Biology subjects

Ren, W.

Publications and source records attributed to Ren, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A Tandem Repeat Atlas for the Genome of Inbred Mouse Strains: A Genetic Variation Resource

Tandem repeats (TRs) are a significant source of genetic variation in the human population; and TR alleles are responsible for over 60 human genetic diseases and for inter-individual differences in many biomedical traits. Therefore, we utilized long-read sequencing and state of the art computational programs to produce a database with 2,528,854 TRs covering 39 inbred mouse strains. As in humans, murine TRs are abundant and were primarily located in intergenic regions. However, there were important species differences: murine TRs did not have the extensive number of repeat expansions like those associated with human repeat expansion diseases and they were not associated with transposable elements. We demonstrate by analysis of two biomedical phenotypes, which were identified over 40 years ago, that this TR database can enhance our ability to characterize the genetic basis for trait differences among the inbred strains.

genetics↗

bioRxiv2025

Sequential Amino Acid Mutagenesis-Driven De Novo Evolution of Adenine Deaminases Enables Efficient In Vivo Base Editing in Primate

Base editing allows for the precise modification of genetic information, providing new avenues for treating diseases1. The adenine base editor ABE8e is currently the most efficient and widely used tool for adenine base editing. ABE8e was developed through multiple rounds of directed evolution of Escherichia coli tRNA adenine deaminase, including phage-assisted continuous evolution (PACE)2,3. While PACE is highly effective, it is a complex system that poses challenges for implementation4. Despite its high efficiency, ABE8e is associated with limitations such as relatively higher bystander editing effects and elevated off-target activity5, which need to be addressed to further enhance its precision and safety. Here, we developed a novel method for the de novo discovery of evolved ABE components, particularly adenine deaminases. This process involves identifying candidate proteins through AI-based structural prediction and clustering, followed by the enhancement of deaminase editing activity through screening libraries created by sequential amino acid saturation mutagenesis. This evolutionary strategy simplifies the approach by employing saturation mutagenesis libraries tailored to specific segments, thereby enabling exploration of an expanded sequence space and increasing the likelihood of discovering adenine deaminases with superior capabilities. The newly developed hpABE5.20 here demonstrates a more refined editing window, reduced DNA off-target effects that are both sgRNA-dependent and -independent, and minimized RNA off-target activity, while maintaining robust editing efficiency relative to ABE8e. Furthermore, hpABE5.20 has been successfully applied for precise and effective therapeutic adenine base editing in cellular disease models, humanized mice, and non-human primates.

bioengineering↗

bioRxiv2025

Dynamic Pathway of Guanidine-III Riboswitch Folding Revealed by Single-Molecule FRET: Mg2+-Assisted Preorganization and Ligand-Induced Kinetic Trapping

Riboswitches are structured RNA elements that regulate gene expression by sensing and binding small molecules. The guanidine-III riboswitch, a critical bacterial regulator responding to guanidine toxicity, undergoes precise conformational changes that remain poorly characterized at a dynamic, mechanistic level. In this study, we employed single-molecule Forster Resonance Energy Transfer (smFRET) coupled with molecular dynamics (MD) simulations to delineate how the guanidine-III riboswitch transitions among distinct conformational states. We identify three principal states [-] an extended (E-state), a compacted prefolded intermediate (P-state), and a folded pseudoknot structure (F-state) [-] with rapid interconversion in the absence of ligand. Magnesium ions significantly stabilize intermediate states via a cooperative, preorganization mechanism, enhancing ligand binding efficiency. Binding of guanidine drastically suppresses the reverse transitions, kinetically trapping the riboswitch into its active folded state primarily through a conformational selection mechanism, with additional contributions from induced-fit dynamics. This work illuminates the unique dynamic pathway by which the guanidine-III riboswitch integrates ionic and ligand cues, ensuring precise gene regulatory responses in bacteria.

biophysics↗

bioRxiv2025

FOSL2 Directly Regulates FSHR and CYP11A1 Transcription: An Essential Transcription Factor for Gonadotropin-Dependent Folliculogenesis

