Biology subjects

Lin, J.

Publications and source records attributed to Lin, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Mesoscopic viscous-to-elastic transition underlies aging of biomolecular condensates

Aging of biomolecular condensates, which progressively leads to solid-like states, is closely linked to biological functions and diseases. However, a unified physical picture that captures the aging dynamics remains elusive. Here, we introduce a phenomenological model in which a condensate is a composite of viscous and elastic elements with coexisting serial and parallel connections. The model naturally yields a relaxation modulus with two relaxation times, unifying the Maxwell and Jeffreys models as special limits. When applied to aging PGL-3 condensates, our model reveals that aging is primarily driven by the conversion of viscous elements into elastic ones. In contrast, the mesoscopic structure topology of the condensates remains approximately invariant. Our stochastic theory of element dynamics also predicts that the condensate viscosity either increases exponentially, in agreement with experiments, or as a power law of the waiting time, governed by a single parameter that depends on temperature and the molecular interaction strength.

biophysics↗

bioRxiv2025

Astrocytic FABP5 drives non-cell-autonomous oligodendrocyte injury in multiple system atrophy by promoting TNF signaling and ferroptotic stress

Multiple system atrophy (MSA) is a fatal -synucleinopathy characterized by progressive parkinsonism, cerebellar and autonomic dysfunction. Currently, the mechanisms driving cerebellar white matter neuroinflammation and degeneration in MSA are poorly understood. Here, we identified fatty acid-binding protein 5 (FABP5) as a key factor regulating cerebellar inflammation in MSA pathogenesis in a detailed study of human, mouse and cultured astrocytes. Firstly, transcriptomic profiling of human MSA cerebellar white matter revealed activation of pro-inflammatory and ferroptotic pathways, with FABP5 identified as a key pathway component that is upregulated. We confirmed that FABP5 is upregulated in reactive astrocytes in the PLP--syn transgenic mouse model, also in LPS-treated primary astrocytes. Fabp5 silencing suppressed TNF signaling, mitigated ferroptosis, and restored mitochondrial function. These findings suggest astrocytic FABP5 as a central intracellular regulator linking glial inflammation, ferroptosis, and mitochondrial injury. Overall, this mechanism suggests that FABP5 drives pathology mediated by astrocytes oligodendroglia in MSA, therefore representing a novel and promising therapeutic target.

neuroscience↗

bioRxiv2025

Random crosslinks generate anomalous scaling of dynamic modulus of biomolecular condensates

Biomolecular condensates are viscoelastic, and their mechanical properties are intimately related to their biological functions. However, the connection between microscopic networks formed by intermolecular crosslinks and viscoelasticity is still elusive. Here, we model biomolecular condensates as random crosslinked polymer solutions to elucidate how random connectivity fundamentally alters their viscoelasticity. We decompose the entire condensate into multiple clusters without loops and demonstrate that for clusters with size n, their eigenvalue distributions exhibit a power-law scaling pn({lambda}) [~]{lambda}-1/3 with a lower cutoff{lambda} min [~]n-3/2. By integrating all clusters, we show that for the entire condensate, random crosslinks generate abundant slow modes involving multiple linear polymers with a constant eigenvalue distribution. The slow modes cause anomalous linear frequency scaling of the dynamic moduli; in particular, they significantly boost the low-frequency storage modulus relative to uncrosslinked systems. Our model rationalizes the anomalous scaling of the dynamic moduli observed in multiple biomolecular condensates.

biophysics↗

bioRxiv2025

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization can play a key role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of the proton mobility in H-bonds. We used neutron crystallography and large quantum mechanics/molecular mechanics-Born Oppenheimer molecular dynamics (QM/MM-BOMD) simulations of human DJ-1 and its bacterial homolog YajL to validate atomic resolution X-ray crystallographic bond length analysis, directly visualizing the shared deuteron in a low-barrier hydrogen bond (LBHB) between Glu14-Asp23 in YajL that is a conventional H-bond in DJ-1. In addition, X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid. Residues in the vicinity of Glu14-Asp23 that might favor LBHB formation in YajL were interrogated by mutagenesis of homologous residues in DJ-1. X-ray bond length analysis and QM/MM-BOMD simulations demonstrate that a distal I21T DJ-1 substitution increases proton delocalization in the Glu-Asp H-bond. In addition, simulations show that the extent of proton mobility in the H-bond influences correlated dimer-spanning motions in YajL and DJ-1. In total, we show that mutations within extended H-bonding networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds, allowing proton delocalization to be engineered using combined bioinformatic, structural, and computational information.

