Biology subjects

Ji, W.

Publications and source records attributed to Ji, W..

At least 19 recordsLinked to original sources

bioRxiv2026

Repetitive transcranial magnetic stimulation targeting motor cortical region induces cell-type-specific transcriptional reprogramming and behavioral recovery in non-human primate model of Rett syndrome

Rett syndrome (RTT), a severe neurodevelopmental disorder caused by mutations in the MECP2 gene, currently lacks effective treatments. The motor cortex is a pivotal hub in RTT and autism spectrum disorders, and its impairments contribute to motor, social, and cognitive deficits. Here we examined the effects of repetitive transcranial magnetic stimulation (rTMS) targeting motor area in non-human primate of RTT (MECP2-mutant monkey) and investigated neuromolecular basis underlying therapeutic effects. We identified a new treatment target, ventral premotor cortex (PMv), for RTT and found that following a 20-day rTMS course, several behavioral and functional connectivity measures showed directional changes. Neuroimaging analyses confirmed that rTMS induced reorganization of large-scale functional connectivity with enhanced functional integration between the somatomotor and the salience networks and normalized coupling between the motor cortex and both the thalamus and the anterior cingulate cortex. Notably, single-nucleus RNA sequencing revealed that rTMS triggered cell-type-specific transcriptional reprogramming: it rescued pathological hyperactivity of excitatory neurons by restoring the expression and regulatory networks of immediate early genes (e.g., FOS, EGR1) and corrected dysregulated intercellular signaling (e.g., NRG, WNT). These findings indicate that targeting motor cortical areas with brain stimulation may treat RTT, which warrants further clinical validation.

neuroscience↗

bioRxiv2026

A FIT2-BLTP1 module sustains lipid droplet phosphatidic acid and restrains overgrowth

Lipid droplets (LDs) are assembled at discrete endoplasmic reticulum (ER) subdomains whose local phospholipid composition, rather than their protein content alone, determines whether a LD nucleates and how large it grows. Phosphatidic acid (PA) is the pivotal lipid of this environment, yet how PA reaches a forming LD has remained unknown. Here we show that the bridge-like lipid transfer protein BLTP1 is required to maintain PA in LD-associated membranes. BLTP1 depletion impaired LD formation and produced fewer but enlarged LDs across mammalian cell types, and lowered LD accumulation during adipogenic differentiation. At the ER, BLTP1 engaged the LD emergence factor FIT2 through its N-terminal transmembrane segment, an interaction that strengthened upon induction of LD formation and was strongly reduced by the disease-associated FIT2 G232R substitution. Co-depletion of FIT2 relieved the LD overgrowth caused by loss of BLTP1. Wild-type BLTP1, but neither a FIT2-binding-defective chimera nor a lipid-transfer-groove mutant, rescued LD formation in BLTP1-depleted cells. Lipidomics of purified LDs showed that BLTP1 loss most strongly lowered PA, most prominently the species PA 36:2, whereas PA and the major phospholipid classes of bulk ER membranes were unchanged. Collectively, we propose that local PA supply by BLTP1 coordinates LD assembly and growth.

cell biology↗

bioRxiv2026

Bacterial RNA polymerase exemplifies a general physical mechanism for accelerating protein-DNA association

