Biology subjects

Shi, Y.

Publications and source records attributed to Shi, Y..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Clustered VEGF Nanoparticles in Microporous Annealed Particle (MAP) Hydrogel Accelerates Functional Recovery and Brain Tissue Repair after Stroke

Ischemic stroke, a blockage in the vasculature of the brain that results in insufficient blood flow, is one of the worlds leading causes of disability. The cascade of inflammation and cell death that occurs immediately following stroke drives vascular and functional loss that does not fully recover over time, and no FDA-approved therapies exist that stimulate regeneration post-stroke. We have previously developed a hydrogel scaffold that delivered heparin nanoparticles with and without VEGF bound to their surface to promote angiogenesis and reduce inflammation, respectively. However, the inclusion of the naked heparin nanoparticles warranted concern over the development of bleeding complications. Here, we explore how microporous annealed particle (MAP) scaffolds functionalized with VEGF coated heparin nanoparticles can both reduce inflammation and promote angiogenesis - without the inclusion of free heparin nanoparticles. We show that our updated design not only successfully promotes de novo tissue formation, including the development of mature vessels and neurite sprouting, but it also leads to functional improvement in a photothrombotic stroke model. In addition, we find increased astrocyte infiltration into the infarct site correlated with mature vessel formation. This work demonstrates how our biomaterial design can enhance endogenous regeneration post-stroke while eliminating the need for excess heparin.

bioengineering↗

bioRxiv2025

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-induced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy. HIGHLIGHTSO_LIPhenotypic screens identified JIB-04 as a potent anti-cancer agent for multiple subtypes of diffuse large B-cell lymphoma C_LIO_LIJIB-04 binds and inhibits KDM4 demethylases resulting in epigenomic rewiring of heterochromatin C_LIO_LIKDM4 demethylases cooperate with KRAB zinc fingers to limit DNA replication stress, and KDM4 inhibition instigates DNA-damage and cGAS-STING activation in several human cancers C_LIO_LIHigh-throughput small molecule screens with semi-synthetic nucleosome substrates and AI-guided molecular docking simulations identify novel KDM4 inhibitors C_LI

genomics↗

bioRxiv2025

TransBrain: A computational framework for translating brain-wide phenotypes between humans and mice

Despite remarkable advances in whole-brain imaging technologies, the lack of quantitative approaches to bridge rodent preclinical and human studies remains a critical challenge. Here we present TransBrain, a computational framework enabling bidirectional translation of brain-wide phenotypes between humans and mice. TransBrain improves human-mouse homology mapping accuracy through: (1) a novel detached region-specific deep neural network trained on integrated multi-modal human transcriptomics to improve cortical correspondence (89.5% improvement over the original transcriptome), which revealed two evolutionarily conserved gradients explaining >50% of cortical organizational variance, and (2) random walk-based graph representation learning to construct a unified cross-species latent space incorporating anatomical hierarchies and structural connectivity. We demonstrated TransBrains utility through three cross-species applications: quantitative assessment of resting-state brain organizational features, inferring human cognitive functions from mouse optogenetic circuits, and translating molecular insights from mouse models to individual-level mechanisms in autism. TransBrain enables quantitative cross-species comparison and mechanistic investigation of both normal and pathological brain functions.

neuroscience↗

bioRxiv2025

Evidence for evolution of a new sex chromosome within the Marchantiales haploid plant lineage

Sex chromosomes have evolved independently in numerous lineages across the tree of life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we study dioicy-monoicy transitions in the ancient liverwort haploid plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that m-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

evolutionary biology↗

bioRxiv2025

Recommendations for Automating Hydrogen/Deuterium Exchange Mass Spectrometry Measurements using Data-Independent Acquisition Methods

Hydrogen/deuterium exchange mass spectrometry (HX-MS) is a method used to study solution-phase protein structure and dynamics. Despite its many applications, HX-MS is limited in throughput because manual data analysis is still the norm. We previously developed HX-MS2 technology to add a second dimension of deuteration data and promote automated data processing. Data-independent acquisition (DIA) techniques enable this approach, but we require optimized methods for best performance. Using an Orbitrap Eclipse for illustration, we show that ion optics and collision energy settings typical of a proteomics DIA experiment generate maximal peptide retrieval from the DIA library. As few as three MS2 sequence ions are sufficient to generate a deuteration measurement with a precision that exceeds what is possible in traditional HX-MS. DIA window sizes are based on the chromatographic resolution of the method. An inter-scan window offset method is the recommended default configuration for most HX-DIA applications, but an intra-scan overlap method can be tuned for highest performance and is recommended when maximum peptide retrieval is desired. A fully automated HX-MS2 solution consists of Trajan HDX automation technology, an Orbitrap Eclipse mass spectrometer and AutoHX software. We demonstrate its robustness on an extensive time-course analysis of phosphorylase B and an epitope analysis of single domain antibodies (VHHs, nanobodies) specific to the receptor binding domain of SARS-CoV2 spike protein.

