Biology subjects

He, H.

Publications and source records attributed to He, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Late-Talking Children Talk More? A Machine Learning Approach to Speech Act Analysis in Early Childhood

Speech acts shape early language development and social cognition, yet little is known about how late-talking (LT) children use them to achieve communicative goals. We compared LT and typically developing (TD) preschoolers (1;09-6;00) across nine dyadic English corpora, using a Conditional Random Field model to annotate speech acts. We analyzed speech act distributions, hierarchical relations, and contingent responses to assess production and comprehension. TD children produced more declarative statements and wh-questions, whereas LT children produced more unclear word-like utterances and showed reduced comprehension ability (1;09-2;07). Speech acts classified LT and TD groups with 72.3% accuracy, improving to 76.6% with linguistic and demographic features. Classification was driven by co-occurring patterns of speech act frequencies. LT children showed delayed onset of speech acts but employed more speech acts after 3;09, focusing on speaker-centered goals, whereas TD children favored collaborative use of speech acts, revealing complex dynamics in the development of communicative skills.

pathology↗

bioRxiv2025

Synaptic and neural pathway redundancy enables the robustness of a sensory-motor reflex and promotes predation escape in C. elegans

As a basic unit of the nervous system, the sensory-motor reflex circuit is fast and robust. However, it is not entirely clear how this robustness is achieved, given that various genetic perturbations can disrupt the function of the sensory neurons. By mapping the molecular basis of neuronal connections in the touch response circuit of Caenorhabditis elegans, we found prevalent genetic redundancy at neural pathway, synaptic, and molecular levels, which ensures that sensory signals can be relayed to command interneurons that control motor output. We also discovered developmental remodeling of the anterior circuit, which leads to the pruning of larval synapses, establishment of a second pathway that activates additional interneurons, and lateralization of the circuit. Finally, we found that the synapses that appeared to be functionally redundant in a simple touch assay contribute to the extent of reversal response in an additive manner, which may help the organism escape from predators.

neuroscience↗

bioRxiv2025

Characterization of the hemodynamic response function in default mode network subregions for task-evoked negative BOLD responses

While the hemodynamic response function (HRF) of the positive blood oxygenated level dependent (BOLD) signal is well characterized in the functional magnetic resonance imaging (fMRI) field, studies investigating the shape and properties of the negative BOLD HRF, often observed in the default mode network (DMN) regions, are rare. In this study, we first investigated the linearity of the task-evoked negative BOLD response (NBR) with respect to stimulus duration. Then, we obtained the shape of the HRF from each region of the DMN, using an in-house developed unbiased and robust iterative deconvolution technique. Our results demonstrated that each region of the DMN represented a unique HRF, which was not only substantially different from the HRF of the positive BOLD signal, but also different from the HRF extracted from the other DMN regions. We replicated these findings using different fMRI datasets with distinct task paradigms. When comparing the HRF across DMN sub-regions and across tasks, our results demonstrated a significantly higher inter-regional variability compared to inter-task variability. Furthermore, our performance correlation analysis illustrated that the HRFs in the DMN sub-regions extracted by our iterative FIR method were not biased by the task performance level. Altogether, we demonstrated the linearity of the NBR, introduced a robust HRF extraction approach to obtain a distinct HRF for each DMN sub-regions, which were different from the HRF of the positive BOLD signal. The results suggest there is possibility that each node of the DMN might have different underlying neural and/or vascular mechanisms.

neuroscience↗

bioRxiv2025

Cholesterol metabolism modulation facilitates CAR-T induced killing of ovarian cancer

