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Biology subjects

Zou, J.

Publications and source records attributed to Zou, J..

At least 109 records · Page 6Linked to original sources

Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

A-to-I mRNA editing occurs during fungal sexual reproduction with an unknown mechanism. Here, we demonstrated that the eukaryotic tRNA-specific heterodimeric deaminase FgTad2-FgTad3, not typically associated with mRNA editing, is responsible for A-to-I mRNA editing in Fusarium graminearum. This editing capacity relies on the interaction between FgTad3 and a sexual stage-specific protein called Ame1. The interaction emerged in Sordariomycetes. Key residues involved in the interaction have been identified. Expression and activity of FgTad2-FgTad3 are regulated through alternative promoters, alternative translation initiation, and post-translational modifications. FgTad2-FgTad3-Ame1 efficiently edits target mRNAs in yeasts, bacteria, and human cells, with significant implications for developing base editors in therapy and agriculture. This study reveals mechanisms, regulation, and evolution of RNA editing in fungi, emphasizing protein-protein interactions in controlling enzyme function.

molecular biology↗

PEPSI: Polarity measurements from spatial proteomics imaging suggest immune cell engagement

Subcellular protein localization is important for understanding functional states of cells, but measuring and quantifying this information can be difficult and typically requires high-resolution microscopy. In this work, we develop a metric to define surface protein polarity from immunofluorescence (IF) imaging data and use it to identify distinct immune cell states within tumor microenvironments. We apply this metric to characterize over two million cells across 600 patient samples and find that cells identified as having polar expression exhibit characteristics relating to tumor-immune cell engagement. Additionally, we show that incorporating these polarity-defined cell subtypes improves the performance of deep learning models trained to predict patient survival outcomes. This method provides a first look at using subcellular protein expression patterns to phenotype immune cell functional states with applications to precision medicine.

bioinformatics↗

Less neutralization evasion of SARS-CoV-2 BA.2.86 than XBB sublineages and CH.1.1

The highly mutated BA.2.86, with over 30 spike protein mutations in comparison to Omicron BA.2 and XBB.1.5 variants, has raised concerns about its potential to evade COVID-19 vaccination or prior SARS-CoV-2 infection-elicited immunity. In this study, we employ a live SARS-CoV-2 neutralization assay to compare the neutralization evasion ability of BA.2.86 with other emerged SARS-CoV-2 subvariants, including BA.2-derived CH.1.1, Delta-Omicron recombinant XBC.1.6, and XBB descendants XBB.1.5, XBB.1.16, XBB.2.3, EG.5.1 and FL.1.5.1. Our results show that BA.2.86 is less neutralization evasive than XBB sublineages. Among all the tested variants, CH.1.1 exhibits the greatest neutralization evasion. In comparison to XBB.1.5, the more recent XBB descendants, particularly EG.5.1 and FL.1.5.1, display increased resistance to neutralization induced by parental COVID-19 mRNA vaccine and a BA.5-Bivalent-booster. In contrast, XBC.1.6 shows a slight reduction but remains comparable sensitivity to neutralization when compared to BA.5. Furthermore, a recent XBB.1.5-breakthrough infection significantly enhances the breadth and potency of cross-neutralization. These findings reinforce the expectation that the upcoming XBB.1.5 mRNA vaccine would likely boost the neutralization of currently circulating variants, while also underscoring the critical importance of ongoing surveillance to monitor the evolution and immune evasion potential of SARS-CoV-2 variants.

microbiology↗

Characterizing tissue structures from spatial omics with spatial cellular graph partition

Spatial transcriptomic and proteomic measurements enable high-dimensional characterization of tissues. However, understanding organizations of cells at different spatial scales and extracting tissue structures of interest remain challenging tasks that require extensive human annotations. To address this need for consistent identification of tissue structures, in this work, we present a novel annotation method Spatial Cellular Graph Partitioning (SCGP) that allows unsupervised identification of tissue structures that reflect the anatomical and functional units of human tissues. We further present a reference-query extension pipeline SCGP-Extension that enables the generalization of existing reference tissue structures to previously unseen samples. Our experiments demonstrate reliable and robust partitionings of both spatial transcriptomics and proteomics datasets encompassing different tissue types and profiling techniques. Downstream analysis on SCGP-identified tissue structures reveals disease-relevant insights regarding diabetic kidney disease and skin disorder, underscoring its potential in facilitating spatial analysis and driving new discoveries.

