Biology subjects

Wu, L.

Publications and source records attributed to Wu, L..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Effect Of Perinatal Perfluorinated Compounds (PFASs) Exposure On Behavior Of SD Rats

Perfluorinated compounds (PFASs) are persistent environmental pollutants recognized for their bioaccumulation and potential neurotoxic effects, particularly in relation to attention deficit hyperactivity disorder (ADHD). This study investigated the effects of perinatal PFAS exposure on Sprague-Dawley (SD) rats, with a focus on behavioral outcomes and dopamine metabolism in the prefrontal cortex (PFC). Pregnant rats were administered PFASs at concentrations of 1 mg/L, 3 mg/L, and 10 mg/L through drinking water during gestation and lactation, with a control group included for comparison. The offspring were subjected to behavioral assessments, including open field, marble burying, and jump tests, to evaluate locomotor activity, attention, and impulsivity. Neurochemical analyses were conducted to measure the expression of tyrosine hydroxylase (TH), aromatic L-amino acid decarboxylase (DDC), and dopamine receptor D1 (Drd1) in the PFC using Western blotting and quantitative PCR (qPCR). The results indicated that high-dose PFAS exposure (10 mg/L) resulted in hyperactivity, attention deficits, and impulsive behavior (p < 0.05), along with decreased TH and DDC expression and altered Drd1 levels, suggesting disrupted dopamine metabolism. These findings imply that perinatal PFAS exposure leads to behavioral abnormalities and disruptions in dopamine-related processes.

animal behavior and cognition↗

bioRxiv2025

CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Design

Protein de novo design is a longstanding challenge in biological field due to the multifaceted physicochemical properties and complexities of proteins. Several deep learning models have emerged for protein de novo design. However, each model exhibits distinct strengths and limitations because of the differences in training strategies or neural network architectures. Therefore, improving the effectiveness of protein design, particularly for functional protein, requires further improvement. To tackle this challenge, we developed CHIEF (Chimera Ensemble Inverse Folding), an attention-based ensemble framework that integrates five pretrained base models (ProteinMPNN-vanilla, ProteinMPNN-soluble, ESM-IF, Frame2seq and PiFold) to leverage their complementary strengths and mitigate limitations. Compared with the base models, CHIEF significantly improved the sequence recovery rate by 16.6-28.0%, while reducing the prediction perplexity by 22.7-34.6%. CHIEF also exhibited superior protein-designing capacity in variable sequence- and structure-based metrics and in large and complex proteins. CHIEF dynamically captured the semantic information from base models in a context-dependent manner and was minimally affected by the ablation of each base model. More importantly, CHIEF demonstrates real-world applicability to design functional malate dehydrogenase (MDH), achieving a 100% success rate. In summary, our study develops an ensemble deep learning model that improves the efficacy of protein sequence design, and will be a valuable platform for protein engineering and drug development.

bioengineering↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

Viral Infection Detector: Ensemble Learning for Predicting Viral Infection in Single-cell Transcriptomics of Virus-Induced Cancers

Oncoviruses cause around 15-20% of all human cancers. As 3 end-based single-cell RNA-sequencing (scRNA-seq) methods become more popular, the relationship between viral infection and tumor progression at the transcriptomic level has been increasingly studied at single-cell resolution. However, the identification of infected cells is challenging as viral reads from infected cells may not be captured, leading to high false negative rates. To recover these infected cells that have been missed, we developed VID, a stacked ensemble machine-learning model that predicts virus-infected cells in scRNA-seq datasets. Using VID, we uncovered biologically meaningful differences between infected and uninfected cells across different oncovirus-mediated cancers and different cell types. Our VID tool provides a user-friendly way to study changes induced by viral infections in scRNA-seq datasets.

bioinformatics↗

bioRxiv2025

China Autism Brain Imaging Consortium: Charting Brain Growth in Chinese Children with Autism