Ovarian cancer is one of the most lethal gynecological cancers worldwide and has one of the highest recurrence rates. Recently developed Chimeric Antigen Receptor T (CAR-T) cell therapy has shown potent clinical efficacy against hematological malignancies. However, solid tumors, including ovarian cancer, possess several mechanisms that hinder T cell activity, and metabolic alteration of cancer cells has been shown to contribute to resistance to immune cell attack against solid tumors. Here, we explored the metabolic response of ovarian cancer cells to CAR-T cell attack using label-free high-content hyperspectral stimulated Raman scattering (h2SRS) imaging. Utilizing visible h2SRS imaging with much improved spatial resolution, we found an altered cholesterol metabolism, featured by increased storage of cholesteryl ester in lipid droplets and free cholesterol, in ovarian cancer cells that survived the CAR-T treatment. Administration of Avasimibe, an inhibitor of cholesteryl esterification, further enhanced CAR-T cytotoxicity. Our study shows the promise of implementing metabolic modulation to facilitate CAR-T cell treatment of solid tumors. Significance StatementOvarian cancer is a major global health challenge, mainly due to relapse driven by chemotherapy resistance development. Meanwhile, immunotherapies such as CAR-T have revolutionized treatment for blood cancers, but their application in solid tumors like ovarian cancer is hindered by limited efficacy. This study uses high-content stimulated Raman scattering (SRS) imaging to reveal metabolic adaptations that help ovarian cancer cells survive CAR-T-mediated cytotoxicity. Guided by these insights, we apply metabolic interventions that enhance CAR-T cytotoxicity efficacy. This approach reveals therapeutic vulnerabilities in ovarian cancer and demonstrates an investigative strategy applicable for overcoming resistance in solid tumors.

cell biology↗

bioRxiv2025

EZH2-TTP-mTORC1 Axis Drives Phenotypic Plasticity and Therapeutic Vulnerability in Lethal Prostate Cancer

Phenotypic plasticity is a recognized mechanism of therapeutic resistance in prostate cancer (PCa), however current knowledge of driver mechanisms and therapeutic interventions are limited. Using genetically engineered mouse models (GEMMs) devoid of Pten and Rb1, we previously demonstrated the chromatin reprogramming factor enhancer of zeste homolog 2 (EZH2) as an important regulator of alternative transcription programs promoting phenotypic plasticity. Here, using a multi-omics approach we demonstrate that EZH2 regulates multilineage cell states dependent on the RNA binding protein Tristetraprolin (TTP) that mediates RNA stability and activation of translation. Combined chemical inhibition of EZH2 and PI3K/mTORC1 resulted in superior anti-tumor activity in murine and human phenotypic plastic models and was most significant when this combination was used with castration or enzalutamide. Together, these data indicate phenotypic plasticity dependence on coordination between EZH2, TTP and mTORC1 signaling that represent novel therapeutic dependencies for this lethal PCa phenotype. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/669104v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@5ef713org.highwire.dtl.DTLVardef@af402forg.highwire.dtl.DTLVardef@19eedcforg.highwire.dtl.DTLVardef@10ee421_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementEZH2 plays a key role in driving cell state transitions in neuroendocrine prostate cancer (NEPC), guiding cancer cells towards a more aggressive, therapy-resistant cell type. This transformation creates a specific vulnerability, as NEPC cells become highly reliant on both EZH2 and PI3K/mTORC1-translation signaling. Targeting this dependency, we demonstrate that combining EZH2 with PI3K/mTORC1 inhibition provides effective suppression of NEPC cell growth, offering a promising therapeutic strategy for treating this challenging and aggressive prostate cancer subtype.

cancer biology↗

bioRxiv2025

Production of unreduced microspores in Arabidopsis flowers cultivated in culture medium suggests a role of sucrose in facilitating meiotic cytokinesis

