Biology subjects

Zhao, P.

Publications and source records attributed to Zhao, P..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Role of channels in the O2 permeabilityof murine red blood cells. I. Stopped-flow and hematological studies

Many have believed that oxygen (O2) crosses red blood cell (RBC) membranes by dissolving in lipids that offer a finite resistance to diffusion or, alternatively, no resistance at all. In this first in a series of three interrelated papers, we examine these idea in murine RBCs. In this first paper, analyses of hemoglobin (Hb) absorbance spectra during O2 off-loading from mouse RBCs indicate that RBC membranes do indeed offer resistance to O2 diffusion, and that the resistance would be far higher if not for the presence of O2-permeable channels. Two agents-- both excluded from the RBC interior--markedly reduce the rate constant for O2 off-loading (kHbO2): p-chloromercuribenzenesulfonate (pCMBS) reduces membrane O2 permeability (PM,O2 by [~]82% (computed from kHbO2 in paper #3), and 4,4-diisothiocyanatostilbene-2,2-disulfonate (DIDS) by [~]56%. Because neither likely produces these effects via membrane lipids, we examined RBCs from mice genetically deficient in aquaporin-1 (AQP1), the Rh complex (RhCx = Rhesus blood group-associated A glycoprotein, RhAG + Rhesus blood group D antigen, RhD), or both. The double knockout (dKO) reduces PM,O2 by [~]55%, and pCMBS+dKO, by [~]91%. Proteomic analyses of RBC membranes, flow cytometry, hematology (see paper #2), and mathematical simulations (paper #3) rule out meaningful contributions from other membrane proteins, RBC geometry, or extracellular unconvected fluid (EUF). Our work represents a paradigm shift for O2 physiology by identifying the first two animal O2 channels, and points to the existence of at least a third, all of which could be subject to physiological regulation and pharmacological intervention. Key PointsO_LISome have held that red-blood-cell (RBC) membranes have a finite O2 permeability, governed by O2 solubility in membrane lipids; others, that membranes offer no resistance whatsoever to O2 diffusion. C_LIO_LIThe present interdisciplinary study comprises three papers. This first paper describes stopped-flow absorbance spectroscopy in which we examine the rate constant of O2 offloading from intact RBCs (kHbO2) from wild-type (WT) mice or those lacking AQP1 and/or RhAG, sometimes treated with p-chloromercuribenzenesulfonate (pCMBS) or 4,4-diisothiocyanatostilbene-2,2-disulfonate (DIDS). C_LIO_LIThe second paper describes RBC morphometry and membrane proteomics. The third introduces a mathematical reaction-diffusion model that generates simulations comporting with physiological data. C_LIO_LIThis first paper shows that pCMBS or DIDS treatments, or deletion of AQP1 and/or RhAG, or combinations thereof, substantially reduce kHbO2. C_LIO_LIThe three papers show that WT RBC membranes offer considerable resistance to O2 diffusion. AQP1 ([~]22%), Rh ([~]36%), and an unknown pCMBS-sensitive protein account for [~]91% of membrane O2 permeability. C_LI

physiology↗

bioRxiv2025

Role of channels in the O2 permeability of murine red blood cells II. Morphological and proteomic studies

