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Liu, H.

Publications and source records attributed to Liu, H..

At least 361 records · Page 20Linked to original sources

The transcription factor ZmbZIP75 promotes both grain filling and kernel dehydration in maize

Selecting both high-yield and low-kernel-moisture varieties is essential for modern maize production, but relevant breeding efforts are hindered by a lack of valuable regulatory genes. Here, we demonstrate that the transcription factor (TF) basic leucine zipper 75 (ZmbZIP75) promotes grain yield and reduces kernel moisture in maize. Knockout of ZmbZIP75 results in defective grain filling and kernel dehydration, whereas ZmbZIP75 overexpression confers increased grain yield per plant and decreased kernel moisture without altering plant architecture. Mechanistically, during the grain filling stage, ZmbZIP75 is transcriptionally induced by maternal-derived basal abscisic acid (ABA) and directly activates multiple core starch synthesis-related genes and key TFs, thereby promoting grain filling and final yield. In the late stage of kernel development, high concentrations of zygotic ABA enhance ZmbZIP75 phosphorylation through SnRK2.10. The phosphorylated ZmbZIP75 subsequently transactivates and interacts with TF VP1 to synergistically promote kernel dehydration. This study thus highlights the potential of ZmbZIP75 for engineering both high-yield and low-kernel-moisture varieties to meet the demands of high-efficient maize production. IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSHigh grain yield in maize is generally associated with elevated kernel moisture at harvest, which is the main limiting factor for modern maize production. Therefore, it is of importance to select varieties with both high-yield and low-kernel-moisture. These traits are largely controlled by grain filling and kernel dehydration, two tightly connected processes during maize kernel development. Abscisic acid (ABA) is well-documented for its vital role in grain filling and dehydration maturation. However, the molecular mechanisms by which ABA coordinates these two processes remain unclear. QuestionWhat are the regulatory factors involved, and how do they mediate ABA signaling to coordinate grain filling and dehydration maturation in maize? FindingsZmbZIP75 is transcriptionally induced by ABA and directly activates multiple core starch synthesis-related genes and key TFs in developing maize endosperm, thereby promoting grain filling. In developing embryo, ABA enhances ZmbZIP75 phosphorylation via SnRK2.10. The phosphorylated ZmbZIP75 then transactivates and interacts with VP1 to synergistically promote kernel dehydration. Moreover, ZmbZIP75 overexpression confers increased grain yield and reduced kernel moisture in maize. Next stepsWhile ZmbZIP75 is directly phosphorylated to mediate ABA signaling during dehydration maturation, ZmbZIP75 is transcriptionally induced by ABA during grain filling. We plan to identify upstream factors that mediate ABA signaling to regulate ZmbZIP75 expression, thereby enhancing our understanding of ABA-promoted grain filling in maize.

plant biology↗

Genetic-Dependent Brain Signatures of Resilience: Interactions among Childhood Abuse, Genetic Risks and Brain Function

Resilience to emotional disorders is critical for adolescent mental health, especially following childhood abuse. Yet, brain signatures of resilience remain undetermined due to the differential susceptibility of the brains emotion processing system to environmental stresses. Analyzing brains responses to angry faces in a longitudinally large-scale adolescent cohort (IMAGEN), we identified two functional networks related to the orbitofrontal and occipital regions as candidate brain signatures of resilience. In girls, but not boys, higher activation in the orbitofrontal-related network was associated with fewer emotional symptoms following childhood abuse, but only when the polygenic burden for depression was high. This finding defined a genetic-dependent brain (GDB) signature of resilience. Notably, this GDB signature predicted subsequent emotional disorders in late adolescence, extending into early adulthood and generalizable to another independent prospective cohort (ABCD). Our findings underscore the genetic modulation of resilience-brain connections, laying the foundation for enhancing adolescent mental health through resilience promotion.

