Biology subjects

Ren, J.

Publications and source records attributed to Ren, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Method of loci training yields unique neural representations that support effective memory encoding

The method of loci is a technique to effectively boost memory, but its impact on the underlying neural representations is poorly understood. Here, we used functional magnetic resonance imaging and representational similarity analysis to compare the neural representations of memory athletes ranked among the worlds top 50 in memory sports to those of mnemonics-naive controls. In a second study, mnemonics-naive individuals underwent a 6-week-long memory training, working memory training, or no intervention. Results showed distinct neural representations in the prefrontal cortex, inferior temporal, and posterior parietal regions as memory athletes and the memory training group studied novel content. Neural representations were also distinct between these experienced individuals, which was related to better memory performance after 4 months. In parallel, the data revealed increased neural pattern similarity in the anterior hippocampus and precuneus, suggesting a more generalised role of these regions in episodic memory formation and retrieval. Our findings highlight how extensive memory training affects neocortical memory engrams. We suggest that the method of loci may bolster memory uniqueness within ones "memory palace", setting the stage for exceptional memory performance.

neuroscience↗

bioRxiv2025

D-LMBmapX: Generalized Deep-Learning Pipeline for Automated Whole-brain Neural Circuitry Profiling Across Any Developmental Stages

Understanding whole-brain circuitry development is essential for uncovering the origins of disorders linked to abnormal neural wiring, yet progress has been limited by the lack of tools for accurate, comprehensive analysis. Brain development is highly dynamic and region-specific, with pronounced inter-individual variability during early stages, and no existing method achieves whole-brain profiling at arbitrary stages. The rapidly changing morphology of developing axons further complicates segmentation. Here, we present D-LMBmapX, a deep learning pipeline for automated whole-brain circuitry profiling across postnatal development. D-LMBmapX constructs sample-inferred atlases from flanking anchor stages, enabling accurate registration at any time point. By developing a foundation model for generalised axon and soma segmentation, it supports quantitative mesoscale developmental connectomics, demonstrated through spatial-temporal profiling of catecholaminergic projections. D-LMBmapX also enables robust cross-modality and cross-dimensional registration, including precise alignment of single 2D slices to 3D references, and offers generalizable strategies for 5D analysis of diverse biomedical spatial datasets.

neuroscience↗

bioRxiv2025

In situ generated vaccine-like pyroptosome for personalized cancer immunotherapy

The efficacy of in situ cancer vaccination has been hampered by poor spatiotemporal orchestration of multiple key steps of cancer-immunity cycle in most tumours and systemic toxicity related to therapeutic strategies. Here, we report a systemic injectable and pyroptosis-enabled nanoadjuvant (SPEN) that precisely evokes the secretion of vaccine-like pyroptosome in tumour area for eliciting robust anti-tumour immunity. SPEN induces vigorous immunogenic pyroptosis, triggering the efficient release of tumour antigen-rich pyroptosomes, DAMPs, and proinflammatory cytokines. Upon the activatable release of a TLR7/8 agonist into pyroptosome, the generated pyroptosome functions as in situ cancer vaccine for cooperatively activating the cancer-immunity cycle while avoiding systemic toxicity. This in situ vaccine boosts both innate and adaptive immune response, facilitating the eradication of primary tumour and long-lasting cancer prevention. Our findings provide new insights into the rational design of pyroptosis-inducing nanomedicines for boosting the cancer-immunity cycle, thus advancing personalized cancer immunotherapy.

cancer biology↗

bioRxiv2025

Title: Cell-autonomous and non-cell-autonomous effects of TRIM72 on ALS disease progression

Dysfunction of RNA-binding proteins, including TDP-43 and FUS, has been associated with amyotrophic lateral sclerosis (ALS); however, the underlying mechanisms are largely unknown. Here, we reported that a neuronal upregulation of TRIM72 (Tripartite Motif Containing 72) in FUS mutation knockin ALS models slows disease progression. TRIM72 interacts with Commander, a protein complex for recycling of membrane proteins, facilitating membrane repair and antioxidation. Exosomal TRIM72 is detected in ALS patient cerebrospinal fluid (CSF) and extracellular application of exosomal TRIM72 protects cell from membrane damage. In a sporadic ALS cohort, CSF TRIM72 level associates ALS disease progression. AAV-mediated neuronal expression of TRIM72 slows down the disease progressions in ALS models and in an ALS patient without adverse effects over a year treatment course. Taken together, our results suggest a universal neuronal protection of a TRIM family protein in cell-autonomous and non-cell-autonomous manners in ALS.

