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Biology subjects

Feng, Z.

Publications and source records attributed to Feng, Z..

At least 55 records · Page 3Linked to original sources

Post-inhibitory rebound firing drives hypothalamic activation for male mating

Many behaviorally relevant limbic circuits are dominated by inhibitory connections, raising the question of how neuronal activation arises in such contexts. In male mating, both activation of mPOA and its inhibitory inputs are essential--a paradox previously ascribed to disinhibition. Here, we show that the mPOA largely lacks local inhibitory circuits, arguing against disinhibition. Instead, in vivo recordings reveal that mount-active mPOA neurons are suppressed prior to behavioral onset, and this inhibition negatively correlates with subsequent activation, consistent with post- inhibitory rebound firing (PIR). A biologically plausible conductance-based model demonstrates that synaptic inhibition interacts with T-type Ca{superscript 2} currents -- the ionic basis of PIR -- to promote mPOA neuron firing. Experimentally, bidirectional manipulations of mPOA T-type Ca{superscript 2} channels confirm this mechanism: knockdown reduces PIR and impairs male mating, while overexpression enhances mating. Together, these results identify PIR as a critical mechanism by which inhibition promotes activation in limbic circuits to drive male mating.

neuroscience↗

Structural and functional analysis of VYD222: a broadly neutralizing antibody against SARS-CoV-2 variants

Extensive mutations in SARS-CoV-2 spike protein have rendered most therapeutic monoclonal antibodies (mAbs) ineffective. However, here we describe VYD222 (pemivibart), a human mAb re-engineered from ADG20 (adintrevimab), which maintains potency despite substantial virus evolution. VYD222 received FDA Emergency Use Authorization for pre-exposure prophylaxis of COVID-19 in certain immunocompromised adults and adolescents. Here we show potent neutralization of this antibody against a broad range of emerging variants, including Omicron KP.3 and KP.3.1.1. X-ray crystal structures of VYD222 complexed with the receptor-binding domains of prototype SARS-CoV-2 and Omicron BA.5 demonstrate the binding epitope spans from the receptor binding site to the conserved CR3022 site. Notably, many of the matured residues between ADG20 and VYD222 occur outside the paratopic region. Deep mutational scanning indicates that SARS-CoV-2s ability to escape VYD222 is constrained by structural compatibility and the need to maintain receptor binding. These findings provide crucial insights into the escape-resistant neutralization of VYD222 against a broad panel of clinically relevant SARS-CoV-2 variants and offer valuable guidance for risk assessment of emergent variants.

biophysics↗

CASP3-GSDME-mediated trophoblast pyroptosis contributes to systemic inflammation

Early-onset preeclampsia (EOPE) is associated with excessive apoptosis and inflammation, but the mechanistic link between these processes remains enigma. Here, we report elevated circulating pro-apoptotic proteins in EOPE patients at early pregnancy, along with concurrent CASP3 activation and GSDME cleavage in a subset of EOPE placentas. Using multiple trophoblast cell lines, we demonstrate that trophoblast cells, which highly express GSDME, undergo a shift from apoptosis to CASP3-dependent pyroptosis, driving inflammation. Notably, pyroptotic trophoblasts further induce pro-inflammatory macrophage polarization within placental villi organoids, establishing a feedback loop that amplifies both trophoblast pyroptosis and inflammatory responses in trophoblast organoids-macrophage assembloids. In vivo, CASP3-GSDME-mediated trophoblast pyroptosis contributes to systemic inflammation in wild-type pregnant mice but not in Gsdme-/- mice. Screening of EOPE prevention drugs reveals Vitamin D as a suppressor of GSDME activation and pyroptosis in trophoblast cells. These findings highlight the CASP3-GSDME axis as a promising therapeutic target for preeclampsia prevention.

cell biology↗

ESM-LoRA-Gly: Improved prediction of N- and O-linked glycosylation sites by tuning protein language models with low-rank adaptation (LoRA)