Autism Spectrum Disorder (ASD) is a lifelong neurodevelopmental condition characterized by atypical brain growth. While advances in neuroimaging and openly sharing large-sample datasets such as the Autism Brain Imaging Data Exchange (ABIDE) have improved understanding of ASD, most studies focus on adolescents and adults, with early brain development-critical for diagnosis and intervention-remaining underexplored. Existing research predominantly involves Western samples, offering limited insight and generalizability into non-Caucasian populations. We introduce the China Autism Brain Imaging Consortium (CABIC) (https://php.bdnilab.com/resources/), a grassroots effort by researchers across the country to aggregate previously collected multi-site structural MRI datasets and phenotypic information from 1,451 autistic children and 1,119 typically developing children, covering an age range from early childhood to school age (1.0 - 12.92 years). Here, we present this resource and depict brain growth charts to push forward a more comprehensive understanding of the brain development in Chinese autism children. We constructed brain growth charts that reveal a developmental shift in autistic children, transitioning from early overgrowth to delayed maturation. Regional analyses identified distinct atypical trajectories across specific brain regions. Individual deviation scores quantified inter-subject variability, characterizing the heterogeneity of brain development in ASD. Comparative analyses between CABIC and ABIDE highlighted differences potentially attributable to ethnicity and culture, advancing our understanding of cross-population neurodevelopmental diversity. CABIC MRI datasets will be shared publicly to foster investigation of the potential neural mechanisms underlying ASD in non-Western populations and support efforts toward precision medicine for autistic individuals across diverse backgrounds.

neuroscience↗

bioRxiv2025

Single-sample, multi-omic mass spectrometry for investigating mechanisms of drug toxicity

Poor therapeutic index is a principal cause of drug attrition during development. A case in point is L-asparaginase (ASNase), an enzyme-drug approved for treatment of pediatric acute lymphoblastic leukemia (ALL) but too toxic for adults. To elucidate potentially targetable mechanisms for mitigation of ASNase toxicity, we performed multi-omic profiling of the response to sub-toxic and toxic doses of ASNase in mice. We collected whole blood samples longitudinally, processed them to plasma, and extracted metabolites, lipids, and proteins from a single 20-{micro}L plasma sample. We analyzed the extracts using multiple reaction monitoring (MRM) of 500+ water soluble metabolites, 750+ lipids, and 375 peptides on a triple quadrupole LC-MS/MS platform. Metabolites, lipids, and peptides that were modulated in a dose-dependent manner appeared to converge on antioxidation, inflammation, autophagy, and cell death pathways, prompting the hypothesis that inhibiting those pathways might decrease ASNase toxicity while preserving anticancer activity. Overall, we provide here a streamlined, three-in-one LC-MS/MS workflow for targeted metabolomics, lipidomics, and proteomics and demonstrate its ability to generate new insights into mechanisms of drug toxicity.

cancer biology↗

bioRxiv2025

Deep Learning-Powered Colloidal Digital SERS for Precise Monitoring of Cell Culture Media

Maintaining consistent quality in biopharmaceutical manufacturing is essential for producing high-quality complex biologics. Yet, current process analytical technologies (PAT) struggle to achieve rapid and highly accurate monitoring of small molecule critical process parameters and critical quality attributes. While Raman spectroscopy holds great promise as a highly sensitive and specific bioanalytical tool for PAT applications, its conventional implementation, surface-enhanced Raman spectroscopy (SERS), is constrained by considerable temporal and spatial intensity fluctuations, limiting the achievable reproducibility and reliability. Herein, we introduce a deep learning-powered colloidal digital SERS platform to address these limitations. Rather than addressing the intensity fluctuations, the approach leverages their very stochastic nature, arising from highly dynamic analyte-nanoparticle interactions. By converting the temporally fluctuating SERS intensities into digital binary "ON/OFF" signals using a predefined intensity threshold by analyzing the characteristic SERS peak, this approach enables digital visualization of single-molecule events and significantly reduces false positives and background interferences. By further integrating colloidal digital SERS with deep learning, the applicability of this platform is significantly expanded and enables detection of a broad range of analytes, unlimited by the lack of characteristic SERS peaks for certain analytes. We further implement this approach for studying AMBIC 1.1, a chemically-defined, serum-free complete media for mammalian cell culture. The obtained highly accurate and reproducible results demonstrate the unique capabilities of this platform for rapid and precise cell culture media monitoring, paving the way for its widespread adoption and scaling up as a new PAT tool in biopharmaceutical manufacturing and biomedical diagnostics.

