Biology subjects

LI, X.

Publications and source records attributed to LI, X..

14 recordsLinked to original sources

bioRxiv2026

TopoFlow: Evolutionarily Conditioned Flow Matching for Protein Conformational Ensemble Generation

Proteins function through dynamic conformational ensembles rather than a single static structure, yet accurately modeling these ensembles remains challenging. Here, we introduce TopoFlow, an evolutionarily conditioned flow-matching framework for protein conformational ensemble generation. TopoFlow uses evolutionary representations from multiple sequence alignments (MSAs) to encode global conformational heterogeneity. It combines this with structural variables from a variational autoencoder (VAE) to capture local flexibility. These complementary representations are then adaptively fused through a conditional modulation module to construct unified conditioning features that guide protein conformational ensemble generation. On the ATLAS molecular dynamics (MD) benchmark, TopoFlow improved the Jensen Shannon metrics for pairwise distances (JS-PwD), radius of gyration (JS-Rg), and time-lagged independent components (JS-TIC) by 10.73%, 5.78% and 7.75%, respectively, relative to BioEmu. Notably, this performance generalizes to experiment-based evaluation, where TopoFlow exhibits strong agreement with experimental observables, including chemical shifts (CS) and small-angle X-ray scattering (SAXS). Ablation analyses further indicated that the evolutionary representations and structural latent variables contributed complementary information to ensemble generation. Our results suggest that TopoFlow, through its integration of evolutionary and structural latent information, offers a promising strategy for generating structurally plausible and conformationally informative protein ensembles.

bioinformatics↗

bioRxiv2026

Endolysosomal damage promotes intraluminal protein condensate formation that limits cytosolic leakage

Endolysosomal membrane damage is a detrimental process in mammalian cells that results in leakage of the luminal contents into the cytosol. However, the nature and extent of the leakage during membrane damage is unknown. Here, we show that endomembrane damage induces the rapid formation of intraluminal condensates in endolysosomes. A subset of resident luminal proteins undergo spatially coordinated condensation upon endomembrane damage. Electron microscopy reveals distinct luminal morphology, and cryo-electron tomography confirms the condensed ultrastructure in their native state. Condensate formation occurs across mechanistically distinct modes of membrane injury and is reversibly dissociated upon lysosomal recovery. Remarkably, these condensates impose a previously unrecognised barrier to endolysosomal escape of therapeutic oligonucleotides. Despite endomembrane damage, luminal oligonucleotide therapeutics are sequestered in damaged endolysosomes through condensate-mediated biophysical immobilisation. Targeting condensate sequestration could represent a novel strategy to improve oligonucleotide-based therapeutics.

cell biology↗

bioRxiv2025

Spen and Nito prevent dedifferentiation of progenitors by translationally repressing E(Spl)mγ

Rapid termination of Notch signaling by asymmetrically segregated Numb is essential for specification of differentiating progeny during asymmetric stem cell division. Using Drosophila type II neuroblasts as a model, here we report that specification of the differentiating progeny also requires the expression of the Notch target E(Spl)m{gamma} in the stem cell to be kept at low levels by the SPEN family proteins, Spen and Nito. We show that loss of Spen or Nito leads to a drastic increase in E(Spl)m{gamma} expression in the stem cell and subsequent dedifferentiation of its progeny. Genetic and biochemical studies demonstrate that Spen and Nito maintain the expression of E(Spl)m{gamma} in the stem cell at low levels by directly binding to two identical novel motifs in the 5UTR to repress its translation. The low expression in the stem cell prevents excessive inheritance of E(Spl)m{gamma} proteins by the differentiating progeny and ensures its rapid removal from the progeny. Together, our work uncovers a novel post-transcriptional mechanism regulating Notch signaling that is critical for cell fate specification during asymmetric stem cell division.

developmental biology↗

bioRxiv2025

ERK and PKA signaling drive the evolutionary expansion of the cortex

The human cerebral cortex, essential for intelligence, cognition, and language, evolved its uniqueness through mechanisms that drive neuronal expansion. Here, we demonstrate that ERK and PKA signaling cooperatively preserve the neurogenic capacity of cortical radial glia (RGs) by inhibiting gliogenic YAP/TAZ and SHH signaling. YAP/TAZ signaling drives cortical RGs toward ependymal fate, while SHH signaling facilitates the generation of cortical tripotential intermediate progenitor cells that produce cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons. During evolution, cortical outer radial glia (oRGs) acquire dominant ERK/PKA signaling through a self-reinforcing feedback mechanism that suppresses both YAP and SHH pathways, thereby significantly enhancing oRG self-renewal capacity and extending the neurogenic period. These findings reveal that cortical neurogenesis, gliogenesis, and evolutionary expansion are coordinately regulated by an integrated ERK, PKA, YAP/TAZ, and SHH signaling, identifying a unifying principle of mammalian cortical development and evolution.