neuroscience↗

bioRxiv2025

Systematic Identification of Microtubule Inner Proteins Reveals JPT2 as a Key Regulator of Lumen Microenvironment and Drug Sensitivity

Microtubules are primarily studied for the interactions of proteins that bind to their outer surfaces and ends, while the regulatory mechanisms within the microtubule lumen, particularly in singlet microtubules critical for essential cellular processes, remain largely unexplored. Our study provides the first systematic identification of key regulatory proteins within the single microtubule lumen. Using proximity-dependent biotin identification (Bio-ID) coupled with mass spectrometry, we identified candidate microtubule inner proteins (MIPs), including Jupiter microtubule-associated homolog 2 (JPT2). JPT2 binds directly to microtubules and specifically localizes within the lumen, where it modulates the luminal environment by inhibiting acetylase MEC17 and independently affects the binding and efficacy of Paclitaxel. Furthermore, our screening identified additional MIPs that influence cellular sensitivity to Paclitaxel, indicating a link between luminal regulation and drug responsiveness. These discoveries reveal JPT2s critical role in singlet microtubule regulation and suggest new therapeutic targets for enhancing cancer drug sensitivity.

cell biology↗

bioRxiv2024

Global and genetic regulation of gene expression in human endothelial and vascular smooth muscle cells

BackgroundThe understanding of genetic and epigenetic regulation of gene expression in endothelial and vascular smooth muscle cells remains fragmented with limited experimental validation. MethodsChromatin conformation (Micro-C), DNA methylation (RRBS), chromatin accessibility (ATAC-seq), and transcriptome profiles (RNA-seq) were mapped in human induced pluripotent stem cell (hiPSC)-derived, isogenic endothelial and vascular smooth muscle cells (iECs and iVSMCs). CTCF and RAD21 were depleted to assess the functional relevance of chromatin architecture, and genome editing was used to evaluate the allelic effect of a blood pressure-associated single nucleotide polymorphism (SNP). ResultsSignificant correlations were identified between gene expression levels and chromatin interactions, chromatin accessibility, and DNA methylation in iECs and iVSMCs, with chromatin interactions showing the strongest association. Chromatin contact regions displayed distinct epigenetic landscapes depending on the types of regulatory element interactions involved. Perturbation of CTCF and RAD21 revealed their differential regulatory effects, particularly on the expression of genes overlapping chromatin contacts, with RAD21 exhibiting a broader regulatory impact. SNPs associated with several vascular traits were enriched in chromatin loops or accessible regions in iECs or iVSMCs. Precise genome editing demonstrated allele-dependent effects of SNP rs9833313 on the expression of SHOX2 located 247.4 kbp away but within the same chromatin loops as the SNP. ConclusionThis study provides an extensive epigenetic landscape of vascular cells that may drive novel research on the role of genetic and epigenetic mechanisms of vascular function and disease as demonstrated by our targeted experiments.

genomics↗

bioRxiv2024

Genome-wide Mapping Eukaryotic Open Chromatin Regions with Double-Stranded DNA Deaminase

A variety of methods such as ATAC-seq and CUT&Tag have been developed for probing chromatin states. However, enzymatic cleavage of DNA in these methods hinders their multi-omics integration with other DNA profiling techniques. Here, by extending our use of dsDNA deaminase (FOOtprinting with DeamInasE, FOODIE), we introduce two new methods for mapping Chromatin Open region by DeamInasE (ChrODIE) and histone modification by ANtibody-associated DeamInasE (ANDIE), respectively. Unlike cleavage-based methods, both ChrODIE and ANDIE leave genomic DNA after deamination unfragmented and amplifiable. This offers the potential for simultaneous or downstream integration with other genomic profiling methods, such as mapping 3D genome interactions.

genomics↗

bioRxiv2024

Development of a novel peripherally acting alpha2A-adrenergic receptor antagonist for anti-diabetic