bioinformatics↗

Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain

Multivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employed an icosahedral DNA origami (ICO) as a display particle for SARS-CoV-2 RBD nanovaccines. The morphology and diameter of the particles were close to those of the virus (91 {+/-} 11 nm). The surface addressability of the DNA origami permitted facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using an in vitro screening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoked stronger and more enduring humoral and T cell immune responses in mouse models compared to soluble RBD antigens. Our vaccines activated similar humoral immunity and slightly stronger cellular immunity compared to mRNA vaccines. These results provide reference principles for the rational design of nanovaccines and exemplify the utility of DNA origami as a display platform for vaccines against infectious disease.

bioengineering↗

TMEM165 acts as a proton-activated Ca2+ importer in lysosomes

Lysosomal calcium (Ca2+) release is critical to cell signaling and is mediated by well-known lysosomal Ca2+ channels. Yet, how lysosomes refill their Ca2+ remains hitherto undescribed. Here, from an RNAi screen, we identify an evolutionarily conserved gene, lci-1, that facilitates lysosomal Ca2+ entry in C. elegans and in mammalian cells. Its human homolog TMEM165, previously designated as a Golgi-resident Ca2+/H+ exchanger (CAX), has a minor lysosomal population of unknown function. Using genetics, lysosomal Ca2+ imaging and electrophysiology, we show that TMEM165 acts as a proton-activated, lysosomal Ca2+ importer in lysosomes. Defects in lysosomal Ca2+ channels cause several neurodegenerative diseases, and knowledge of lysosomal Ca2+ importers may provide new avenues to explore the physiology of Ca2+ channels.

cell biology↗

Is your data alignable? Principled and interpretable alignability testing and integration of single-cell data

Single-cell data integration can provide a comprehensive molecular view of cells, and many algorithms have been developed to remove unwanted technical or biological variations and integrate heterogeneous single-cell datasets. Despite their wide usage, existing methods suffer from several fundamental limitations. In particular, we lack a rigorous statistical test for whether two high-dimensional single-cell datasets are alignable (and therefore should even be aligned). Moreover, popular methods can substantially distort the data during alignment, making the aligned data and downstream analysis difficult to interpret. To overcome these limitations, we present a spectral manifold alignment and inference (SMAI) framework, which enables principled and interpretable alignability testing and structure-preserving integration of single-cell data. SMAI provides a statistical test to robustly determine the alignability between datasets to avoid misleading inference, and is justified by high-dimensional statistical theory. On a diverse range of real and simulated benchmark datasets, it outperforms commonly used alignment methods. Moreover, we show that SMAI improves various downstream analyses such as identification of differentially expressed genes and imputation of single-cell spatial transcriptomics, providing further biological insights. SMAIs interpretability also enables quantification and a deeper understanding of the sources of technical confounders in single-cell data.

bioinformatics↗

Human iPSC-derived Microglia Cells Integrated into Mouse Retina and Recapitulated Features of Endogenous Microglia Cells

Microglia exhibit both maladaptive and adaptive roles in the pathogenesis of neurodegenerative diseases and have emerged as a cellular target for central nervous system (CNS) disorders, including those affecting the retina. Replacing maladaptive microglia, such as those impacted by aging or over-activation, with exogenous microglia that can enable adaptive functions has been proposed as a potential therapeutic strategy for neurodegenerative diseases. To investigate microglia replacement as an approach for retinal diseases, we first employed a protocol to efficiently generate human-induced pluripotent stem cells (hiPSC)-derived microglia in quantities sufficient for in vivo transplantation. These cells demonstrated expression of microglia-enriched genes and showed typical microglial functions such as LPS-induced responses and phagocytosis. We then performed xenotransplantation of these hiPSC-derived microglia into the subretinal space of adult mice whose endogenous retinal microglia have been pharmacologically depleted. Long-term analysis post-transplantation demonstrated that transplanted hiPSC-derived microglia successfully integrated into the neuroretina as ramified cells, occupying positions previously filled by the endogenous microglia and expressed microglia homeostatic markers such as P2ry12 and Tmem119. Further, these cells were found juxtaposed alongside residual endogenous murine microglia for up to eight months in the retina, indicating their ability to establish a stable homeostatic state in vivo. Following retinal pigment epithelial (RPE) cell injury, transplanted microglia demonstrated responses typical of endogenous microglia, including migration, proliferation, and phagocytosis. Our findings indicate the feasibility of microglial transplantation and integration in the retina and suggest that modulating microglia through replacement may be a therapeutic strategy for treating neurodegenerative retinal diseases.

neuroscience↗

Disease-associated gut microbiome and metabolome changes in chronic low back pain patients with bone marrow lesions