Live-imaging microscopy technology has been increasingly applied for meiosis study in plants, which largely relies on the set up of a healthy ex vivo culture system for inflorescences ensuring that the captured chromosomes dynamics approaches the natural features of meiosis. Here, we report that Arabidopsis thaliana flowers cultivated in a culture medium (CCM) composed of the half-strength Murashige and Skoog basal salt, MES, Myo-inositol, sucrose and agar produce diploid microspores due to occurrence of meiotic restitution. Cytological studies revealed adjacent nuclei distribution and incomplete cytokinesis at late meiosis II in meiocytes within the CCM flowers. Immunolocalization of -tubulin and the microtubule-associated protein MAP65-3 showed that the orientation of spindles at metaphase II and the organization of radial microtubule arrays at the tetrad stage are interfered, which explains the production of meiotically-restituted microspores. Moreover, the CCM flowers showed a gradually impaired expression of Aborted Microspores (AMS), a key transcription factor regulating tapetum development and meiotic cytokinesis. Interestingly, an increased supply of sucrose in culture medium promoted the expression of AMS and partially rescued haploid microspore formation in the CCM flowers. Taken together, this study suggests a role of sucrose in facilitating meiotic cytokinesis and gametophytic ploidy stability in plants. One-sentence summaryArabidopsis flowers cultivated in culture medium produce unreduced microspores due to interfered meiotic cytokinesis, which is partially rescued by increased sucrose supply.

plant biology↗

bioRxiv2025

Mid-Infrared Photothermal Imaging of Fatty Acid Desaturation Reaction in Cancer Cells

Direct visualization of metabolic conversions within living systems is essential for understanding metabolic activities yet challenging due to the absence of reaction-specific reporters and the limited sensitivity of current imaging modalities. Herein, we report an approach to monitor fatty acids (FAs) desaturation, primarily catalyzed by stearoyl-CoA desaturase, in cancer cells using deuterium (D)-labeled palmitic acid (PA-d31) as the reaction-specific reporter and mid-infrared photothermal (MIP) microscopy as the bond-selective imaging modality. The desaturation of PA-d31 produced a peak at 2246 cm-1 in the cell-silent region, corresponding to the stretching vibration of unsaturated C-D bonds (D-C=C-D) in unsaturated fatty acids. Penalized least squares fitting was employed to remove water background for enhancing the visibility of this peak. Our study revealed heterogeneous spatial distributions of both saturated FAs and their desaturated metabolites within lipid droplet pools in cancer cells. Furthermore, we observed an increase in fatty acid unsaturation level in OVCAR5 cells under cisplatin-induced stress. By directly visualizing fatty acid desaturation, this study offers new insights into fatty acid metabolism and opens avenues for evaluating new therapeutic strategies targeting fatty acid metabolism.

biochemistry↗

bioRxiv2025

Contrastive Learning-Enhanced Drug Metabolite Prediction Drives the Discovery of an Orally Bioavailable RSK4 Inhibitor for Esophageal Cancer

Drug metabolism liabilities are a major bottleneck in drug development, necessitating accurate metabolite prediction tools. While AI-driven methods have advanced, challenges remain in achieving high-precision, robustness, broad reaction coverage and seamless integration into the drug development workflow. To address this, we first constructed the most comprehensive human-specific drug metabolism database to date, encompassing 11,665 human metabolic reactions and 2,497 high-quality rules. Leveraging this resource, we developed ConMeter (Contrastive learning and feature interaction based Metabolic Reaction prediction), a novel model integrating chemical feature interaction and contrastive learning. ConMeter demonstrates significant improvements, achieving [~]80% accuracy in identifying at least one metabolite within the top 5 predictions and showing an average 25% relative enhancement in ranking true positives compared to state-of-the-art methods. The comprehensive database also expands the range of predictable metabolic reactions. To demonstrate the utility of ConMeter, we integrated it into a metabolite prediction-guided drug design strategy aimed at addressing the low oral bioavailability of a metabolically vulnerable RSK4 lead compound -- a pervasive issue among known RSK inhibitors. This strategy successfully yielded R636, a novel RSK4 inhibitor exhibiting remarkably improved bioavailability (a 63-fold increase, reaching 63% absolute bioavailability) while maintaining its potent activity. Notably, R636 showed favorable safety profile and significant anti-tumor efficacy against esophageal squamous cell carcinoma (ESCC) in vitro and in two distinct patient-derived xenograft (PDX) mouse models. This work introduces ConMeter as a powerful and practical tool for high-accuracy metabolite prediction, demonstrating its potential to accelerate lead optimization, exemplified by the discovery of R636 as a promising orally bioavailable candidate for ESCC.