biochemistry↗

bioRxiv2025

Enforced E-selectin ligand installation enhances homing and efficacy of adoptively transferred T cells

Adoptive T-cell transfer has revolutionized the treatment of hematological malignancies. However, this approach has had very limited success in treating solid tumors, largely due to inadequate infiltration of vascularly administered T cells at tumor sites. The shear-resistant interaction between endothelial E-selectin and its cognate ligand expressed on leukocytes, sialyl Lewis X (sLeX), is an essential prerequisite for extravasation of circulating leukocytes. Here, we report that enforced E-selectin ligand expression (enforced sLeX display) on antigen-specific T cells can be achieved by fucosylating cells via cell surface treatment with the human 1-3-fucosyltransferase, FUT6 ("exofucosylation"), or via Golgi-targeted FUT6 overexpression ("Golgi-fucosylation"). However, despite comparable E-selectin binding, only sLeX-modified T cells engendered by exofucosylation, not by Golgi-fucosylation, exhibited enhanced parenchymal infiltration of target malignant sites. This heightened homing yielded significantly improved therapeutic efficacy in various murine syngeneic and xenograft cancer models, including subcutaneous solid tumors, lymphoma and leukemia, as well as lung and bone marrow metastases. Therefore, exofucosylation represents a promising strategy to improve the efficacy of adoptive T-cell therapy, particularly in the treatment of solid tumors and metastatic disease.

cancer biology↗

bioRxiv2025

Extreme high-diversity barcoded HIV library enables single cell multi-omics analysis of viral expression and fate determination

HIV-1 persists as a global health challenge due to its ability to establish latent reservoirs that evade eradication by antiretroviral therapy (ART). This study introduces a high-diversity barcoded HIV-1 library combined with a novel peptide barcode system to enable single-cell multi-dimensional analysis of viral integration, transcription, splicing, and translation of distinct viral mRNA isoform. Our method revealed over 80 distinct HIV-1 splicing isoforms and uncovered significant temporal variation in mRNA diversity, driven by integration site and chromatin context. By linking HIV-1 5UTR with peptide barcoding, we quantified the translation efficiency of alternative 5' UTRs and demonstrated correlations with abundance of each viral mRNA isoform. Additionally, we showed that latency reversal agents, such as SAHA and Bryostatin, selectively reactivate proviruses depending on their genomic and chromatin context and leads to distinct viral RNA splicing program. This platform revealed the diversity of HIV-infected cells at levels of transcripts as well as at proteins, and subsequently the fate determination. The detailed understanding of the stochastic diversity and dynamic nature of HIV-1 latency, inform the development of targeted therapies to eliminate latent reservoirs.

microbiology↗

bioRxiv2025

Niacin protects against vascular calcification via enhanced SIRT1 and SIRT6 signaling and promoted VSMC autophagy

BackgroundVascular calcification (VC) is a common pathologic state that often accompanies calcium-phosphorus metabolism disorder and chronic kidney diseases (CKDs) in aging individuals. Vascular smooth muscle cell (VSMC) has been widely acknowledged as one of the main cell types that involved in this process. Niacin, a lipid-lowering reagent, has been demonstrated to be beneficial in atherosclerotic disease. The correlation and mechanism between niacin and vascular calcification have not been reported so far. Methods and resultsRCS analysis based on large clinical databases indicated that diet that riches in niacin can protect against abdominal artery calcification (AAC). Our data showed that niacin treatment remarkably reduced VSMC osteogenic differentiation and senescence-associated markers under osteogenic stimulation. Moreover, niacin treatment alleviated CKD and vitamin D3-induced vascular calcification in C57BL/6J mice. Mechanistically, we for the first time demonstrated that niacin supplementation inhibited vascular calcification via maintaining both Sirtuin 1 (SIRT1) and Sirtuin 6 (SIRT6) levels. Moreover, we verified that niacin activated SIRT1 and SIRT6 promoted VSMC autophagy flux. ConclusionsThese findings may help to develop novel therapeutic strategies in the treatment and prevention of vascular calcification.