biochemistry↗

bioRxiv2025

Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

Cellular stresses induce transcription readthrough, whereby RNA polymerase II elongates past a genes polyadenylation cleavage site without RNA cleavage. Readthrough has been reported in several cancer types. Here, we use long-read sequencing of nascent RNA to quantify transcriptional readthrough in chronic myelogenous leukemia (CML) cells and characterize early responses to the targeted therapeutic, imatinib. We show that the amount, length, and gene-specificity of readthrough increase within 1 hour, while gene expression and alternative splicing alterations emerge later. Strikingly, imatinib-dependent mRNA isoform changes involved "readthrough chimeras", in which exons from an upstream gene are alternatively spliced to exons in a downstream gene. Modifications in mRNA isoforms and chimera levels detected at 18 hours were also found in imatinib-resistant K562 as well as CML patient cells, suggesting a cascade of early changes in the fidelity of transcription and splicing, leading to long-term adjustment in gene expression and the development of therapy resistance. TeaserPrecision RNA sequencing was used to discover the earliest response of leukemia cells treated with targeted therapy: transcriptional readthrough.

molecular biology↗

bioRxiv2025

Brain Dynamics of Mental Manipulation

Humans effortlessly juggle their internal thoughts, but the neuronal dynamics that support mental manipulation are largely unknown. Leveraging the high spatiotemporal fidelity of intracranial recordings in humans (N = 30), we provide evidence that mental sound manipulation involves the inhibition of sensory cortex and the coordinated engagement of memory and control networks. This modulation manifests in two ways. First, there is a shift in the balance between faster (> 30 Hz) and slower (< 30 Hz) dynamics in primary and secondary auditory areas, suggesting a decrease in local excitability. Second, there is a distributed increase in oscillatory synchrony (6-10 Hz), which predicts imagery vividness and task performance. This evidence points to a key role of local excitability and inter-areal synchrony in the manipulation of thought.

neuroscience↗

bioRxiv2025

Fixing Hybrid Rice: >99% Efficient Apomixis with Near-Normal Seed Set

Apomixis, a form of clonal seed reproduction, offers a transformative approach to agriculture by enabling the stable fixation of hybrid vigor and elite heterozygosity across generations. However, the practical implementation of synthetic apomixis has been hindered by highly variable clonal efficiency or significant yield penalties. In this study, through integrated transcriptomic analyses, we identified a sperm-specific transcription factor in rice that likely functions as a key initiator of embryogenesis. Ectopic expression of this factor in egg cells effectively induces parthenogenesis and produces haploid progeny. When combined with clonal gametogenesis, this system achieved nearly complete synthetic apomixis, with clonal seed production rates exceeding 99% across all derived hybrid rice lines. Moreover, we generated apomictic hybrid lines that not only consistently produced over 99% clonal seeds but also exhibited seed yields comparable to conventional F1 hybrids. These findings establish a scalable and agriculturally viable platform for synthetic apomixis, achieving stable fixation of heterosis through clonal seeds and paving the way for the commercial deployment of self-perpetuating hybrid crops.

plant biology↗

bioRxiv2025

An ultra-long acting insulin enables glucose-synchronised release

Delayed and weak glucose-responsive kinetics, coupled with short plasma exposure and complicated formulation, remain major obstacles to the clinical translation of glucose-responsive insulin formulations. Here we report a rapidly absorbable, ultra-long acting, and glucose-responsive insulin analogue via engineering recombinant human insulin with two phenylboronic acids. The insulin analogue has a long circulating half-life (t1/2{beta} [~]150 h) due to its unique, unprecedented, glucose-responsive binding to blood circulation-associated proteins. This interaction drives the formation of a unique systemic reservoir that allows synchronised dynamic response in insulin levels to glucose fluctuations. In type 1 diabetic mice and minipigs, a single subcutaneous dose can maintain normoglycaemia for over one week (47.5-fold compared to insulin glargine). After the last injection of four consecutive weekly administrations in mice, the glucose-lowering effect can last 800 hours. Administering this glucose-responsive insulin analogue with a fully automated insulin delivery system can leverage dual closed loops and achieve a glucose time in range of over 85% and a coefficient of variation of approximately 30%, better than the recommended targets for human therapy. Importantly, no toxicity was identified in the study.

