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Lv, S.

Publications and source records attributed to Lv, S..

17 recordsLinked to original sources

Temporal decoding of blood flow derived mechanical cues driving liver regeneration

Liver regeneration is initiated by rapid vascular changes, yet how blood flow-derived mechanical cues are decoded by liver sinusoidal endothelial cells (LSECs) remains unclear. Here, we found that partial hepatectomy generates temporally distinct mechanical cues in vivo, with a transient rise in shear stress followed by progressive sinusoidal dilation and endothelial stretch. To dissect these forces, we developed a liver regeneration chip that reconstructs sinusoidal architecture and enables independent or coupled manipulation of shear stress and mechanical stretch. Shear-dominant, stretch-dominant, and coupled mechanical modalities induce divergent LSEC regenerative programs involving extracellular matrix remodeling, cell-cycle regulation, cytoskeletal organization, and angiocrine signaling. Mechanistically, force-specific pathways, including Wnt, HIF-1, NF-{kappa}B, and Piezo1-associated signaling, mediate these outputs. Inhibition of these pathways after partial hepatectomy impairs hepatocyte proliferation and survival. These findings reveal that LSECs temporally decode blood flow-derived mechanical forces into distinct regenerative outputs, establishing endothelial mechanotransduction as an upstream regulator of liver regeneration. HIGHLIGHTS{blacksquare} Partial hepatectomy decouples transient shear from progressive stretch in vivo. {blacksquare}A liver regeneration chip recreates structure and distinct mechanical modalities in sinusoids. {blacksquare}Distinct mechanical modalities encode divergent LSEC regenerative programs. {blacksquare}Force-specific LSEC mechanotransduction supports hepatocyte proliferation and survival.

bioengineering↗

Normative models of individualized functional brain networks reveal language network expansion in autism

Autism spectrum disorder is a highly heterogeneous neurodevelopmental disorder, hindering mechanistic insights and the identification of biomarkers for clinical diagnosis. Recently, precision functional mapping has been developed to identify abnormalities in brain network topologies associated with various psychiatric disorders, yet its application in autism remains limited. Here, we utilized precision functional mapping and a large, multisite neuroimaging dataset (N = 1,182) to construct individualized functional networks in individuals with autism. We developed normative models using network surface area from healthy controls (n = 628) to characterize typical brain network organization across age, allowing for the quantification of individual-specific deviations in individuals with autism (n = 554). We found widespread and heterogeneous deviations from the normative model, with the language network emerging as the most significantly altered region, thereby emerging as an epicenter of functional disruption in autism. Individuals with autism were clustered into three subtypes involving distinct functional network topologies, associated with behavioral profiles marked by impairments in perception, language processing, or socio-emotional functioning. We further linked these atypical brain features to cortical gene expression patterns, revealing enriched pathways related to neurodevelopment, language, and signaling processes. Together, these findings reveal autism-specific deviations in individualized functional brain networks, offering potential clinical relevance for understanding and stratifying autism.

neuroscience↗

The Cryo-EM structure of TRPC1 and TRPC5 heterotetramer

Ion channel heteromers display distinct electrophysiological and ligand-binding properties, allowing precise modulation of cellular functions in specific tissues. Among the TRPC subtypes, the TRPC1/4/5 heteromers are the most abundant isoform in the human brain and represent a primary target for treating anxiety and depression. However, the structural organization of TRPC1/4/5 heteromers remain unclear, limiting the advancement of research on these channels. Here, we report the cryo-EM structure of TRPC1/5 heterotatramer at a resolution of 2.84 [A]. It consists of an asymmetric structure with three TRPC5 subunits and one TRPC1 subunit. Further structural and functional analysis revealed that the TRPC1 subunit contributes to an asymmetrical ion conduction pathway, a characteristic that differentiates it from TRPC5 homomers. The unique features of the TRPC1 pore loop and its interface interactions with TRPC5 were shown to play crucial roles in modulating the ion conduction properties and gating mechanisms of the heteromeric complex. In addition, we identified key residues within the gating regions that influence channel activation and ion permeability, elucidating the structural basis for the functional divergence between the TRPC1/C5 heterotetramer and TRPC5 homotetramer. Notably, TRPC5 residues were found to dominate gating mechanisms, underscoring the complex interplay between subunit composition and functional outcomes in TRPC channels. Our findings provide novel insights into the structural and functional dynamics of TRPC1/C5 heteromers, paving the way for targeted therapeutic strategies in TRPC5-related disorders.