cancer biology↗

bioRxiv2025

Spatial profiling of chromatin accessibility reveals alteration of glial cells in Alzheimer's disease mouse brain

Abnormal epigenetic modifications, including altered chromatin accessibility, have been implicated in the development and progression of Alzheimers disease (AD). In this study, we applied spatially resolved chromatin accessibility profiling by performing spatial assay for transposase-accessible chromatin using sequencing (ATAC-seq) to analyze brain tissues from 5xFAD AD model and C57BL/6J control mice. Our analysis identified seven major cell types across 11 brain regions and further characterized glial subtypes--microglia and astrocytes-- revealing subtype-specific chromatin accessibility changes in 5xFAD mice relative to controls. These alterations were associated with AD-related pathways, including neuroinflammation and immune dysregulation, and synaptic dysfunction and neuronal signaling in microglia, as well as lysosomal and proteasomal activity, lipoprotein metabolism, and mitochondrial dysfunction in astrocytes. We also characterized cell-type-specific enrichments of motifs and transcription factors, including enrichment of Bcl11a in microglia. Furthermore, we linked chromatin accessibility changes in 5xFAD mice to human AD risk genes, highlighting altered epigenetic signatures in genes such as Trem2. Supporting the spatial ATAC-seq findings, flow cytometry validated a selective increase in VISTA (encoded by Vsir) protein expression in 5xFAD microglia, supporting the spatial ATAC-seq findings and indicating a shift toward a pro-inflammatory, disease-associated microglial (DAM-like) phenotype. These findings underscore the utility of spatial chromatin accessibility profiling for uncovering brain-region specific cell identities and epigenetic mechanisms underlying AD pathogenesis.

bioinformatics↗

bioRxiv2025

Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus

For the first time, we assembled two highly continuous, completely gap-free reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP), which are widely distributed in southern China with similar phenotypic traits (Figures 1A, 1B, and Figure S1), yet ripe fruits display distinct sugar accumulation levels (Table S1), making them ideal candidates for investigating the mechanisms underlying sugar accumulation in the Rubus genus. The XMM (213.53 Mb, 28,204 genes) and DHP (218.26 Mb, 28,569 genes) genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (translocations, inversions, segmental duplications), and presence/absence variation (PAV). Using Hi-C interaction heatmaps and Sanger sequencing, we validated interspecific structural inversions. Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved key genes (RhSTP13 and RhSTP7) associated with sugar accumulation in Rubus genus and displayed distinct roles through transient expression assay. To facilitate functional genomics study, we also established a comprehensive Rubus database, RubusDB, a freely accessible repository consolidating all genomic, transcriptomic and phenotypic data of Rubus genus. These findings provide a foundational framework for elucidating the genetic basis of sugar accumulation, genome diversification, and trait improvement in Rubus species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/646780v2_fig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1baca20org.highwire.dtl.DTLVardef@2c01eaorg.highwire.dtl.DTLVardef@131dc00org.highwire.dtl.DTLVardef@62a04f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO Phenotypic characterization, de novo genome assemblies, variation, and evolution of Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP). (A) Illustration of XMM whole plants, stem, flower bud and flower, respectively. (B) Illustration of DHP whole plants, stem, flower bud and flower, respectively. (C) The chromosome karyotype analysis of XMM. Bar = 10 {micro}m. (D) Circular diagram of XMM and DHP reference genomes. (a) Chromosomes are represented by centromeres (dark red) and telomeres (blue); (b) CEN18 density; (c) CEN17 density; (d) Gene density; (e) TE density; (f) PAV density; (g) SNP density; (h) Collinear lines at the center of diagram highlight homoeologous chromosomes relationships and non-homoeologous regions. (E) Genomic alignments between XMM and DHP. Inversions, duplications and translocations are marked with orange, blue and green ribbons, respectively. (F) Identification of large inversions in chromosome 7 between XMM and DHP. The three heatmaps show the chromatin interaction matrix, including mapping Hi-C data of DHP against DHP genome (left), mapping Hi-C data of DHP against XMM genome (middle) and mapping Hi-C data of XMM against XMM genome (right). The lower panel illustrates gene alignments between XMM and DHP. (G) Synteny, structural rearrangements, monomer, and identity distribution in the 16-20 Mbp region of chromosome 6 between XMM and DHP. (H) Local genome synteny of chromosome 5, with a structural variation that is present only in XMM. The PAV region includes a gene related to sugar transporter (MFS1, XMM05G025540). (I) Gene-level matchings of MFS genes in the PAVs region between XMM and DHP. (J) Phylogenetic relationships and divergence times between raspberries and other Rosaceae species. The black numbers close to the divergence nodes indicate the divergence times and the red bars represent the 95% confidence intervals. The red and black numbers indicate expanded and contracted ortholog groups at the corresponding node. Scale bar corresponds to 10 Mya. C_FIG