Glycosylation associates with many diseases ranging from cancer to neurodegeneration and understanding these disease mechanisms requires the precise identification of glycosylation sites. Computational prediction of glycosylation sites has been useful to complement laborious experimental methods, while existing tools lack sufficient accuracy and scalability. Here, we introduce ESM-LoRA-Gly, a method that employs Low-Rank Adaptation (LoRA) to fine-tune the ESM2-3B protein language model for predicting both N- and O-linked glycosylation sites. According to the evaluation on the benchmark datasets, ESM-LoRA-Gly outperforms existing state-of-the-art techniques. The improvement is particularly significant (>100% in Matthews correlation coefficient) for the O-linked dataset. By substantially reducing trainable parameters while maintaining predictive power, ESM-LoRA-Gly enables computationally efficient proteome-scale predictions. This approach should be instrumental for advancing glycoproteomic research and accelerating therapeutic discovery for glycosylation-related diseases.

bioinformatics↗

One Thousand SARS-CoV-2 Antibody Structures Reveal Convergent Binding and Near-Universal Immune Escape

Since the emergence of SARS-CoV-2, understanding how antibodies recognize and adapt to viral evolution has been central to vaccine and therapeutic developments. To date, over 1,100 SARS-CoV-2 antibody structures--16% of all known antibody-antigen complexes--have been resolved, marking the largest structural biology effort towards a single pathogen. Here, we present a comprehensive analysis of this landmark dataset to investigate the principles of antibody recognition and immune escape. Human immunoglobulins (IgGs) and camelid single-chain antibodies dominate the dataset, collectively mapping 99% of the receptor-binding domain surface. Despite remarkable sequence and conformational diversity, antibodies exhibit striking convergence in their paratope structures, revealing evolutionary constraints in epitope selection. Structural and functional analyses reveal near-universal immune escape of antibodies, including all clinical monoclonals, by advanced variants such as KP3.1.1. On average, over one-third of antibody epitope residues are mutated. These findings support pervasive immune escape, underscoring the need to effectively leverage multi-epitope targeting strategies to achieve durable immunity.

microbiology↗

In Vivo Evolution of Monoclonal Antibody CR3022 to Achieve Cross-Neutralization of SARS-CoV-2 and Implications for Vaccine Strategies Against SARS-Related Viruses

The epitope that monoclonal CR3022 binds to represents a promising target for broad protection against a wide range of human and zoonotic coronaviruses. We developed a powerful model to evaluate antibody affinity maturation in vivo using immunoglobulin (Ig)-humanized mice that express the predicted germline heavy chain of antibody CR3022. SARS-CoV/SARS-CoV-2 sequential immunization led to the convergent evolution of the germline CR3022 through somatic hypermutation (SHM) that resembled the affinity-matured CR3022 from a human, but now also adapted to key variants and divergent sarbecoviruses. While simple prime-boost strategies drove CR3022-epitope targeting, an intensive vaccination protocol elicited dominant responses to other epitopes. X-ray crystal structures revealed that SARS-CoV-2-neutralizing CR3022-like antibodies exhibit enhanced affinity by increasing polar and electrostatic interactions. Overall, these findings show CR3022-like clones can be readily adapted through SHM to increase breadth and potency to sarbecoviruses by relatively minor shifts in affinity with appropriate vaccination strategies.

immunology↗

HuiduRep: A Robust Self-Supervised Framework for Learning Neural Representations from Extracellular Recordings

Extracellular recordings are transient voltage fluctuations in the vicinity of neurons, serving as a fundamental modality in neuroscience for decoding brain activity at single-neuron resolution. Spike sorting, the process of attributing each detected spike to its corresponding neuron, is a pivotal step in brain sensing pipelines. However, it remains challenging under low signal-to-noise ratio (SNR), electrode drift, and cross-session variability. In this paper, we propose HuiduRep, a robust self-supervised representation learning framework that extracts discriminative and generalizable features from extra-cellular recordings. By integrating contrastive learning with a denoising autoencoder, HuiduRep learns latent representations robust to noise and drift. With HuiduRep, we develop a spike sorting pipeline that clusters spike representations without ground truth labels. Experiments on hybrid and real-world datasets demonstrate that HuiduRep achieves strong robustness. Furthermore, the pipeline outperforms state-of-the-art tools such as KiloSort4 and MountainSort5. These findings demonstrate the potential of self-supervised spike representation learning as a foundational tool for robust and generalizable processing of extracellular recordings.

