8b6e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Novel Tissue Mechanics-Guided Cellular Flows Enable the Evolution of Feather Follicles

Complex tissue architecture is achieved through multiple rounds of morphological transitions. Here, we analyzed cellular flows and tissue mechanics during avian skin development. We showed how novel cellular flows initiate chemo-mechanical circuits that guide epithelial protrusion, folding, invagination, and spatial cell fate specification. In the initial feather bud formation, stiff dermal condensates protrude vertically out of the locally softened epithelial sheet. As the bud elongates, it stretches the epithelial cells at the base, which mechanically activates YAP and causes the epithelial sheet to fold downward and form a stiff cylindrical wall that invaginates into the skin. This stiff epithelial tongue is essential to the compaction and formation of the tightly packed dermal papillae. These topological transformational events are mechanically interconnected, and the completion of the previous circuit initializes the next one. On the contrary, during scale development, its rigid epithelial sheet restricts dermal cell flows, preventing other further topological transformation. We generated a topological transformation model to show how the process enables the novel evolution of feather follicles.

developmental biology↗

Roles of K-channel activity in feather bud morphogenesis

Bioelectricity plays a key role in shaping tissues during early development. In developing chick skin, we previously demonstrated that a transient standing electrical current loop forms within individual feather buds as they start to elongate. Current flows into the feather bud tip via calcium channels, facilitating collective distal dermal cell movement, thus determining bud orientations. Here, we further evaluate the hypothesis that potassium channels carry the current that flows out of the bud base. We found potassium channel blockers convert periodic feather primordia into horizontal stripes and alter bud aspect ratios by disrupting the bud elongation process. Bioelectric characterization showed the entire current loop is altered, not only the outward current at the base, but also the inward current at the feather bud tip. In situ hybridization shows beta-catenin and Sonic Hedgehog, both feather bud markers, are reduced, resulting in altered periodic patterning and bud shaping. These findings show that a complex multiscale interdependency of ion channel function across a multicellular cell collective is essential for periodic feather patterning and shaping of 3-dimensional feather architecture during skin morphogenesis. Summary StatementCalcium channels at the feather bud tip and potassium channels at the base maintain a standing current loop, creating an essential multicell collective for proper feather bud patterning and morphology.

developmental biology↗

Strategies to improve the efficiency of homing gene drives with multiplexed gRNAs

CRISPR homing gene drive holds great potential for pest control, but its success is challenged by the generation of resistance alleles. To mitigate the impact of resistance, multiplexed gRNA strategies have been demonstrated. However, unless both outmost sites are cleaved simultaneously, poor homology during DNA repair may compromise efficiency, leading to decline in drive conversion efficiency when the number of gRNAs is higher than two. Here, to better estimate the rate of drive efficiency decline, we designed and assessed the efficiency of single gRNA drives with imperfect homologous arms, refining a detailed gRNA multiplexing model. To mitigate the greater than expected efficiency loss, we further evaluated two new strategies: (1) extended homology arms to span all target sites with mutations in the PAMs and (2) a population-level multiplexing gRNAs system involving two or more drives, each carrying two gRNAs. Specifically, the population-level multiplexing system has four adjacent gRNA target sites, and the drives have small mutations in their homologous arms to prevent cleavage by the other drive. Mutations in both strategies did not impair efficiency, but they were not consistently inherited, and undesired cutting in the homologous arms decreased drive efficiency. We simulated homing suppression drive using a dual 2-gRNA population-level gRNA multiple xing strategy based on our experimental evaluation. Despite being somewhat more vulnerable to functional resistance than a standard 4-gRNA drive, the higher individual drive efficiency of the population-level multiplexing system increased successful population elimination outcomes. Thus, population-level multiplexing can be a useful for improving suppression drive power.

genetics↗

Phosphorylation of the α subunit inhibits proteasome assembly and regulates cell division in archaea