biophysics↗

Tachykinin1-expressing neurons in the parasubthalamic nucleus control active avoidance learning

Active avoidance is a type of instrumental behavior that requires an organism actively to engage in specific actions to avoid or escape from a potentially aversive stimulus and is crucial for the survival and well-being of organisms. It requires a widely distributed, hard-wired neural circuits spanning multiple brain regions, including the amygdala and thalamus. However, less is known about whether and how the hypothalamus encodes and controls active avoidance learning. Here we identify a previously unknown role for the parasubthalamic nucleus (PSTN), located in the lateral subdivision of the posterior hypothalamus, in the encoding and control of active avoidance learning. Fiber photometry calcium imaging shows that the activity of tachykinin1-expressing PSTN (PSTNTac1) neurons progressively increases during this learning. Cell-type specific ablation and optogenetic inhibition of PSTNTac1 neurons attenuates active avoidance learning, whereas optogenetic activation of these cells promotes this learning via a negative motivational drive. Moreover, the PSTN mediates this learning differentially through its downstream targets. Together, this study identifies the PSTN as a new member of the neural networks involved in active avoidance learning and offers us potential implications for therapeutic interventions targeting anxiety disorders and other conditions involving maladaptive avoidance learning.

neuroscience↗

Wnt specifically induces FZD5/8 endocytosis and degradation and the involvement of RSPO-ZNRF3/RNF43 and DVL

Frizzled (FZD) proteins are the principal receptors of the Wnt signaling pathway. However, whether Wnt ligands induce FZD endocytosis and degradation remains elusive. The transmembrane E3 ubiquitin ligases ZNRF3 and RNF43 were reported to promote the endocytosis and degradation of FZD receptors to inhibit Wnt signaling, and their function is antagonized by R-spondin (RSPO) proteins. However, the dependency of RSPO-ZNRF3/RNF43-mediated FZD endocytosis and degradation on Wnt stimulation, as well as the specificity of this degradation for different FZD, remains unclear. Here, we demonstrated that Wnt induces FZD5/8 endocytosis and degradation in a ZNRF3/RNF43-dependent manner. ZNRF3/RNF43 selectively targets FZD5/8 for degradation upon Wnt stimulation. RSPO1 enhances Wnt signaling by specifically stabilizing FZD5/8. Wnt promotes the interaction between FZD5 and RNF43. We further demonstrated that DVL proteins promote ligand-independent endocytosis of FZD but are dispensable for Wnt-induced FZD5/8 endocytosis and degradation. Our results reveal a novel negative regulatory mechanism of Wnt signaling at the receptor level and illuminate the mechanism by which RSPO-ZNRF3/RNF43 regulates Wnt signaling, which may provide new insights into regenerative medicine and cancer therapy.

