Search bioRxiv⌕ Search

Biology subjects

Guo, F.

Publications and source records attributed to Guo, F..

At least 37 records · Page 2Linked to original sources

Identification of a neural circuit that enables safe, long-term torpor in mice

Torpor, a state of regulated hypothermia and hypometabolism, is a critical survival strategy in certain mammals. Previous studies established the primacy of neuron control in initiating acute torpor. However, whether neuromodulation can safely sustain torpor over the long term, and the specific governing pathways, remain unanswered challenges limiting its translational potential. Here we identify a distinct preoptic neuronal population expressing General control nonderepressible 2 ( G neurons) in mice that is essential and sufficient for torpor induction. Strikingly, sustained and selective activation of G neurons induces a stable, weeks-long torpid state (G neuron-driven long-term torpor, GLT), from which animals arouse without obvious behavioral deficits or tissue pathology. In contrast, long-term torpor driven by pan-neuronal activation of the same brain region (PLT) causes multiple post-recovery damages, underscoring the unique safety profile of selective pathway of G neurons. In a mouse cancer model, GLT directly suppressed tumor proliferation and markedly sensitized tumors to chemotherapy, achieving profound therapeutic outcomes. Together, we delineate a distinct neuronal population safely enabling prolonged torpor. This establishes a specific paradigm for inducing a stable and sustained hypometabolic state, providing a transformative platform for fundamental physiological research and pioneering clinical strategies against chronic pathologies such as cancer.

neuroscience↗

PARP1 regulates the genomic ribonucleotide processing activity of TOP1 to prevent the formation of toxic TOP1-DNA adducts and the associated mutations.

Ribonucleotides are frequently incorporated into our genome during replication. Canonically, RNase H2 is responsible for the removal of these embedded ribonucleotides. Alternatively, DNA topoisomerase 1 (TOP1) has also been shown to have genomic ribonucleotide processing activity. When this process occurs at short tandem repeat (STR) sequences, it can lead to 2-5 bp deletions. These deletions are the result of two sequential cuts by TOP1 at sites of ribonucleotide incorporation. In this study, we have determined that PARP1 regulates the TOP1-mediated excision of ribonucleotides by preventing the formation of TOP1-DNA adducts that occur through a second cleavage following the initial ribonucleotide cut by TOP1. We biochemically defined the mechanism by which this regulatory inhibition of TOP1 occurs, which involves both PARP1 physically restricting TOP1 from the cleavage site followed by the inhibitory PARylation of TOP1. We also show that this activity means that PARP1 prevents the TOP1-dependent deletions at STRs in cells. In the absence of both a functional RNase H2 complex and PARP1, we demonstrated that cells appear to be in a senescent state provoked by the accumulation of TOP1-DNA adducts, which are a result of TOP1 being unimpeded to remove genomic ribonucleotides. Our work has elucidated the role of PARP1 in preventing the deleterious consequences of the processing of genomic ribonucleotides by TOP1. Understanding this mechanism could help us develop therapies that better sensitize tumors to PARP inhibitors, especially in cancers that present loss-of-function RNase H2 mutations (seen in certain chronic lymphocytic leukemia and prostate cancers).

biochemistry↗

The tongue-brain axis mediates a hidden amino acid appetite

Selecting a diet containing all essential amino acids (EAAs) is critical for health. Following EAA deprivation, animals can select a nutritiously complete food source; however, the underlying mechanisms in vertebrates remain unclear. In mice, we show that leucine deficiency activates hypothalamic agouti-related protein (AgRP) neurons, which project to the paraventricular thalamus (PVT) via {gamma}-aminobutyric acid and are required for EAA deficiency-induced leucine appetite in mice. Furthermore, the peripheral tongue amino acid sensor general control nonderepressive-2 (GCN2) mediates acute EAA appetite via AgRP neurons. Together, these findings identify a tongue-AgRP-PVT circuit underlying EAA appetite, which is important for the rapid and accurate selection of essential nutrients.

neuroscience↗

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

Injury-transduced SerpinOLs modulate neuroinflammation and glial activation in the diseased and non-diseased CNS