In this second of three papers, we examine red blood cell (RBC) morphometry and RBC-membrane proteomics from our laboratory mouse strain (C57BL/6Case). In paper #1, using stopped-flow absorbance spectroscopy to ascertain the rate constant for oxyhemoglobin (HbO2) deoxygenation (kHbO2), we find substantial kHbO2 reductions with (1) membrane-protein inhibitors p-chloromercuribenzenesulfonate (pCMBS) or 4,4-diisothiocyanatostilbene-2,2-disulfonate (DIDS); (2) knockouts of aquaporin-1 (AQP1-KO), or Rhesus blood-group-associated A-glycoprotein (RhAG-KO), or double knockouts (dKO); or (3) inhibitor+dKO. In paper #3, reaction-diffusion mathematical modeling/simulations reveal that kHbO2 could fall secondary to slowed intracellular O2/HbO2/Hb diffusion. Here in paper #2, blood smears as well as still/video images and imaging flow cytometry (IFC) of living RBCs show that [~]97.5% to [~]98.6% of control (not drug-treated) cells are biconcave disks (BCDs) across all genotypes. Pretreatment with pCMBS raises non-BCD abundance to [~]8.7% for WT and [~]5.7% for dKO; for DIDS pretreatment, the figures are [~]41% and [~]21%, respectively. Modeling (paper #3) accommodates for these shape changes. Light-scattering flow cytometry shows no significant difference in RBC size or shape among genotypes. IFC reveals minor differences among genotypes in RBC major diameter (OMajor), which (along with mean corpuscular volume, paper #1) yields RBC thickness for simulations in paper #3. Label-free liquid chromatography/tandem mass spectrometry (LC/MS/MS) proteomic analyses of RBC plasma-membrane ghosts confirm the deletion of proteins targeted by our knockouts, and rule out changes in the 100 proteins of greatest inferred abundance. Thus, genetically induced changes in kHbO2 must reflect altered abundance of AQP1 and /or the Rh complex. Key PointsO_LIO2-offloading from red blood cells (RBCs) depends not only on membrane O2 permeability and oxyhemoglobin dissociation, but also on RBC size and shape. In this second of three papers, we use blood smears, still/video images of living RBCs, and imaging flow cytometry to examine morphometry of RBCs from paper #1. C_LIO_LIWe find that mouse RBCs of all genotypes--wild-type, aquaporin-1 knockout (AQP1-KO), Rhesus blood group-associated A-glycoprotein knockout (RhAG-KO), and double knockout--are dominantly biconcave discs, with [~]1.4% to [~]2.5% poikilocytosis (shape change, SC). Drug pre-treatment increases %SC. C_LIO_LIUsing label-free liquid chromatography/tandem mass spectrometry to assess apparent abundance of RBC-ghost proteins, we find no significant differences among genotypes for any of the [~]100 most abundant protein species except, as appropriate, AQP1, RhAG, or Rhesus blood group D antigen. C_LIO_LIThus, the substantial effects observed in paper #1 cannot be attributed to differences in morphometry or protein content. C_LI

physiology↗

bioRxiv2025

Role of channels in the O2 permeability of murine red blood cells. III. Mathematical modeling and simulations.

In this third of three papers, we develop a reaction-diffusion model for O2 offloading from a red blood cell (RBC), treated as a sphere with diameter approximating RBC thickness. Stopped-flow (SF) analysis (paper #1) of hemoglobin/oxyhemoglobin (Hb/HbO2) absorbance spectra during O2 efflux from intact murine RBCs show that membrane-impermeant inhibitor p-chloromercuribenzenesulfonate (pCMBS) reduces the HbO2-deoxygenation rate constant (kHbO2) by [~]61%. SF experiments show that kHbO2 falls by (1) 9% for aquaporin-1 knockouts (AQP1-KOs), (2) 17% for Rhesus A-glycoprotein knockouts (RhAG-KOs), (3) 30% for double knockouts (dKOs), and (4) [~]78% in dKOs/pCMBS. Here, we simulate HbO2 dissociation in the intact RBC (i.e., kHbO2); HbO2, Hb, and O2 diffusion through RBC cytosol; transmembrane O2 diffusion; and O2 diffusion through extracellular unconvected fluid (EUF) to bulk extracellular fluid. Informed by automated-hematology data (paper #1) and imaging-flow-cytometry data (paper #2), simulations predict that observed kHbO2 decreases cannot reflect changes only in RBC size/shape or [Hb/HbO2]. Instead, membrane O2 permeability (PM,O2) must fall by (1) 22% to account for AQP1-KO data, (2) 36% for RhAG-KOs, (3) 55% for dKOs, and (4) 91% for dKOs/pCMBS. Exploring predicted kHbO2 sensitivities to eight key parameters (e.g., [Hb/HbO2], diffusion constants, kHbO2[->]Hb+O2, thicknessEUF, diameterSphere) shows that no reasonable changes explain the kHbO2 data. We introduce a linear-combination approach to accommodate for the presence of poikilocytes. Finally, contrary to common beliefs, the model predicts that, in the absence of inhibitors, the RBC membrane represents >30% of total diffusive "resistance" to O2 offloading, even for a WT mouse. Key PointsO_LIIn this third of three papers, we develop a novel reaction-diffusion model for O2 offloading from a red blood cell (RBC), treated as a sphere with diameter approximating RBC thickness. C_LIO_LIUsing physical constants and parameter values from the literature and papers #1 and #2, we generate simulations that reproduce observed hemoglobin desaturation (rate constant, kHbO2) of intact RBCs from wild-type mice. C_LIO_LITo simulate kHbO2 decreases (9%, 17%, 30%) observed in RBCs from knockouts (KOs: aquaporin-1, Rhesus A-glycoprotein, both) we must decrease membrane O2 permeability (PM,O2) by far greater percentages (22%, 36%, 55%). C_LIO_LIAnalyses of simulated-kHbO2 sensitivity to kinetic and geometric parameters suggest that reasonable parameter-value changes cannot explain experimentally observed kHbO2 decreases in RBCs from KOs. Thus, experimentally observed kHbO2 decreases must reflect decreases in PM,O2. C_LIO_LITo accommodate for poikilocytes, we develop a linear-combination approach (poikilocytes + biconcave disks, BCDs) to extract the kHbO2 and PM,O2 of just BCDs. C_LI