Bacterial RNA polymerases (RNAPs) have two flexibly tethered subunit C-terminal domains (-CTDs) that bind DNA. Interaction between -CTDs and some promoter DNA motifs is known to accelerate transcription initiation, but the physical mechanism by which it does so is unclear. We used single-molecule multiwavelength fluorescence microscopy to test how the diffusion-limited binding kinetics of core RNAP to non-promoter DNA differ from those of mutant RNAPs that lack one or both -CTDs. We find that even though -CTDs and their tethers are small compared to the complete RNAP molecule, the presence of two -CTDs accelerates DNA binding by [~]10-fold and [~]55-fold respectively relative to RNAP constructs in which one or both -CTDs are deleted. In contrast, the presence of -CTDs did not have a detectable effect on RNAP-DNA complex lifetimes in the absence of RNA synthesis. We explain how -CTDs achieve the dramatic acceleration of RNAP binding to DNA using a quantitative three-state kinetic model that includes a transient binding intermediate where only the -CTD(s) are bound to DNA, tethering the rest of the RNAP in the vicinity of DNA. The model and assumed parameters are validated using Brownian dynamics simulations of the DNA association reactions for two-, one-, or zero-CTD RNAP constructs. The combination of single-molecule experiments, mathematical theory, and simulations suggests that adding a flexible DNA-binding tether is a general physical mechanism which can accelerate the diffusion-limited binding of a large protein like RNAP to DNA and quantitatively defines the conditions under which this acceleration can occur. Significance StatementLarge enzymes that must associate with DNA to perform their biological functions are expected to bind DNA only slowly because of slow enzyme diffusion. However, some DNA-binding enzymes have one or more additional small DNA-binding domains that can diffuse rapidly but are attached to the enzyme through an unstructured flexible tether. Combining single-molecule experiments, theory, and computation, we present evidence for a general mechanism by which such tethered domains can accelerate enzyme binding to DNA by orders of magnitude, while not significantly changing the duration of the DNA-bound state. We demonstrate this effect for the flexibly-tethered -subunit C-terminal domain of bacterial RNA polymerase. The mechanism may allow the polymerase to rapidly bind DNA while minimizing non-functional sequestration on the genome.

biophysics↗

bioRxiv2026

Convergent antigenic drift of the influenza hemagglutinin lateral patch across time and species

The lateral patch epitope of the H1 hemagglutinin (HA) was a dominant target of antibodies following exposure to the 2009 pandemic H1N1 virus. However, the conservation and potential for antigenic drift in the lateral patch remain unresolved. Here, we used lateral patch-specific monoclonal antibodies (mAbs) to understand the antigenicity of the lateral patch of human, avian, and swine H1Nx viruses spanning from 1918 to 2022. We identified discrete mutations that evaded lateral patch-targeting mAbs in pre- and post-2009 H1N1 viruses, leading to genetic differences in lateral patch-targeting antibodies in individuals across birth years. We observed that the lateral patch remains well conserved across zoonotic sources, suggesting existing lateral patch antibodies could protect against a future H1Nx pandemic. Together, these data support that lateral patch antigenic drift has shaped the human B cell repertoire against influenza viruses and that the lateral patch remains an attractive target for pandemic preparedness.

microbiology↗

bioRxiv2026

Structural insights into antibody responses against influenza A virus in its natural reservoir

While influenza A virus undergoes rapid antigenic drift in humans, at least some subtypes, such as H3, have relatively stable antigenicity in natural waterfowl reservoirs, despite the presence of immune pressure. However, the underlying mechanisms remain poorly understood. This study identified and characterized 187 antibodies to H3 hemagglutinin from experimentally infected mallard ducks, 18 of which were further analyzed by cryo-EM. Compared with human H3 antibodies, duck H3 antibodies exhibited higher glycan-binding propensity, more balanced immunodominance hierarchy, and targeted distinct epitopes. Other unique features of duck H3 antibodies included a convergent CDR H3-independent heavy chain-only binding mode and an N-glycosylated CDR H3 as decoy receptor. By annotating duck immunoglobulin germline genes, we also demonstrated the importance of gene conversion in duck H3 antibodies. Overall, our findings provide insights into how millennia of coevolution have shaped the interplay between influenza A virus antigenic drift and antibody responses in the natural reservoir.