bioinformatics↗

rAAV-miniBEND: A targeted vector for brain endothelial cell gene delivery and cerebrovascular malformation modeling

Defects in brain endothelial cells (brainECs) can cause severe cerebrovascular malformations, including arteriovenous malformation (AVM) and cerebral cavernous malformation (CCM). The lack of appropriate tools for cerebrovascular disease modeling and local genetic manipulation of the brain vasculature hinders research on cerebrovascular malformations. Here we develop a recombinant adeno-associated virus (rAAV) tool miniBEND (rAAV-based mini-system for brain endothelial cells, rAAV-miniBEND), which combines a minimal promoter and an optimized cis-acting element (cis-element) isolated from the mouse gene Tek. This system achieves gene expression specifically in mouse and rat brainECs. Using rAAV-miniBEND, we achieve high-efficiency and high-specificity gene expression in brainECs through intracranial injection at various developmental stages and through intravenous administration at all postnatal stages in mice. Furthermore, we use rAAV-miniBEND to model sporadic CCMs mediated by MAP3K3I441M and AVMs mediated by BrafV600E. We demonstrate that somatic expression of BrafV600E in brainECs induces an AVM phenotype, and that brainEC proliferation are important for AVM development. Thus, our rAAV-miniBEND system provides a valuable and widely applicable tool for cerebrovascular disease modeling and local or global brainEC gene delivery.

neuroscience↗

Structural innovations and neurogenic continuity define avian brain development and evolution

Understanding how neurogenic diversity and brain architecture emerge is crucial for deciphering the mechanisms of brain plasticity and cognitive evolution. Here, we present a comprehensive single-cell and spatial transcriptomic atlas of the budgerigar brain, a highly cognitive avian species. We uncover a striking dorsoventral symmetry in excitatory neuron distribution, precisely organized along the lamina mesopallialis intermedia (LMI), a key boundary structure. Cross-species comparisons further reveal the origins of this unique avian pallial organization, offering new insight into avian brain evolution. Our study also highlights distinct developmental trajectories and asynchronous maturation patterns between telencephalic and optic tectum excitatory neurons, underscoring their contribution to innate circuit assembly. Furthermore, we identify adult neural stem cells (NSCs) with evolutionarily conserved transcriptomic signatures across avian species, emphasizing their role in brain plasticity and adaptation. These findings refine fundamental models of avian brain development and elucidate conserved principles of cognitive plasticity.

evolutionary biology↗

Structural insight into the transcription activation mechanism of the phage Mor/C family activators

Bacteriophage Mu, a temperate phage that infects E. coli K-12 and other enteric bacteria, precisely controls its replication cycle through hijacking host RNA polymerase (RNAP) by the middle operon regulator Mor and the late gene transcription activator C. Though a dimeric arrangement and significant conformational changes are proposed for the distinct Mor/C family activators, the underlying transcription activation mechanism remains unclear. In this study, we present two cryo-EM structures of the transcription activation complex (Mor-TAC and C-TAC) with phage Mu middle and late gene promoters, respectively. Remarkably, the Mor/C activators bind to promoter DNA as a centrosymmetric tetramer rather than as the proposed dimer, concurrently stabilizing by the N-terminal dimerization domains and C-termini. The C-terminal DNA binding domains and two anti-{beta}-strands simultaneously interact with two adjacent DNA major grooves. The activators also engage a variety of interactions with the conserved domains (CTD, {sigma}70R4, and {beta} FTH) of RNAP, providing evidences for a recruitment mechanism. In addition, single-molecule FRET assays show that C significantly enhances RPitc formation, suggesting a different multi-step activation mechanism for C. Collectively, these findings reveal the unique transcription activation mechanism of tetrameric Mor/C family activators, unraveling a novel mode of phage hijacking and bacterial transcription regulation.