physiology↗

bioRxiv2025

DMBT1 promotes SARS-CoV-2 infection and its SRCR-derived peptide inhibits SARS-CoV-2 infection

DMBT1 is a large scavenger receptor cysteine rich (SRCR) B protein that has been reported as a tumor suppressor gene and a co-receptor for HIV-1 infection. Here we found DMBT1 is a major mucosal protein bound to SARS-CoV-2. Overexpression of DMBT1 in 293T cells enhanced infection by SARS-CoV-2 in ACE2 dependent manner. Blocking experiments using overlapping peptide library of SRCR domain of DMBT1 showed that CQGRVEVLYRGSWGTV peptide, which contains bacteria-binding VEVLXXXXW motif, could inhibit SARS-CoV-2 infection. High concentration of the peptide can significantly inhibit the replication of SARS-CoV-2 in hamsters. Single cell sequencing analysis showed the highest expression abundance of DMBT1 at airway submucosal glands. These results demonstrate that membrane DMBT1 can promote SARS-CoV-2 infection, and serve as a candidate target for antiviral development. Author SummaryWe discovered that a protein named as DMBT1, which is found in our mucous membranes, plays a significant role in SARS-CoV-2 infection. DMBT1 is a large glycoprotein that has previously reported linked to tumor suppression and HIV-1 infection. Our single-cell sequencing analysis revealed that DMBT1 is most abundant in the airway submucosal glands. In our study, we found that when DMBT1 is overexpressed in cells, it enhances SARS-CoV-2 infection. Using a peptide library from DMBT1, we pinpointed a specific peptide, CQGRVEVLYRGSWGTV, which can inhibit SARS-CoV-2 infection. At high concentrations, it significantly reduces the viruss ability to replicate in hamsters. These findings suggest that DMBT1 on the cell membrane can promote SARS-CoV-2 infection and highlight DMBT1 as a potential target for developing antiviral treatments.

microbiology↗

bioRxiv2025

Generalization but not strengthening of negative memories drives the development of depression-like behaviors

Individuals with depression exhibit intensified and generalized negative memories. However, how prior memories actually influence onset and/or progression of depression, particularly whether the strengthening or the generalization of prior memories play a key role, is poorly understood. Here, we introduced behavioral paradigms to differentiate between memory strengthening and generalization, and found that negative experiences that produced memory overgeneralization, but not strengthening, induced depression-like behaviors. Furthermore, we identified that the medial prefrontal cortex (mPFC) to the bed nucleus of the stria terminals (BNST) projection functionally linked memory generalization to depression, together with single-cell calcium imaging which revealed a significant overlap in the mPFCBNST neuronal ensemble encoding depression-like behaviors with that encoding generalized memory, but not memory strength. Circuit-based transcriptomic analysis and chromophore-assisted light inactivation demonstrated that triggering actin remodeling in the mPFCBNST neurons, a memory consolidation mechanism enhanced generalization while reducing memory strength, also induced depression-like behaviors. Collectively, these findings suggest generalization of negative memories as a primary factor that drives depression-like behaviors, highlighting the importance of early identification of individuals at risk for depression who exhibit overgeneralized negative memories, and targeting overgeneralized negative memories in the treatment of depression.

animal behavior and cognition↗

bioRxiv2025

TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

Cis-regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce Transposase-Accessible Chromosome Conformation Capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals that chromatin interaction frequency aligns with genome size and gene expression, exhibiting distinct loop structures between C3 and C4 plants, particularly in C4-specific enzymes coding genes. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. Asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in Taspl7&15 mutant. TAC-C provides new insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat. TeaserTAC-C Reveals Chromatin Interactions and SPL-Mediated Photosynthesis Regulation in Crops.