Chronic low back pain (LBP) is the leading cause of global disability. Vertebral bone marrow lesions (BMLs), one etiological factor for chronic LBP, are MRI signal changes in the vertebral bone marrow that extend from the disc endplate. The adipogenesis of bone marrow mesenchymal stem cells (BM-MSCs) could explain fatty replacement (FR) in normal bone marrow. FR is the most common type of BMLs. Here we show how the gut microbiome and serum metabolome change and how they interact in LBP patients with or without FR. The serum metabolome of chronic LBP patients with FR is characterized by decreased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has important capability to regulate BCAA degradation pathway. Ruminococcus gnavus, Roseburia hominis and Lachnospiraceae bacterium 8 1 57FAA are identified as the main species driving the association between biosynthesis of BCAAs and BM-MSCs metabolism in LBP with FR individuals. In vitro work demonstrates that BCAAs can induce the adipogenesis of BM-MSCs by activating the SIRT4 pathway. Our findings provide a deep insight into understanding the role of the disturbed gut ecosystem in FR and LBP.

cell biology↗

OrtR regulates the oxidative stress response of Streptococcus mutans

Dental caries is the most common chronic infectious diseases around the world and disproportionately affects the marginalized socioeconomic group. Streptococcus mutans, considered a primary etiological agent of caries, must depend on the coordinated physiological response to tolerate the oxidative stress generated by commensal species within dental plaque, which is a critical aspect of its pathogenicity. Here, we identified and characterized a novel TetR family regulator SMU_1361c, encoded by the TnSmu2 operon, which appears to be acquired by the bacteria via horizontal genes transfer. Surprisingly, smu_1361c functions as a transcriptional repressor to regulate gene expression outside its operon, involved in the oxidative stress response of S. mutans. The smu_1361c overexpression strain UA159/pDL278-1361c was more susceptible to oxidative stress and less competitive against hydrogen peroxide generated by commensal species Streptococcus gordonii and Streptococcus sanguinis. Transcriptomics analysis revealed that smu_1361c overexpression resulted in the significant downregulation of 22 genes mainly belonging to three gene clusters responsible for the oxidative stress response. The conversed DNA binding motif of SMU_1361c was determined by electrophoretic mobility shift and DNase I footprinting assay with purified SMU_1361c protein, therefore, smu_1361c is directly involved in gene transcription related to the oxidative stress response. Crucially, our finding provides a new understanding of how S. mutans deals with the oxidative stress that is required for pathogenesis and will facilitate the development of new and improved therapeutic approaches for dental caries.

microbiology↗

Lysine vitcylation is a novel vitamin C-derived protein modification that enhances STAT1-mediated immune response

Vitamin C (vitC) is a vital nutrient for health and also used as a therapeutic agent in diseases such as cancer. However, the mechanisms underlying vitCs effects remain elusive. Here we report that vitC directly modifies lysine without enzymes to form vitcyl-lysine, termed "vitcylation", in a dose-, pH-, and sequence-dependent manner across diverse proteins in cells. We further discover that vitC vitcylates K298 site of STAT1, which impairs its interaction with the phosphatase PTPN2, preventing STAT1 Y701 dephosphorylation and leading to increased STAT1-mediated IFN pathway activation in tumor cells. As a result, these cells have increased MHC/HLA class-I expression and activate immune cells in co-cultures. Tumors collected from vitC-treated tumor-bearing mice have enhanced vitcylation, STAT1 phosphorylation and antigen presentation. The identification of vitcylation as a novel PTM and the characterization of its effect in tumor cells opens a new avenue for understanding vitC in cellular processes, disease mechanisms, and therapeutics.

biochemistry↗

TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses

Whole-transcriptome spatial profiling of genes at single-cell resolution remains a challenge. To address this limitation, spatial gene expression prediction methods have been developed to infer the spatial expression of unmeasured transcripts, but the quality of these predictions can vary greatly. Here we present TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) as a general framework for estimating uncertainty for spatial gene expression predictions and providing uncertainty-aware methods for downstream inference. Across eleven benchmark datasets, TISSUE provides well-calibrated prediction intervals for predicted expression values. Moreover it consistently reduces false discovery rates for differential gene expression analysis, improves clustering and visualization of predicted spatial transcriptomics, and improves the performance of supervised learning models trained on predicted gene expression profiles. Applying TISSUE to a MERFISH spatial transcriptomics dataset of the adult mouse subventricular zone, we identified subtypes within the neural stem cell lineage and developed subtype-specific regional classifiers. TISSUE is publicly available as a flexible wrapper method for existing spatial gene expression prediction methods to assist researchers with implementing uncertainty-aware analyses of spatial transcriptomics data.