developmental biology↗

bioRxiv2025

Mouse Cortical Cellular Diversification Through Lineage Progression of Radial Glia

Cortical radial glia (RGs) sequentially generate pyramidal neurons (PyNs) and glia. In this study, we investigated the cell intrinsic programs underlying cortical cellular diversification using time-series scRNA-seq and snATAC-seq on purified mouse cortical progenitors across embryonic and postnatal stages. Our data revealed that RGs transition from early to late over time, sequentially producing intermediate neuronal progenitors (INPs) and intermediate glial progenitors (IGPs). While INPs expand exclusively to generate PyNs, IGPs progress from young to old, sequentially producing cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons. We constructed comprehensive molecular maps that reflect cell lineage progression. In particularly, we found that chromatin accessibility drives cortical cellular diversification by restricting broadly expressed transcription factors to specific stages and cell types. Developmental changes in chromatin accessibility confine Lhx2-induced neurogenesis to early-stage RGs, leading to the loss of neurogenic competence and the acquisition of gliogenic competence as corticogenesis progresses.

neuroscience↗

bioRxiv2024

Chemically Induced Nuclear Pore Complex Protein Degradation via E3 Ligase TRIM21

Despite the exciting progress of the bifunctional degrader molecules, also known as proteolysis-targeting chimeras (PROTACs), the rapidly expanding field is still significantly hampered by the lacking of available E3 ligase ligands. Our research bridges this gap by uncovering a series of small-molecule ligands to the E3 ligase TRIM21 through DNA-Encoded Library (DEL) technology. We confirmed their interaction with TRIM21 using crystallography and demonstrated their anti-proliferative effects across various cancer cell types. Furthermore, proteomic studies identified that the mRNA Export Factor GLE1, and the Nuclear Pore Complex Protein NUP155, were significantly down-regulated upon TRIM21 ligand treatment. This degradation required TRIM21 and was ubiquitin-proteasome-dependent. More specifically, NUP155 was the primary target for the TRIM21 ligands, while GLE1 was considered a passenger target upon the initial degradation of NUP155. Using immunofluorescence techniques, we further demonstrated that the degradation of GLE1 and NUP155 proteins impaired the integrity of the nuclear envelope, leading to cell death. Highlighted by this research, a novel mode of action has been discovered for the TRIM21 E3 ligase ligand, acting as a monovalent degrader that triggers de novo interaction with functional complex proteins and induces their degradation.

cell biology↗

bioRxiv2024

Orchestrating the Acquisition of Oligodendrocyte Precursor Cell versus Olfactory Bulb Interneuron Fates through Olig1/2 during Mammalian Cortical Gliogenesis and Gliomagenesis

The hijacking of developmental gliogenesis programs is a hallmark of glioblastoma (GBM), in which glial precursor cells (GPCs) typically differentiate into both neurons and glial cells. In GBM, this process is disrupted, leading to the overproduction of proliferative glial-like cells. Our study demonstrates that the knockout of Olig1/2 in both normal development and gliomagenesis causes GPCs to shift from generating highly proliferative oligodendrocyte precursor cells to producing non-proliferative olfactory bulb interneurons. Mechanistically, Olig1/2 play dual roles by orchestrating distinct transcriptional programs in GPCs, particularly inhibiting the expression of Gsx2 through direct binding to its multiple enhancers. Additionally, we provide compelling evidence that human H3.3G34R/V-mutant tumors, a subtype of high-grade gliomas, originate from dorsal cortical-derived GPCs rather than from the previously assumed progenitors in the ventral basal ganglia. Collectively, our findings reveal a previously unrecognized role of Olig1/2 in both gliogenesis and gliomagenesis, offering deeper insights into the connections between normal neural development and tumorigenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/623106v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@10ea118org.highwire.dtl.DTLVardef@1725006org.highwire.dtl.DTLVardef@1e3ce25org.highwire.dtl.DTLVardef@f300ee_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Elucidating the Diversity and Potential Function of Ribosomally Synthesized and Post-translationally Modified Peptides in the Human Microbiome