plant biology↗

bioRxiv2025

Targeted ubiquitination of NaV1.8 reduces sensory neuronal excitability

Chronic pain and addiction are a significant global health challenge. Voltage-gated sodium channel NaV1.8, a pivotal driver of pain signaling, is a clinically validated target for the development of novel, non-addictive pain therapeutics. Small molecule inhibitors against NaV1.8 have shown promise in acute pain indications, but large clinical effect sizes have not yet been demonstrated and efficacy in chronic pain indications are lacking. An alternative strategy to target NaV1.8 channels for analgesia is to reduce the number of channels that are present on nociceptor membranes. We generated a therapeutic heterobifunctional protein, named UbiquiNaV, that contains a NaV1.8-selective binding module and the catalytic subunit of the NEDD4 E3 Ubiquitin ligase. We show that UbiquiNav significantly reduces channel expression in the plasma membrane and reduces NaV1.8 currents in rodent sensory neurons. We demonstrate that UbiquiNaV is selective for NaV1.8 over other NaV isoforms and other components of the sensory neuronal electrogenisome. We then show that UbiquiNaV normalizes the distribution of NaV1.8 protein to distal axons, and that UbiquiNaV normalizes the neuronal hyperexcitability in in vitro models of inflammatory and chemotherapy-induced neuropathic pain. Our results serve as a blueprint for the design of therapeutics that leverage the selective ubiquitination of NaV1.8 channels for analgesia.

neuroscience↗

bioRxiv2025

Title: Cell-autonomous and non-cell-autonomous effects of TRIM72 on ALS disease progression

Dysfunction of RNA-binding proteins, including TDP-43 and FUS, has been associated with amyotrophic lateral sclerosis (ALS); however, the underlying mechanisms are largely unknown. Here, we reported that a neuronal upregulation of TRIM72 (Tripartite Motif Containing 72) in FUS mutation knockin ALS models slows disease progression. TRIM72 interacts with Commander, a protein complex for recycling of membrane proteins, facilitating membrane repair and antioxidation. Exosomal TRIM72 is detected in ALS patient cerebrospinal fluid (CSF) and extracellular application of exosomal TRIM72 protects cell from membrane damage. In a sporadic ALS cohort, CSF TRIM72 level associates ALS disease progression. AAV-mediated neuronal expression of TRIM72 slows down the disease progressions in ALS models and in an ALS patient without adverse effects over a year treatment course. Taken together, our results suggest a universal neuronal protection of a TRIM family protein in cell-autonomous and non-cell-autonomous manners in ALS.

neuroscience↗

bioRxiv2024

Integrative Omics reveals genetic basis and TaMYB7-A1's function in wheat WUE and drought resilience

Improving water use efficiency (WUE) and drought resistance in wheat is critical for ensuring global food security under changing climate conditions. Here, we integrated multi-omic data, including population-scale phenotyping, transcriptomics, and genomics, to dissect the genetic and molecular mechanisms underlying WUE and drought resilience in wheat. Genome-wide association studies (GWAS) revealed 8,135 SNPs associated with WUE-related traits, identifying 258 conditional and non-conditional QTLs, many of which co-localized with known drought-resistance genes. Pan-transcriptome analysis uncovered tissue-specific expression patterns, core and unique gene functions, and dynamic sub-genomic biases in response to drought. eQTL mapping pinpointed 146,966 regulatory loci, including condition-specific hotspots enriched for genes involved in water regulation, osmoregulation, and photosynthesis. Integration of Weighted gene co-expression network analysis (WGCNA), Summary-data-based Mendelian Randomization (SMR) and GWAS, eQTLs identified 207 candidate causal genes as key regulators for WUE-related traits in wheat, such as TaMYB7-A1. Functional analyses found that TaMYB7-A1 enhances drought tolerance by promoting root growth, reducing oxidative stress, and improving osmotic regulation, enabling better water access and survival under stress. It also increases photosynthesis efficiency and WUE, boosting yield under drought without compromising performance in well-watered conditions, making it ideal target for breeding. Our findings provide a comprehensive omic framework for understanding the genetic architecture of WUE and drought resistance, offering valuable targets for breeding resilient wheat varieties.

plant biology↗

bioRxiv2024

Development of a Novel Hybprinter-SAM for Functionally Graded Tissue Engineering Constructs with Patterned and Localized Biochemical Signals