Yohimbine, a potent alpha2A-adrenergic receptor (2AAR) antagonist, was found therapeutic potential for type 2 diabetes through improving insulin release. However, the adverse side effects mediated by its actions in the brain hampered its use. Here, based on molecular docking analysis and structural modification, we have developed a novel peripherally acting yohimbine derivative (CDS479-2). CryoEM data found that yohimbine and CDS479-2 have similar interactions with the structure of 2AAR. Importantly, CDS479-2 shows similar 2AAR antagonist activity as yohimbine, but with very limited access to the brain, and thus avoiding the unwanted central effects such as hypertension and anxiety. Acute administration of CDS479-2 by injection or gavage lowered blood glucose levels and improved glucose tolerance in the high-fat diet-induced obesity (DIO) mice, an animal model for human type 2 diabetes. Remarkably, DIO mice received 2 weeks of daily administration of CDS479-2, but not yohimbine, exhibited sustained normoglycaemia, and increased density of the insulin-producing beta cells, in which important proliferation genes were found upregulated. Moreover, the overall protein expression levels of their pancreas were more similar to that of the healthy chow-fed mice. Thus, CDS479-2 may indicate a new direction for type 2 diabetes treatment. Importantly, the strategy we employed in this study will inspire the optimization for drugs that with both peripheral and central targets. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/628818v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d3d7corg.highwire.dtl.DTLVardef@1afbad3org.highwire.dtl.DTLVardef@12a1aborg.highwire.dtl.DTLVardef@1341a02_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex

Thyroid hormones (THs) are required for proper maturation of parvalbumin-expressing GABAergic interneurons in the mouse neocortex, which function is essential to maintain a proper balance between neuronal excitation and inhibition. However, the timeline of this TH action has yet to be elucidated. Here, we used several mouse models expressing dominant negative mutations of the TH nuclear receptor 1 (TR1), to better define the time window during which THs promote the maturation of parvalbumin neurons. The action of THs during the first three postnatal weeks appears to be necessary to initiate the elaboration of a specialized extracellular matrix called the perineuronal net. Transcriptome analysis identified a small set of putative target genes for TR1, which are at the origin of the postnatal remodeling of the repertoire of ions channels and the elaboration of perineuronal nets. These data suggest that THs act as a timer to define the temporal boundaries of the critical period of heightened cortical plasticity, which plays a fundamental role in the development of neuronal circuits. Significance statementThyroid hormones exert a major influence on late neurodevelopment, acting directly on gene expression by binding to nuclear receptors present in all cell types. This study reports the discovery of a direct link between the transcriptional regulation exerted by the thyroid hormones in GABAergic neurons and the timing of the critical period of heightened plasticity. This provides a general framework to understand the pathology associated with altered thyroid hormone signaling.

developmental biology↗

bioRxiv2024

HDAC6-Mediated FoxO1 Acetylation And Phosphorylation Control Periodontal Inflammatory Responses

Post-translational modifications (PTMs) are critical regulators of protein function and cellular signaling. While histone deacetylation by histone deacetylases (HDACs) is well established, the role of specific HDACs in modulating non-histone protein PTMs, particularly in an infectious context, is poorly understood. Here, we reveal a pivotal role for HDAC6 in orchestrating periodontal inflammation through its dual regulatory effects on FoxO1 acetylation and phosphorylation. Using Porphyromonas gingivalis, a key periodontal pathogen, as a model pathogen, we observed that infection induces HDAC6 activation, driving inflammatory responses via modulating FoxO1 activity. HDAC6 depletion increased FoxO1 acetylation and phosphorylation, leading to its cytoplasmic sequestration and subsequent suppression of FoxO1- mediated pro-inflammatory cytokine production in macrophages. Mechanistically, HDAC6 deficiency not only directly enhances the acetylation of FoxO1 but also upregulates the expression of Rictor, a critical component of the mTORC2 complex, thereby promoting Akt phosphorylation and subsequently FoxO1 phosphorylation. This results in its cytoplasmic retention and attenuated inflammatory transcriptional activity. Functional studies demonstrated that HDAC6 depletion suppressed the production of key inflammatory mediators, including TNF, IL-6, IL-12p40, and MIP-2, while promoting macrophage polarization toward anti-inflammatory M2 phenotypes. In vivo, using oral gavage infection and ligature-induced mouse periodontitis models, HDAC6 deficiency significantly reduced inflammatory cell infiltration in gingival tissues and protected against alveolar bone loss. These findings establish HDAC6 as a central regulator of periodontal inflammation, acting through the coordinated modulation of FoxO1 acetylation and phosphorylation. Beyond its role in oral pathology, HDAC6 may serve as a promising therapeutic target for managing inflammatory diseases linked to immune dysregulation.

molecular biology↗

bioRxiv2024

A motif preferred adenine base editor with minimal bystander and off-targets editing

