Biology subjects

Lin, K.

Publications and source records attributed to Lin, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Transcriptional activity generates chromatin motion that drives nuclear blebbing

Abnormal nuclear morphology is a hallmark of human diseases, including cancers and age-related disorders. Previously, maintenance of nuclear morphology and integrity was thought to be solely dependent on a force balance between nuclear mechanical resistance and actin antagonism. However, our recent work revealed that inhibiting RNA polymerase II suppresses nuclear blebbing independent of altering force balance, but the mechanism remains unknown. Through removing cell culture media serum and then adding it back, we can decrease and then restore transcriptional activity. Decreasing transcriptional activity decreases nuclear bleb formation, stability, and rupture while returning transcriptional activity restores nuclear blebbing. These modulations of transcriptional activity did not alter nuclear or actin mechanics. The mean square displacement (MSD) of chromatin domains labeled via transfected Cy3-dNTPs revealed that transcription activity regulates chromatin motion. To determine if increasing chromatin motion is a mechanism to increase nuclear blebbing, we used an established RAD51 inhibitor BO2. We verified BO2 increases chromatin domain motion which resulted in increased nuclear blebbing. We reveal the mechanism by which transcriptional activity drives nuclear blebbing is through chromatin motion. Thus, two hallmarks of human disease are directly linked via transcriptional activity and abnormal nuclear shape. Statement of SignificanceO_LINuclear blebs are hallmarks of disease progression that cause dysfunction, but how they are formed remains unanswered. C_LIO_LIWe find that chromatin motion generated by transcriptional activity is essential for both nuclear bleb formation and stability. This was independent of changes in nuclear stiffness or actin antagonism. C_LIO_LIThis finding provides a key advancement in our understanding of nuclear bleb formation. Furthermore, it reveals transcriptional activity as a novel contributor to nuclear blebbing in addition to the paradigm of nuclear shape determined as a force balance between nuclear resistance and actin antagonism. C_LI

cell biology↗

bioRxiv2025

Genetic risk in endolysosomal network genes correlates with endolysosomal dysfunction across neural cell types in Alzheimer's disease

Late-onset Alzheimer disease (LOAD) has a complex genomic architecture. LOAD risk variants suggest multiple pathways, including the endolysosomal network (ELN), contribute to the pathobiology of Alzheimer disease (AD). Whether genetic risk in specific pathways correlates with corresponding biological dysfunction remains largely unknown. We developed an endolysosomal pathway-specific polygenic risk score (ePRS) using 14 well-established AD risk alleles implicating ELN genes. We investigated the association between ePRS and AD neuropathology, then examined cell-specific endolysosomal morphology and transcriptomic profiles in post-mortem dorsolateral prefrontal cortex samples from donors stratified by ePRS burden. We found that the ePRS was significantly associated with AD diagnosis and neuropathological measures, comparable to a pathway-agnostic PRS despite representing far fewer loci. High ePRS correlated with increased neuronal endosome volume, number and perinuclear aggregation independent of AD pathology. Single-nucleus RNA sequencing revealed cell type-specific transcriptomic changes associated with ePRS status, influencing glutamatergic signaling, protein homeostasis, responses to DNA damage and immune function. Neurons, astrocytes, oligodendrocytes, and microglia each showed varied gene expression patterns associated with ePRS burden. Together, these results provide evidence that AD genetic risk variants harboring ELN genes correlate with endolysosomal dysfunction in human brain tissue. These findings suggest that pathway-specific genetic risk contributes to corresponding cellular pathology in AD and nominates candidate mechanisms by which ELN AD variants contribute to pathogenesis.

neuroscience↗

bioRxiv2025

HighPlay：Cyclic Peptide Sequence Design Based on Reinforcement Learning and Protein Structure Prediction

The structural diversity and good biocompatibility of cyclic peptides has led to their emergence as potential therapeutic agents. Traditional cyclic peptide design relies on natural template modification and combinatorial chemical library screening, but suffers from bottlenecks such as limited molecular diversity, high cost, and time-consuming.AI technologies have improved design efficiency by predicting target binding patterns and generating scaffold structures, but they still require extensive laboratory screening. In this study, we propose HighPlay, which integrates reinforcement learning (Monte Carlo Tree Search) with the HighFold structure prediction model to design cyclic peptide sequences for protein targets, dynamically exploring the sequence space without the need of predefined target information. The model was applied to the design of cyclic peptide sequences for three different targets, which were screened and verified by molecular dynamics simulation, and showed good binding affinity. Specifically, the cyclic peptide sequences designed for TEAD4 target showed micromolar-level affinity in further experimental validation.