biochemistry↗

EpiMII: Integrating Structure and Graph Neural Networks for MHC-II Epitope and Neoantigen Design

MHC-II neoantigens play a critical role in immunotherapy, either as direct effectors or through their influence on CD8+ T cells. However, only a small fraction of tumor DNA mutations qualify as functional neoantigens, and current prediction tools often lack accuracy, leading to the low immunogenicity of predicted neoantigens in vivo. Here, we present EpiMII, a Graph Neural Network model for MHC-II epitope design, which learns from the structural features of epitopes to predict their sequences. To train EpiMII, we constructed a reliable, large dataset containing 142,934 MHC-II epitope structures. This approach achieves a 4.2x improvement over ProteinMPNN, with a sequence recovery rate of 78.0% for known MHC-II epitopes in the Protein Data Bank. As a case study, we designed a neoantigen from hepatocellular carcinoma. All five designed epitopes significantly activated CD4+ T cells in vitro and induced secretion of IFN-{gamma} and TNF-. Notably, one epitope treatment significantly reduced tumor volume in mice in vivo. EpiMII offers a novel and efficient approach for identifying MHC-II epitopes/neoantigens, potentially contributing to vaccine development.

immunology↗

A theory of ecological invasions and its implications for eco-evolutionary dynamics

Predicting the outcomes of species invasions is a central goal of ecology, a task made especially challenging due to ecological feedbacks. To address this, we develop a general theory of ecological invasions applicable to a wide variety of ecological models: including Lotka-Volterra models, consumer resource models, and models with cross feeding. Importantly, our framework remains valid even when invading evolved (non-random) communities and accounts for invasion-driven species extinctions. We derive analytical expressions relating invasion fitness to invader abundance, shifts in the community, and extinction probabilities. These results can be understood through a new quantity we term "dressed invasion fitness", which augments the traditional notion of invasion fitness by incorporating ecological feedbacks. We apply our theory to analyze short-term evolutionary dynamics through a series of invasions by mutants whose traits are correlated with an existing parent. We demonstrate that, generically, mutants and parents can coexist, often by driving the extinction of low-abundance species. We validate theoretical predictions against experimental datasets spanning ecosystems from plants to microbial protists. Our work highlights the central role of ecological feedbacks in shaping community responses to invasions and mutations, suggesting that parent-mutant coexistence is widespread in eco-evolutionary dynamics.

ecology↗

Block-Champagne: A novel Bayesian framework for Imaging E/MEG Source

Estimating the extents of E/MEG source activities is vital for exploring brain dynamics at high spatiotemporal resolution. However, conventional ESI models exclusively overemphasize on the accurate estimation of the source locations and struggle to reconstruct the extents due to the ill-posed nature of the problem, which requires effective integration of biophysical constraints and proficiency in signal processing methods. In this study, a novel Bayesian framework - Block-Champagne is introduced to provide accurate estimation of extended sources (i.e., both locations and extents). Specifically, a blocksparsity constraint is employed to model the local homogeneity of sources, which can be updated automatically to reconstruct source with arbitrary extents. Furthermore, prior constraints from other modalities, such as fMRI maps, can be incorporated to model interactions between remote sources to further enhance source reconstruction. The performance of Block-Champagne was quantitatively evaluated through simulation experiments, demonstrating its overall superiority under various complex scenarios (i.e., SNR, extent size, & number of extents) compared to benchmark algorithms (including LORETA, EBI-Convex, tsCham, L21-Sissy, & SI-STBF). Moreover, validation results obtained from deep-brain stimulation EEG, epilepsy data, and face-processing multi-modal data further proved the practical feasibility of Block-Champagne. In conclusion, our study reveals the superiority of the proposed BlockChampagne in accurate reconstruction of extended source, positioning Block-Champagne as a highly promising tool for realistic applications where source locations and extents are of equivalent importance.