neuroscience↗

RAD50 is a potential biomarker for breast cancer diagnosis and prognosis

BACKGROUNDRAD50 is one of the most critical genes in DNA double-strand break processing, which can lead to a single 3 strand of DNA overhang and is potentially involved in forcing incomplete DNA repair. This research study aims to investigate the role of RAD50 in breast cancer diagnosis and prognosis. METHODSBreast cancer mRNA expression data was collected from TCGA and the difference between cancer and non-cancer in gene expression of RAD50 was analyzed. The survival association of RAD50 was also analyzed. RESULTSRAD50 expression is significantly lower in cancer than in normal tissue. High expression of RAD50 is associated with worse survival. ConclusionRAD50 is a potential biomarker for breast cancer diagnosis and prognosis

cancer biology↗

Enzymatic Degrading Chlorophenol Wastewater by Mixed Strains of Immobilized White Rot Fungi

To address chlorophenol wastewater pollution, immobilized mixed white rot fungi (WRF) strain microsphere was designed as a solid degradation agent, using lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac) to degradating the wastewater. Considering the diverse physical and chemical properties of the fungal sphere, the immobilization agent formula is optimized and comprehensive environmental factor design response surface analysis are implemented to determine the delivery conditions. Consequently, the 2,4-DCP treatment rate and extracellular enzyme activity for a 1:1 encapsulation of T. versicolor and P. sajor-caju significantly outperform those of individual strains. Using polyvinyl alcohol (PVA), sodium alginate (SA), and biochar as carriers, with sodium dihydrogen phosphate solution as crosslinker and SiO2/zeolite as additives, immobilizing mixed bacteria yielded a high-quality solid agent. This achieved a 99.33% 2,4-DCP degradation rate over 96 hours, with optimal dosage, pH, and initial 2,4-DCP concentration at 11.5 g/L, 5.5, and 40 mg/L. The degradation of 2,4-DCP by WRF selectively removes adjacent chlorine atoms to produce 4-CP, enhancing the dechlorination efficiency. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/611973v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1653067org.highwire.dtl.DTLVardef@4cc31dorg.highwire.dtl.DTLVardef@19daa33org.highwire.dtl.DTLVardef@1115c5_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

scDrugAtlas: an integrative single-cell drug response atlas for unraveling tumor heterogeneity in therapeutic efficacy

Tumor heterogeneity often leads to substantial differences in responses to same drug treatment. The presence of pre-existing or acquired drug-resistant cell sub-populations within a tumor survive and proliferate, ultimately resulting in tumor relapse and metastasis. The drug resistance is the leading cause of failure in clinical tumor therapy. Therefore, accurate identification of drug-resistant tumor cell subpopulations could greatly facilitate the precision medicine and novel drug development. However, the scarcity of single-cell drug response data significantly hinders the exploration of tumor cell resistance mechanisms and the development of computational predictive methods. In this paper, we propose scDrugAtlas, a comprehensive database devoted to integrating the drug response data at single-cell level. We manually compiled more than 100 datasets containing single-cell drug responses from various public resources. The current version comprises large-scale single-cell transcriptional profiles and drug response labels from 1,023 samples (cell line, mouse, PDX models, patients and bacterium), across 78 unique drugs and 24 major cancer types. Particularly, we assigned a confidence level to each response label based on the tissue source (primary or relapse/metastasis), drug exposure time and drug-induced cell phenotype. We believe scDrugAtlas could greatly facilitate the Bioinformatics community for developing computational models and biologists for identifying drug-resistant tumor cells and underlying molecular mechanism. The scDrugAtlas database is available at: http://drug.hliulab.tech/scDrugAtlas/.

bioinformatics↗

The Greenland shark (Somniosus microcephalus) genome provides insights into extremelongevity

The Greenland shark (Somniosus microcephalus) is the longest-lived vertebrate known, with an estimated lifespan of [~] 400 years. Here, we present a chromosome-level assembly of the 6.45 Gb Greenland shark, rendering it one of the largest non-tetrapod genomes sequenced so far. Expansion of the genome is mostly accounted for by a substantial expansion of transposable elements. Using public shark genomes as a comparison, we found that genes specifically duplicated in the Greenland shark form a functionally connected network enriched for DNA repair function. Furthermore, we identified a unique insertion in the conserved C-terminal region of the key tumor suppressor p53. We also provide a public browser to explore its genome.