cell biology↗

bioRxiv2025

Psilocybin induces sex- and context-specific recruitment of the stress axis

Psychedelics have reemerged as potential treatments for mental health disorders, yet their impact on stress-related brain regions remains poorly understood. Here, we provide the first real-time, in vivo evidence of psilocybin-induced neuronal activation, specifically in hypothalamic corticotropin-releasing hormone neurons. Notably, psilocybin elicited more pronounced responses in female mice and produced context-related alterations in threat assessment. Our findings provide valuable insight into the impact of psychedelics on a key stress center in the brain.

neuroscience↗

bioRxiv2025

Antidepressants promote developmental-like plasticity through remodeling of extracellular matrix

Antidepressants are widely used to treat mood and anxiety disorders, yet the cellular and molecular mechanisms underlying their therapeutic effects remain poorly understood. Here, we show that the selective serotonin reuptake inhibitor (SSRI) fluoxetine rejuvenates the dentate gyrus (DG) by reactivating a latent developmental plasticity program in mature neurons, which is required for re-engaging critical period-like synaptic remodeling and antidepressant-like behavioral effects. Single nuclei transcriptomic profiling across all hippocampal cell types revealed a strikingly selective response in the DG, where mature neurons re-engaged a developmental-like transcriptional state, an effect distinct from adult neurogenesis. Chronic fluoxetine treatment induced expression of SOX11, a developmental transcription factor involved in neurodevelopment and axonal regeneration that is normally silenced in the adult brain. Reactivation of SOX11 in mature DG neurons was necessary for both the antidepressant-like behavioral effects of fluoxetine and the re-engagement of critical period-like synaptic remodeling. Notably, SOX11 reactivation was also induced by physiological stimuli, including environmental enrichment and peripheral axon regeneration, suggesting that mature neurons retain access to a conserved developmental plasticity program throughout adulthood. We further identified evidence of this form of developmental plasticity in the adult human brain, an effect distinct from adult neurogenesis. At the structural level, fluoxetine remodeled novel extracellular matrix (ECM) structures within the DG distinct from canonical perineuronal nets, and targeted ECM degradation was sufficient to reactivate SOX11 in mature neurons, identifying the ECM as a key regulator of neuronal rejuvenation. Altogether, these findings demonstrate that mature neurons retain an intrinsic capacity to re-engage dormant developmental programs, and that antidepressants harness this regenerative plasticity to drive neural circuit remodeling and antidepressant-like effects.

neuroscience↗

bioRxiv2025

Hydrogen-bonded organic framework nanotransducers enabled sono-optogenetics for Parkinsonian rats

Cell-type-specific activation of parvalbumin (PV)-expressing neurons in the external globus pallidus (GPe) through optogenetics has shown promise in facilitating long-lasting movement dysfunction recovery in mice with Parkinsons disease. However, its translational potential is hindered by adverse effects stemming from the invasive implantation of optical fibers into the brain. In this study, we have developed a non-invasive optogenetics approach, utilizing focused ultrasound-triggered mechanoluminescent nanotransducers to enable remote photon delivery deep in the brain for genetically targeted neuromodulation. These mechanoluminescent nanotransducers consist of sonosensitized hydrogen-bonded frameworks and chemiluminescent L012, serving as a nanoscale light source through ultrasound-induced cascade reactions. This system offers high ultrasound-triggered brightness and long-lasting light emission, facilitating repeatable deep brain stimulation. Our sono-optogenetics technology demonstrated effective modulation in the mouse motor cortex for limb motion control and activation of PV-GPe neurons for rescuing movement dysfunction over time in dopamine-depleted Parkinsons disease rats. This approach demonstrates the pathway for achieving genetically targeted and non-invasive neuromodulation for long-lasting treatment of Parkinsons disease, towards non-human primate models and clinical applications.

bioengineering↗

bioRxiv2024

Multi-omics analysis of long-term cultured human islets

Beta-cell dysfunction in pancreatic islets, characterized as either the loss of beta-cell mass or the resistance of beta-cell to glucose, is the leading cause of progression to diabetes. Islet transplantation became a promising approach to replenish functional beta-cell mass. However, not much known about changes in islets used for transplantation after isolation. We have subjected human islets into long-term in vitro culture (LTC) and characterized those survived islets. While most of the dysregulated genes were downregulated during LTC, specific groups of mRNA or miRNA were upregulated, and they are involved in specific pathways. In general, alpha-cells and beta-cells of LTC-islets have elevated expressions of MAFB and MAFA genes, respectively. We also found that exocrine cells were eliminated faster than endocrine cells, and beta-cells were lost at a higher rate than alpha-cells. Interestingly, one specific group of cells that have characteristics of immature alpha-cells or beta-cells, were enriched in LTC-islets, revealing the possibility of transdifferentiation of alpha-cells to beta-cells, or dedifferentiation of beta-cells to alpha-cells, under in vitro culture. Our results suggest that there are intrinsic cellular and molecular mechanisms in pancreatic cells that are associated with their maturity and correlated with their survival ability under unfavorable living conditions.