bioinformatics↗

bioRxiv2025

Adaptive Plasticity Tumor Cells Modulate MAPK-Targeting Therapy Response in Colorectal Cancer

MAPK pathway inhibitors (MAPKi) are increasingly used in the treatment of advanced colorectal cancer, but often produce short-lived responses in patients. Although acquired resistance by de novo mutations in tumors have been found to reduce response in some patients, additional mechanisms underlying the limited response durability of MAPK targeting therapy remain unknown. Here, we denote new contributory tumor biology and provide insight on the impact of tumor plasticity on therapy response. Analysis of MAPKi treated patients revealed activation of stemness programs and increased ASCL2 expression, which are associated with poor outcomes. Greater ASCL2 with MAPKi treatment was also seen in patient-derived CRC models, independent of driver mutations. We find ASCL2 denotes a distinct cell population, arising from phenotypic plasticity, with a proliferative, stem-like phenotype, and decreased sensitivity to MAPKi therapy, which were named adaptive plasticity tumor (APT) cells. MAPK pathway suppression induces the APT phenotype in cells, resulting in APT cell enrichment in tumors and limiting therapy response in preclinical and clinical data. APT cell depletion improved MAPKi treatment efficacy and extended MAPKi response durability in mice. These findings uncover a cellular program that mitigates the impact of MAPKi therapies and highlights the importance of addressing tumor plasticity to improve clinical outcomes.

cancer biology↗

bioRxiv2025

Multicilia dynamically transduce Shh signaling to regulate choroid plexus functions

Choroid plexus is a major site for cerebrospinal fluid (CSF) production, characterized by a multiciliated epithelial monolayer that regulates CSF production. We demonstrate that defective choroid plexus ciliogenesis or Intraflagellar transport yields neonatal hydrocephalus, at least in part, due to increased water channel Aqp1 and ion transporter Atp1a2 expression. We demonstrate choroid plexus multicilia as sensory cilia, transducing both canonical and non-canonical Shh signaling. Interestingly, it is the non-canonical Shh signaling that represses Aqp1 and Atp1a2 expression by Smo/Gi/cAMP pathway. Choroid plexus multicilia exhibit unique ciliary ultrastructure, carrying features of both primary and motile cilia. Unlike most cilia that elongate during maturation, choroid plexus ciliary length decreases during development, causing a decline of Shh signaling intensity in developing choroid plexus, a derepression of Aqp1 and Atp1a2, and ultimately, an increased CSF production. Hence, developmental dynamics of choroid plexus multicilia dampens the Shh signaling intensity to promote CSF production.

developmental biology↗

bioRxiv2025

Specificity Protein 1 is essential for the limb trajectory of ephrin-mediated spinal motor axons

The precise organization of neural circuits requires highly specific axon guidance, facilitated by cell-surface guidance receptors on axonal growth cones that help neurons reach their target destinations. Despite a limited repertoire of known guidance receptors and ligands, neural systems achieve complex axonal networks, suggesting that additional regulatory mechanisms exist. One proposed strategy is the co-expression of ligands and their receptors on the same axons, allowing modulation of receptor responsiveness to guidance cues. To investigate this mechanism, we studied the spinal lateral motor column (LMC) motor neurons, which make a binary axon pathfinding decision toward limb targets. We hypothesized that specificity protein 1 (Sp1), a transcription factor, regulates ephrin expression in LMC neurons, thereby modulating receptor functions via cis-attenuation to ensure accurate axonal pathfinding. Our results show that Sp1 is indeed expressed in LMC neurons during critical axonal extension periods. Manipulating Sp1 activity disrupted LMC axon trajectory selection, and RNA-Seq analysis indicated that Sp1 regulates genes associated with axon guidance, including ephrins. We found that Sp1 knockdown affected ephrin/Eph cis-binding and trans-signaling, highlighting Sp1s role in controlling axonal projections through ephrin gene regulation. Additionally, coactivators p300 and CBP are essential for Sp1s regulatory function. These findings identify Sp1 as a key transcription factor in LMC neurons, essential for ephrin expression and ephrin/Eph-mediated axon guidance, providing insights into the molecular mechanisms of neural circuit formation.

neuroscience↗

bioRxiv2024

Cycledesigner Leveraging RFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets

Cyclic peptides are potentially therapeutic in clinical applications, due to their great stability and activity. Yet, designing and identifying potential cyclic peptide binders targeting specific targets remains a formidable challenge, entailing significant time and resources. In this study, we modified the powerful RFdiffusion model to allow the cyclic peptide structure identification and integrated it with ProteinMPNN and HighFold to design binders for specific targets. This innovative approach, termed cycledesigner, was followed by a series of scoring functions that efficiently screen. With the combination of effective cyclic peptide design and screening, our study aims to further broaden the scope of cyclic peptide binder design.

bioinformatics↗

bioRxiv2024

A Molecular Image-based Explainable Artificial intelligence Framework Identifies Novel Candidate Antibiotics

The continued growth of antibiotic resistance and the slowing of antibiotic discovery poses a large challenge in fighting infectious diseases. Recent advances in Artificial intelligence (AI) technologies offer a time- and cost-effective solution for the rapid development of effective antibiotics. In this study, we presented an explainable AI framework from a pre-trained model using 10 million drug-like molecular images. Specifically, we created a fine-tuned ImageMol from experimental Staphylococcus aureus inhibition assays which contained 24,521 molecules consisting of 516 active compounds and 24,005 non-active compounds. Our optimized AI model achieved a strong AUROC of 0.926. The model was then used to predict the antibiotic activities from 10,247 FDA-approved, clinically investigational, or experimental molecules from the DrugBank database. After further filtering, 340 molecules were identified to have antibacterial behavior while simultaneously being dissimilar to known antibiotics. Finally, 76 candidates were identified as FDA-approved drugs for other applications. Thus, those candidates can be repurposed into needed novel antibiotics. We further illustrated explainable molecular images for top predicted candidate drugs via Gradient-weighted Class Activation Mapping (Grad-CAM) heatmap analysis. In summary, the presented molecular image-based AI model in drug discovery could be highly favorable due to its high performance, speed, and biological interpretation.

pharmacology and toxicology↗

bioRxiv2024

Microglia-specific transduction via AAV11 armed with IBA1 promoter and miRNA-9 targeting sequences

Microglia, as resident immune cells in the central nervous system (CNS), are closely related to human health and the pathogenesis of various CNS diseases, making them compelling targets for therapeutic interventions. However, functional and therapeutic studies of microglia remain significant challenges largely due to the lack of tools capable of efficiently and specifically transducing microglia. Herein, we evaluated the specificity and efficiency of various adeno-associated virus (AAV) vectors armed with the mIBA1 promoter and miRNA-9 targeting sequences in transducing microglia within the caudate putamen (CPu) brain region, and found that AAV11 mediates more specific and efficient transduction of microglia. Subsequently, we further demonstrated that AAV11 also exhibits high transduction specificity for microglia across various brain areas and within the spinal cord. Finally, by reducing the injection dosage, we employed AAV11 for sparse labeling of microglia. This work provides a promising tool for advancing both the functional investigation and therapeutic targeting of microglia.

neuroscience↗

bioRxiv2024

An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish

The larval zebrafish is a vertebrate model for in vivo monitoring and manipulation of whole-brain neuronal activity. Tracing its neural circuits remains challenging. Here, we report an applicable methodology tailored for larval zebrafish to achieve efficient retrograde trans-monosynaptic tracing from genetically defined neurons via EnvA-pseudotyped glycoprotein-deleted rabies viruses. By combinatorially optimizing multiple factors involved, we identified the CVS strain trans-complemented with advanced expression of N2cG at 36 {degrees}C as the optimal combination. It yielded a tracing efficiency of up to 20 inputs per starter cell. Its low cytotoxicity enabled the viable labeling and calcium imaging of infected neurons 10 days post-infection, spanning larval ages commonly used for functional examination. Cre-dependent labeling was further developed to enable cell-type-specific input tracing and circuit reconstruction. We mapped cerebellar circuits and uncovered the ipsilateral preference and subtype specificity of granule cell-to-Purkinje cell connections. Our method offers an efficient way for tracing neural circuits in larval zebrafish.