Oligodendroglial dysfunction is common in CNS diseases and injuries, but the molecular and functional responses of oligodendroglia to CNS pathologies remain poorly defined. Here, we report that oligodendrocytes (OLs) respond to demyelinating diseases by dysregulating serine protease inhibitor clade A member 3N (SERPINA3N). Homeostatic OLs transition to Serpina3n-expressing OLs (SerpinOLs) under other diseased conditions including stroke, endotoxicity, neurodegeneration, neurotrauma, and non-diseased healthy aging conditions. Mechanistically, general neuroinflammation or inflammatory mediators is insufficient for SerpinOL transition. Instead, oligodendrocyte damage/injury, even in the absence of neuroinflammation or glial activation, is sufficient for the transition. Phenotypically, SerpinOLs are characterized by molecular signatures of inflammatory and immune regulation and STAT3 signaling activation. Functionally, SerpinOLs exacerbate neuroinflammation and promote glial activation toward pro-inflammatory and neurodegenerative states. Together, our findings suggest SerpinOLs are a common population of injury-transduced OLs that amplify neuroinflammation and glial activation in the diseased and non-diseased CNS through SERPINA3N secretion. Our findings provide new insights into myelination-independent role of OLs in regulating CNS pathophysiology.

neuroscience↗

Transcriptomic and functional characterization indicate sexual dimorphism of discrete circadian neuron subtypes

While many sexually dimorphic behaviors exhibit distinct time-of-day preferences, our understanding of how sex shapes the molecular and circuit properties of central brain neurons remain limited. Here, we uncover the transcriptomic and circuit basis of sexual dimorphism within the Drosophila circadian network. By leveraging single-cell RNA sequencing of male and female clock neurons, we identify specific subsets of dorsal lateral neurons (LNds), dorsal neurons 1p (DN1ps), and dorsal neurons 3 (DN3s) with dramatic dimorphic gene expression profiles. These sex differences are primarily characterized by cell-type-specific expression of genes involved in neural connectivity, particularly cell adhesion molecules (CAMs). Focusing on the dimorphic Cry-negative E3 LNds, we show that they form functionally active, synaptic connections with downstream doublesex-expressing pC1 and pCd-1 neurons, which serve as central regulators of dimorphic behaviors. Moreover, we demonstrate that formation and maintenance of these connections are mediated at least in part by sex-enriched CAMs, dpr9 in males and dpr3 in females. Thus, our work reveals sexual differentiation mechanisms at both the molecular and circuit levels, identifying specific molecules that sculpt sex-specific pathways to link the circadian clock to dimorphic outputs.

molecular biology↗

IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by A Low-Affinity Antibody

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. We report P5-1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low-affinity yet high-potency" phenotype, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, we show that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design. Graphical AbstractLow-affinity antibodies are frequently disregarded in discovery pipelines. This work reports P5-1C8, a Class 1 SARS-CoV-2 antibody with weak trimer binding (KD-to-IC50 > 3,700-fold) yet potent neutralization of Omicron JN.1. Structural, biophysical, functional and coarse-grained simulations collectively demonstrate that transient inter-spike IgG bridging seeds higher-order aggregation, which in turn drives neutralization and provides a mechanistic framework. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/691454v1_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1d4f132org.highwire.dtl.DTLVardef@1274400org.highwire.dtl.DTLVardef@e186a6org.highwire.dtl.DTLVardef@4f1870_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Modelling mental disorders in zebrafish. Neurexins severely modulate anxiety, social behaviours and aggression.

Can we reproduce mental disorders in zebrafish? To explore this question, we manipulated the neurexin gene family. Neurexin (nrxn) genes encode synaptic cell-adhesion molecules that have been repetitively associated with neurodevelopmental and mental disorders. While the zebrafish animal model offers tremendous advantages for dissecting neural development/function, no robust nrxn zebrafish models are currently available. In this study, we generated the first collection of zebrafish knockout lines for each nrxn gene, with mutations ranging from transmembrane domain- to full genomic locus-deletions. Surprisingly, all homozygous lines developed normally, presenting no gross neurodevelopmental or obvious early behavioural abnormalities. However, this absence of early phenotypes translated into profound, paralog-specific behavioural alterations emerging during juvenile-to-adult stages. All neurexin knockouts affected mating behaviour, complicating the generation and maintenance of homozygous lines. Except for this shared behavioural alteration, nrxn1, but not nrxn2 or nrxn3, led to marked changes in social behaviour and aggression. In contrast, nrxn2 mutants exhibited severe anxiety-like behaviours, including bottom-dwelling and repetitive freezing/seizure events. Strikingly, nrxn1 full-locus deletion mutants showed opposing behaviour, spending most of their time near the surface. The two also displayed opposite responses to open/closed field transitions; confinement alleviated nrxn2 anxiety but enhanced nrxn1 surface-dwelling. Meanwhile, nrxn3 mutants behaved normally in all our initial tests. In summary, our study introduces a complete set of zebrafish mutants covering the whole nrxn gene family, presenting striking juvenile/adult behavioural alterations despite the absence of noticeable early defects; echoing the delayed onset of human psychiatric disorders such as schizophrenia. This work demonstrates the value of zebrafish to study mental disorders and unlock a novel platform to unravel the pathogenic contribution of neurexin and associated subtle neurodevelopmental changes/timing that drive the emergence of mental illnesses.