biophysics↗

bioRxiv2025

Niacin protects against vascular calcification via enhanced SIRT1 and SIRT6 signaling and promoted VSMC autophagy

BackgroundVascular calcification (VC) is a common pathologic state that often accompanies calcium-phosphorus metabolism disorder and chronic kidney diseases (CKDs) in aging individuals. Vascular smooth muscle cell (VSMC) has been widely acknowledged as one of the main cell types that involved in this process. Niacin, a lipid-lowering reagent, has been demonstrated to be beneficial in atherosclerotic disease. The correlation and mechanism between niacin and vascular calcification have not been reported so far. Methods and resultsRCS analysis based on large clinical databases indicated that diet that riches in niacin can protect against abdominal artery calcification (AAC). Our data showed that niacin treatment remarkably reduced VSMC osteogenic differentiation and senescence-associated markers under osteogenic stimulation. Moreover, niacin treatment alleviated CKD and vitamin D3-induced vascular calcification in C57BL/6J mice. Mechanistically, we for the first time demonstrated that niacin supplementation inhibited vascular calcification via maintaining both Sirtuin 1 (SIRT1) and Sirtuin 6 (SIRT6) levels. Moreover, we verified that niacin activated SIRT1 and SIRT6 promoted VSMC autophagy flux. ConclusionsThese findings may help to develop novel therapeutic strategies in the treatment and prevention of vascular calcification.

cell biology↗

bioRxiv2025

SAMHD1 enhances HIV-1-induced apoptosis in monocytic cells via the mitochondrial pathway

Sterile alpha motif (SAM) and histidine-aspartate (HD) domain-containing protein 1 (SAMHD1) inhibits HIV-1 replication in non-dividing cells by reducing the intracellular dNTP pool. SAMHD1 enhances spontaneous apoptosis in cells, but its effects on HIV-1-induced apoptosis and the underlying mechanisms remain unknown. Here we uncover a new mechanism by which SAMHD1 enhances HIV-1-induced apoptosis in monocytic cells through the mitochondrial pathway. We found that endogenous SAMHD1 enhances apoptosis levels induced by HIV-1 infection in dividing THP-1 cells. Mechanistically, SAMHD1 expression decreases the mitochondrial membrane potential and promotes cytochrome c release induced by HIV-1 infection in THP-1 cells, thereby enhancing mitochondrial apoptotic pathway. SAMHD1-enhanced apoptosis is associated with increased expression of the pro-apoptotic protein BCL-2-interacting killer (BIK) in cells. We further demonstrated that BIK contributes to SAMHD1-enhanced apoptosis during HIV-1 infection. Overall, our results reveal an unappreciated regulatory mechanism of SAMHD1 in enhancing HIV-1-induced apoptosis via the mitochondrial pathway in monocytic cells.

microbiology↗

bioRxiv2025

Transplant immunosuppressant therapies induce unique functional changes in lymph node and re-shape gut immune homeostasis