cell biology↗

Cryo-EM structures of human cone visual pigments

Trichromatic color vision in humans constitutes a pivotal evolutionary adaptation, endowing individuals with the capacity to discern and discriminate a diverse spectrum of colors. This unique visual capability confers a selective advantage crucial for successful adaptation, survival, and reproductive success in the natural environment. Color vision in humans is facilitated by the red, green, and blue cone visual pigments within cone photoreceptor cells. These pigments consist of a G-protein-coupled receptor opsin apoprotein and a chromophore covalently linked to opsins. Despite the elucidated structure of rhodopsin, the structures of cone visual pigments have yet to be determined. Here, we present the cryo-EM structures of three human cone visual pigments in complex with G proteins. Our structural analysis reveals detailed interactions between cone opsins, all-trans-retinal, and G proteins, indicating their active state. We also provide a concise summary and analysis of mutations in human cone opsins, elucidating potential relationships between residue substitutions and spectral tuning. Notably, S1162.67Y, A2335.52S, Y2776.44F were found to induce a blue shift in the absorption spectrum of the red-pigment, while the substitutions W2816.48Y and K3127.43A resulted in the absence of the absorption spectrum. The structural elucidation of human cone visual pigments significantly contributes to our understanding of how distinct types of cone cells perceive light across varying wavelengths. Furthermore, it provides a deeper insight into the functioning of the human trichromatic vision system, probing the mechanisms enabling humans to perceive a broad spectrum of colors.

biophysics↗

Cryo-EM structure and biochemical analysis of human chemokine receptor CCR8

The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein coupled receptor that has emerged as a promising therapeutic target in cancer and autoimmune diseases. Although the structures of human CCR8 in complex an antagonist antibody Fab1 and an endogenous agonist ligand CCL1 have been solved, the structure of ligand-free CCR8 remains to be determined. Here, we solved the cryo-electron microscopy (cryo-EM) structure of the human CCR8-Gi complex in the absence of a ligand. Structural analysis and comparison revealed that CCR8 in our apo structure undergoes some conformational change and is similar to that in the CCL1-CCR8 complex structure, indicating an active state. In addition, the key residues of CCR8 involved in the recognition of LMD-009, a potent nonpeptidic agonist, were investigated by mutating CCR8 and testing the calcium flux induced by LMD-009-CCR8 interaction. Two mutants of CCR8, Y1133.32A, and E2867.39A, showed a dramatically decreased ability in mediating calcium mobilization, indicating their key interaction with LMD-009. These structural and biochemical analyses provided molecular insights into the agonism and activation of CCR8 and will also facilitate CCR8-targeted therapy.

biophysics↗

De novo design and optimization of aptamers with AptaDiff

Aptamers are single-stranded nucleic acid ligands, featuring high affinity and specificity to target molecules. Traditionally they are identified from large DNA/RNA libraries using in vitro methods, like Systematic Evolution of Ligands by Exponential Enrichment (SELEX). However, these libraries capture only a small fraction of theoretical sequence space, and various aptamer candidates are constrained by actual sequencing capabilities from the experiment. Addressing this, we proposed AptaDiff, the first in silico aptamer design and optimization method based on the diffusion model. Our Aptadiff can generate aptamers beyond the constraints of high-throughput sequencing data, leveraging motif-dependent latent embeddings from variational autoencoder, and can optimize aptamers by affinity-guided aptamer generation according to Bayesian optimization. Comparative evaluations revealed AptaDiffs superiority over existing aptamer generation methods in terms of quality and fidelity across four high-throughput screening data targeting distinct proteins. Moreover, Surface Plasmon Resonance (SPR) experiments were conducted to validate the binding affinity of aptamers generated through Bayesian optimization for two target proteins. The results unveiled a significant boost of 87.9% and 60.2% in RU values, along with a 3.6-fold and 2.4-fold decrease in KD values for the respective target proteins. Notably, the optimized aptamers demonstrated superior binding affinity compared to top experimental candidates selected through SELEX, underscoring the promising outcomes of our AptaDiff in accelerating the discovery of superior aptamers. Key PointsO_LIWe proposed AptaDiff, the first in silico aptamer design method based on the diffusion model. Aptadiff can generate aptamers beyond the constraints of high-throughput sequencing data. C_LIO_LIAptadiff can optimize aptamers through affinity-guided generation via Bayesian optimization within a motif-dependent latent space, and the affinity of the optimized aptamers to the target protein is better than the best experimental candidate from traditional SELEX screening. C_LIO_LIAptadiff consistently outperforms the current state-of-the-art method in terms of quality and fidelity across high-throughput screening data targeting distinct proteins. C_LI

bioinformatics↗

Neutralization of SARS-CoV-2 BQ.1.1 and XBB.1.5 by Breakthrough Infection Sera from Previous and Current Waves in China