Engineering native-mimetic tissue constructs is challenging due to their intricate biological and structural gradients. To address this, Hybprinter-SAM was developed by integrating three bioprinting technologies: syringe extrusion (SE), acoustic droplet ejection (ADE) and molten material extrusion (MME). This system enables not only the creation of mechanical gradients by combining soft and rigid materials but also precise patterning and controlled localization of biochemical signals within printed scaffolds. This capability is beneficial in replicating the complexity of native tissues to enhance functionality. Both the printing process and biomaterials were optimized to balance printability, mechanical integrity, and biocompatibility. As a proof of concept, Hybprinter-SAM was used in a bone-tendon regeneration study to engineer a multi-material construct with patterned fibroblast growth factor 2 (FGF-2), resulting in markers indicative of fibrocartilage development. These findings highlight the potential of Hybprinter-SAM as a versatile platform for diverse tissue engineering applications that require complex, functionally graded tissue constructs.

bioengineering↗

bioRxiv2024

p300/CBP-catalyzed acetylation safeguards minor zygotic genome activation via activating DUX

Zygotic genome activation (ZGA), the first transcriptional event at the onset of life, is crucial for early embryonic development. However, the mechanisms that initiate and regulate ZGA in mammals remain poorly understood. In this study, we demonstrate that p300/CBP-catalyzed acetylation plays a vital role in regulating ZGA. Inhibition of p300/CBP acetyltransferase activity results in impaired minor ZGA and a subsequent 2-cell arrest. By profiling the dynamic landscape of p300 during the ZGA stage, we elucidate the distinct patterns of p300 establishment in promoter and enhancer regions. Moreover, p300 recruits RNA polymerase (Pol II) to pre-configure in the promoter regions of ZGA genes, and orchestrates the gradual establishment of enhancer activity during the early 2-cell stage to activate ZGA. Furthermore, p300 enhances minor ZGA by promoting the expression of DUX. Restoring DUX levels, which are diminished due to p300/CBP inhibition, rescues ZGA and embryonic development by re-establishing Pol II enrichment on minor ZGA genes. Overall, our findings elucidate the mechanism by which p300/CBP regulates ZGA through acetylation and activation of the key transcription factor DUX. HighlightsO_LIp300/CBP plays a stage-specific role during preimplantation development phase. C_LIO_LIp300 displays distinctive dynamic changes in promoter and enhancer regions during ZGA stage. C_LIO_LIp300/CBP-catalyzed acetylation facilitates the pre-configuration and elongation of Pol II at ZGA gene regions. C_LIO_LIDUX recruits p300 and Pol II to activate minor ZGA genes independently of p300s catalytic activity. C_LI

developmental biology↗

bioRxiv2024

Replication stress marker phospho-RPA2 predicts response to platinum and PARP inhibitors in homologous recombination-proficient ovarian cancer

BackgroundOvarian cancer treatment includes cytoreductive surgery, platinum-based chemotherapy, and often poly (ADP-ribose) polymerase (PARP) inhibitors. Homologous recombination (HR)-deficiency is a well-established predictor of therapy sensitivity. However, over 50% of HR-proficient tumors also exhibit sensitivity to standard-of-care treatments. Currently, there are no biomarkers to identify which HR-proficient tumors will be sensitive to standard-of-care therapy. Replication stress may serve as a key determinant of response. MethodsWe evaluated phospho-RPA2-T21 (pRPA2) foci via immunofluorescence as a potential biomarker of replication stress in formalin-fixed, paraffin-embedded tumor samples collected at diagnosis from patients treated with platinum chemotherapy (discovery cohort: n = 31, validation cohort: n = 244) or PARP inhibitors (n = 87). Recurrent tumors (n = 37) were also analyzed. pRPA2 scores were calculated using automated imaging analysis. Samples were defined as pRPA2-High if > 16% of cells had [≥] 2 pRPA2 foci. ResultsIn the discovery cohort, HR-proficient, pRPA2-High tumors demonstrated significantly higher rates of pathologic complete response to platinum chemotherapy than HR-proficient, pRPA2-Low tumors. In the validation cohort, patients with HR-proficient, pRPA2-High tumors had significantly longer survival after platinum treatment than those with HR-proficient, pRPA2-Low tumors. Additionally, the pRPA2 assay effectively predicted survival outcomes in patients treated with PARP inhibitors and in recurrent tumor samples. ConclusionOur study underscores the importance of considering replication stress markers alongside HR status in therapeutic planning. Our work suggest that this assay could be used throughout a patients treatment course to expand the number of patients receiving effective therapy while reducing unnecessary toxicity.