BackgroundLifelong immunosuppressive therapy is required to prevent allograft rejection in organ transplantation. Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in severe off-target complications. It remains a significant unmet medical need in transplant medicine. ResultsIn this study we investigated immunosuppressant effects of four major immunosuppressant classes, including tacrolimus, prednisone, mycophenolate mofetil (MMF), and fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking after up to 30-day chronic exposure. Despite their distinct mechanisms of action and not designed to target the gut, all immunosuppressive drugs induced profound and time-dependent alterations in both intestine gene expression and gut microbiome composition. Progressive alterations from moderate early, drug-specific changes to a strikingly convergent microbial dysbiosis, marked by significant expansion of pathobionts of Muribaculaceae, occurred across all drug classes. Concurrently, all drugs uniformly induced significant suppression of mucosal immunity including B cell, immunoglobulin, and antigen recognition. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, marked by a progressive shift toward pro-inflammatory phenotypes in gut-draining mesenteric LNs and a gradual loss of tolerogenic architecture in peripheral LNs. Drug-specific metabolic alterations and distinct phases of intestinal transcriptional responses were also characterized. Notably, MMF and FTY demonstrated the most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cell distribution and LN remodeling. ConclusionsTogether, these findings highlight the underappreciated complexity and temporal dynamics immunosuppressants effects, particularly their impact on the gut and compartmentalized regulation of alloimmune in lymphoid tissues. Understanding these relationships offers new opportunities for refining immunosuppressive strategies to reduce treatment-related off-target complications and improve long-term organ transplant outcomes.

immunology↗

bioRxiv2025

Single-base m6A epitranscriptomics reveals novel HIV-1 host interaction targets in primary CD4+ T cells

N6-methyladenosine (m6A) is the most prevalent cellular mRNA modification and plays a critical role in regulating RNA stability, localization, and gene expression. m6A modification plays a vital role in modulating the expression of viral and cellular genes during HIV-1 infection. HIV-1 infection increases cellular RNA m6A levels in many cell types, which facilitates HIV-1 replication and infectivity in target cells. However, the function of m6A modification in regulating HIV-1 infection of primary CD4+ T cells remains unclear. Here, we demonstrate that HIV-1 infection of Jurkat CD4+ T cells and primary CD4+ T cells promotes the interaction between the m6A writer complex subunits methyltransferase-like 3 and 14 (METTL3/METTL14). Using single-base m6A-specific RNA sequencing, we identified several differentially m6A-modified cellular mRNAs, including perilipin 3 (PLIN3), during HIV-1 infection in primary CD4+ T cells. Interestingly, HIV-1 infection increased PLIN3 mRNA level by enhancing its stability, but PLIN3 protein level was decreased. Knocking down PLIN3 in primary CD4+ T cells reduced HIV-1 production but enhanced virion infectivity. In contrast, in Jurkat cells, PLIN3 mRNA and protein expression levels were unaffected by HIV-1 infection, and knocking out PLIN3 did not impact HIV-1 production or infectivity. These results indicate that the interplay between HIV-1 and PLIN3 is cell-type specific and only observed in primary CD4+ T cells. Overall, our results highlight the importance of m6A RNA modification in HIV-1-infected primary CD4+ T cells and suggest its significance as a regulatory mechanism in HIV-1 infection. Author SummaryN6-methyladenosine (m6A) is a common chemical modification on mRNA that helps control RNA stability, localization, and gene expression. m6A modification of viral and cellular RNA is important for HIV-1 infection. In this study, we found that HIV-1 infection of CD4+ T cells enhanced the interaction between two proteins, METTL3 and METTL14, which are responsible for adding m6A modifications to RNA. Using m6A-specific RNA sequencing, we identified several mRNAs with altered m6A modifications during HIV-1 infection, including one called PLIN3. Interestingly, HIV-1 infection stabilized and increased PLIN3 mRNA levels, but reduced PLIN3 protein expression in primary CD4+ T cells. When we knocked down PLIN3 in primary CD4+ T cells, it decreased HIV-1 production but made the HIV-1 particles more infectious. In contrast, in the Jurkat CD4+ T cell line, HIV-1 infection did not affect PLIN3 expression and knockout of PLIN3 did not alter HIV-1 production or infectivity, suggesting that the effect is specific to primary CD4+ T cells. Our findings show the importance of m6A RNA modification in HIV-1 infection by regulating host genes like PLIN3 and suggest a unique regulatory mechanism in HIV-1 infected primary CD4+ T cells.

microbiology↗

bioRxiv2024

Direct and abscopal anti-tumor responses elicited by peripheral nerve schwannoma irradiation synergize with anti-PD1 treatment in vestibular schwannoma models