genomics↗

bioRxiv2025

HDL Nanodiscs Loaded with Liver X Receptor Agonist Decreases Tumor Burden and Mediates Long-term Survival in Mouse Glioma Model

Glioblastoma multiforme (GBM) is highly aggressive primary brain tumor with a 5-year survival rate of 7%. Previous studies have shown that GBM tumors have a reduced capacity to produce cholesterol and instead depend on the uptake of cholesterol produced by astrocytes. To target cholesterol metabolism to induce cancer cell death, synthetic high-density lipoprotein (sHDL) nanodiscs delivering Liver-X-Receptor (LXR) agonists and CpG oligonucleotides for targeting GBM were investigated. LXR agonists synergize with sHDL nanodiscs by increasing the expression of the ABCA1 cholesterol CpG oligonucleotides are established adjuvants used in cancer immunotherapy that work through the toll-like receptor 9 pathway. In the present study, treatment with GW-CpG-sHDL nanodiscs increased the expression of cholesterol efflux transporters on murine GL261 cells leading to enhanced cholesterol removal. Experiments in GL261-tumor-bearing mice revealed combining GW-CpG-sHDL nanodiscs with radiation (IR) therapy significantly increases median survival compared to GW-CpG-sHDL or IR alone. Furthermore, 66% of long-term survivors from the GW-CpG-sHDL +IR treatment group showed no tumor tissue when rechallenged.

cancer biology↗

bioRxiv2025

Functional landscape of circular RNAs in human cancer cells

Circular RNAs (circRNAs) constitute a novel class of noncoding RNAs showcasing distinct tissue- and cell-specific expression patterns. Despite the extensive profiling of circRNAs, their individual functions remain poorly understood. To fill this gap, we designed a genome-wide library of 65,300 shRNAs, targeting 9,663 clinically relevant circRNAs and 3,981 of their linear parental genes, and conducted functional screening in seven types of human cancer. We identified a total of 1,342 essential circRNAs (13.9% screened) that impact cell proliferation in at least one cell line, and in 96.5% of the cases, the linear counterparts are not essential. While a shared common subset emerges as functional regulators across all examined cell lines, the majority of circRNAs are functional in a cell type-specific manner. For a comprehensive presentation of the functional circRNA landscape in cancer, we introduce FunCirc, an online database encompassing functional circRNAs across cancer cell lines, coupled with circRNA expression profiles from diverse cancer and tissue types. Our work enhances the understanding of circRNA functions in cancer and provides the scientific community with a resource to further investigate their intricate roles.

cancer biology↗

bioRxiv2025

scKAN: Interpretable Single-cell Analysis for Cell-type-specific Gene Discovery and Drug Repurposing via Kolmogorov-Arnold Networks