genomics↗

Epidermal Growth Factor Receptor Signaling Governs the Host Inflammatory Response to Invasive Aspergillosis

The epidermal growth factor receptor (EGFR) has been identified as an epithelial cell receptor for Mucorales fungi and Candida albicans. Blocking EGFR with small molecule inhibitors reduces disease severity in mouse models of mucormycosis and oropharyngeal candidiasis. In contrast, cases of invasive aspergillosis have been reported in cancer patients who were treated with EGFR inhibitors, suggesting that EGFR signaling may play a protective role in the host defense against this infection. Here, we analyzed transcriptomic data from the lungs of mice with invasive aspergillosis and found evidence that Aspergillus fumigatus infection activates multiple genes that are predicted to function in the EGFR signaling pathway. We also found that A. fumigatus infection activates EGFR in both a human small airway epithelial (HSAE) cell line and in the lungs of immunosuppressed mice. EGFR signaling in HSAE cells is required for maximal endocytosis of A. fumigatus and for fungal-induced proinflammatory cytokine and chemokine production. In a corticosteroid immunosuppressed mouse model of invasive pulmonary aspergillosis, inhibition of EGFR with gefitinib decreased whole lung chemokine levels and reduced accumulation of phagocytes in the lung, leading to a decrease in fungal killing, an increase in pulmonary fungal burden, and accelerated mortality. Thus, EGFR signaling is required for pulmonary epithelial cells to orchestrate the host innate immune defense against invasive aspergillosis in immunosuppressed hosts. ImportanceWhen A. fumigatus infects the lungs, it invades epithelial cells that line the airways. During this process, the fungus interacts with epithelial cell receptors. This interaction stimulates epithelial cells to endocytose the fungus. It also induces these cells to secret proinflammatory cytokines and chemokines that recruit phagocytes to the site of infection where they can kill the fungus. Here, we show that in small airway epithelial cells, the epidermal growth factor receptor (EGFR) acts a sensor for A. fumigatus that triggers the production of chemokines in response to fungal infection. In corticosteroid-immunosuppressed mice, blocking EGFR with the kinase inhibitor, gefitinib reduces chemokine production in the lungs. This leads to decreased accumulation of neutrophils and dendritic cell in the lungs, reduced A. fumigatus killing, and increased mortality. These results provide a potential explanation as to why some cancer patients who are treated with EGFR inhibitors develop invasive aspergillosis.

microbiology↗

Mechanisms of traditional Chinese medicine in modulating cardiac microvascular endothelial cells in various injury models: A comprehensive systematic review

BackgroundThe structural and functional failure of cardiac microvascular endothelial cells (CMECs) is a primary contributor to coronary microvascular dysfunction (CMD). Traditional Chinese medicine (TCM) has been identified as a potential therapeutic approach for preserving CMECs and mitigating CMD. ObjectiveThis systematic review aims to present the latest evidence on TCM intervention mechanisms in CMECs under diverse injury models. MethodsThis systematic review was performed following the parameters of the PRISMA statement (Preferred Reporting Items for Systematic Reviews and Meta-Analysis). A comprehensive literature search was conducted using PubMed, Embase, Web of Science, Scopus, China National Knowledge Infrastructure and China Biology Medicine disc. Reference lists of selected articles were reviewed to identify relevant studies. The search was not limited by year and was conducted solely in English. Eligible studies comprised publications describing in vitro studies that presented the latest evidence on TCM intervention mechanisms in CMECs under diverse injury models. ResultsA total of 63 papers were included in this study. According to the cell processing approach, 19 studies on ischemia or hypoxic injury models, 16 studies on Ischemia/reperfusion (I/R) or hypoxia/reoxygenation (H/R) injury models, 10 studies on inflammatory injury models, 5 studies on metabolic injury models, 3 studies on angiotensin II injury models, and 10 studies on other models. TCM exhibits structural and functional intervention capabilities in diverse damage conditions of CMECs. Its mechanism of action involves antioxidant, anti-apoptotic, anti-inflammatory effects, as well as regulation of energy metabolism through signaling pathways such as HIF-1/VEGF, PI3K/AKT, MAPK, and NF-{kappa}B. ConclusionsThe CCM and its constituents modulate CMECs through multiple signaling pathways in response to various injury models, thereby conferring protection on the coronary microcirculation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/611361v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@188068forg.highwire.dtl.DTLVardef@166c434org.highwire.dtl.DTLVardef@1db6c16org.highwire.dtl.DTLVardef@952182_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation

Rice (Oryza sativa) is one of the most important staple food crops worldwide, and its wild relatives serve as an important gene pool in its breeding. Compared with cultivated rice species, African wild rice (Oryza longistaminata) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previous O. longistaminata genome assemblies have been hampered by gaps and incompleteness, restricting detailed investigations into their genomes. To streamline breeding endeavors and facilitate functional genomics studies, we generated a 343-Mb telomere-to-telomere (T2T) genome assembly for this species, covering all telomeres and centromeres across the 12 chromosomes. This newly assembled genome has markedly improved over previous versions. Comparative analysis revealed a high degree of synteny with previously published genomes. A large number of structural variations were identified between the O. longistaminata and O. sativa. A total of 2,466 segmentally duplicated genes were identified and enriched in cellular amino acid metabolic processes. We detected a slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome of O. longistaminata provides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.

genomics↗

Subunit-specific conductance of single HCN pacemaker channels at femtosiemens resolution

Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels are tetramers that generate rhythmic electrical activity in neuronal and cardiac pacemaker cells 1. The channels are activated by hyperpolarisation of the membrane voltage and additionally tuned by the second messenger cAMP at sympathetic stimulation. There are four mammalian isoforms, HCN1-4 2-4. The single-channel conductance,{gamma} , of HCN channels remains debated, with conflicting results ranging from near 1.5 pS for HCN2 5,6 to tens of pS for HCN1 7, HCN2 7 and HCN4 7,8, though the pore structure, viewed to determine the conductance 9,10, is either identical or highly conserved. To resolve this controversy, we analyzed all four mouse isoforms mHCN1-4 at femtosiemens resolution. We show that mHCN1, mHCN3 and mHCN4 also generate small conductance values, even smaller than that of mHCN2 with the sequence{gamma} mHCN2=1.54 pS >{gamma} mHCN1=0.84 pS >{gamma} mHCN3=0.54 pS {asymp}{gamma} mHCN4=0.51 pS. As shown by systematic mutagenesis and molecular dynamic simulations, the differences in the conductance are neither generated by the selectivity filter nor the inner gate 9, but by defined negative charges in the outer channel vestibule increasing cation occupation. In line with these results, heteromers of mHCN2 with either mHCN1, mHCN3 or mHCN4 lead to graded single-channel currents in-between those of the respective homomeric channels. Our approach at femtosiemens resolution provides insight into the function of recombinant and native HCN channels at the level of single subunits and is thus promising for the development of subunit-specific drugs acting on these clinically highly relevant channels 11.

physiology↗

Yeast-MetaTwin for Systematically Exploring Yeast Metabolism through Retrobiosynthesis and Deep Learning

Underground metabolism plays a crucial role in understanding enzyme promiscuity, cellular metabolism, and biological evolution, yet experimental exploration of underground metabolism is often sparse. Even though yeast genome-scale metabolic models have been reconstructed and curated for over 20 years, more than 90% of the yeast metabolome is still not covered by these models. To address this gap, we have developed a workflow based on retrobiosynthesis and deep learning methods to comprehensively explore yeast underground metabolism. We integrated the predicted underground network into the yeast consensus genome-scale model, Yeast8, to reconstruct the yeast metabolic twin model, Yeast-MetaTwin, covering 16,244 metabolites (92% of the total yeast metabolome), 2,057 metabolic genes and 59,914 reactions. We revealed that Km parameters differ between the known and underground network, identified hub molecules connecting the underground network and pinpointed the underground percentages for yeast metabolic pathways. Moreover, the Yeast-MetaTwin can predict the by-products of chemicals produced in yeast, offering valuable insights to guide metabolic engineering designs.