SARS-CoV-2 is continuing to evolve and diversify, with an array of various Omicron sub-lineages, including BA.5, BA.2.75, BN.1, BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5, now circulating globally at recent time. In this study, we evaluated the neutralization sensitivity of a comprehensive panel of Omicron subvariants to sera from different clinical cohorts, including individuals who received homologous or heterologous booster vaccinations, vaccinated people who had Delta or BA.2 breakthrough infection in previous waves, and patients who had BA.5 or BF.7 breakthrough infection in the current wave in China. All the Omicron subvariants exhibited substantial neutralization evasion, with BQ.1, BQ.1.1, XBB.1, and XBB.1.5 being the strongest escaped subvariants. Sera from Omicron breakthrough infection, especially the recent BA.5 or BF.7 breakthrough infection, exhibited higher neutralizing activity against all Omicron sub-lineages, indicating the chance of BA.5 and BF.7 being entirely replaced by BQ or XBB subvariants in China in a short-term might be low. We also demonstrated that the BQ and XBB subvariants were the most resistant viruses to monoclonal antibodies. Continuing to monitor the immune escape of SARS-CoV-2 emerging variants and developing novel broad-spectrum vaccines and antibodies are still crucial.

immunology↗

Depletion of collagen IX alpha2 interferes osteochondral homeostasis of the knee joint which ultimately causing osteoarthritis-like articular cartilage damage

As one of the branched chains of Type IX collagen (Col9), Collagen IX alpha2 (Col92) has been reported to be associated with several orthopedic conditions. To probe the relationship between Col92 and knee osteoarthritis (KOA), we performed a systematic analysis of Col92-deficient (Col9-/-) mice using whole-mount skeletal staining, Micro-CT (CT), biomechanics, histomorphometry, immunohistochemistry (IHC), immunofluorescence (IF) and Enzyme-linked immunosorbent (Elisa). Although whole-mount skeletal staining displayed no difference in bone length and ossification between Col9-/- mice and wild-type (Col92+/+) mice at mid-gestation and adult stages, the knee joint exhibited dramatic discrepancies. Specifically, the subchondral bone (SCB) in the knee joint of Col9-/- mice became sparse and deformed in the early stage, with altered bone morphometric parameters, reduced load-bearing capacity, dysfunctional bone homeostasis (decreased osteogenesis capacity and elevated bone resorption capacity), diminished cartilage proteoglycans and disrupted cartilage extracellular matrix (ECM) anabolism and catabolism compared with the Col92+/+ mice. In the late stage, the cartilage degeneration in Col92-/- mice were particularly pronounced compared to Col92+/+ mice, as evidenced by severe cartilage destruction and a marked reduction in cartilage thickness and area. Overall, Col92 is essential for maintaining osteochondral homeostasis in the knee joint of mice, and the absence of this gene is accompanied by distinct sclerosis of the SCB and a reduction in load-bearing capacity; in the late stage, in the lack of SCB stress inhibition, excessive load is consistently exerted on the cartilage, ultimately leading to osteoarthritic-like articular cartilage damage. Hence, Col92 may serve as a potential candidate biomarker associated with KOA.

physiology↗

The radio-protective effects of (-)-Epigallocatechin-3-gallate (EGCG): regulating macrophage function in radiation-induced intestinal injury.