bioinformatics↗

Human Attention during Goal-directed Reading Comprehension Relies on Task Optimization

The computational principles underlying attention allocation in complex goal-directed tasks remain elusive. Goal-directed reading, i.e., reading a passage to answer a question in mind, is a common real-world task that strongly engages attention. Here, we investigate what computational models can explain attention distribution in this complex task. We show that the reading time on each word is predicted by the attention weights in transformer-based deep neural networks (DNNs) optimized to perform the same reading task. Eye-tracking further reveals that readers separately attend to basic text features and question-relevant information during first-pass reading and rereading, respectively. Similarly, text features and question relevance separately modulate attention weights in shallow and deep DNN layers. Furthermore, when readers scan a passage without a question in mind, their reading time is predicted by DNNs optimized for a word prediction task. Therefore, we offer a computational account of how task optimization modulates attention distribution during real-world reading.

neuroscience↗

Leveraging medical Twitter to build a visual-language foundation model for pathology AI

The lack of annotated publicly available medical images is a major barrier for innovations. At the same time, many de-identified images and much knowledge are shared by clinicians on public forums such as medical Twitter. Here we harness these crowd platforms to curate OpenPath, a large dataset of 208,414 pathology images paired with natural language descriptions. This is the largest public dataset for pathology images annotated with natural text. We demonstrate the value of this resource by developing PLIP, a multimodal AI with both image and text understanding, which is trained on OpenPath. PLIP achieves state-of-the-art zero-shot and transfer learning performances for classifying new pathology images across diverse tasks. Moreover, PLIP enables users to retrieve similar cases by either image or natural language search, greatly facilitating knowledge sharing. Our approach demonstrates that publicly shared medical information is a tremendous resource that can be harnessed to advance biomedical AI.

pathology↗

High Volume Rate 3-D Ultrasound Imaging Using Fast-Tilting and Redirecting Reflectors

3-D ultrasound imaging has many advantages over 2-D imaging such as more comprehensive tissue evaluation and less operator dependence. Although many 3-D ultrasound imaging techniques have been developed in the last several decades, a low-cost and accessible solution with high imaging volume rate and imaging quality remains elusive. Recently we proposed a new, high volume rate 3-D ultrasound imaging technique: Fast Acoustic Steering via Tilting Electromechanical Reflectors (FASTER), which uses a water-immersible and fast-tilting acoustic reflector to steer ultrafast plane waves in the elevational direction to achieve high volume rate 3-D ultrasound imaging with conventional 1-D array transducers. However, the initial implementation of FASTER imaging only involves a single fast-tilting acoustic reflector, which is inconvenient to use because the probe cannot be held in the regular upright position. Also, conventional FASTER imaging can only be performed inside a water tank because of the necessity of using water for acoustic conduction. To address these limitations of conventional FASTER, here we developed a novel ultrasound probe clip-on device that encloses a fast-tilting reflector, a redirecting reflector, and an acoustic wave conduction medium. The new FASTER 3-D imaging device can be easily attached to or removed from clinical ultrasound transducers, allowing rapid transformation from 2-D to 3-D ultrasound imaging. In vitro B-mode imaging studies demonstrated that the proposed method provided comparable imaging quality (e.g., spatial resolution and contrast-to-noise ratio) to conventional, mechanical-translation-based 3-D imaging while providing a much faster 3-D volume rate (e.g., 300 Hz vs [~]10 Hz). In addition to B-mode imaging, we also demonstrated 3-D power Doppler imaging and 3-D super-resolution ultrasound localization microscopy with the newly developed FASTER device. An in vivo imaging study showed that the FASTER device could clearly visualize the 3-D anatomy of the basilic vein of a healthy volunteer, and customized beamforming was implemented to accommodate the speed of sound difference between the acoustic medium and the imaging object (e.g., soft tissue). These results suggest that the newly developed redirecting reflector and the clip-on device could overcome key hurdles for future clinical translation of the FASTER 3-D imaging technology.

bioengineering↗

Targeting SERCA2 in organotypic epidermis reveals MEK inhibition as a therapeutic strategy for Darier disease.