molecular biology↗

bioRxiv2024

A gated hydrophobic funnel within BAX binds long-chain alkenals to potentiate pro-apoptotic function

Mitochondria maintain a biochemical environment that cooperates with BH3-only proteins (e.g., BIM) to potentiate BAX activation, the key event to initiate physiological and pharmacological forms of apoptosis. The sphingosine-1-phosphate metabolite 2-trans-hexadecenal (2t-hexadecenal) is one such component described to support BAX activation, but molecular mechanisms remain largely unknown. Here, we utilize complementary biochemical and biophysical techniques to reveal that 2t-hexadecenal non-covalently interacts with BAX, and cooperates with BIM to stimulate early-activation steps of monomeric BAX. Integrated structural and computational approaches reveal 2t-hexadecenal binds an undefined region - a hydrophobic cavity formed by core-facing residues of 5, 6, and gated by 8 - we now term the "BAX actuating funnel" (BAF). We define alkenal length and 8 mobility as critical determinants for 2t-hexadecenal synergy with BIM and BAX, and demonstrate that proline 168 allosterically regulates BAF function. Collectively, this work imparts detailed molecular insights advancing our fundamental knowledge of BAX regulation and identifies a regulatory region with implications for biological and therapeutic opportunities.

cell biology↗

bioRxiv2024

A Brain Reward Circuit Inhibited By Next-Generation Weight Loss Drugs

Glucagon-like peptide-1 receptor agonists (GLP1RAs) effectively reduce body weight and improve metabolic outcomes, yet established peptide-based therapies require injections and complex manufacturing. Small-molecule GLP1RAs promise oral bioavailability and scalable manufacturing, but their selective binding to human versus rodent receptors has limited mechanistic studies. Here, we developed humanized GLP1R mouse models to investigate how small-molecule GLP1RAs influence feeding behavior. This approach revealed that these compounds regulate both homeostatic and hedonic feeding through parallel neural circuits. Beyond engaging canonical hypothalamic and hindbrain networks that control metabolic homeostasis, GLP1RAs recruit a discrete population of Glp1r-expressing neurons in the central amygdala, which selectively suppress the consumption of palatable foods by reducing dopamine release in the nucleus accumbens. Stimulating these central amygdalar neurons curtail hedonic feeding, whereas targeted deletion of the receptor in this cell population specifically diminishes the anorectic efficacy of GLP1RAs for reward-driven intake. These findings reveal a dedicated neural circuit through which small molecule GLP1RAs modulate reward processing, suggesting broad therapeutic potential in conditions of dysregulated dopamine signaling including substance use disorder and binge eating.

neuroscience↗

bioRxiv2024

Modulating Cellular Deformability via 3D Dextran Hydrogel Cultivation to Regulate the Microcirculation of Mesenchymal Stem Cells in Murine Spleen and Liver

For mesenchymal stem cell (MSC) therapy to be effective, the vascular system may be used to deliver and steer the cells to the target tissue. However, the expanded MSCs in petri dishes are usually have a limited deformability and commonly excluded by the capillary networks when homing to the downstream organs via microcirculation. Here, we propose to utilize specially designed 3D dextran hydrogels and tuning the microscopic heterogeneity of hydrogel composition to make the administrated cells mechanically comply with the structure and mechanics of the capillary. The cell deformability in petri dishes, microcosmically homogeneous (HOM) and heterogeneous (HET) dextran hydrogels were investigated in vitro by measuring cell moduli through atomic force microscope (AFM), analyzing the expression of cytoskeletal protein via flow cytometry and fluorescent imaging. The in vitro experimental results demonstrate a progressive increase in cell deformability from 2D dishes, to HOM-hydrogel derived cells, and then to HET-hydrogel derived cells. The in vivo mouse experiment indicates the cells could deform accordingly and pass through easily with reduced resistance inside the mouse organs. It is suggested that the main destination of hMSC microcirculation could be selected between the spleen and liver of mice, by tuning cell mechanics that depends on the stimulus from microcosmically HOM or HET hydrogel, which lays a potential foundation for the mechanically modified MSC therapy for lesions in the organs.

biophysics↗

bioRxiv2024

Scalable emulation of protein equilibrium ensembles with generative deep learning