cancer biology↗

bioRxiv2024

Profiling amino acid substitution on proteomic scale unveils novel protein regulation in cancer diseases

Amino acid (AA) substitutions play a critical role in regulating cellular activities, including complex signaling and cell cycle processes. Recent research on AA substitutions has primarily relied on genomic and transcriptomic data. The identification at the proteomic scale remains underexplored, despite evidence suggesting that DNA and RNA biosynthesis are not the sole sources of these substitutions. This gap persists due to challenges in analyzing large-scale proteomic data. In this study, we address this limitation by analyzing multiple independent datasets across five cancer types using PIPI-C, a novel mass spectrometry data analysis tool. And we propose AA substitutomics, a pipeline for characterizing AA substitutions arising after protein translation and dissecting the regulatory functions of key proteins with AA substitutions. Among our identified AA substitutions, 87% are novel findings and not recorded in genomic/transcriptomic databases, which indicates that the post-translational AA substitutions are prevalent. Our findings reveal biologically significant AA substitutions linked to cancer, such as F43S and E91D in hemoglobin subunit beta, P584T in filamin A, and A175N in fructose-bisphosphate aldolase B. Furthermore, our pipeline enables direct investigation of drug resistance and immune escape. By capturing functional protein-level alterations beyond genomic and transcriptomic profiling, it establishes a robust framework to advance cancer research.

cancer biology↗

bioRxiv2024

Systems genetic dissection of Alzheimer's disease brain gene expression networks

In Alzheimers disease (AD), changes in the brain transcriptome are hypothesized to mediate the impact of neuropathology on cognition. Gene expression profiling from postmortem brain tissue is a promising approach to identify causal pathways; however, there are challenges to definitively resolve the upstream pathologic triggers along with the downstream consequences for AD clinical manifestations. We have functionally dissected 30 AD-associated gene coexpression modules using a cross-species strategy in fruit fly (Drosophila melanogaster) models. Integrating longitudinal RNA-sequencing and behavioral phenotyping, we interrogated the unique and shared transcriptional responses to amyloid beta (A{beta}) plaques, tau neurofibrillary tangles, and/or aging, along with potential links to progressive neuronal dysfunction. Our results highlight hundreds of conserved, differentially expressed genes mapping to human AD regulatory networks. To confirm causal modules and pinpoint AD network drivers, we performed systematic in vivo genetic manipulations of 357 conserved, prioritized targets, identifying 141 modifiers of A{beta}- and/or tau-induced neurodegeneration. We discover an up-regulated network that is significantly enriched for both AD risk variants and markers of immunity / inflammation, and which promotes A{beta} and tau-mediated neurodegeneration based on fly genetic manipulations in neurons. By contrast, a synaptic regulatory network is strongly downregulated in human brains with AD and is enriched for loss-of-function suppressors of A{beta}/tau in Drosophila. Additional experiments suggest that this human brain transcriptional module may respond to and modulate A{beta}-induced glutamatergic hyperactivation injury. In sum, our cross-species, systems genetic approach establishes a putative causal chain linking AD pathology, large-scale gene expression perturbations, and ultimately, neurodegeneration.

systems biology↗

bioRxiv2024

IgGM: A Generative Model for Functional Antibody and Nanobody Design

AO_SCPLOWBSTRACTC_SCPLOWImmunoglobulins are crucial proteins produced by the immune system to identify and bind to foreign substances, playing an essential role in shielding organisms from infections and diseases. Designing specific antibodies opens new pathways for disease treatment. With the rise of deep learning, AI-driven drug design has become possible, leading to several methods for antibody design. However, many of these approaches require additional conditions that differ from real-world scenarios, making it challenging to incorporate them into existing antibody design processes. Here, we introduce IgGM, a generative model for the de novo design of immunoglobulins with functional specificity. IgGM produces antibody sequences and structures simultaneously for a given antigen, consisting of three core components: a pre-trained language model for extracting sequence features, a feature learning module for identifying pertinent features, and a prediction module that outputs designed antibody sequences and the predicted complete antibody-antigen complex structure. IgGM has demonstrated its effectiveness in not only predicting structures but also designing novel antibodies and nanobodies. This makes it highly applicable in a wide range of practical situations related to antibody and nanobody design. 1

bioinformatics↗

bioRxiv2024

Coat protein of TCV suppresses RNA decay via ubiquitination and autophagy pathways to facilitate viral infection