Accidental and medical radiation exposure may cause radiation-induced intestinal injury (RIII), a catastrophic disease requiring efficient therapies. (-)-Epigallocatechin-3-gallate (EGCG), a major constituent of green tea, has been shown to have potent biological activity as well as strong anti-inflammation effects. Here, we demonstrate that EGCG treatment not only protects mice against total body irradiation (TBI)-induced toxicity and weight loss but also alleviates whole abdominal irradiation (WAI)-induced intestinal injury. EGCG promotes proliferation and survival of intestinal stem cells, inhibits radiation-induced apoptosis and inflammation. At the same time, EGCG preserves the composition of the gut microbiota in WAI mice. In vitro, we demonstrate that EGCG regulates the release of radiation-induced inflammatory factors by inhibiting inflammatory pathways such as toll-like receptor signaling pathway in peritoneal macrophages. Mechanistically, the radioprotective effect of EGCG was likely attributable to its preservation on macrophages and the colonized gut microbiota composition, thus relieving the intestinal inflammation. EGCG provides a novel strategy to mitigate RIII and improve the prognosis of patients after radiotherapy.

cell biology↗

Integrated analysis reveals FOXA1 and Ku70/Ku80 as direct targets of ivermectin in prostate cancer

Ivermectin is a widely used antiparasitic drug and shows promising anticancer activity in various cancer types. Although multiple signaling pathways modulated by ivermectin have been identified, few studies have focused on the exact target of ivermectin. Herein, we report the pharmacological effects and direct targets of ivermectin in prostate cancer (PCa). Ivermectin caused G0/G1 arrest, induced cell apoptosis, DNA damage, and decreased androgen receptor (AR) signaling in PCa cells. Using integrated omics profiling, including RNA-seq and thermal proteome profiling, we found that the forkhead box protein A1 (FOXA1) and non-homologous end joining (NHEJ) repair executer Ku70/Ku80 were the direct targets of ivermectin. The binding of ivermectin and FOXA1 reduced the chromatin accessibility of AR and the G0/G1 cell cycle regulator E2F1, leading to cell proliferation inhibition. The binding of ivermectin and Ku70/Ku80 impaired the NHEJ repair ability. Cooperating with the downregulation of homologous recombination repair after AR inhibition, ivermectin triggered synthetic lethality. Our findings demonstrate the anticancer effect of ivermectin in prostate cancer, indicating that its use may be a new therapeutic approach for PCa.

cancer biology↗

The Human walking kinematic model combined with upper and lower limb movement

The purpose of this study is to build a relatively complete human walking kinematic model. This model is combined with the rolling-foot model (lower limb) and multi-rod swinging model (upper limb) connected by COM. We calculated the velocity of COM and other critical joints of the upper limb by marker point capture experiment using the high-speed camera. This research shows that the hand joint velocity measured through the experiment can achieve high coincidence with that calculated by the theoretical model given specific inputs. Moreover, the common pattern of upper limb angles is also studied for an accurate description. The proposed kinematic model is expected to forecast desired motion intention for better compliance by the rehabilitation and assistive robots.

biophysics↗

Dysfunction of the histone demethylase IBM1 in Arabidopsis reshapes the root-associated bacteria community

Root-associated bacteria communities are influential to plant growth and stress tolerance. Epigenetic regulation plays important roles in many plant biological processes, but its potential impacts on the assembly of root microbiota remain unclear. Here we report that dysfunction of the histone demethylase IBM1 in Arabidopsis substantially alters root-associated soil bacteria community. We compared two alleles of ibm1 mutant (ibm1-1 and ibm1-4) with wild type Arabidopsis regarding the root-associated bacteria community by 16S rRNA gene sequencing. The constrained principal coordinate analysis (PCoA) showed that the ibm1 mutants are both clearly separated from Col-0 along the major coordinates. Among the 29 families which have a relative abundance more than 0.5% in at least one sample, 10 and 11 families were commonly affected by ibm1-1 and ibm1-4 alleles in the rhizosphere and the endosphere compartment, respectively. Notably, the ACMs (Abundant Community members) belonging Pseudomonadaceae showed increased relative abundance in the ibm1 mutant alleles compared to Col-0 in both the rhizosphere and the endosphere compartments. The ACMs belonging to Oxalobacteraceae mostly showed decreased relative abundance in ibm1 mutants compared to Col-0 in endosphere compartment. These findings demonstrate an influential function of IBM1-mediated epigenetic regulation in shaping the root-associated microbiota.