Archaea of the order Sulfolobales possess a eukaryotic-like cell division machinery and display a eukaryotic-like cell cycle, however, the cell division and cell cycle control mechanisms remain enigmatic. Here, we demonstrate that phosphorylation of the subunit by a eukaryotic-like protein kinase ePK2 affects 26S proteasome assembly and controls cell division in Saccharolobus islandicus. ePK2 exhibits cell cycle-dependent expression at both transcriptional and translational levels. Deletion or overexpression of ePK2 results in impaired cytokinesis, with the deletion cells being unable to generate single chromosome cells after synchronization and the overexpression cells exhibiting growth retardation and cell enlargement. Interestingly, overexpression of ePK2 leads to a coherent reduction in cellular proteasome activity and degradation of cell division proteins. We identify S200 and T213 of the proteasome subunit as specific target sites for ePK2 phosphorylation. Functional and structural analyses of site-directed mutants at S200 and T213 suggest that S200 phosphorylation disrupts the assembly of 20S into 26S proteasome whereas T213 phosphorylation interferes the de novo ring assembly. Collectively, our study uncovers an ingenious and efficient mechanism of proteasome phosphorylation-mediated cell division regulation, a prototype of the eukaryotic cell cycle regulation system, in Sulfolobales archaea.

microbiology↗

A synthetic biology toolkit for interrogating plasmid-dependent methylotrophy and enhancing methanol-based biosynthesis of Bacillus methanolicus

Bacillus methanolicus represents a thermophilic methylotroph whose methanol utilization depends on plasmid-encoded genes. It serves as a unique model for deciphering plasmid-dependent methylotrophy and an ideal chassis for low-carbon biomanufacturing using CO2-derived C1 substrates. Despite its evolutionary uniqueness and industrial potential, the lack of synthetic biology tools has hindered both mechanistic understanding and strain engineering. Here, we present a comprehensive synthetic biology platform comprising a high-efficiency electroporation protocol, a CRISPR method enabling robust and multiplex genome editing, diverse neutral loci for gene integration and overexpression, and a cloud-based genome-scale metabolic model iBM822 for user-friendly biodesign. Leveraging this toolkit, we systematically dissected plasmid-dependent methylotrophy, host restriction-modification systems, and functional significance of the chromosomal methylotrophic genes through targeted deletion. To address plasmid loss-induced strain degeneration, we integrated the large endogenous plasmid pBM19 into the chromosome for stable and intact methylotrophic growth. Finally, by integrating metabolic modeling with CRISPR editing, we engineered L-arginine feedback regulation to achieve the first L-arginine biosynthesis from methanol. This study establishes a synthetic biology framework for B. methanolicus, promoting mechanistic exploration of methylotrophy and low-carbon biomanufacturing.

synthetic biology↗

Digital Twin Brain Predicts rTMS Effects on Brain State Dynamics in Chronic Tinnitus

Predicting repetitive transcranial magnetic stimulation (rTMS) effects on whole-brain dynamics in clinical populations is crucial for developing personalized therapies and advancing precision medicine in brain disorders. This study provides the first proof-of-concept demonstrating that the Digital Twin Brain (DTB) can forecast rTMS effects on brain state dynamics in individuals with brain disorders (chronic tinnitus). First, we identified two aberrant brain states that predominantly overlapped with the somatomotor and default mode networks, respectively. Subsequently, we developed DTB for patients and derived regional responses for each brain region, revealing distinct roles of the parieto-occipital and frontal regions. Mechanistically, we examined the biological plausibility using tinnitus-specific risk genes and investigated the multi-scale neurobiological relevance. Clinically, we found that DTB can predict rTMS effects in an independent, longitudinal dataset (all r > 0.78). Particularly, the predictive capacity exhibits a state-specific nature. Overall, this work proposes a novel DTB-based framework for predicting rTMS effects in clinical populations and provides the first empirical evidence supporting its clinical utility. This approach may be generalizable to other brain disorders and neuromodulation techniques, promoting broader advancements in brain health.