neuroscience↗

Causality-oriented regulatory inference and rational transcriptomic reprogramming design with CASCADE

Systematically elucidating the causal structure of gene expression regulation is the foundation for identifying key regulators of cellular function and designing rational interventions thereof. While advances in high-content perturbation screens enables experimental probing of causal regulatory effects, the massive genomic scale, measurement noise and confounding factors pose significant challenges for existing causal discovery and inference algorithms. Here, we present CASCADE, an end-to-end framework that integrates de novo causal discovery with prior regulatory knowledge for genome-wide causal discovery and inference. In addition to its superior performance on causal regulatory structure discovery and counterfactual inference for unseen perturbation effects, CASCADE enables, for the first time, causality-oriented rational intervention design for transcriptomic programming towards various targeted cells within a unified framework.

bioinformatics↗

Parallel and non-parallel features of adaptive radiation in Yucatan pupfishes

Understanding the extent of parallelism across adaptive radiations remains a central problem in evolutionary biology. We used whole-genome resequencing of 123 individuals to compare the adaptive radiation of Cyprinodon pupfishes in Lake Chichancanab, Mexico, to an independent radiation of San Salvador Island (SSI) pupfishes in the Bahamas, and assess the repeatability of adaptive genetic architecture, sources of adaptive variation, and stages of selection. Despite rapid craniofacial divergence of trophic specialists within 8-15 kya, only two candidate genes (0.5%; 2/426) were shared between Caribbean radiations. Although adaptive introgression played a major role in SSI, we found minimal evidence of adaptive introgression in Chichancanab, likely due to the geographic isolation of this inland lake. Instead, de novo mutations provided a substantial source of adaptive variation (30.6%) for the endemic zooplanktivore, 15 times higher than the endemic scale-eater on SSI. However, in parallel with SSI, we found strong evidence that adaptive divergence occurred in stages, first on regulatory and standing genetic variation, then on de novo and nonsynonymous mutations. Consistent with adaptive variants near opsin and spermatogenesis genes, functional categories unique to Chichancanab, we found greater visual acuity and divergent sperm morphology in lab-reared zooplanktivores relative to generalists using laboratory assays. Consistent with extensive adaptive de novo mutations in WNT10A and rapid diversification of tooth size in the zooplanktivore, we found that experimental inhibition of the Wnt pathway in generalists resulted in narrower oral teeth. We conclude that de novo mutations, not introgression, can drive rapid adaptive radiations in isolated environments.

evolutionary biology↗

Assessing molecular, cellular and transcriptomic bases of laminar perfusion and cytoarchitecture coupling in the human cortex

Understanding how cellular architecture organizes cortical function requires mesoscopic approaches that resolve structure-function coupling in vivo. Here we introduce cerebral blood flow (CBF) and cell-body staining intensity (CSI) similarity index (CCSI), a localized similarity index between the CBF estimates from ultra-high-field 7T arterial spin labeling images and CSI from the BigBrain histology images to serve as a quantitative marker of laminar perfusion-cytoarchitecture coupling. CCSI revealed a reproducible, region- specific alignment between laminar vascular and cellular profiles across the cortex. Going beyond CBF, CCSI selectively tracked mitochondrial respiratory capacity and colocalized with capillary endothelial and mature non-myelination oligodendrocyte populations forming neurovascular interfaces. Transcriptomic enrichment highlighted pathways related to vascular remodeling, oxidative metabolism, and lipid-myelin homeostasis, indicating that CCSI reflects integrated metabolic-structural specialization. At the systems level, CCSI strengthened structure-function gradient correspondence in transmodal cortices, such as the default mode network. Together, these findings establish CCSI as a physiologically grounded, non-invasive marker of perfusion-cytoarchitecture alignment, providing a cross-scale framework linking cortical microstructure, metabolism, and functional organization.

neuroscience↗

FOLR1-targeted Actinium-225-based Alpha-particle Therapy Eliminates Ovarian Cancer