immunology↗

bioRxiv2026

Elimination of intramuscular immunoglobulin accumulation alleviates Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is a devastating neuromuscular disorder due to loss of dystrophin, a cytoskeletal protein critical for muscle integrity and functionality. Despite recent therapeutic advances, there remains a significant unmet need for more effective and accessible therapeutics. Here, we discovered an early accumulation of immunoglobulin G (IgG) in the sarcolemma, which exacerbates tissue inflammation and disease progression. The IgG accumulation primarily resulted from ectopic localization of Fc{gamma}R1, a high-affinity IgG Fc receptor, on dystrophin-deficient myofibers. In two independent murine models, eliminating IgG accumulation via B cell depletion provided sustained benefit to alleviate DMD progression. Our findings uncover a novel disease accelerator in DMD and demonstrate the potential to target this mechanism as therapeutics for broader population of patients with DMD.

immunology↗

bioRxiv2026

MOSPD3 mediates the ER recruitment of ATG2A to promote autophagy

ATG2A transfers glycerophospholipids from the endoplasmic reticulum (ER) to support expansion of the isolation membrane at ER membrane contact sites. While a role for ATG18/WIPI4 in targeting ATG2A to the IM is well established, how ATG2A is recruited to the ER remains unclear. In this study, we found that MOSPD3, an atypical VAP family protein, acts an adaptor that recruits ATG2A to the ER. MOSPD3 colocalizes with ATG2A and is specifically enriched at ER sites juxtaposed with the IM during autophagosome formation. Recruitment is mediated by direct interactions between the FFNT (two phenylalanines in a neutral tract) motif in the N-terminal region (NT) of ATG2A and the major sperm protein (MSP) domain of MOSPD3. Co-expression of MOSPD3 with ATG2A-NT, but not a MOSPD3-binding-defective mutant ATG2A-NT-T362A, markedly rescued the autophagic defect caused by ATG2A/B double knockout (DKO). MOSPD3 depletion abolishes ATG2A recruitment to the ER and impedes autophagic flux. Together, this study demonstrates that MOSPD3 functions as an ER adaptor for ATG2A in autophagy.

cell biology↗

bioRxiv2025

HGS+ enlarged vesicular compartment serves as site for coronavirus assembly at later infection stage

The precise site of coronavirus assembly remains poorly characterized. In this study, we observed that coronavirus infection induces the host factor hepatocyte growth factor-regulated tyrosine kinase substrate (HGS) to form distinct HGS enlarged vesicular compartments at later infection stage. Confocal and live-cell super-resolution microscopy showed that viral structural proteins colocalize with these HGS enlarged vesicular compartments. Correspondingly, APEX2-based electron microscopy (APEX2-EM) and immuno-EM analyses confirmed the presence of assembled virions within these unique HGS compartments, identifying them as sites of virion assembly. This was further supported by cryogenic correlated light and electron microscopy (cryo-CLEM), which captured ongoing virion formation occurring within HGS enlarged vesicles. Crucially, whole cell volume EM revealed that HGS deficiency abolishes these vesicular compartments and markedly reduces assembled virions. Lastly, we demonstrated that HGS vesicular compartments are rearranged from Golgi and endosome/lysosome by coronavirus infection. Together, these findings establish that coronavirus-induced HGS vesicular compartments function as essential platforms for virion assembly at later infection stage.

microbiology↗

bioRxiv2025

Targeting the host factor HGS-viral membrane protein interaction in coronavirus infection

While current antivirals primarily target viral proteins, host-directed strategies remain underexplored. Here, we performed a genome-wide CRISPRi screening to identify the host protein, Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (HGS), as essential for the pan-coronaviruses infection both in vitro and in vivo. Mechanistically, HGS directly interacts with the viral membrane (M) protein, facilitating its trafficking to the ER-Golgi intermediate compartment (ERGIC) for virion assembly. Conversely, HGS deficiency caused M retention in the ER, blocking assembly. Leveraging this interaction, we designed M-derived peptides and screened over 5,000 FDA-approved drugs, identifying riboflavin tetrabutyrate (RTB). Both the peptides and RTB bind HGS and disrupt its interaction with the M protein, leading to M retention in the ER and subsequent blockade of virion assembly. These agents demonstrated broad anti-pan-coronavirus activity in vitro and in vivo. Collectively, our findings establish HGS as a druggable host target and identify RTB as a promising broad-spectrum antiviral candidate.