Following the sequence and structure revolutions, predicting the dynamical mechanisms of proteins that implement biological function remains an outstanding scientific challenge. Several experimental techniques and molecular dynamics (MD) simulations can, in principle, determine conformational states, binding configurations and their probabilities, but suffer from low throughput. Here we develop a Biomolecular Emulator (BioEmu), a generative deep learning system that can generate thousands of statistically independent samples from the protein structure ensemble per hour on a single graphical processing unit. By leveraging novel training methods and vast data of protein structures, over 200 milliseconds of MD simulation, and experimental protein stabilities, BioEmus protein ensembles represent equilibrium in a range of challenging and practically relevant metrics. Qualitatively, BioEmu samples many functionally relevant conformational changes, ranging from formation of cryptic pockets, over unfolding of specific protein regions, to large-scale domain rearrangements. Quantitatively, BioEmu samples protein conformations with relative free energy errors around 1 kcal/mol, as validated against millisecond-timescale MD simulation and experimentally-measured protein stabilities. By simultaneously emulating structural ensembles and thermodynamic properties, BioEmu reveals mechanistic insights, such as the causes for fold destabilization of mutants, and can efficiently provide experimentally-testable hypotheses.

molecular biology↗

bioRxiv2024

A gene co-expression network-based analysis of mesenchymal stromal cells reveals novel genes and molecular pathways underlying heterotopic ossification

BackgroundHeterotopic ossification (HO) represents a frequently seen refractory disease second to musculoskeletal injury, in which bone tissue ectopically exists within soft tissue, resulting in serious extremity loss-of-function. This work focused on identifying regulating factors and gene network associated with HO pathology. Material and MethodsWe randomized the heterotopic ossification dataset GSE94683 as HO and NON-HO group. Weighted gene co-expression network analysis (WGCNA) was applied in identifying HO related modules. We discovered differentially expressed genes (DEGs) between the two groups. Then, we integrated protein-protein interaction (PPI) network, co-expression network, enrichment analysis, gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) for identifying the HO-related pathways. We also employed GSE126118 test set to investigate hub genes related to HO. Eventually, potential therapeutics for reversing abnormal hub gene levels were predict by DGIdb. ResultsWe discovered twelve HO status modules and 1,483 DEGs in HO samples compared with NON-HO counterparts. Four hub genes were obtained from the overlap of HO related PPI and coexpression networks. Training and test sets were adopted for verification, and three abnormally high hub gene expression in HO were obtained. Functional enrichment of DEGs indicated that these genes were involved in the stem cell pluripotency regulatory pathways, cytokine-cytokine receptor interaction, as well as rap1 pathway. Based on the results from GSEA and GSVA, many hub gene sets were mainly enriched in immune responses. ConclusionWe identified a gene coexpression network associated with regulatory factors in HO, which provided a new perspective on the pathogenesis and provided potential biomarkers or therapeutic targets.

bioinformatics↗

bioRxiv2024

p300/CBP-catalyzed acetylation safeguards minor zygotic genome activation via activating DUX

Zygotic genome activation (ZGA), the first transcriptional event at the onset of life, is crucial for early embryonic development. However, the mechanisms that initiate and regulate ZGA in mammals remain poorly understood. In this study, we demonstrate that p300/CBP-catalyzed acetylation plays a vital role in regulating ZGA. Inhibition of p300/CBP acetyltransferase activity results in impaired minor ZGA and a subsequent 2-cell arrest. By profiling the dynamic landscape of p300 during the ZGA stage, we elucidate the distinct patterns of p300 establishment in promoter and enhancer regions. Moreover, p300 recruits RNA polymerase (Pol II) to pre-configure in the promoter regions of ZGA genes, and orchestrates the gradual establishment of enhancer activity during the early 2-cell stage to activate ZGA. Furthermore, p300 enhances minor ZGA by promoting the expression of DUX. Restoring DUX levels, which are diminished due to p300/CBP inhibition, rescues ZGA and embryonic development by re-establishing Pol II enrichment on minor ZGA genes. Overall, our findings elucidate the mechanism by which p300/CBP regulates ZGA through acetylation and activation of the key transcription factor DUX. HighlightsO_LIp300/CBP plays a stage-specific role during preimplantation development phase. C_LIO_LIp300 displays distinctive dynamic changes in promoter and enhancer regions during ZGA stage. C_LIO_LIp300/CBP-catalyzed acetylation facilitates the pre-configuration and elongation of Pol II at ZGA gene regions. C_LIO_LIDUX recruits p300 and Pol II to activate minor ZGA genes independently of p300s catalytic activity. C_LI

developmental biology↗