Mutation of the ATP2A2 gene encoding sarco-endoplasmic reticulum calcium ATPase 2 (SERCA2) was linked to Darier disease more than two decades ago; however, there remain no targeted therapies for this disorder causing recurrent skin blistering and infections. Since Atp2a2 knockout mice do not phenocopy its pathology, we established a human tissue model of Darier disease to elucidate its pathogenesis and identify potential therapies. Leveraging CRISPR/Cas9, we generated human keratinocytes lacking SERCA2, which replicated features of Darier disease, including weakened intercellular adhesion and defective differentiation in organotypic epidermis. To identify pathogenic drivers downstream of SERCA2 depletion, we performed RNA sequencing and proteomic analysis. SERCA2-deficient keratinocytes lacked desmosomal and cytoskeletal proteins required for epidermal integrity and exhibited excess MAP kinase signaling, which modulates keratinocyte adhesion and differentiation. Immunostaining patient biopsies substantiated these findings with lesions showing keratin deficiency, cadherin mis-localization, and ERK hyper-phosphorylation. Dampening ERK activity with MEK inhibitors rescued adhesive protein expression and restored keratinocyte sheet integrity despite SERCA2 depletion or chemical inhibition. In sum, coupling multi-omic analysis with human organotypic epidermis as a pre-clinical model, we found that SERCA2 haploinsufficiency disrupts critical adhesive components in keratinocytes via ERK signaling and identified MEK inhibition as a treatment strategy for Darier disease.

cell biology↗

Modulation of WNT, Activin/Nodal and MAPK Signaling Pathways Increases Arterial Hemogenic Endothelium and Hematopoietic Stem/Progenitor Cell Formation During Human iPSC Differentiation

Several differentiation protocols enable the emergence of hematopoietic stem and progenitor cells (HSPCs) from human induced pluripotent stem cells (iPSCs), yet optimized schemes to promote the development of HSPCs with self-renewal, multilineage differentiation and engraftment potential are lacking. To improve human iPSC differentiation methods, we modulated WNT, Activin/Nodal and MAPK signaling pathways by stage-specific addition of small molecule regulators CHIR99021, SB431542 and LY294002, respectively, and measured the impact on hematoendothelial formation in culture. Manipulation of these pathways provided a synergy sufficient to enhance formation of arterial hemogenic endothelium (HE) relative to control culture conditions. Importantly, this approach significantly increased production of human HSPCs with self-renewal and multilineage differentiation properties, as well as phenotypic and molecular evidence of progressive maturation in culture. Together, these findings provide a stepwise improvement in human iPSC differentiation protocols and offer a framework for manipulating intrinsic cellular cues to enable de novo generation of human HSPCs with functionality in vivo. Significance StatementThe ability to produce functional HSPCs by differentiation of human iPSCs ex vivo holds enormous potential for cellular therapy of human blood disorders. However, obstacles still thwart translation of this approach to the clinic. In keeping with the prevailing arterial-specification model, we demonstrate that concurrent modulation of WNT, Activin/Nodal and MAPK signaling pathways by stage-specific addition of small molecules during human iPSC differentiation provides a synergy sufficient to promote arterialization of HE and production of HSPCs with features of definitive hematopoiesis. This simple differentiation scheme provides a unique tool for disease modeling, in vitro drug screening and eventual cell therapies.

cell biology↗

Human subcortical pathways automatically detect collision trajectory without attention and awareness

Detecting imminent collisions is essential for our survival and is likely supported by evolutionarily conserved mechanisms in the brain. Using high-resolution 7T fMRI, we investigated subcortical pathways for detecting collision trajectories in healthy human subjects and hemianopic patients. When healthy participants focused their attention on a central fixation task, their superior colliculus (SC), ventromedial pulvinar (vmPul) and ventral tegmental area (VTA) elicited stronger responses to a peripheral object approaching on head-collision courses compared to near-miss trajectories. Correlation and path analyses of collision-sensitive responses revealed collision sensitivity in the SC-vmPul and SC-VTA pathways without attention and cortical influence. Both behavioral performance and SC responses showed higher sensitivity to looming stimuli from the upper visual field. For hemianopic patients with unilateral lesions of the geniculostriate pathway, the ipsilesional SC, vmPul and VTA showed collision sensitivity to looming stimuli in their blind visual field, in the absence of their awareness. Stronger responses in the SC were also associated with better detection performance of the collision events. These findings clearly demonstrate that human tectofugal pathways, without attention and awareness, automatically detects approaching objects on a collision course, supporting blindsight to impending visual threats. HighlightsO_LISC-vmPul and SC-VTA pathways show collision sensitivity without attention and cortical influence in healthy participants. C_LIO_LIBoth behavioral performance and SC responses show higher sensitivity to looming stimuli from the upper visual field. C_LIO_LIThe ipsilesional SC, vmPul and VTA of hemianopic patients automatically detects collision trajectories in their blind visual field without awareness. C_LIO_LISC response is associated with "blindsight" detection of impending collisions. C_LI

neuroscience↗