neuroscience↗

TUCL-Seq for miRNA single molecule sequencing

MicroRNAs (miRNAs) are pivotal regulatory molecules in gene expression, and their precise quantification is essential for elucidating their roles in diverse biological processes. This research paper introduces a pioneering workflow for the single molecule sequencing (SMS) of miRNA, integrating advanced miRNA sample preparation with SMS sequencing. Central to our approach is TUCL-Seq, which is an automated, on-chip miRNA library preparation method designed to streamline the sequencing process. This innovative approach incorporates the addition of sequencing adaptor to RNA samples in solution, and converts it to cDNA on a sequencing flow cell for sequencing. Coupled with single molecule sequencing instrument and base-call software, our workflow significantly reduces sample-to-result time, and decreases the need for manual interventions compared to traditional SMS and next-generation sequencing methods. We demonstrate the efficacy of TUCL-Seq by accurately quantifying synthetic miRNA samples with a 24-hour workflow, showcasing its potential for high-throughput miRNA profiling. Our findings highlight the promise of this integrated workflow for advancing miRNA research and applications in diagnostics and therapeutics.

biochemistry↗

Mapping cellular targets of covalent cancer drugs in the entire mammalian body

As our understanding of biological systems reaches single-cell and high spatial resolutions, it becomes imperative that pharmacological approaches match this precision to understand drug actions. This need is particularly urgent for the targeted covalent inhibitors that are currently re-entering the stage for cancer treatments. By leveraging the unique kinetics of click reactions, we developed volumetric clearing-assisted tissue click chemistry (vCATCH) to enable deep and homogeneous click labeling across the 3D mammalian body. With simple and passive incubation steps, vCATCH offers cellular resolution drug imaging in the entire adult mouse. We combined vCATCH with HYBRiD imaging and virtual reality to visualize and quantify in vivo targets of two clinical cancer drugs, afatinib and ibrutinib, which recapitulated their known pharmacological distribution and revealed previously unreported tissue and cell type engagement potentially linked to off-target effects. vCATCH provides a body-wide, unbiased platform to map covalent drug engagements at unprecedented scale and precision.

pharmacology and toxicology↗

A new class of OLD family ATPases functions in cell cycle progression in thermoacidophilic archaea

Overcoming lysogenization defect (OLD) proteins are diverse ATPases-nucleases functioning in antiphage defense in bacteria. However, the role of these proteins in archaea is currently unknown. Here, we describe a new class of archaeal OLD family ATPases and show that they do not appear to be involved in antiviral defense but play an essential role in cell cycle progression. The gene in Saccharolobus islandicus REY15A, named as Cran1 (Cell cycle related ATPase and nickase 1), cannot be deleted and exhibits cyclic expression patterns, with a peak expression during the transition from M-G1 to S cell cycle phase. Cran1 overexpression leads to significant growth retardation, cell size enlargement, and increased cellular DNA content. Cran1 displays potent nickase and ATPase activities in vitro, with the nickase activity being dependent on the presence of the ATPase domain. Notably, Cran1 copurifies with chromatin-associated proteins, such as Cren7 and a histone deacetylase homolog, suggesting its involvement in chromatin-related activities. Collectively our results suggest that Cran1 plays an important role in cell cycle progression, revealing a novel function of OLD family proteins.

microbiology↗

ZBP1 Senses Splicing Aberration through Z-RNA to promote Cell Death

RNA splicing, a highly regulated process performed by the spliceosome, is crucial for eukaryotic gene expression and cellular function. Numerous cellular stresses including oncogenic insults dysregulate RNA splicing, often provoking inflammatory responses and cell death. However, the molecular signal produced by spliceosome aberration and how cell sensed and respond to it remain elusive. Here we show that spliceosome inhibition induces the widespread formation of unique, left-handed nucleic acids, Z-form nucleic acids (Z-NAs) from the nucleus. These Z-NAs were double-stranded RNA (dsRNA), rather than DNA-RNA hybrids, that were predominantly derived from transcripts of mis-spliced intronic RNA. Spliceosome inhibition induced the egress of these Z-RNA from the nucleus to the cytoplasm in an active manner. Sensing of the accumulation of Z-RNA in the cytosol by the host sensor ZBP1 triggered cell death, mainly for RIPK3-MLKL dependent necroptosis. Collectively, these findings delineate a previously uncharacterized mechanism in which Z-NA sensing by ZBP1 responds to global aberrations of RNA splicing to trigger inflammatory cell death.