The meticulous orchestration of gonadotropin-dependent folliculogenesis constitutes the cornerstone of female reproductive cyclicity and fertility, with FSH/FSHR signaling recognized as the master regulator. Achieving the necessary amplification of this signaling is essential for successful GTH-dependent folliculogenesis, yet the mechanisms remain inadequately defined. Our study utilizes single-cell and spatial transcriptomics to identify FOSL2 as an FSH-inducible transcription factor, exhibiting precise spatiotemporal co-expression with FSHR. FOSL2 knockdown in vitro resulted in notable reductions in granulosa cell proliferation, induced apoptosis, and disrupted gonadotropin-dependent folliculogenesis. In vivo studies using conditional FOSL2 deletion in mouse granulosa cells corroborated these results, demonstrating a complete halt in GTH-dependent folliculogenesis and resultant infertility. Mechanistic exploration unveiled that FSH/FSHR initiates FOSL2 expression via the cAMP/PKA/CREB cascade, while FOSL2 in turn enhances FSHR transcription through direct promoter binding, thereby establishing a self-amplifying loop. This loop represents a molecular switch, modeled to the all-or-nothing dynamics of GTH-dependent folliculogenesis. The evolutionary conservation of this mechanism was confirmed through cross-species analyses in sheep, where FOSL2 deficiency similarly attenuated FSH/FSHR signaling and inhibited follicular growth. Our findings advance the understanding of folliculogenesis by revealing a novel FOSL2-centered amplification loop for FSH/FSHR signaling, highlighting the indispensable role of FOSL2 in reproductive biology.

cell biology↗

bioRxiv2025

Enzymes can activate and mobilize the cytoplasmic environment across scales

Biomolecular condensates have so far been studied in terms of their structural, compositional, and functional properties. However, condensate enzymatic activity --a key aspect of cellular metabolism-- remains unexplored due to the complexity of the system. In this study, using a combination of experimental, computational and theoretical techniques, we have discovered that the non-equilibrium activity which originates from catalytic reactions couples with the environment through various feedback mechanisms across five orders of magnitude of length scales. We observe that condensed enzymes catalyse more rapidly in the presence of crowding proteins and show that the increased enzymatic activity within these droplets stems from the emergence of lower-energy protein conformations induced by the highly crowded environment. Despite the crowding in the environment of the droplet, which might suggest an effective increase in its overall viscosity, we find that it becomes more agile, as evidenced by the observation of enhanced diffusion and macroscopic flow, due to the enzymatic activity. These findings shed new light on the dynamic interplay between enzymatic activity, composition and crowding in condensates, and their roles on the mobility and accessibility of various functional units in these environments, offering a novel perspective on liquidliquid phase separation in metabolically active conditions.

biochemistry↗

bioRxiv2025

Stress-activated neuronal ensemble in the supramammillary nucleus stores anxiety but not memory

Anxiety is a prevalent negative emotional state induced by stress; however, the neural mechanism underlying anxiety is still largely unknown. We used acute and chronic stress to induce anxiety and test anxiety-like behavior; immunostaining, multichannel extracellular electrophysiological recording and Ca2+ imaging to evaluate neuronal activity; and virus-based neuronal tracing to label circuits and manipulate circuitry activity. Here, we identified a hypothalamic region, the supramammillary nucleus (SuM), plays important role in anxiety-like behavior. We then characterized a small ensemble of stress-activated neurons (SANs) that are recruited by stress. These SANs respond specifically to stress, and their activation robustly increases anxiety-like behavior in male mice. We also found that ventral subiculum (vSub)-SuM projection but not dorsal subiculum (dSub)-SuM projections encode anxiety-like behavior and that inhibition of these vSub-SuM projections has an antianxiety effect. These results indicate that the reactivation of stress-activated supramammillary cells and relevant neural circuits are important neural processes underlying anxiety-like behavior.

neuroscience↗

bioRxiv2025

A Murine Database of Structural Variants Enables the Genetic Architecture of a Spontaneous Murine Lymphoma to be Characterized

A more complete map of the pattern of genetic variation among inbred mouse strains is essential for characterizing the genetic architecture of the many available mouse genetic models of important biomedical traits. Although structural variants (SVs) are a major component of genetic variation, they have not been adequately characterized among inbred strains due to methodological limitations. To address this, we generated high-quality long-read sequencing data for 40 inbred strains; and designed a pipeline to optimally identify and validate different types of SVs. This generated a database for 40 inbred strains with 573,191SVs, which included 10,815 duplications and 2,115 inversions, which also has 70 million SNPs and 7.5 million insertions/deletions. Analysis of this SV database identified an SV that is one component of a bi-genic model for lymphoma susceptibility in SJL mice, which provides mechanistic insight into the genetic basis for susceptibility to murine (and potentially human) lymphomas.