Single-cell analysis has revolutionized our understanding of cellular heterogeneity, yet current approaches face challenges in efficiency and interpretability. In this study, we present scKAN, a framework that leverages Kolmogorov-Arnold Networks for interpretable single-cell analysis through three key innovations: efficient knowledge transfer from large language models through a lightweight distillation strategy; systematic identification of cell-type-specific functional gene sets through KANs learned activation curves; and precise marker gene discovery enabled by KANs importance scores with potential for drug repurposing applications. The model achieves superior performance on cell-type annotation with a 6.63% improvement in macro F1 score compared to state-of-the-art methods. Furthermore, scKANs learned activation curves and importance scores provide interpretable insights into cell-type-specific gene patterns, facilitating both gene set identification and marker gene discovery. We demonstrate the practical utility of scKAN through a case study on pancreatic ductal adenocarcinoma, where it successfully identified novel therapeutic targets and potential drug candidates, including Doconexent as a promising repurposing candidate. Molecular dynamics simulations further validated the stability of the predicted drug-target complexes. Our approach offers a comprehensive framework for bridging single-cell analysis with drug discovery, accelerating the translation of single-cell insights into therapeutic applications.

bioinformatics↗

bioRxiv2025

Depicting pathogenesis of osteomyelitis by single cell RNA-sequencing and an involvement of Morrbid in the autoinflammatory disease

Autoinflammatory diseases (AIDs) are defined as abnormal activation of the innate immune system leading to spontaneous and uncontrolled inflammation. The AIDs affect bone tissue and lead to chronic recurrent multifocal osteomyelitis (CRMO). However, the etiology and treatment of CRMO remain elusive. A mouse strain, Pstpip2cmo/cmo (cmo: chronic multifocal osteomyelitis), exhibits phenotypic characteristics similar to human CRMO. Morrbid is a long non-coding RNA gene and has been indicated in leukemogenesis in our previous studies. In this study, we demonstrated that Morrbid and Pstpip2 are co-expressed in mature myeloid cells and hypothesized a role of Morrbid in osteomyelitis. The Pstpip2-/- mice have the same phenotype as Pstpip2cmo/cmo, mimicking CRMO, while loss of Morrbid in Pstpip2-/-mice significantly inhibited the initiation and progression of CRMO symptoms, as well as the dysregulated activation of myeloid cells and the excessive release of inflammatory cytokines. Furthermore, single-cell RNA-sequencing (scRNA-seq) analysis from the Pstpip2-/- mice and the compound mutant mice supports that reduction of osteoclasts and inflammatory cells caused by Morrbid loss. The study systematically profiles the etiology of CRMO by scRNA-seq and warrants that inhibiting the lifespan of inflammatory myeloid cells by targeting Morrbid is an effective therapeutic strategy for osteomyelitis. HighlightsO_LIWe generated a frameshift mutant mouse strain Pstpip2-/-, which have a classic CRMO-like phenotype as same as Pstpip2cmo/cmo and could be used for testing various anti-inflammation perturbations. C_LIO_LILoss of Morrbid significantly inhibited the autoinflammatory symptoms in Pstpip2-/- mice, suggesting that Morrbid is a novel target for mitigating CRMO. C_LIO_LIscRNA-seq analysis of the affected bone marrow cells in Pstpip2-/-revealed the abnormalities of osteoclasts (OC), neutrophils (NE) and granulocyte macrophage progenitors (GMP) in both their fractions and inflammatory activities. C_LIO_LIUpon loss of Morrbid, we observed reduced composition and proliferation of OC and decreased activity of Nfkb2 and Rela in the compound mutants. C_LI

immunology↗

bioRxiv2024

Base-modified nucleotides mediate immune signaling in bacteria

Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. While cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of other messengers remains largely unexplored. Here, we reveal a bacterial anti-phage system that mediates immune signaling through nucleobase modification. Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine 5-triphosphate (dITP) as immune messengers. The dITP signal activates downstream effector to mediate cellular NAD+ depletion, resulting in population-level defense through the death of infected cells. To counteract immune signaling, phages deploy specialized enzymes that deplete cellular dAMP, the precursor of dITP messengers. Our findings uncover a nucleobase modification-based anti-phage signaling pathway, establishing noncanonical nucleotides as a new type of immune messengers in bacteria.