bioengineering↗

bioRxiv2025

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

Oncogenesis involves widespread genetic and epigenetic alterations, yet the full spectrum of somatic variation genome-wide remains unresolved. We generated a near-telomere-to-telomere (T2T) diploid assembly of a donor paired with deep short- and long-read sequencing of their melanoma. This revealed that 16% of somatic variants occur in sequences absent from GRCh38, with satellite repeats acting as hotspots for UV-induced damage due to sequence-intrinsic mutability and inefficient repair. Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation, leading to remodeling of centromere kinetochore binding domains during tumor evolution. Single-molecule telomere reconstructions uncovered cycles of attrition, deletion, and telomerase-mediated extension that shape cancer telomeres. Finally, diploid chromatin maps exposed that copy number alterations and epimutations, rather than point mutations, predominate in rewiring cancer regulatory programs. These findings define the full landscape of a cancers somatic variation and their functional impact, establishing a blueprint for T2T studies of mosaicism.

genomics↗

bioRxiv2025

Direct cell reprogramming by a designed agonist inducing HER2-FGFR proximity

Growth factor induced receptor dimerization and activation of downstream pathways can modulate cell fate decisions. Here, we investigate the potential of de novo designed synthetic ligands, termed Novokines, to reprogram cell identity by inducing proximity of novel pairs of receptor subunits. We find that a design, H2F, that brings together HER2 (which has no known natural ligand) and the FGF receptor has potent signaling activity. H2F induces robust signaling and reprograms fibroblasts into myogenic cells. Unlike native FGF ligands, H2F selectively activates the MAPK pathway without engaging PLC{gamma}-mediated Ca{superscript 2} signaling. FRET assays confirm H2F-mediated HER2-FGFR proximity, and phosphoproteomic analysis reveals activation of MAPK effectors. H2F-induced ERK phosphorylation is abolished in cells expressing a kinase-dead FGFR1 (K514M) mutant, confirming the requirement for FGFR catalytic activity. H2F treatment significantly increases myofiber formation from adult patient-derived primary myoblasts, demonstrating its capacity to promote myogenic regeneration. Our findings demonstrate that synthetic receptor pairings can rewire signaling outputs to drive regeneration, providing a programmable platform for cell fate engineering.

biochemistry↗

bioRxiv2025

Viral tRNA-like structure hijacks host ribosomes for poly(A)-independent translation

Positive-sense RNA viruses often use 3' tRNA-like structures (TLSs) instead of poly(A) tails to capture the host translation machinery. While TLSs resemble canonical tRNAs and engage host factors, their ability to directly recruit ribosomes has remained unresolved. Here, we present cryo-electron microscopy snapshots of the histidine-accepting TLS (TLSHis) from tobacco mosaic virus bound to the 60S subunit, the 80S ribosome, and the 80S-tRNAiMet initiation complex. Across these states, TLSHis is consistently anchored to the L1 stalk of 60S, even under cycloheximide treatment, yet remains dynamic on the 40S subunit. Structural analysis shows that TLSHis transitions from the E-site to an adjacent Z-site to accommodate initiator tRNA. Functional assays show that TLSHis preferentially associates with ribosomal subunits over polysomes and can substitute for a poly(A) tail to promote robust cap-dependent translation. Together, these findings reveal how a viral tRNA mimic hijacks host ribosomes to promote poly(A)-independent translation.

molecular biology↗

bioRxiv2025

scLinguist: A pre-trained hyena-based foundation model for cross-modality translation in single-cell multi-omics