neuroscience↗

bioRxiv2024

The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma

Despite recent advances in therapeutic treatments, multiple myeloma (MM) remains an incurable malignancy. Epigenetic factors contribute to the initiation, progression, relapse, and clonal heterogeneity in MM, but our knowledge on epigenetic mechanisms underlying MM development is far from complete. The SAGA complex serves as a coactivator in transcription and catalyzes acetylation and deubiquitylation. Analyses of datasets in the Cancer Dependency Map Project revealed many SAGA components are selective dependencies in MM. To define SAGA-specific functions, we focused on ADA2B, the only subunit in the lysine acetyltransferase (KAT) module that specifically functions in SAGA. Integration of RNA-seq, ATAC-seq, and CUT&RUN results identified pathways directly regulated by ADA2B include MTORC1 signaling, MYC, E2F, and MM-specific MAF oncogenic programs. We discovered that ADA2B is recruited to MAF and MYC gene targets, and that MAF shares a majority of its targets with MYC in MM cells. Furthermore, we found the SANT domain of ADA2B is required for interaction with both GCN5 and PCAF acetyltransferases, incorporation into SAGA, and ADA2B protein stability. Our findings uncover previously unknown SAGA KAT module-dependent mechanisms controlling MM cell growth, revealing a vulnerability that might be exploited for future development of MM therapy.

molecular biology↗

bioRxiv2024

Canonical AREs are tumor suppressive regulatory elements in the prostate

The androgen receptor (AR) is the central determinant of prostate tissue identity and differentiation, controlling normal, growth-suppressive prostate-specific gene expression1. It is also a key driver of prostate tumorigenesis, becoming "hijacked" to drive oncogenic transcription2-5. However, the regulatory elements determining the execution of the growth suppressive AR transcriptional program, and whether this can be reactivated in prostate cancer (PCa) cells remains unclear. Canonical androgen response element (ARE) motifs are the classic DNA binding element for AR6. Here, we used a genome-wide strategy to modulate regulatory elements containing AREs to define distinct AR transcriptional programs. We find that activation of these AREs is specifically associated with differentiation and growth suppressive transcription, and this can be reactivated to cause death in AR+ PCa cells. In contrast, repression of AREs is well tolerated by PCa cells, but deleterious to normal prostate cells. Finally, gene expression signatures driven by ARE activity are associated with improved prognosis and luminal phenotypes in human PCa patients. This study demonstrates that canonical AREs are responsible for a normal, growth-suppressive, lineage-specific transcriptional program, that this can be reengaged in PCa cells for potential therapeutic benefit, and genes controlled by this mechanism are clinically relevant in human PCa patients.

cancer biology↗

bioRxiv2024

Chromatin regulator Kdm6b is required for the establishment and maintenance of neural stem cells in mouse hippocampus

Neural stem cells (NSCs) in the mouse hippocampal dentate gyrus (DG) - a structure important to learning and memory - generate new neurons postnatally and throughout adult life. However, the regulators that enable this lifelong neurogenesis remain incompletely understood. Here we show that the chromatin regulator KDM6B is required for both the establishment and maintenance of NSCs in the mouse DG. Conditional deletion of Kdm6b in embryonic DG precursors results in an adult hippocampus that is essentially devoid of NSCs, and hippocampal-dependent behaviors are defective. Kdm6b-deletion causes precocious neuronal differentiation, and the NSC population fails to become established in the postnatal DG. Using single cell RNA sequencing (scRNA-seq), we observed that Kdm6b-deletion disrupts the transcriptomic signature of NSC maintenance. Furthermore, deleting Kdm6b in adult DG NSCs induces early neuronal differentiation, and the NSC population is not properly maintained. These data illustrate the critical role that Kdm6b plays in adult DG neurogenesis, which may help understand how mutations in this chromatin regulator result in cognitive disorders in human patients.

neuroscience↗

bioRxiv2024

Natural selection exerted by historical coronavirus epidemic(s): comparative genetic analysis in China Kadoorie Biobank and UK Biobank

BackgroundPathogens have been one of the primary sources of natural selection affecting modern humans. The footprints of historical selection events - "selective sweeps" - can be detected in the genomes of present-day individuals. Previous analyses of 629 samples from the 1000 Genomes Project suggested that an ancient coronavirus epidemic [~]20,000 years ago drove multiple selective sweeps in the ancestors of present-day East Asians, but not in other worldwide populations. ResultsUsing a much larger genetic dataset of 76,719 unrelated individuals from each of the China Kadoorie Biobank (CKB) and UK Biobank (UKB) to identify regions of long-range linkage disequilibrium, we further investigated signatures of past selective sweeps and how they reflect previous viral epidemics. Using independently-curated lists of human host proteins which interact physically or functionally with viruses (virus-interacting proteins; VIPs), we found enrichment in CKB for regions of long-range linkage disequilibrium at genes encoding VIPs for coronaviruses, but not DNA viruses. By contrast, we found no clear evidence for any VIP enrichment in UKB. These findings were supported by additional analyses using saltiLASSi, a selection-scan method robust to false positives caused by demographic events. By contrast, for GWAS signals for SARS-Cov2 susceptibility (critical illness, hospitalisation, and reported infection), there was no difference between UKB and CKB in the number located at or near signals of selection, as expected for a novel virus which has had no opportunity to impact the CKB/UKB study populations. ConclusionsTogether, these results provide evidence of selection events consistent with historical coronavirus epidemic(s) originating in East Asia. These results show how biobank-scale datasets and evolutionary genomics theory can provide insight into the study of past epidemics. The results also highlights how historic infectious diseases epidemics can shape the genetic architecture of present-day human populations.