microbiology↗

bioRxiv2025

BLTP1-dependent phospholipid efflux prevents mitochondrial lipid overload and apoptosis at FKBP8-tethered ER-mitochondrial contact

Maintenance of mitochondrial phospholipid homeostasis is critical for organellar function and cell survival, yet mechanisms enabling phospholipid efflux from mitochondria remain undefined. We identify BLTP1 as a phospholipid transporter that exports phospholipids from mitochondria to maintain lipid homeostasis. The outer mitochondrial membrane protein FKBP8 recruits BLTP1 to ER-mitochondrial contact sites, establishing a dedicated lipid export pathway. BLTP1 deficiency triggers pathological accumulation of phosphatidic acid (PA), phosphatidylglycerol (PG), and cardiolipin (CL) within mitochondria. This lipid overload is associated with elevation of mitochondrial reactive oxygen species (ROS), bioenergetic dysfunction, and apoptosis. Critically, depleting intramitochondrial lipid transfer proteins (e.g., PRELID1) or enzymes in the CL synthesis pathway (e.g., PTPMT1, CRLS1) prevents apoptosis caused by BLTP1 deficiency. Our findings defines a BLTP1-FKBP8-dependent mechanism for mitochondrial phospholipid efflux that is essential for mitochondrial function and cell survival.

cell biology↗

bioRxiv2025

Unveiling the Chain Mediation Model of Sleep Quality and Fatigue in Linking Subjective Exercise Experience to Depression in Adolescent

While the positive correlation between physical exercise and depression has been widely replicated in cross-sectional research, the prognostic value of subjective exercise experience for depression continues to be disputed, and the mediating processes are not well understood. This study aims to elucidate the predictive role of subjective exercise experience in depression and examine the chain mediating effects of sleep quality and fatigue. We administered validated self-report questionnaires to assess these constructs in a sample of 538 Chinese high school students. The results demonstrated that adolescents depressive symptoms are influenced by subjective exercise experience, and this effect mediated through two independent pathways: sleep quality and fatigue. Moreover, subjective exercise experience can predict adolescent depression via either the sleep quality pathway or the fatigue pathway. The identification of mediating dual pathways provides empirical support for developing targeted exercise interventions that specifically address sleep disturbances and fatigue management in depressed adolescents.

physiology↗

bioRxiv2025

Association of handgrip strength asymmetry and weakness with successful aging among older adults in China

BackgroundSuccessful aging (SA) is important for the increasing population aging. The role of handgrip strength(HGS) asymmetry and weakness in successful aging remains unclear. This study aimed to elucidate the association of HGS asymmetry and weakness with successful aging in older adults. MethodsWe included participants aged [≥] 60 years from the 2015 China Health and Retirement Longitudinal Study (CHARLS).SA absence of major diseases, absence of major chronic diseases, no impairment in physical function, high cognitive functioning, good mental health, and active participation in life. HGS asymmetry and weakness were measured using the maximum value of the HGS. Logistic regression modeling was used to examine the association of individuals with HGS asymmetry and weakness with SA. Restricted cubic spline (RCS) modeling was used to explore potential nonlinear relationships. ResultsOf the 5,031 individuals included, the median age of the study population was 67 years IQR: 63-73 years, 45.6% female. Only 6.3% met the criteria for successful aging. HGS asymmetry (OR = 0.597,95 % CI: 0.472-0.754) and weakness (OR = 0.643,95 % CI: 0.417-0.964) were both independent influences on SA. Participants were less likely to have SA when both HGD asymmetry and frailty were present (OR = 0.426,95 % CI: 0.240-0.757). Further subgroup analyses revealed significant associations between HGS status and each of the components of SA, particularly with regard to physical functioning. There was an n-shaped relationship between HGS asymmetry and SA. ConclusionHGS asymmetry is associated with a reduced likelihood of weak SA. Improving or maintaining HGS symmetry and frailty may contribute to SA in older adults.