Single-cell multi-omics provides complementary insights into cellular states, heterogeneity, and regulatory programmes. However, paired assays remain costly, low-throughput, and technically challenging, whereas large-scale single-modality data such as scRNA-seq are abundant but do not capture protein-level biology. Here we present scLinguist, a foundation model for cross-modality translation introduces a three-stage framework: self-supervised pretraining on large-scale unimodal datasets to learn modality-specific representations, post-pretraining on limited paired data to capture cross-modality relationships, and inference to predict missing modalities (e.g., protein from RNA) in fine-tuning or zero-shot settings. Systematic benchmarking shows that scLinguist consistently outperforms state-of-the-art methods in predicting protein abundance from RNA across diverse biological contexts. It achieves high predictive performance while preserving cellular heterogeneity and further enables mechanistic and generalizable inference under simulated gene perturbations. Furthermore, scLinguist exhibits strong transferability across health states and datasets. By leveraging abundant unimodal data and minimizing dependence on paired assays, scLinguist establishes a scalable and versatile framework for cross-modality translation in single-cell analysis.

cell biology↗

bioRxiv2025

Imlifidase and EndoS enables semi-allogeneic bone marrow engraftment in sensitized mice under reduced intensity conditioning

Patients in need of a hematopoietic stem cell transplant frequently have pre-existing donor-specific antibodies (DSA) which can impair engraftment. These patients often require intensified conditioning regimens, even in the setting of partially matched (semi-allogeneic) donors. Reducing the toxicity of conditioning and desensitization protocols is therefore a major goal. We previously showed that enzymatic desensitization of donor-specific IgG using imlifidase and EndoS improved murine bone marrow engraftment in donor sensitized, autoimmune-prone recipient mice. Conditioning included a 6 Gy total body irradiation, cyclophosphamide, bortezomib, and T cell depletion. In non-autoimmune prone semi-allogeneic recipients sensitized to the donor, we demonstrate that desensitisation with imlifidase and EndoS permits long-term donor bone marrow engraftment and induces tolerance to subsequent allogeneic skin grafts under a 3 Gy irradiation protocol. Enzymatic inactivation of DSA facilitates donor hematopoietic stem cell engraftment in allo-sensitized semi-allogeneic recipients in a reduced intensity conditioning protocol.

immunology↗

bioRxiv2025

JointMap identified SERPINA3+ chondrocytes as a therapeutic target for osteoarthritis

BackgroundOsteoarthritis (OA) is a prevalent degenerative joint disease that affects nearly half of the population aged over 65. Recent single-cell transcriptional studies have identified heterogeneous OA-specific chondrocyte subtypes, yet a unified subtype-classification remains incomplete. MethodsIn this study, we integrated a total of 545,946 cells to develop JointMap, an interspecies atlas. The chondrocyte subtypes were analyzed using machine learning algorithms were validated via human samples, animal models, and in vitro cell culture. We performed KAS-seq and analyzed the spatial characters for JointMap. ResultsBased on clinical diagnosis and cross-omic indexes, we identified a novel OA-elevated chondrocyte subtype, SERPINA3+ chondrocytes. Notably, we uncovered their upregulated chondrogenesis function and intercellular communication patterns as potential therapeutic targets. ConclusionsIn summary, JointMap provides a unified framework for the systematic annotation of chondral tissues across species and helps in the identification of druggable networks for articular diseases.

bioinformatics↗

bioRxiv2025

Maximized field-of-view deep-brain calcium imaging through gradient-index lenses

Advances in genetically encoded fluorescent indicators have enabled increasingly sensitive optical recordings of neural activity. However, light scattering in the mammalian brain tissue restricts optical access to deeper regions. To address this limitation, researchers often employ implanted gradient-index (GRIN) lenses to reach deep brain areas. Nevertheless, the severe optical aberrations of GRIN lenses significantly reduce the effective field of view (FOV). In this work, we present a simple and robust imaging approach that combines low-NA telecentric scanning (LNTS) of laser excitation with high-NA fluorescence collection to increase the FOV. This configuration effectively eliminates common aberrations such as astigmatism and field curvature, resulting in a FOV [~]100% as large as the GRIN lens facet area -- corresponding to a [~]400% increase in imaging area compared with conventional approaches. We validate this method through both structural and functional in vivo imaging. The highly consistent imaging performance, fully maximized imaging FOV, and the very simple optical design make this method well-suited for broad dissemination in neuroscience research.

neuroscience↗

bioRxiv2025

A simplified and highly efficient cell-free protein synthesis system for prokaryotes