neuroscience↗

Somatic repetitive element insertions Define New Biomarkers in Pan-cancer genome

Repetitive elements insertions (REIs), including tandem repeat insertions (TRIs) and transposable element insertions (TEIs), constitute >90% of large-scale (>50bp) somatic insertions and are linked to diseases and cancer biomarkers. However, the genomic landscape of large-scale REIs in pan-cancer has not been well-characterized due to short-read sequencing limitations. Here, we detected somatic REIs in 325 cancer genomes across 12 cancer types using long-read whole-genome sequencing and customized algorithms. The diverse sequence patterns of somatic TRIs and the insertion mechanisms of somatic TEIs were characterized across different cancer types. We identified 152 high-frequency somatic TRIs, with 10 showing pan-cancer characteristics, including TRIs in SHROOM2, PALMD, and the enhancer of PTPRZ1. The MHC class II gene cluster exhibited the highest somatic TEI abundance, affecting [~]40% tumors. Adenocarcinomas and squamous cell carcinomas exhibited differing TEI distributions within this region. Our study highlights REIs as important but under-explored markers for personalized cancer diagnosis and immunotherapy.

genomics↗

Target-Specificity and Repeatability in Neuro-Cardiac-Guided TMS for Heart-Brain Coupling

The dorsolateral prefrontal cortex (DLPFC) is a principal target for transcranial magnetic stimulation (TMS) in treating major depressive disorder, with therapeutic effects thought to be mediated by its connectivity with the subgenual anterior cingulate cortex. As both regions are involved in autonomic regulation, short-term heart rate changes following DLPFC stimulation may serve as physiological markers to identify stimulation targets. We employed neuro-cardiac guided TMS in a cohort of healthy participants to examine the effects of stimulation intensity and DLPFC target specificity on heart-brain coupling (HBC). We used generalized additive models to assess nonlinear effects of stimulation intensity and target location on HBC, while accounting for pain ratings and other side effects. Intra-subject repeatability across three sessions was evaluated using intraclass correlation coefficients. We observed a non-linear modulation of HBC depending on stimulation intensity and target location, with greater effects at the F3 lateral and F3 posterior targets compared to sham. By evaluating these effects across sessions within participants, we demonstrate the robustness of our results beyond the influence of pain and other side effects on HBC modulation. Exploratory analyses of the directionality show a consistent decrease in HR only at the F3 lateral target with suprathreshold stimulation. These results demonstrate that HBC is modulated in a target- and intensity-specific manner, with particularly consistent effects at F3 lateral sites within the DLPFC. The findings enhance the understanding of TMS-modulated heart-brain interactions, offering a potential framework for optimizing individualized rTMS treatment protocols for depression.

neuroscience↗

EPSD 2.0: An Updated Database of Protein Phosphorylation Sites across Eukaryotic Species

As one of the most crucial post-translational modifications (PTMs), protein phosphorylation regulates a broad range of biological processes in eukaryotes. Biocuration, integration and annotation of reported phosphorylation events will deliver a valuable resource for the community. Here, we present an updated database, the eukaryotic phosphorylation site database 2.0 (EPSD 2.0), which includes 2,769,163 experimentally identified phosphorylation sites (p-sites) in 362,707 phosphoproteins from 223 eukaryotes. From the literature, 873,718 new p-sites identified through high-throughput phosphoproteomic research were first collected, and 1,078,888 original phosphopeptides together with primary references were reserved. Then, this dataset was merged into EPSD 1.0, comprising 1,616,804 p-sites within 209,326 proteins across 68 eukaryotic organisms [1]. We also integrated 362,190 additional known p-sites from 10 public databases. After redundancy clearance, we manually re-checked each p-site and annotated 88,074 functional events for 32,762 p-sites, covering 58 types of downstream effects on phosphoproteins, and regulatory impacts on 107 biological processes. In addition, phosphoproteins and p-sites in 8 model organisms were meticulously annotated utilizing information supplied by 100 external platforms encompassing 15 areas. These areas included kinase/phosphatase, transcription regulators, three-dimensional structures, physicochemical characteristics, genomic variations, functional descriptions, protein domains, molecular interactions, drug-target associations, disease-related data, orthologs, transcript expression levels, proteomics, subcellular localization, and regulatory pathways. We expect that EPSD 2.0 will become a useful database supporting comprehensive studies on phosphorylation in eukaryotes. The EPSD 2.0 database is freely accessible online at https://epsd.biocuckoo.cn/.