synthetic biology↗

Functional characterisation of neuropeptides that act as ligands for both calcitonin-type and pigment-dispersing factor-type receptors in a deuterostome

The calcitonin (CT) family of related peptides exerts diverse physiological effects in mammals via two G-protein coupled receptors: CTR and the CTR-like receptor CLR. Phylogenetic analysis of CT-type signaling has revealed the presence of CT-type peptides and CTR/CLR-type proteins in both deuterostome and protostome invertebrates. Furthermore, experimental studies have demonstrated that in the protostome Drosophila melanogaster the CT-like peptide DH31 can act as a ligand for a CTR/CLR-type receptor and a pigment-dispersing factor (PDF) receptor. Here we investigated the signaling mechanisms and functions of CT-type neuropeptides in a deuterostome invertebrate, the sea cucumber Apostichopus japonicus (phylum Echinodermata). In A. japonicus, a single gene encodes two CT-type peptides (AjCT1 and AjCT2) and both peptides act as ligands for a CTR/CLR-type receptor (AjCTR) and two PDF-type receptors (AjPDFR1, AjPDFR2), but with differential activation of downstream cAMP/PKA, Gq/Ca2+/PKC and ERK1/2 signaling pathways. AjCT1/AjCT2-encoding transcripts were detected in the central nervous system and a variety of organ systems and neuropeptide expression was visualized immunohistochemically using an antiserum to a starfish CT-type peptide (ArCT). In vitro pharmacological experiments demonstrated that AjCT1 and/or AjCT2 cause dose-dependent relaxation of longitudinal muscle and intestine preparations. Furthermore, in vivo pharmacological experiments, combined with gain-and loss-of-function experiments, revealed a potential physiological role for AjCT2/AjPDFR2 signaling in promoting feeding and growth in A. japonicus. To our knowledge, this is the first study to obtain evidence that CT-type peptides can act as ligands for both CTR/CLR-type and PDF-type receptors in a deuterostome. Moreover, it provides the first evidence for appetite-stimulating and growth-promoting effects of CT-type neuropeptides in bilaterians. Given the economic importance of A. japonicus as a foodstuff, the discovery of CT-type peptides as potential regulators of feeding and growth in this species may offer novel strategies for aquaculture applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/610391v3_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@663885org.highwire.dtl.DTLVardef@108bea3org.highwire.dtl.DTLVardef@11bd14dorg.highwire.dtl.DTLVardef@14a2008_HPS_FORMAT_FIGEXP M_FIG C_FIG A schematic showing proposed molecular mechanisms by which CT-type signaling regulates feeding and growth in A. japonicus. AjCT1 and AjCT2 are represented by purple and yellow circles, respectively. For cell signaling, black arrows indicate that this process is activated, whilst the pink arrow indicates that ERK1/2 is activated in the AjCT1/AjPDFR1, AjCT2/AjPDFR1 and AjCT2/AjPDFR2 signaling pathways.

neuroscience↗

Blocking Toxin Function and Modulating the Gut Microbiota: Caffeic Acid and its Derivatives as Potential Treatments for Clostridioides difficile Infection

Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea that seriously threatens public health. The disruption of normal gut microbiota by the use of broad-spectrum antimicrobial agents enables C. difficile to proliferate in the colon. The emergence and prevalence of hypervirulent C. difficile strains result in increased morbidity, mortality, and high recurrence rates of CDI, thus creating a pressing need for novel therapeutics. The multi-domain toxins TcdA and TcdB are the primary determinants of CDI pathogenesis, rendering them ideal drug targets in the anti-virulence paradigm. In this study, we identified caffeic acid and its derivatives from natural compounds library as active inhibitors of TcdB via a cell-based high-throughput phenotypic screening. Further mechanistic investigations revealed that caffeic acid phenethyl ester (CAPE) could directly bind to TcdB, thus suppressing InsP6-induced autoproteolysis and inhibiting glucosyltransferase activity. CAPE treatment remarkably reduces the pathology of CDI in a murine infection model in terms of alleviated diarrhea symptoms, decreased bacterial colonization, and relieved histopathological lesions. Moreover, CAPE treatment of C. difficile-challenged mice induces a remarkable increase in the diversity and composition of the gut microbiota and alterations of gut metabolites (e.g., adenosine, D-proline, and melatonin), which might partially contribute to the therapeutic outcomes of CAPE against CDI. Our results reveal the potential of CAPE as a therapeutic for the management of CDI, or CAPE might serve as a lead compound for the development of antivirulence drugs targeting TcdB.

microbiology↗

Three-dimension transcriptomics maps of whole mouse embryo during organogenesis

Understanding mammalian development heavily relies on classical animal models like the house mouse (Mus musculus). Advanced spatial transcriptomics has enabled biologists to break new ground in studies of molecular dynamics and cellular patterning during embryonic development with spatiotemporal resolution. To construct a comprehensive developmental trajectory, current three-dimensional (3D) spatial transcriptomic profiling leverages mouse embryos from gastrulation (E5.5) to organogenesis (E13.5) in continuity. However, a crucial phase for early organogenesis between E9.5 and E11.5 was deficient. To unveil the mystery of this stage, we present the 3D transcriptomics of mouse embryos at E9.5 and E11.5, with a widely applicable reconstruction workflow that bypasses sophisticated bioinformatic calculations. As our 3D atlas is generated at single-cell resolution, we demonstrate how organogenetic processes can be interpreted at different levels of granularity, from local cellular interactions to whole embryonic regionalization. We release the open-access database MOSTA3D (Mouse Organogenesis Spatiotemporal Transcriptomic Atlas in Three-dimensional) and hope a broader community will contribute to extending this framework from conception to senility in the near future.

developmental biology↗

Identifying drug-resistant individual cells within tumors by semi-supervised domain adaptation

The presence of pre-existing or acquired drug-resistant cells within the tumor often leads to tumor relapse and metastasis. Single-cell RNA sequencing (scRNA-seq) enables elucidation of the subtle differences in drug responsiveness among distinct cell subpopulations within tumors. A few methods have employed scRNA-seq data to predict the drug response of individual cells to date, but their performance is far from satisfactory. In this study, we propose SSDA4Drug, a semi-supervised few-shot transfer learning method for inferring drug-resistant cancer cells. SSDA4Drug extracts pharmacogenomic features from both bulk and single-cell transcriptomic data using semi-supervised adversarial domain adaptation. This allows us to transfer knowledge of drug sensitivity from bulk-level cell lines to single cells. We conduct extensive performance evaluation experiments across multiple independent scRNA-seq datasets, demonstrating SSDA4Drugs superior performance over current state-of-the-art methods. Remarkably, with only one or two labeled target-domain samples, SSDA4Drug significantly boosts the predictive performance of single-cell drug responses. Moreover, SSDA4Drug accurately recapitulates the temporally dynamic changes of drug responses during continuous drug exposure of tumor cells, and successfully identifies reversible drug-responsive states in lung cancer cells, which initially acquire resistance through drug exposure but later restore sensitivity during drug holidays. Also, our predicted drug responses consistently align with the developmental patterns of drug sensitivity observed along the evolutionary trajectory of oral squamous cell carcinoma cells. In addition, our derived SHAP values and integrated gradients effectively pinpoint the key genes involved in drug resistance in prostate cancer cells. These findings highlight the exceptional performance of our method in determining single-cell drug responses. This powerful tool holds the potential for identifying drug-resistant tumor cell subpopulations, paving the way for advancements in precision medicine and novel drug development.