genetics↗

bioRxiv2024

A Systematic Comparison of Single-Cell Perturbation Response Prediction Models

Predicting single-cell transcriptional responses to perturbations is central to dissecting gene regulation and accelerating therapeutic design, yet the field lacks a rigorous, task-spanning assessment of model behavior. We present a large-scale benchmark of 13 representative methods and baselines across 25 datasets spanning diverse perturbation modalities and species, including two primary immune-cell drug-response resources. We evaluated three core tasks--generalization to unseen single-gene perturbations, prediction of combinatorial interactions, and transfer across cell types--using 24 metrics covering expression-level accuracy, relative changes, differential expression recovery, and distributional similarity. Across tasks, performance depended strongly on perturbation effect size and evaluation perspective: expression-level agreement was highest for small-effect perturbations resembling controls, whereas delta- and DE-based metrics improved with larger effects, providing clearer signals. Models shared a conservative bias, with fine-tuned foundation models compressing variance and underestimating synergistic effects in combinations. PerturbNet showed superior recovery of DE signatures in Tasks 1 and 2, while no method consistently generalized across cell types in Task 3, where biological consistency dominated outcomes. This benchmark establishes current methodological limits, clarifies that different metrics probe distinct biological signals rather than redundant summaries of the same prediction problem, and provides a foundation for developing virtual-cell models that more faithfully capture heterogeneous perturbation responses. Teaser: A large-scale benchmark reveals strengths and limits of models predicting single-cell perturbation responses.

bioinformatics↗

bioRxiv2024

In vivo genome editing of human hematopoietic stem cells for treatment of blood disorders by mRNA delivery

Ex vivo autologous hematopoietic stem cells (HSCs) gene therapy provides promising new treatments for hematological disorders. However, current methods involve complex processes and chemotherapeutic conditioning, leading to limited accessibility for treatment and significant side effects. Here, we developed an antibody-free targeted lipid nanoparticles (LNPs) for mRNA delivery to HSCs in vivo, enabling efficient base editing of the HBG target in human HSCs to reactivate fetal hemoglobin in derived erythroid cells. Delivery of ABE8e/sgRNA mRNA with optimized structure LNPs achieves efficient in vivo base editing of HBG in transfusion-dependent {beta}-thalassemia (TDT) patients derived HSCs engrafted in immunodeficient NCG-X mice, showing restored globin chain balance in erythroid cells. Our research indicated that utilizing LNPs for delivery of genome editor achieves efficient editing of endogenous genes of human HSCs. Notably, this non-viral delivery system eliminates the need for harvesting or mobilizing HSCs, providing a potent and one-time treatment potential for blood disorders like sickle cell disease (SCD) and TDT. HighlightsO_LIAntibody-free targeted LNPs system achieves efficient mRNA delivery and base editing in human bone marrow cells including HSCs via one-time intravenous injection. C_LIO_LIDelivery of ABE8e/sgRNA mRNA with optimized LNPs achieves efficient in vivo base editing of HBG in TDT patients derived HSCs engrafted in immunodeficient NCG-X mice, showing restored globin chain balance in erythroid cells. C_LIO_LILNPs efficiently deliver gene editing system to the BM for in vivo editing of human HSCs, providing preclinical evidence for the next generation non-viral gene therapy for blood disorders. C_LI

bioengineering↗

bioRxiv2024

Study on the phenotypic diversity and comprehensive evaluation analysis of 43 ornamental peonies of Sect. Paeonia.

The peony of Sect. Paeonia was a perennial herbaceous plant with numerous ornamental varieties and riched diversity in flower color and shape. It has ornamental, edible, and medicinal value and a long history of cultivation in China. The study of phenotypic diversity of plants is an important foundation for plants of Sect. Paeonia breeding. This study conducted phenotypic diversity analysis, principal component analysis, and cluster analysis on 43 varieties of Sect. Paeonia germplasm resources. Phenotypic traits included 30 qualitative traits and 7 quantitative traits. Through genetic diversity analysis, principal component analysis, comprehensive evaluation, and cluster analysis, we ultimately concluded that plant samples had relatively rich genetic phenotype traits. In principal component analysis, the first 12 principal components have covered the vast majority of information for phenotypic traits. The comprehensive evaluation results of phenotypic traits indicate that the F values of each variety in the germplasm sample were all positive number. The degree of stamen petals played a key role in determining the phenotypic diversity of plants, and the shape of the cotyledons and leaflets may determine the plants stress resistance performance, which provides a reference for breeding new varieties of peonies of Sect. Paeonia.

plant biology↗

bioRxiv2024

From Sight to Insight: A Multi-task Approach with the Visual Language Decoding Model