cell biology↗

Formaldehyde induces and promotes Alzheimer's disease pathologies in a 3D human neural cell culture system

Alzheimers disease (AD) arises from complex multilevel interactions between genetic, epigenetic, and environmental factors. Recent studies suggest that exposure to the environmental and occupational toxicant formaldehyde (FA) may play a significant role in AD development. However, the effects of FA exposure on A{beta} and tau pathologies in human neural cell 3D culture systems remain unexplored. To investigate FAs role in AD initiation, we differentiated 3D-cultured immortalized human neural progenitor ReN cells (ReNcell VM) into neurons and glial cells, followed by FA treatment. FA exposure for 12 weeks resulted in a dose-dependent increase in A{beta}40, A{beta}42, and phosphorylated tau levels. To further examine FAs role in AD progression, we established a 3D human neural cell culture AD model by transfecting ReN cells with AD-related mutant genes, including mutant APP and PSEN1, which recapitulate key AD pathological events. Our findings demonstrate that FA exposure significantly elevated A{beta}40, A{beta}42, and phosphorylated tau levels in this 3D-cultured AD model. These results suggest that FA exposure contributes to the initiation and progression of AD pathology in 3D-cultured human neural cells.

neuroscience↗

Multi-lineage transcriptional and cell communication signatures define pathways in individuals at-risk for developing rheumatoid arthritis that initiate and perpetuate disease

Rheumatoid arthritis (RA) is a systemic autoimmune disease arising from loss of tolerance and autoantibody development in at-risk individuals. Targeted therapies yield variable responses and current preventive strategies delay but do not stop disease onset. We propose that a set of transcription factors (TFs) and their downstream pathways regulate inflammatory cell communication networks in at-risk populations and RA. These networks enable multiple pathogenic cell types and mediators and could account for variable responses to targeted agents. To test this hypothesis, we identified anti-citrullinated protein antibody (ACPA)-positive at-risk individuals, patients with early and established RA and healthy controls. Single cell chromatin accessibility and transcriptomic profiles from blood mononuclear r cells were integrated and identified share pathogenic mechanisms, especially SUMOylation, RUNX2, YAP1, NOTCH3, and {beta}-Catenin Pathways. Surprisingly, this signature was found in multiple cell types. Individualized gene expression patterns were then confirmed in RA synovium. Cell communication analysis revealed that multiple lineages can deliver a core set of pro-inflammatory mediators to receiver cells. Longitudinal analysis showed that the signature cell types evolve in individual at-risk participants. Cell-type-specific signature pathways could contribute to the differing clinical responses to targeted therapies. This study describes how a common clinical phenotype could arise from multiple pathogenic mechanisms.

systems biology↗

Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions

We introduce Hydrogen-Exchange Experimental Structure Prediction (HX-ESP), a method that integrates hydrogen exchange (HX) data with molecular dynamics (MD) simulations to accurately predict ligand binding modes, even for targets requiring significant conformational changes. Benchmarking HX-ESP by fitting two ligands to PAK1 and four ligands to MAP4K1 (HPK1), and comparing the results to X-ray crystallography structures, demonstrated that HX-ESP successfully identified binding modes across a range of affinities significantly outperforming flexible docking for ligands necessitating large conformational adjustments. By objectively guiding simulations with experimental HX data, HX-ESP overcomes the long timescales required for binding predictions using traditional MD. This advancement promises to enhance the accuracy of computational modeling in drug discovery, potentially accelerating the development of effective therapeutics.

biophysics↗