bioinformatics↗

Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein

The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigated how mutations and a deletion in the KP.3.1.1 spike protein (S) affect ACE2 binding and antibody escape. Mass spectrometry revealed a new glycan site at residue N30 and altered glycoforms at neighboring N61. Cryo-EM structures showed that the N30 glycan and rearrangement of adjacent residues did not significantly change the overall spike structure, up-down ratio of the receptor-binding domains (RBDs), or ACE2 binding. Furthermore, a KP.3.1.1 S structure with hACE2 further confirmed an epistatic effect between F456L and Q493E on ACE2 binding. Our analysis shows SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.

immunology↗

Identification of SLC35A1 as an essential host factor for the transduction of multi-serotype recombinant adeno-associated virus (AAV) vectors

We conducted a genome-wide CRISPR/Cas9 screen in suspension 293-F cells transduced with rAAV5. The highly selected genes revealed after two rounds of screens included the previously reported KIAA039L, TM9SF2, and RNF121, along with a cluster of genes involved in glycan biogenesis, Golgi apparatus localization and endoplasmic reticulum penetration. In this report, we focused on solute carrier family 35 member A1 (SLC35A1), a Golgi apparatus-localized cytidine 5-monophosphate-sialic acid (CMP-SIA) transporter. We confirmed that SLC35A1 knockout (KO) significantly decreased rAAV5 transduction to a level lower than that observed in KIAA0319L or TM9SF2 KO cells. Although SLC35A1 KO drastically reduced the expression of 2,6-linked SIA on the cell surface, the expression of 2,3-linked SIA, as well as the cell binding and internalization of rAAV5, were only moderately affected. Moreover, SLC35A1 KO significantly diminished the transduction of AAV multi-serotypes, including rAAV2 and rAAV3 which do not utilize SIAs for primary attachment. Notably, the SLC35A1 KO markedly increased transduction of rAAV9 and rAAV11, which primarily attach to cells via binding to galactose. Further analyses revealed that SLC35A1 KO significantly decreased vector nuclear import. More importantly, although the C-terminal cytoplasmic tail deletion ({Delta}C Tail) mutant of SLC35A1 did not drastically decrease SIA expression, it significantly decreased rAAV transduction, as well as vector nuclear import, suggesting the C-tail is critical in these processes. Furthermore, the T128A mutant significantly decreased SIA expression, but still supported rAAV transduction and nuclear import. These findings highlight the involvement of the CMP-SIA transporter in the intracellular trafficking of rAAV vectors post-internalization. IMPORTANCErAAV is an essential tool for gene delivery in the treatment of genetic disorders, yet the mechanisms of rAAV transduction remain partially understood. GPR108 is vital for the transduction of most rAAV vectors, but not for rAAV5. We aimed to identify host factors that impact AAV5 transduction akin to GPR108. Using a genome-wide CRISPR/Cas9 screen in 293-F cells, we identified SLC35A1, a Golgi apparatus-localized CMP-sialic acid transporter that transports CMP-sialic acid from cytoplasm into the Golgi apparatus for sialylation, is essential to rAAV transduction. Further studies across various AAV serotypes showed SLC35A1 significantly affects vector nuclear import post-internalization. These results underscore the crucial role of SLC35A1 in intracellular trafficking beyond the initial cell attachment of rAAV.

microbiology↗