Highlight statementThe findings highlight that TCV manipulates 26S proteasome and autophagy pathways to obstruct antiviral RNA decay defenses and ultimately enhance its ability to infect host cells. RNA decay is a pervasive process in eukaryotic cells. Viruses utilize the host cells intracellular machinery to gain access to essential molecules and subcellular structures required for infection during the pathogenesis process. The study demonstrates that turnip crinkle virus (TCV) infection enhances the expression of Arabidopsis Dcp1 (AtDcp1), which negatively regulates the accumulation of TCV RNA, indicating its involvement in antiviral defense. Nevertheless, TCV circumvents the antiviral defense based on RNA decay, as indicated by the capsid protein (CP) of TCV stabilizing the known nonsense-mediated RNA decay targeted transcripts. In vivo, CP physically interacts with AtDcp1, promoting AtDcp1 degradation via ubiquitination and autophagy pathways. This is evidenced by the observation that the degradation is inhibited by both 26S proteasome and autophagy inhibitors. Furthermore, CP elevates the polyubiquitination of Dcp1-Flag and the quantity of pre-autophagosome or autophagosome structures. These data indicate that CP suppresses RNA decay by interacting with AtDcp1 and mediating its degradation through the 26S proteasome and autophagy pathways, effectively subduing antiviral RNA decay. This study uncovers a previously unidentified virulence strategy in the ongoing conflict between plants and viruses.

pathology↗

bioRxiv2024

5UTR translational inhibition of neuroblastoma dependency factors using the CR-1-31-B rocaglate

Current therapies for neuroblastoma are often ineffective and survivors suffer from severe long-term therapy related side-effects, underscoring the need for identification of novel drugging strategies. We performed an in-depth evaluation of phenotypic and molecular responses following exposure of neuroblastoma cells to the rocaglate CR-1-31-B, scrutinizing its mode-of-action through integrative ribosome footprinting and shotgun proteome profiling. We could show that CR-1-31-B significantly reduces tumor growth in vivo without apparent toxicity. By means of combined ribosome footprinting and transcriptome analysis we uncovered that CR-1-31-B treatment downregulates translation efficiencies of several major neuroblastoma dependencies including MYCN, CCND1 and ALK as well as factors involved in the G2/M checkpoint. Upregulated targets are enriched for oxidative phosphorylation pathway components and DNA repair. At the proteome level, CR-1-31-B imposed downregulation of a FOXM1 driven signature, including the FOXM1 target gene TPX2. We show that neuroblastoma cells are dependent on TPX2 for growth and DNA repair and further demonstrate enhanced CHK1 sensitivity upon TPX2 knockdown. Next, we also observed synergistic effects of CHK1 inhibition with CR-1-31-B. In conclusion, our data support CR-1-31-B as a potent novel therapeutic agent in neuroblastoma, in particular in combination with DNA damage or replication stress inducing agents.

cancer biology↗

bioRxiv2024

MiniXL: An open-source, large field-of-view epifluorescence miniature microscope for mice capable of single-cell resolution and multi-brain region imaging

Capturing the intricate dynamics of neural activity in freely behaving animals is essential for understanding the neural mechanisms underpinning specific behaviors. Miniaturized microscopy enables investigators to track population activity at cellular level, but the field of view (FOV) of these microscopes have been limited and does not allow multiple-brain region imaging. To fill this technological gap, we have developed the eXtra Large field-of-view Miniscope (MiniXL), a 3.5g lightweight miniaturized microscope with an FOV measuring 3.5 mm in diameter and an electrically adjustable working distance of 1.9 mm {+/-} 200 m. We demonstrated the capability of MiniXL recording the activity of large neuronal population in both subcortical area (hippocampal dorsal CA1) and deep brain regions (medial prefrontal cortex, mPFC and nucleus accumbens, NAc). The large FOV allows simultaneous imaging of multiple brain regions such as bilateral mPFCs or mPFC and NAc during complex social behavior and tracking cells across multiple sessions. As with all microscopes in the UCLA Miniscope ecosystem, the MiniXL is fully open-source and will be shared with the neuroscience community to lower the barriers for adoption of this technology.

neuroscience↗