Despite the advancement in therapies, ovarian cancer treatment is challenging due to poor prognosis and high relapse associated with acquired resistance. Targeting overexpression of FOLR1 in ovarian cancers has proven to be an attractive strategy. The recent FDA approval of FOLR1 targeted antibody drug conjugate has shown promising results albeit resistance with repeated use appears inevitable. Emerging targeted alpha-particle therapies, particularly Actinium-225 (225Ac), for treating refractory cancers have opened avenues for improved therapeutic options. The success of alpha-particle therapy relies on tumor specific delivery of the alpha emitters. Herein we describe the first example of FOLR1-targeted 225Ac alpha-particle therapy for treatment of ovarian cancer. Longitudinal PET imaging demonstrated high tumor-specific uptake of FOLR1 in SKOV3 xenografts. FOLR1-targeted 225Ac demonstrated high therapeutic efficacy achieving marked tumor regression, 80% survival and 40% complete response. The therapy resulted in tumor specific double stranded DNA damage, and no obvious toxicity was observed in normal tissues. Estimated human dosimetry showed high absorbed dose for tumor and minimal absorbed dose for healthy tissues establishing its safety. In totality, FOLR1-targeted 225Ac alpha-particle therapy is an efficacious and safe treatment with high feasibility for clinical translation to fight against ovarian cancer.

bioengineering↗

Arousal increases locus coeruleus blood flow, salience-related brain responses, and modulates negative-valence attentional biases

The amygdala helps prioritize emotional over neutral information. However, it responds similarly to positive and negative stimuli, and so is unlikely to be the source of valence-specific effects within affective networks. We hypothesized that the locus coeruleus (LC) is a key contributor to negative biases in attention. Using ultra-high field 7T magnetic resonance imaging, we tested how arousal modulates processing of emotional faces during an oddball task in twenty-two young adults during two separate sessions. Arousal induced by isometric handgrip increased LC cerebral blood flow and amplified brain responses to target and angry faces, but not to happy faces. The amygdala exhibited valence-general responses that were not modulated by arousal. LC connectivity with the default mode network decreased during processing target and angry faces, and arousal further modulated responses in the salience network and visual cortex. Behaviorally, arousal enhanced recognition of angry faces only when allocating attentional resources and memory performance was linked to left LC brain activity. These findings highlight the LC as a key structure through which arousal shapes valence processing, biases attention, and informs mechanisms related to affective disorders.

neuroscience↗

Assessing computational strategies for the evaluation of antibody binding affinities.

Accurate evaluation of binding affinity is critical in drug discovery to identify molecules that bind strongly to their targets while minimizing off-target effects. Although binding affinity calculations are theoretically well-defined, they require exhaustive sampling of configurational space, a step that often requires significant computational resources. In this study, we compare different methods for calculating the binding energy of antibodies targeting a peptide derived from the N-terminus of CXCR2, a GPCR-family protein. Contrary to some previous reports, we find that equilibrium MMPBSA calculations yield better agreement with experimental binding affinities than non-equilibrium potential of mean force evaluations, underscoring the system-dependent performance of these methods. We also observed a modest improvement in accuracy when MMPBSA is combined with replica exchange molecular dynamics, albeit at a significantly higher computational cost. Calculation based on Rosetta force field, instead, produced results that did not correlate with the experimental data. We attribute these findings to two factors, which could limit the applicability of some methodologies that are widely used in the computation the binding energy: the high potency of the antibodies studied and the dominance of hydrophobic interactions between the antibodies and the peptide. Overall, this work provides important insights for optimizing in silico antibody screening strategies.

biophysics↗

The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability

Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome assembly spanning 129.4 Mb across 12 chromosomes, encompassing 15,321 predicted protein-coding genes. Leveraging whole-genome sequencing of eight mutation accumulation (MA) lines propagated for an average of 482 generations (spanning over 20 years), we estimated a spontaneous single nucleotide mutation (SNM) rate of 2.23 x 10-9 and an indel mutation rate of 2.75 x 10-10 per site per generation. The SNM spectrum was strongly biased toward C:G > T:A transitions. Comparative analyses with natural population data revealed that exonic mutations observed in the MA lines were significantly less likely to be present in standing variation than intronic or intergenic mutations, suggesting that purifying selection in natural populations acts to remove deleterious alleles. We also identified 48 de novo loss-of-heterozygosity (LOH) events, comprising 8 heterozygous deletions and 40 gene conversion events. The genome-wide gene conversion rate was estimated at 2.62 x 10-5 per heterozygous site per generation. These findings provide a comprehensive view of the mutation spectrum, selective pressures, and mechanisms underlying genome stability in D. obtusa.