NF2-related schwannomatosis (NF2-SWN) is a progressive and disabling disease requiring effective treatments. The hallmark of NF2-SWN is bilateral vestibular schwannomas (VSs), which progressively enlarge, leading to permanent sensorineural hearing loss and severely impacting patients quality of life. Currently, there are no FDA-approved drugs for VS or the associated hearing loss. Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, but have not yet been systematically investigated in non-malignant tumors such as VS. In our studies, we demonstrated that combining anti-PD1 (PD1) treatment with radiation therapy (RT) provides three significant therapeutic benefits: i) Enhanced PD1 efficacy and immune memory: RT induces immunogenic cell death and activates the STING pathway, enhancing PD1 efficacy and generating long-term immune memory, ii) Reduced RT dose and associated tissue injury: The combination strategy reduces the required RT dose necessary for effective tumor control, potentially minimizing RT injury to surrounding normal tissues, and iii) Elicited abscopal effects on cerebellopontine angle (CPA) schwannomas: RT to peripheral nerve tumor induces a systemic abscopal effect, which synergizes with PD-1 to effectively control intracranial schwannomas without direct irradiation, sparing the cochlea from radiation exposure and avoiding auditory radiation injury. Together, our findings provide a compelling rationale for deploying ICIs in combination with radiotherapy as a novel treatment approach for patients with VS and NF2-SWN.

cancer biology↗

bioRxiv2024

Enhanced Tumor Control and Hearing Loss Prevention Achieved with Combined Immune Checkpoint Inhibitor and Anti-VEGF Therapy in Vestibular Schwannoma Model

BackgroundNF2-related schwannomatosis (NF2-SWN) is a debilitating condition that calls for robust treatment options. The defining feature of NF2-SWN is the presence of bilateral vestibular schwannomas (VSs), which grow over time and can result in irreversible sensorineural hearing loss, significantly affecting the quality of life for those affected. At present, there are no FDA-approved medications specifically for treating VS or related hearing loss. VS management involves radiotherapy or surgical resection, while bevacizumab, an anti-vascular endothelial growth factor (VEGF) monoclonal antibody (VEGF) may be used off-label in NF2-SWN to shrink the tumor. However, not all patients respond, and the effect is not always durable. There is a critical need for effective medications that can stop the growth of VS and prevent hearing loss associated with these tumors. While immune checkpoint inhibitors have transformed cancer therapy, their potential has not been thoroughly explored in non-malignant tumors such as VS. MethodsWe characterize the effects of anti-PD1 (PD1) treatment on tumor growth and hearing function in two syngeneic, immune-competent VS models. ResultsWe demonstrated that combining VEGF treatment with PD1 significantly enhances the efficacy of each monotherapy. Specifically, i) VEGF enhances PD1 efficacy by normalizing the tumor vasculature to improve drug delivery and immune cell infiltration, and by activating T cell and NK cell anti-tumor cytotoxicity via NKG2D upregulation; and ii) combining PD1 with VEGF treatment effectively controls tumors that progressed despite VEGF treatment. ConclusionThese findings provide a strong foundation for the development of PD1 with VEGF combination therapies for patients with NF2-SWN. Key pointsWe filled a critical gap in NF2 research: 1) we characterized the effects of immunotherapy on tumor growth and hearing function in non-malignant vestibular schwannomas 2) We showed combined anti-VEGF and anti-PD1 enhances the efficacy of each monotherapy Importance of the studyTreatment options for patients with NF2-SWN are limited or are associated with significant co-morbidities. There are no approved medical treatments for NF2-related tumors. While immune checkpoint inhibitors have transformed cancer therapy, their potential has not been thoroughly explored in non-malignant tumors such as VS. Our work filled this critical gap in NF2-SWN research. For the first time, we systemically evaluated ICI efficacy on tumor growth and hearing function in non-malignant schwannomas. Furthermore, we demonstrated that combining VEGF treatment with PD1 significantly enhances the efficacy of each monotherapy. Specifically: i) VEGF enhances PD1 efficacy by normalizing the tumor vasculature to improve drug delivery and immune cell infiltration, and by activating T cell and NK cell anti-tumor cytotoxicity via NKG2D upregulation; and ii) combining PD1 with VEGF treatment effectively controls tumors that progress despite VEGF treatment. Our findings provide a strong foundation for the development of PD1 with VEGF combination therapies for patients with NF2-SWN.