microbiology↗

Latent defense response to non-pathogenic microbial factors impairs plant-rhizobacteria mutualism

Unlike pathogens that trigger plant defense responses, commensal or beneficial microbes are compatible with plants and do not elicit a defense response. An assumption underlying the compatibility is that plants are inert in mounting a defense response to non-pathogenic microbial factors. However, the mechanisms underlying this inertness in defense are unknown. Here a forward genetic screen led to the isolation of an Arabidopsis mutant displaying a new type of immunity which we named as latent defense response (LDR) to a beneficial rhizobacterium. The mutant, known as gp1 for Growth-Promotion 1, is impaired in rhizobacteria-induced plant growth-promotion due to disrupted oleic acid homeostasis and consequent activation of defense responses. Several bacterial volatile compounds trigger LDR in gp1 but not wild type plants. GP1 dysfunction strongly represses colonization of the beneficial rhizobacterium and alters root-associated microbiota. Our findings reveal a hidden layer of plant defense, LDR, which is suppressed by GP1 to allow mutualistic association between plants and beneficial rhizobacteria. One Sentence SummaryA hidden layer of host immunity against non-pathogenic microbes leads to plant incompatibility with beneficial rhizobacteria.

plant biology↗

The relationship between the waiting time of postoperative radiotherapy and the prognosis of high grade glioma:a systemic review and meta-analysis.

Objective: The relationship between the waiting time of postoperative radiotherapy and the prognosis of patients with high-grade glioma is still inconclusive, and we addressed this issue through a systematic review and meta-analysis. Methods: Twenty studies published between 1975 and 2019 about waiting times (WT) of radiotherapy with high-grade glioma were retrieved for meta-analysis.The meta-analysis was performed by converting the effect sizes of different WT into regression coefficients ({beta}) and standard error (SE) to indicate the daily impact of delay on OS. Results: A total of 8462 high-grade glioma patients were included in the 20 studies, and no correlation between WT delay and OS was found in the unadjusted model through meta-analysis (HR=1, 95%CI=0.99-1.01, p=0.962). Meta-regression was used to adjust for other prognostic factors and no clear evidence of the relationship between WT delay and OS was found. Conclusion: This meta-analysis suggests that there is no clear evidence for the effect of delayed radiotherapy on OS with high-grade glioma patients.

cancer biology↗

Loss of function mutation of mouse Snap29 on a mixed genetic background phenocopy abnormalities found in CEDNIK and 22q11.2 Deletion Syndrome patients

Synaptosomal-associated protein 29 (SNAP29) is a member of the SNARE family of proteins involved in maintenance of various intracellular protein trafficking pathways. SNAP29 maps to the 22q11.2 region and is deleted in 90% of patients with 22q11.2 deletion syndrome (22q11.2DS). However, the contribution of hemizygosity of SNAP29 to developmental abnormalities in 22q11.2DS remains to be determined. Mutations in SNAP29 are responsible for the developmental syndrome called CEDNIK (cerebral dysgenesis, neuropathy, ichthyosis, and keratoderma). On an inbred C57Bl/6J genetic background, only the ichthyotic skin defect associated with CEDNIK was reported. In this study, we show that loss of function mutation of Snap29 on a mixed genetic background not only models skin abnormalities found in CEDNIK, but also phenocopy ophthalmological, neurological, and motor defects found in these patients and a subset of 22q11.2DS patients. Thus, our findings indicate that mouse models of human syndromes should be analyzed on a mixed genetic background. Our work also reveals an unanticipated requirement for Snap29 in male fertility, and support contribution of hemizygosity for SNAP29 to the phenotypic spectrum of abnormalities found in 22q11.2DS patients.

developmental biology↗