evolutionary biology↗

A paradigm shift of SERPINA3N in neurobehavioral development and brain injury

Murine serine protease inhibitor clade A member 3N (SERPINA3N) and its human ortholog SERPINA3 are dysregulated in neurological disorders. SERPINA3N has been proposed as a protective factor, enhancing neurobehavioral development under homeostasis and mitigating neuronal/glial and vascular damage under neurological conditions. Here, we employed powerful, non-invasive genetic tools to revisit the concept of SERPINA3N in brain development and injury. Brain-specific SERPINA3N overexpression neither alters neuronal or glial development nor improves cognitive ability under homeostasis. In stark contrast, SERPINA3N drives a pro-inflammatory response to brain injury and exacerbates blood-brain barrier dysfunction. Its overexpression promotes neurodegeneration through apoptosis-mediated neuronal loss and disrupts oligodendroglial differentiation and myelination following neonatal brain injury. Collectively, our findings challenge the prevailing paradigm of SERPINA3N in neurodevelopment and injury, revealing that while SERPINA3N is dispensable for neurobehavioral development, it aggravates neural injury and vascular damage under pathological conditions.

neuroscience↗

Epilepsy-Associated SCN2A-L1342P Mutation Drives Network Hyperexcitability and Widespread Transcriptomic Changes in Human Cortical Organoids

ObjectiveSCN2A pathogenic mutations, such as the recurrent heterozygous Nav1.2-L1342P, are monogenic causes of epilepsy. In this human-induced pluripotent stem cell model system, we aim to investigate the molecular and cellular mechanisms underlying the SCN2A-L1342P-associated pathology. MethodsUsing a human male iPSC reference line (KOLF) carrying the Nav1.2-L1342P mutation, we generated 3D cortical organoids for functional studies. Patch clamp and multi-electrode array (MEA) recordings, immunocytochemistry, and RNA sequencing were used to characterize the disease phenotypes. ResultsNav1.2-L1342P organoid neurons displayed increased intrinsic excitability, and amplified excitatory post-synaptic currents, which are consistent with an increase in excitatory synapse formation revealed by PSD95/SYN1 immunostaining. Moreover, elevated network firing activity, as demonstrated by MEA, indicates a pronounced network hyperexcitability. Transcriptomic profiling of organoids carrying the Nav1.2-L1342P mutation further revealed significant alterations in synaptic, glutamatergic, and developmental pathways. SignificanceOur findings demonstrate that the Nav1.2-L1342P mutation drives a multifaceted disease phenotype, including network hyperexcitability and disruption of pathways related to neuronal and synaptic functions. These results advance our understanding of SCN2A-related Developmental and Epileptic Encephalopathy (DEE), laying a foundation for personalized interventions. Key PointsO_LIKey Point 1: Human neurons carrying epilepsy-causing SCN2A-L1342P display intrinsic hyperexcitability in cortical organoids. C_LIO_LIKey Point 2: Synaptic transmission is enhanced in organoids carrying the SCN2A-L1324P mutation, consistent with the presence of elevated excitatory synapses, which leads to increased network hyperexcitability. C_LIO_LIKey Point 3: Transcriptomics analysis reveals that the SCN2A-L1342P mutation causes significant differential changes in forebrain developmental genes, synaptic and glutamatergic signaling pathways, and enhances cellular senescence and apoptosis. C_LI

neuroscience↗

Exogenous Photoreceptor-Specific N-Glycosylated PROM1 Rescues Retinal Degeneration in Patient and Mouse Models

PROM1 is widely expressed across various tissues. However, its pathogenic mutations are exclusively associated with inherited retinal dystrophy (IRD). The mechanisms underlying this retina-specific vulnerability remain poorly understood, and no effective treatment currently exists for PROM1-IRD. Here, we utilized urine cells, hiPSCs, hiPSC-RPE cells, retinal organoids (ROs) and Prom1-/- mice to address these challenges. During photoreceptor development in ROs, PROM1 co-localized with ciliary marker ARL13B and outer segment (OS) marker PRPH2. It exhibited photoreceptor-specific mRNA splicing isoforms and unique N-glycosylation. In IRD patient-specific models with the PROM1 c.619G>T (p.E207X) homozygous mutation, we observed nonsense-mediated mRNA decay and altered splicing, leading to complete loss of PROM1 protein and OS-like structure disruption, faithfully recapitulating PROM1-IRD pathology. To rescue these defects, we engineered a photoreceptor-specific AAV7m8-CRXp-hPROM1, which successfully restored PROM1 expression and OS-like structures in patient-derived ROs. Therapeutic efficacy was further validated in Prom1-/- mice, where subretinal delivery of AAV8-CRXp-hPROM1 led to photoreceptor-specific expression of human PROM1, significantly preserving OS morphology and improving visual function. These findings not only provide the first solid preclinical evidence supporting gene therapy for PROM1-IRD, but also reveal photoreceptor-specific vulnerability to PROM1 mutations, offering a novel conceptual framework for investigating and treating related IRDs.

neuroscience↗