cancer biology↗

bioRxiv2024

Nematode-Trapping Fungus Arthrobotrys oligospora is Hungry for COQ7 to Alleviate Environmentally Triggered Iron Overload

Choosing the right and appropriate amount of substances in a changing environment is essential for the growth and survival of all species. We found that elevated oxygen levels significantly enhanced the iron-rich trapping devices of a nematode-trapping fungus (NTF), Arthrobotrys oligospora. Interestingly, genomic analysis revealed that all NTFs lacked coq7, a key gene involved in ubiquinol (UQ) biosynthesis and iron chelation. Notably, A. oligospora utilizes UQ instead of UQ for low-aerobic respiration. Transcriptional, metabolic, mutational, and phenotypic analyses revealed that A. oligospora produces a chemotaxonomic class of highly oxygenated arthrobotrins with characteristics similar to UQ skeleton, for high-aerobic respiration. Disruption of arthrobotrin biosynthesis in the {Delta}art mutant not only enhanced UQ biosynthesis, but also triggered trapping device formation and nematicidal activity under elevated oxygen conditions. The addition of UQ to both wild-type and {Delta}art mutants strongly inhibited trapping device development. Remarkably, the iron-rich trapping devices preferentially capture N2 nematodes harboring iron-chelating COQ7 with ferritin properties. Time-calibrated evolutionary analyses, combined with geological data, indicated that the NTF ancestor lost the coq7 gene after acquiring the arthrobotrin biosynthetic gene cluster during the "superoligotrophy" period, characterized by dramatic shifts in global oxygen levels and temperature changes. Our results demonstrate that oxygen is a critical factor in inducing iron overload, highlighting the origin and role of coq7 loss in the evolution of predatory behavior of NTFs. Our finding that NTFs capture nematodes for iron chelation therapy, rather than for food, explains a long standing debate about the limited carnivorous ability of trapping devices.

microbiology↗

bioRxiv2024

Evidence for white matter intrinsic connectivity networks at rest and during a task: a large-scale study and templates

Understanding white matter (WM) functional connectivity is crucial for unraveling brain function and dysfunction. In this study, we present a novel WM intrinsic connectivity network (ICN) template derived from over 100,000 fMRI scans, identifying 97 robust WM ICNs using spatially constrained independent component analysis (scICA). This WM template, combined with a previously identified gray matter (GM) ICN template from the same dataset, was applied to analyze a resting-state fMRI (rs-fMRI) dataset from the Bipolar-Schizophrenia Network on Intermediate Phenotypes 2 (BSNIP2; 590 subjects) and a task-based fMRI dataset from the MIND Clinical Imaging Consortium (MCIC; 75 subjects). Our analysis highlights distinct spatial maps for WM and GM ICNs, with WM ICNs showing higher frequency profiles. Modular structure within WM ICNs and interactions between WM and GM modules were identified. Task-based fMRI revealed event-related BOLD signals in WM ICNs, particularly within the corticospinal tract, lateralized to finger movement. Notable differences in static functional network connectivity (sFNC) matrices were observed between controls (HC) and schizophrenia (SZ) subjects in both WM and GM networks. This open-source WM NeuroMark template and automated pipeline offer a powerful tool for advancing WM connectivity research across diverse datasets.

neuroscience↗

bioRxiv2024

FastReseg: using transcript locations to refine image-based cell segmentation results in spatial transcriptomics