bioinformatics↗

Anchor Point Engineering on Anticalin Scaffolds for Enhanced Particle Adhesion to CTLA-4 Under Shear Stress

Achieving high binding strength and efficient delivery of molecular cargo to cells expressing biomarker targets is a significant challenge in drug delivery. Here, we investigated how altering the surface immobilization residue (i.e. anchor point) within a non-antibody binding scaffold called Anticalin can enhance particle adhesion to the immune checkpoint protein CTLA-4 on mammalian cells under shear stress. By introducing bio-orthogonal clickable amino acids into Anticalin at various positions and applying tension to the protein complex using single-molecule AFM force spectroscopy and bead-based adhesion assays, we elucidate the relationship between anchor point position and mechanostability of the Anticalin:(CTLA-4) complex. Multi-regression analysis of the physicochemical properties of the anchor points revealed that the distance from the anchor point on Anticalin to CTLA-4s center of mass was a major determinant of binding strength under shear flow. These results demonstrate how anchor point engineering can enhance particle adhesion and cellular delivery to CTLA-4 targets and provides a heuristic for choosing surface immobilization points of targeting proteins such that they withstand high mechanical forces.

biophysics↗

Ribosomal RNA transcription governs splicing through ribosomal protein RPL22

Ribosome biosynthesis is a cancer vulnerability executed by targeting RNA polymerase I (Pol I) transcription. We developed advanced, specific Pol I inhibitors to identify drivers of this sensitivity. By integrating multi-omics features and drug sensitivity data from a large cancer cell panel, we discovered that RPL22 frameshift mutation conferred Pol I inhibitor sensitivity in microsatellite instable cancers. Mechanistically, RPL22 directly interacts with 28S rRNA and mRNA splice junctions, functioning as a splicing regulator. RPL22 deficiency, intensified by 28S rRNA sequestration, promoted the splicing of its paralog RPL22L1 and p53 negative regulator MDM4. Chemical and genetic inhibition of rRNA synthesis broadly remodeled mRNA splicing controlling hundreds of targets. Strikingly, RPL22-dependent alternative splicing was reversed by Pol I inhibition revealing a ribotoxic stress-initiated tumor suppressive pathway. We identify a mechanism that robustly connects rRNA synthesis activity to splicing and reveals their coordination by ribosomal protein RPL22.

molecular biology↗

A novel functional coordination in UNC-13 regulates neurotransmitter release

Munc13 plays a crucial role in short-term synaptic plasticity by regulating synaptic vesicle (SV) exocytosis and neurotransmitter release at the presynaptic terminals. However, the intricate mechanisms governing these processes have remained elusive due to the presence of multiple functional domains within Munc13, each playing distinct roles in neurotransmitter release. Here we report a coordinated mechanism in the C. elegans Munc13 homolog UNC-13 that controls the functional switch of UNC-13 during synaptic transmission. Mutations disrupting the interactions of C1 and C2B with diacylglycerol (DAG) and phosphatidylinositol 4,5-bisphosphate (PIP2) on the plasma membrane induced the gain-of-function state of UNC-13L, the long UNC-13 isoform, resulting in enhanced SV release. Concurrent mutations in both domains counteracted this enhancement, highlighting the functional interdependence of C1 and C2B. Intriguingly, the individual C1 and C2B domains exhibited significantly stronger facilitation of SV release compared to the presence of both domains, supporting a mutual inhibition of C1 and C2B under basal conditions. Moreover, the N-terminal C2A and X domains exhibited opposite regulation on the functional switch of UNC-13L. Furthermore, we identified the polybasic motif in the C2B domain that facilitates SV release. Finally, we found that disruption of C1 and C2B membrane interaction in UNC-13S, the short isoform, leads to functional switch between gain-of-function and loss-of-function. Collectively, our findings provide a novel mechanism for SV exocytosis wherein UNC-13 undergoes functional switches through the coordination of its major domains, thereby regulating synaptic transmission and short-term synaptic plasticity.

neuroscience↗