physiology↗

bioRxiv2025

BLTP2 orchestrates lysobisphosphatidic acid synthesis and exosome biogenesis via SCAMP3-dependent ER contacts in tumorigenesis

Multivesicular bodies (MVBs) contain intraluminal vesicles (ILVs) designated for degradation in lysosomes or release as exosomes for cell-to-cell communication. The mechanisms governing ILV/exosome formation are not fully understood. Here, we show that the integral endoplasmic reticulum (ER) membrane protein bridge-like lipid transfer protein 2 (BLTP2; KIAA0100) is indispensable in ILV/exosome formation and that secretory carrier membrane protein 3 (SCAMP3) recruits BLTP2 to ER-MVB membrane contact sites (MCSs) in a Rab5-dependent manner. Our results indicate that this recruitment is hindered by NEDD4-mediated ubiquitination of SCAMP3. Depletion of BLTP2 was found to impede ILV/exosome formation and selectively diminish the levels of cone-shaped phospholipids, including bis(monoacylglycero)phosphate (BMP) and the BMP precursor phosphatidylglycerol (PG) within endosomes. BLTP2 knockout also hampered cell proliferation and tumorigenicity, which could be restored to a significant extent by supplementation with exosomes from wild-type cells. Since BLTP2 is associated with acute monocytic leukemia and is highly expressed in breast cancer, our findings suggest that BLTP2 transfers the BMP/LBPA precursor PG to MVBs for BMP/LBPA synthesis and promotes ILV/exosome formation at SCAMP3-dependent ER-MVB MCSs, a process crucial for cell proliferation and tumorigenesis.

cell biology↗

bioRxiv2025

Reshaping epistatic network modules enhances wheat yield potential

Increasing wheat yield is a key approach to ensuring global food security and an enduring focus in crop breeding. Here, we assembled a panel of 3,030 wheat lines to dissect the genetic mechanisms of yield improvement. We conducted large-scale field trials across five ecological environments over two consecutive years to evaluate yield performance and constructed a haplotype atlas using the Wheat 660K genotype array. 234 quantitative trait loci (QTLs) and 522 haplotype blocks (HBs) were identified for 14 traits through genome-wide association studies (GWAS), including 10 QTLs and 35 HBs associated with grain yield. Genomic analysis revealed that wheat yield improvement is primarily driven by changes in the epistatic network rather than the introduction of new haplotype segments. SNPs or HBs explain 53.3%-62.9% of the phenotypic variation in yield, whereas epistasis explains 70.4%, highlighting the role of epistasis in yield improvement. Moreover, yield improvement is significantly correlated with the accumulation of favorable epistatic modules. Pedigree-based analysis revealed that the modules remained relatively stable under the pressure of breeding selection, while new favorable modules were also created during hybrid breeding, highlighting that crop design breeding should be based on genetic modules. This study provides insights into genetic mechanism of wheat yield improvement and guidance for designing future wheat in the era of artificial intelligence.

genetics↗

bioRxiv2025

Layered stomatal immunity contributes to resistance of Vitis riparia against downy mildew Plasmopara viticola

Downy mildew (DM), caused by Plasmopara viticola, is one of the most serious grapevine diseases. Resistant grapevines are a well-known tool for mitigating pathogen-caused damage. We evaluated 29 global grapevine cultivars from 7 species for the sensitivity to P. viticola. Chardonnay belonging to the sensitive species V. vinifera and Qingdahean belonging to the well-known resistant species V. riparia were chosen for further investigation on the resistance mechanism against DM. Unlike Chardonnay, Qingdahean exerted an inhibitory effect on stomatal targeting, suppression of stomatal closure, stomatal penetration of P. viticola, and the development of primary hyphae and haustoria during the early phase of infection, and contained higher levels of malondialdehyde (MDA), which was significantly increased by P. viticola infection, toxic to the pathogen and had an interfering effect on the stomatal targeting. Furthermore, Qingdahean resisted pathogen invasion through the rapid induction of guard cell death and the hypersensitive responses (HR) of other cell types. These findings suggest that resistance to P. viticola consists of layered stomatal immunity in addition to the well-known HR in V. riparia, which is overcome by the pathogen in V. vinifera.