Visual neural decoding aims to unlock the mysteries of how the human brain interprets the visual world. While early studies made some progress in decoding visual activity for singular type of information, they failed to concurrently reveal the multi-level interweaving linguistic information in the brain. Here, we developed a novel Visual Language Decoding Model (VLDM) capable of decoding categories, semantic labels, and textual descriptions from visual perceptual activities simultaneously. We selected the large-scale NSD dataset to ensure the efficiency of the decoding model in joint training and evaluation across multiple tasks. For category decoding, we achieved the effective classification of 12 categories with an accuracy of nearly 70%, significantly surpassing the chance level. For label decoding, we attained the precise prediction of 80 specific semantic labels with a 16-fold improvement over the chance level. For text decoding, the scores of the decoded text surpassed the corresponding baseline levels by remarkable margins on six evaluation metrics. This study contributes significantly to extensive applications in multi-layered brain-computer interfaces, potentially leading to more natural and efficient human-computer interaction experiences.

neuroscience↗

bioRxiv2023

Systematic comparison of sequencing-based spatial transcriptomic methods

Recent advancements of sequencing-based spatial transcriptomics (sST) have catalyzed significant advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare six sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, significantly impacting the effective resolutions. Furthermore, we observed that spatial transcriptomic data demonstrate unique attributes beyond merely adding a spatial axis to single-cell data, including an enhanced ability to capture patterned rare cell states along with specific markers, albeit being influenced by multiple factors including sequencing depth and resolution. Our study assists biologists in sST platform selection, and helps foster a consensus on evaluation standards and establish a framework for future benchmarking efforts that can be used as a gold standard for the development and benchmarking of computational tools for spatial transcriptomic analysis.

genomics↗

bioRxiv2023

High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy

In recent years, notable progress has been achieved in both the hardware and algorithms of structured illumination microscopy (SIM). Nevertheless, the advancement of 3DSIM has been impeded by challenges arising from the speed and intricacy of polarization modulation. In this study, we introduce a high-speed modulation 3DSIM system, leveraging the polarization maintaining and modulation capabilities of a digital micro-mirror device (DMD) in conjunction with an electro-optic modulator. The DMD-3DSIM system yields a 2-fold enhancement in both lateral (133 nm) and axial (300 nm) resolution compared to wide-field imaging, and can acquire a data set comprising 29 sections of 1024x1024 pixels, with 15 ms exposure time and 6.75 s per volume. The versatility of the DMD-3DSIM approach was exemplified through the imaging of various specimens, including fluorescent beads, nuclear pores, microtubules, actin filaments, and mitochondria within cells, as well as plant and animal tissues. Notably, polarized 3DSIM elucidated the orientation of actin filaments. Furthermore, the implementation of diverse deconvolution algorithms further enhances three-dimensional resolution. The DMD-based 3DSIM system presents a rapid and reliable methodology for investigating biomedical phenomena, boasting capabilities encompassing 3D superresolution, fast temporal resolution, and polarization imaging.

cell biology↗

bioRxiv2023

Integrin beta4 promotes DNA damage drug resistance in triple-negative breast cancer via TNFAIP2/IQGAP1/Rac1

Anti-tumor drug resistance is a challenge for human triple-negative breast cancer treatment. Our previous work demonstrated that TNFAIP2 activates RAC1 to promote triple-negative breast cancer cell proliferation and migration. However, the mechanism by which TNFAIP2 activates RAC1 is unknown. In this study, we found that TNFAIP2 interacts with IQGAP1 and Integrin {beta}4. Integrin {beta}4 activates RAC1 through TNFAIP2 and IQGAP1 and confers DNA damage-related drug resistance in triple-negative breast cancer. These results indicate that the Integrin {beta}4/TNFAIP2/IQGAP1/RAC1 axis provides potential therapeutic targets to overcome DNA damage-related drug resistance in triple-negative breast cancer.

cancer biology↗

bioRxiv2023

LINC01117 inhibits invasion and migration of lung adenocarcinoma through influencing EMT process