microbiology↗

bioRxiv2024

A CRISPR-associated Rossman-fold Ring Nuclease and Adenosine Deaminase Fusion Allosterically Converts ATP to ITP

The recently identified CARF (CRISPR-associated Rossman-fold) family of proteins play a critical role in prokaryotic defense, mediating cOA (cyclic oligoadenylate)-stimulated ancillary immune responses in the type III CRISPR-Cas systems. Whereas most previously characterized CARF proteins contain nucleic acids or protein degradation effectors, a subset comprises CARF-fused adenosine deaminase (ADA) (Cad1) and has a yet to be determined function. Here we present biochemical and structural analyses of a ring nuclease Cad1, revealing its unexpected role in deaminating adenosine-5'-triphosphate to inosine-5'-triphosphate in a cOA-dependent manner. Despite an overall structural similarity to canonical ADA enzymes, the ADA domain of Cad1 possesses unique structural features underlying its specificity for ATP. Supported by mutational analysis, we demonstrate an allosteric link between the cOA-binding CARF and the ADA domain, suggesting that Cad1 is a cOA-stimulated effector that influences cellular metabolic processes. HighlightsO_LITaqCad1 converts ATP to ITP in a magnesium- and cOA-dependent manner C_LIO_LICryo-EM structures reveal TaqCad1 forms a homohexamer C_LIO_LICryo-EM structures reveal how cA4 is degraded and modulates the ADA active site C_LI

cell biology↗

bioRxiv2024

Network-based amyloid-beta pathology predicts subsequent cognitive decline in cognitively normal older adults

The deposition of amyloid-{beta} (A{beta}) protein in the human brain is a hallmark of Alzheimers disease and is related to cognitive decline. However, the relationship between early A{beta} deposition and future cognitive impairment remains poorly understood, particularly concerning its spatial distribution and network-level effects. Here, we employed a cross-validated machine learning approach and investigated whether integrating subject-specific brain connectome information with A{beta} burden measures improves predictive validity for subsequent cognitive decline. Baseline regional A{beta} pathology measures from positron emission tomography (PET) imaging predicted prospective cognitive decline. Incorporating structural connectome, but not functional connectome, information into the A{beta} measures improved predictive performance. We further identified a neuropathological signature pattern linked to future cognitive decline, which was validated in an independent cohort. These findings advance our understanding of how A{beta} pathology relates to brain networks and highlight the potential of network-based metrics for A{beta}-PET imaging to identify individuals at higher risk of cognitive decline.

neuroscience↗

bioRxiv2024

De novo non-compartmentalized microorganism for directed evolution of nanobodies

The creation of de novo microorganisms is a fascinating task, and microorganisms offer a wide range of applications for humanity. Herein, we designed a de novo microorganism, termed Syn-phage, as an artificial unencapsulated mimic of naturally occurring phage capable of evolving nanobodies with improved properties. Syn-phage composes unified genomic and phenotypic materials with phenotypic proteins encoded from its genetic information. Since Syn-phage can undergo amplification in E. coli. host, we established a protocol for the evolution of nanobodies with improved avidity or affinity, allowing super-resolution live-cell immunoimaging of endogenous proteins, a challenge posed in immunolabeling with antibodies. Utilizing a Syn-phage evolved nanobody, we visualized the microtubule nucleation factor hTPX2, recorded the dynamics of it during mitotic progression, and imaged it at a resolution beyond the diffraction limit of light via an AI-powered imaging pipeline. Hence, this study demonstrated the possibility to design de novo microorganisms for capitative applications.

biochemistry↗