Cell-free protein synthesis (CFPS) systems are a powerful platform with immense potential in fundamental research, biotechnology, and synthetic biology. Conventional prokaryotic CFPS systems, particularly those derived from Escherichia coli (E. coli), often rely on complex reaction buffers containing up to thirty-five components, limiting their widespread adoption and systematic optimization. Here, we present an optimized E. coli cell-free protein synthesis (eCFPS) system, which is significantly streamlined for high efficiency. Through systematic screening, we successfully reduced the essential core reaction components from 35 to a core set of 7. The thorough optimization of these seven key components ensured that protein expression levels were not only maintained but even substantially improved. Furthermore, we developed a much simpler procedure for preparing the bacterial cytosolic extracts, a "fast lysate" protocol that eliminates the traditional time-consuming runoff and dialysis steps, thereby enhancing the overall accessibility and robustness of eCFPS. This optimized and user-friendly eCFPS efficiently synthesizes challenging proteins, including functional, self-assembling vimentin, and active restriction endonuclease BsaI despite its strong cytotoxicity, and serves as a powerful tool that will facilitate diverse applications in basic life science research and beyond.

biochemistry↗

bioRxiv2025

Crosslinking of Lipid Nanoparticles Enhances the Delivery Efficiency and Efficacy of mRNA Vaccines

Lipid nanoparticles (LNPs) have enabled the effective delivery of RNA therapeutics and mRNA vaccines. However, their broader applications are limited by the suboptimal stability and endosomal escape efficiency. Here, we present an easy-to-adopt post-assembly crosslinking approach to enhance the structural and functional stability of mRNA LNPs. By leveraging a series of cholesterol derivatives and crosslinking methods, we induce crosslinks of the lipid components following mRNA LNP assembly to form the crosslinked LNPs (cLNPs). We systematically evaluated crosslinking parameters and identified optimal conditions that enhance both the physical stability and transfection efficiency of cLNPs. Our findings demonstrate that cLNPs exhibit improved structural integrity under storage and lyophilization conditions, as well as increased extracellular stability and endosomal escape efficiency, resulting in improved performance of mRNA LNPs both in vitro and in vivo. This crosslinking strategy represents a critical advance in LNP engineering, enabling more resilient LNPs and broadening the applicability of LNP-based therapies for gene therapy and vaccine delivery. Our work lays the foundation for developing next-generation LNPs with superior stability and delivery efficiency, broadening the impact of RNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

KICDB: A Causality-Oriented Multi-Omics Database for Kinase Inhibitor-Induced Cardiotoxicity

BackgroundKinase inhibitors (KIs) are mainstays of targeted cancer therapy, but their clinical utility is frequently limited by cardiotoxicity. A systematic resource to explore the underlying causal mechanisms is urgently needed. MethodsWe present the KICDB (Kinase Inhibitor Cardiotoxicity Database), a comprehensive and interactive web server. KICDB is built upon a framework integrating large-scale transcriptomics meta-analysis with causal inference. ResultsThis database centralizes the findings from a comprehensive meta-analysis of 26 kinase inhibitors (KIs) across 7 studies (n=5291) identified 8,907 significant gene expression changes in human cardiomyocytes. To establish causality, we performed a two-pronged Mendelian randomization (MR) analysis testing hundreds of downstream genes and a panel of 43 key kinase proteins against 46 cardiovascular outcomes. This large-scale analysis revealed 26 significant causal associations, implicating novel molecular mediators in KI-induced cardiotoxicity. ConclusionsKICDB serves as a valuable and accessible platform for the cardio-oncology community. By integrating transcriptomic signatures with causal inference data, the database empowers researchers to formulate mechanistic hypotheses, accelerate biomarker validation, and guide the design of future cardioprotective strategies. URL: https://zhang-lab-database.shinyapps.io/KICDB/ Key PointsO_LIWe developed KICDB, a comprehensive and publicly accessible web server, to systematically investigate the causal mechanisms of KI-induced cardiotoxicity. C_LIO_LIKICDB integrates a large-scale meta-analysis of transcriptomic data from 26 KIs with a robust Mendelian randomization (MR) framework to move beyond correlation and infer causality. C_LIO_LIThe analysis identified 8,907 significant gene expression changes and 26 significant causal associations between KI-associated genes and 46 cardiovascular outcomes. C_LI

bioinformatics↗