The human microbiome holds tremendous potential for generating specialized peptides, specifically ribosomally synthesized and post-translationally modified peptides (RiPPs), significantly affecting human health by mediating interactions with other microbes and the human host. However, the capacity of our microbiome to produce these peptides and their links with human health are poorly understood. This study systematically analyzes 306,481 human microbiota-associated genomes, uncovering a broad array of yet-to-be-discovered RiPPs. These RiPPs are distributed across various body sites but show a specific enrichment in the gut and oral microbiome. Big data omics analysis reveals that numerous RiPP families are inversely related to various diseases, suggesting their potential protective effects on health. For a proof of principle study, guided by biosynthetic prediction, nine autoinducing peptides (AIPs) were chemically synthesized for in vitro and ex vivo assay. Our findings revealed that five AIPs effectively inhibited the biofilm formation of disease-associated pathogens, with one demonstrating significant anti-inflammatory capabilities. Furthermore, when ex vivo testing gut bacteria from mice with inflammatory bowel disease, we observed that two AIPs could regulate the microbial community and reduce harmful species. These findings highlight the vast potential of human microbial RiPPs in regulating microbial communities and maintaining human health, emphasizing their potential for therapeutic development.

microbiology↗

bioRxiv2024

The Alexander Disease Protein GFAP Drives Mitochondrial Fission

Mitochondrial plasticity, coordinated by fission and fusion, is crucial to ensure cellular functions. Mitochondrial fission is mediated by the GTPase Drp1 at the constriction site, which is proposed to be driven by the actin-myosin contractile force. However, the mechanism that propels constriction remains unclear, and the potential involvement of additional mechanisms in this process remains an open question. Here, using structured illumination microscopy and electron microscopy, we show that the type-III intermediate filament glial fibrillary acidic protein (GFAP) closely surrounds mitochondria fission sites and associates with accumulated Drp1 molecules. Remarkably, loss of GFAP results in hyperfused mitochondria under physiological condition and even Ca2+-induced mitochondrial fission. Additionally, mutations of GFAP, the cause of Alexander disease, result in an elevated recruitment of Drp1 to GFAP, leading to significantly increased mitochondrial fissions. Taking together, these findings suggest a novel mechanism of mitochondrial division mediated by type-III intermediate filaments.

cell biology↗

bioRxiv2022

ATG5- and ATG7-mediated autophagy regulates pollen tube guidance and male fertility in Arabidopsis thaliana

Autophagy functions as a crucial cellular scavenger by targeting cytoplasmic cargo to specific lysosome/vacuole for degradation. Autophagy-related (ATG) core proteins including ATG5 and ATG7 are evolutionarily conserved factors that are spatiotemporally orchestrated to regulate multiple processes of autophagy in yeast, mammalian and plant cells. However, autophagy is believed to be functionally dispensable in Arabidopsis thaliana since severe defects during plant growth, development and reproduction have not been observed in most of the ATG loss-of-function mutants, including atg5 and atg7, under standard cultivation conditions. In this study, we report that autophagy does in fact play roles in regulating pollen tube growth guidance and male fertility in Arabidopsis thaliana. A detailed re-assessment of atg5 and atg7 mutants revealed greatly reduced autophagy activity in germinated pollens and the seed formation within siliques is partially abolished. Next, we demonstrated that both the pollen germination ratio and pollen tube length of the mutants decreased at the beginning of germination by time-lapse tracking of pollen germination in vitro and in vivo. Additionally, we observed occurrences of pollen tube twisting and stacking during their growth towards the ovules. Finally, we found abnormal pollen grains containing only a single sperm cell or an undivided generative nucleus. Collectively, these results indicate that ATG5- and ATG7-mediated autophagy is functionally involved in regulating pollen germination, tube growth guidance and sperm cell development in Arabidopsis thaliana.

plant biology↗

bioRxiv2022

Environmental factors shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench

Hailed as "The Fourth Pole", the Mariana Trench is the deepest part of the ocean. The microbial diversity in it is extremely complicated, which might be caused by the unique environmental factors such as high salinity, low temperature, high hydrostatic pressure, and limited nutrition. Based on 4 seawater samples and 4 sediment samples obtained from the Mariana Trench, we isolated and fostered the microorganism clones with kinds of culture mediums and high-throughput culturing. By using the molecular identification methods based on PCR of 16S rDNA and ITS gene, 1266 bacterial strains in total were isolated and identified, which affiliated to 7 classes, 16 orders, 25 families and 36 genera in four phyla : Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Strains in genera Halomonas, Pseudoaltermonas were the dominant bacteria isolated from the samples. With Mantel tests on the sample-environmental parameter matrix, the sample-environmental organic matter diversity matrix and the sample-microbial diversity matrix, we concluded that the environmental parameters and the organic matters in the condition can shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench.

microbiology↗

bioRxiv2021

Mesenchymal stem cell subpopulations and their heterogeneity of response to inductions revealed by single-cell RNA-seq

Mesenchymal stem/stromal cells (MSCs) are promising cell source for regenerative medicine and treatment of autoimmune disorders. Comparing MSCs from different tissues at single cell level is fundamental for optimizing clinical applications. Here we analyzed single cell RNA-seq data of MSCs from 4 tissues, namely umbilical cord, bone marrow, synovial tissue and adipose tissue. We identified 3 major cell subpopulations, namely osteo-MSCs, chondro-MSCs, adipo/myo-MSCs, across all MSC samples. MSCs from umbilical cord exhibited the highest immunosuppression, potentially indicating it is the best immune modulator for autoimmune diseases. The differentiation potentials of MSC subpopulations, which are strongly associated with their subtypes and tissue sources, showed pronounced subpopulation differences. We found MSC subpopulations expanded and differentiated when their subtypes consist with induction directions, while the other subpopulations shrank. We identified the genes and transcription factors underlying each induction at single cell level and subpopulation level, providing better targets for improving induction efficiency.

genetics↗

bioRxiv2020

Fast and easy single-molecule pulldown assay based on agarose microbeads

The recently developed single-molecule pulldown (SiMPull) assay by Jain and colleagues is a highly innovative technique but its wide application is hindered by the high technical barrier and time consumption. We report an innovative, agarose microbead-based approach for SiMPull. We used commercially available, pre-surface-functionalized agarose microbeads to capture the protein of interest together with its binding partners specifically from cell extracts and observed these interactions under a microscope at the single-molecule level. Relative to the original method, microbead-based SiMPull is considerably faster, easier to use, and more reproducible and yet provides similar sensitivity and signal-to-noise ratio; specifically, with the new method, sample-preparation time is substantially decreased (from [~]10 to [~]3 h). These crucial features should facilitate wide application of powerful and versatile SiMPull in common biological and clinical laboratories. Notably, by exploiting the simplicity and ultrahigh sensitivity of microbead-based SiMPull, we used this method in the study of rare auditory hair cells for the first time.

biochemistry↗

bioRxiv2019

Light stimulation into dorsal raphe nucleus contributes to antidepressant effect for a stressed rat model

BackgroundLight therapy is frequently demonstrated by clinical trials to be effective to seasonal or non-seasonal major depression. However, the pathway underlying the light effect on mood remains unclear. Since a retino-raphe pathway was previously indicated to modulate 5-HT production, we hypothesize that the retinal projection into dorsal raphe nucleus (DRN) may play an important role in the light therapy for depression.\n\nMethodsA rat model of 14-day corticosterone administration (40 mg/kg/day subcutaneous injection) was mainly used to test the effect of light therapy on non-seasonal depressant-like behavior, and the involved neural circuitry and neurochemistry as well.\n\nResultsBehavior results revealed that the bright light therapy especially with the blue light of 470 nm and 400 lux, effectively reversed the depression-like responses in those stressed rats. After elimination of retino-raphe projection using immunotoxin (Saporin) the effect of light therapy was significantly attenuated. Whereas activation of retino-raphe projection using HM3q chemogenetics was shown an effect similar to fluoxetine treatment. Furthermore, 5-HT3A positive GABA cells in the DRN were activated with high c-Fos expression that involved in an inhibition of 5-HT synthesis and a subsequent depressive behavior. While light therapy through retino-raphe projection deactivated the hyperaction of those GABA cells in the DRN; that eventually contributed to the antidepressant effect from light therapy.\n\nConclusionsOur results indicate that the retino-raphe circuitry engaged antidepressant effect in DRN that contributed to the light therapy to the non-seasonal depression. 5-HT3A positive GABA cells in DRN was indicated to mediate this function of retino-raphe projection.

neuroscience↗