Spatial transcriptomics (ST) is a rapidly advancing field, yet it is challenged by persistent issues with cell segmentation accuracy, which can bias biological interpretations by making cells appear more similar to their neighbors than they truly are. FastReseg introduces a novel class of algorithm that employs transcriptomic data not to redefine cell boundaries but to rectify inaccuracies within existing image-based segmentation outputs. By combining the rich information from image-based methods with the 3D precision of transcriptomic analysis, FastReseg enhances cell segmentation accuracy. A key innovation of FastReseg approach is its transcript scoring system, which scores each transcript for its goodness-of-fit within host cell using log-likelihood ratio. This scoring system facilitates the quick identification and correction of spatial doublets, i.e. cells erroneously segmented due to close proximity or spatial overlap in 2D. FastReseg approach offers several advantages: it reduces the risks of circularity in deriving cell boundaries from expression data and minimizes spatial-dependent biases arising from erroneous segmentation. It also addresses computational challenges often associated with existing transcript-based methods by introducing a heuristic, modular workflow that efficiently processes large datasets, a critical feature given the increasing size of spatial transcriptomics datasets. Its modular workflow allows for individual components to be optimized and seamlessly integrated back into the overall pipeline, accommodating ongoing advancements in segmentation technology. By enabling efficient management of large datasets and providing a scalable solution for refining cell segmentation, FastReseg is poised to enhance the quality and interpretability of spatial transcriptomics data even as underlying image-based cell segmentation techniques evolve.

bioinformatics↗

bioRxiv2024

Changes in urinary proteins of unaffected individuals with a family history of frontotemporal dementia

Frontotemporal dementia (FTD) is a common type of neurodegenerative dementia and the primary cause of dementia in individuals under 65 years old. Current studies typically consider family members carrying relevant gene mutations as genetic risk populations, while individuals with a family history of FTD but without known mutations are sometimes included as healthy controls in research, with their potential pathophysiological changes not being fully addressed. This study performed urinary proteomics analysis on individuals with a family history of FTD but without known mutations and healthy controls to investigate whether there are differential urinary proteins and biological pathways in FTD family members who remain undiagnosed with FTD or common mutations under existing diagnostic methods. The results showed 428 significantly differentially expressed proteins (P<0.01; FC[≥]2.0 or [≤]0.5) between the two groups, among which multiple proteins have been reported to be involved in FTD or nervous system functions, particularly Progranulin (PGRN), recognized as an effective biomarker for FTD. The 146 enriched biological pathways (P<0.01) of differentially expressed proteins included multiple pathways directly related to neurons and the nervous system, such as glial cells. The differences in urinary proteins between individuals with a family history of FTD without known mutations and healthy controls indicate that urinary proteomics holds unique potential in exploring unknown pathogenic factors of FTD, providing a new perspective for deepening disease understanding and optimizing prevention and treatment strategies.

biochemistry↗

bioRxiv2024

Influenza Virus Enhances Bacterial Growth in the Lungs through Weakening Capsule Receptor-Mediated Bacterial Capture by Neutrophils

Certain serotypes of encapsulated bacteria are more associated with severe pneumonia than others, but the biological reason behind this association has remained largely unknown. This study has uncovered a causal relationship between capsule serotype and virulence phenotype of Streptococcus pneumoniae, a leading cause of community-acquired pneumonia, in mice using isogenic bacteria. Certain high-virulence (HV) serotypes persist in the lungs and lead to severe pneumonia, whereas the low-virulence (LV) serotypes are effectively cleared. The capsule type-dependent difference in virulence is determined by the capsule-binding receptors, which recognize the capsular polysaccharides of the LV serotypes (but not the HV serotypes) and enable pathogen capture by neutrophils through complement activation. The capsule receptor-driven immunity of lung neutrophils is significantly compromised by pre-infection of influenza virus, which enhances the survival and virulence of the LV S. pneumoniae serotypes, and recurs in the heightened pathogenicity of Haemophilus influenzae. This study not only unravels the long-sought mechanistic mystery of serotype-dependent virulence in bacterial lung infections, but also provides an explanation for the well-known pathogenesis synergism between influenza virus and respiratory bacteria. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/622589v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1464164org.highwire.dtl.DTLVardef@16f34e5org.highwire.dtl.DTLVardef@1f9ad46org.highwire.dtl.DTLVardef@df104d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