plant biology↗

bioRxiv2025

Systematic Identification of Microtubule Inner Proteins Reveals JPT2 as a Key Regulator of Lumen Microenvironment and Drug Sensitivity

Microtubules are primarily studied for the interactions of proteins that bind to their outer surfaces and ends, while the regulatory mechanisms within the microtubule lumen, particularly in singlet microtubules critical for essential cellular processes, remain largely unexplored. Our study provides the first systematic identification of key regulatory proteins within the single microtubule lumen. Using proximity-dependent biotin identification (Bio-ID) coupled with mass spectrometry, we identified candidate microtubule inner proteins (MIPs), including Jupiter microtubule-associated homolog 2 (JPT2). JPT2 binds directly to microtubules and specifically localizes within the lumen, where it modulates the luminal environment by inhibiting acetylase MEC17 and independently affects the binding and efficacy of Paclitaxel. Furthermore, our screening identified additional MIPs that influence cellular sensitivity to Paclitaxel, indicating a link between luminal regulation and drug responsiveness. These discoveries reveal JPT2s critical role in singlet microtubule regulation and suggest new therapeutic targets for enhancing cancer drug sensitivity.

cell biology↗

bioRxiv2024

Identification of Differentially Expressed Genes and Proteins Related to Diapause in Lymantria Dispar: Insights for the Mechanism of Diapause from Transcriptome and Proteome Analyses

Spongy moth (Lymantria dispar Linnaeus) is a globally recognized quarantine leaf-eating pest. Spongy moths typically enter diapause after completing embryonic development and overwinter in the egg stage. They spend three-quarters of their life cycle (approximately nine months) in the egg stage, which requires a period of low-temperature stimulation to break diapause and continue growth and development. In this study, we explored the molecular mechanism underlying the diapause process in spongy moth. We performed bioinformatics analysis on four Asian populations of spongy moth and one Asian-European hybrid population through a transcriptome analysis combined with proteomics. The results revealed that 1,842 genes were differentially expressed upon diapause initiation, while 264 genes were identified upon diapause termination. Eight diapause-related genes were screened out from the three-level pathways that were significantly enriched by differentially expressed genes at the time of diapause and diapause termination, and the phylogenetic tree and protein three-dimensional structure model were constructed. This study elucidates the diapause mechanism of spongy moth at the gene and protein levels, providing theoretical insights into the early and precise prevention and control of spongy moth. This study can facilitate the development of an efficient, environmentally friendly control system for managing spongy moth populations in the field.

genomics↗

bioRxiv2024

Design principles of transcription factors with intrinsically disordered regions

Transcription Factors (TFs) are proteins crucial for regulating gene expression. Effective regulation requires the TFs to rapidly bind to their correct target, enabling the cell to respond efficiently to stimuli such as nutrient availability or the presence of toxins. However, the search process is hindered by slow diffusive movement and the presence of false targets - DNA segments that are similar to the true target. In eukaryotic cells, most TFs contain an Intrinsically Disordered Region (IDR), which is commonly assumed to behave as a long, flexible polymeric tail composed of hundreds of amino acids. Recent experimental findings indicate that the IDR of certain TFs plays a pivotal role in the search process. However, the principles underlying the IDRs role remain unclear. Here, we reveal key design principles of the IDR related to TF binding affinity and search time. Our results demonstrate that the IDR significantly enhances both of these aspects. Furthermore, our model shows good agreement with experimental results, and we propose further experiments to validate the models predictions.

biophysics↗