BackgroundStudying the mechanism of action of LincRNAs in lung adenocarcinoma (LUAD) is of great importance for an in-depth understanding of the molecular mechanism of lung adeno carcinogenesis and development. ObjectiveTo identify long-stranded non-coding RNAs that are specifically highly expressed in LUAD cells and to investigate their function in LUAD cells to provide new potential targets for targeting LUAD therapy. MethodsThis study used publicly available data downloaded from The Cancer Genome Atlas (TCGA) database. Construction of siRNA and overexpression plasmid-packed lentiviral constructs were used to knock down and increase the expression of LINC01117 in LUAD cells. The effect of LINC01117 on LUAD cell migration and invasion was verified by scratch assays and Transwell assays. Western blot assays were performed to verify the effect of knocking down LINC01117 expression on key proteins of the EMT process. ResultsLINC01117 expression was upregulated in LUAD tissues and cell lines. Clinical correlation and prognostic analyses showed that LINC01117 was associated with poorer clinical features (staging and N classification) and poorer prognosis and could be analyzed as an independent prognostic factor. Cell migration and invasion were significantly inhibited in the knockdown group compared to the control group; in contrast, cell migration and invasion were promoted in the overexpression group. The expression of N-cadherin and vimentin, molecular markers of the EMT process, was elevated in the overexpression group, and the expression of E-cadherin was decreased. Conclusions: LINC01117 was highly expressed in LUAD cells, and inhibition of LINC01117 expression significantly inhibited the migration and invasion of LUAD cells, while overexpression of LINC01117 significantly promoted the migration and invasion of LUAD cells, and may affect the migration ability of LUAD cells through the EMT process. It suggests that LINC01117 may play a key role in the occurrence and development of LUAD.

molecular biology↗

bioRxiv2022

Visualization of mitochondrial cristae and mtDNA evolvement and interactions with super-resolution microscopy

Mitochondrial cristae host the respiratory chain complexes composed of mitochondrial DNA (mtDNA)-encoded and nuclear-encoded proteins and are responsible for ATP production. Movement of mtDNA located in the matrix is limited due to blockade by the cristae; yet, the dynamic interaction between the inner membrane and mtDNA remains unknown due to the insufficient spatiotemporal resolution of conventional microscopy and the lack of appropriate in vivo probes targeted to the mitochondrial inner membrane. Here, we developed a novel fluorescence probe to visualize the inner membrane using low-power stimulated emission depletion (STED) microscopy. Dual-color imaging of the inner membrane and mtDNA demonstrated that mtDNA is more likely to spread at mitochondrial tips or branch points under an overall even distribution. Interestingly, exploration of forming this distribution propensity uncovered that the mitochondrial dynamics are closely related to the location of mtDNA, and further insight found that fusion always occurs near mtDNA in order to minimize the pressure for cristae remodeling. In healthy cells, mitochondrial dynamics based on cristae remodeling promotes the even distribution of mtDNA, on the contrary, when cristae structure fails in apoptosis and ferroptosis, leading to mtDNA distribution disorder. Observation of active changes during apoptosis further captured the dynamic process of inner membrane herniation and mtDNA leakage along with cristae remodeling. Under ferroptosis, the mitochondria shrank into ellipsoids and mtDNA converged at the center of mitochondria. The rich dynamics between the cristae and mtDNA, revealed at unprecedented spatiotemporal resolution, show the motive and outgrowth of mtDNA distribution.

biophysics↗

bioRxiv2022

Monitoring mouse brain perfusion with hybrid magnetic resonance optoacoustic tomography

Progress in brain research critically depends on the development of next-generation multi-modal imaging tools that are capable of capturing transient functional events and multiplexed contrasts noninvasively and concurrently. A number of outstanding questions, such as those pertaining to the link between blood-oxygen-level-dependent (BOLD) signaling, oxygen saturation and underlying neural activity, could potentially be addressed by truly integrating several complementary neuroimaging readouts into one hybrid system, thus enabling a holistic view of dynamic events in vivo. Here we developed a hybrid magnetic resonance and optoacoustic tomography (MROT) system for murine brain imaging by incorporating an MR-compatible spherical matrix array transducer and fiberbased light illumination into a 9.4T small animal scanner, whilst further designing an optimized radiofrequency coil for whole-brain interrogation. The utility of the system is demonstrated by acquiring complementary angiographic and soft tissue anatomical contrast along with simultaneous dual-modality visualization of contrast agent dynamics in vivo.

bioengineering↗

bioRxiv2022

Novel leaf-root coordination driven by leaf water storage tissues in mangroves

Interactions among root and leaf traits (in particular, leaf hydraulic and leaf economics traits) are fundamental in generating diverse strategies in land plants, yet it remains a knowledge gap in mangrove plants that experiences saline stress distinct from most other vascular plants. Here, we tested the trait relationships in mangrove plants and compared them with typical land plants (non-mangrove). Consistent with non-mangrove plants, leaf hydraulic and economics traits were decoupled in mangrove plants. However, mangrove leaf economics traits correlated strongly with root hydraulic traits, which are normally decoupled in non-mangrove plants. Moreover, we observed a unique scaling relationship between leaf dry mass per area and root hydraulic traits in mangroves. The novel coordination between leaves and roots arises from the wide-presence of leaf water storage tissues in mangroves, and this potentially represents a new paradigm with which we look into the ecology, physiology and evolution of this important vegetation.

ecology↗