genomics↗

bioRxiv2023

Oblique Line Scan Illumination Enables Expansive, Accurate and Sensitive Single Protein Measurements in Solution and in Living Cells

Single-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enable in situ measurements in cells from which data-rich metrics can be extracted. SMT has been successfully applied to a variety of biological questions and model systems, aiming to unravel the spatiotemporal regulation of molecular mechanisms that govern protein function, downstream pathway effects, and cellular function. While powerful, SMLM often suffers from low throughput and illumination inhomogeneity, along with microscope and user-induced technical biases. Due to technical limitations in scaling SMLM techniques, a tradeoff between spatiotemporal resolution and throughput has been made historically, restricting broad application of these technologies. Here we address these limitations using Oblique Line Scan (OLS), a robust single-objective light-sheet based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a 250 x 190 m field of view. We demonstrate OLS-enabled SMT on Halo-Tagged proteins in living cells capturing protein motion up to 14 m2 /s. By exploiting the adaptability of the acquisition frame rate and the improved rejection of out of focus light, we extend the utility of OLS beyond cellular compartments with in-solution SMT (isSMT) for single-molecule measurement of ligand-protein interactions and disruption of protein-protein interactions (PPI). We illustrate the versatility of OLS by showcasing two-color SMT, STORM, and single molecule fluorescence recovery after photobleaching (FRAP). OLS expands the range of SMLM applications and paves the way for robust, high-throughput single-molecule investigations of protein dynamics required for drug screening and systems biology studies, both in cells and in solution.

biophysics↗

bioRxiv2023

eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings

BackgroundSingle-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. ResultsWe develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. ConclusionseSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.

genomics↗

bioRxiv2023

A "suicide" BCG strain provides enhanced immunogenicity and robust protection against Mycobacterium tuberculosis in macaques

Intravenous (IV) BCG delivery provides robust protection against Mycobacterium tuberculosis (Mtb) in macaques but poses safety challenges. Here, we constructed two BCG strains (BCG-TetON-DL and BCG-TetOFF-DL) in which tetracyclines regulate two phage lysin operons. Once the lysins are expressed, these strains are killed in immunocompetent and immunocompromised mice yet induced similar immune responses and provided similar protection against Mtb challenge as wild type BCG. Lysin induction resulted in release of intracellular BCG antigens and enhanced cytokine production by macrophages. In macaques, cessation of doxycycline administration resulted in rapid elimination of BCG-TetOFF-DL. However, IV BCG-TetOFF-DL induced increased pulmonary CD4 T cell responses compared to WT BCG and provided robust protection against Mtb challenge, with sterilizing immunity in 6 of 8 macaques, compared to 2 of 8 macaques immunized with WT BCG. Thus, a "suicide" BCG strain provides an additional measure of safety when delivered intravenously and robust protection against Mtb infection.

immunology↗

bioRxiv2023

Development of an Engineered Mycobacterium tuberculosis Strain for a Safe and Effective Tuberculosis Human Challenge Model

Human challenge experiments could greatly accelerate the development of a tuberculosis (TB) vaccine. Human challenge for tuberculosis requires a strain that can both replicate in the host and be reliably cleared. To accomplish this, we designed Mycobacterium tuberculosis (Mtb) strains featuring up to three orthogonal kill switches, tightly regulated by exogenous tetracyclines and trimethoprim. The resultant strains displayed immunogenicity and antibiotic susceptibility similar to wild-type Mtb under permissive conditions. In the absence of supplementary exogenous compounds, the strains were rapidly killed in axenic culture, mice and nonhuman primates. Notably, the strain that contained three kill switches had an escape rate of less than 10-10 per genome per generation and displayed no relapse in a SCID mouse model. Collectively, these findings suggest that this engineered Mtb strain could be a safe and effective candidate for a human challenge model.

microbiology↗