48% of hereditary disease are caused by single C-to-T base conversion, which makes efficient A-to-G base editing tools (ABEs) have great potential in the treatment of these diseases. However, the existing efficient ABE, while catalyzing A-to-G conversion, will bring more A and C bystander editing and off-target events, which poses safety concerns for their clinical application. Here, we developed ABE10 (ABE8e with TadA-8e A48E) for efficient and accurate editing of As in YA motifs with YAY>YAR (Y=T or C, R=A or G) hierarchy through structure-oriented rational design. Compared with ABE3.1, currently the only motif (YAC) preference ABE version, ABE10 exhibited A-to-G editing efficiency improvement with an average up to 3.1-fold in indicated YA motif while maintaining reduced bystander Cs editing and minimized DNA or RNA off-targets. Also, we showed ABE10 corrected pathogenic mutation with high efficiency and precision in human cells. Moreover, by ABE10, we efficiently and precisely generated hypocholes-terolemia and tail-loss mouse models mimicking human associated disease and mouse PCSK9 base editing in vivo for hypercholesterolemia gene therapy, indicating their great potential in broad applications for and disease modeling and gene therapy.

molecular biology↗

bioRxiv2024

Comprehensive Evaluation of AlphaFold-Multimer, AlphaFold3 and ColabFold, and Scoring Functions in Predicting Protein-Peptide Complex Structures

Determining the three-dimensional structures of protein-peptide complexes is crucial for elucidating biological processes and designing peptide-based drugs. Protein-peptide docking has become essential for predicting complex structures. AlphaFold-Multimer, ColabFold and AlphaFold3 provided groundbreaking tools to enhance the protein-peptide docking accuracy. This study evaluates these three tools for predicting protein-peptide complex structures using Template-Based (TB) and Template-Free (TF) methods. AlphaFold-Multimer excels in TB predictions and performs moderately in TF scenarios in the prediction pool, but TF outperforms TB in the first-ranked models. ColabFold demonstrates versatility in both TB and TF settings. AlphaFold3 generates high-quality structures for more proteins, but the medium accuracy is not as good as AlphaFold-Multimer using a large model pool. We also assessed the performance of various scoring functions in ranking predicted protein-peptide complex structures. While the scoring function built in AlphaFold demonstrates the best performance, some other scoring functions, e.g., FoldX-Stability and HADDOCK-mdscore, provide complementary values. The findings suggest the potential for enhancing scoring functions targeting AlphaFold-based predictions by combining multiple scoring functions or using a consensus approach from many prediction models.

bioinformatics↗

bioRxiv2024

SenSeqNet: A Deep Learning Framework for Cellular Senescence Detection from Protein Sequences

Cellular senescence, characterized by the irreversible cessation of division in normally proliferating cells due to various stressors, presents a significant challenge in the treatment of age-related diseases. Understanding and accurately detecting cellular senescence is crucial for identifying potential therapeutic targets. However, traditional wet lab assays for detecting cellular senescence are time-consuming and labor-intensive, limiting research and drug development efficiency. There is an urgent need for computational tools allowing swift and accurate detection of cellular senescence from protein sequences. We propose SenSeqNet, a novel deep learning framework for detecting cellular senescence directly from protein sequences. The framework begins with feature extraction using the Evolutionarily Scaled Model (ESM-2), a state-of-the-art protein language model that captures evolutionary information and complex sequence patterns. The extracted embeddings are then passed through a hybrid architecture consisting of long short-term memory (LSTM) networks and convolutional neural networks (CNNs) to further refine and learn from the embedded information. SenSeqNet achieved a final accuracy of 83.55% on independent testing, surpassing various machine learning and deep learning architectures. This performance underscoring the robustness and effectiveness of SenSeqNet for detecting cellular senescence from protein sequences. These results provide a solid foundation for future research on aging and age-related therapeutics.

bioinformatics↗

bioRxiv2024

Establishment and Molecular Characterization of Patient-Derived Organoids for Primary Central Nervous System Lymphoma

Primary central nervous system lymphoma (PCNSL) exhibits substantial heterogeneity, both intra-tumoral and intertumoral, posing challenges in developing effective treatment methods. Existing in vitro models fail to simulate the inherent microenvironment and the cellular and mutational diversity of native tumors and require a prolonged generation time. To address this concern, we described an organoid culture method for patient-derived PCNSL organoids (CLOs) and evaluated them through extensive molecular characterization. These CLOs accurately mimicked the histological attributes, gene expression landscapes and mutational profiles of their original tumors through rigorous histopathological analysis, RNA sequencing and whole-exome sequencing. Notably, CLOs were generated within 2 weeks, demonstrating rapid development and reliability. Furthermore, therapeutic profiling was performed on three selected CLOs using four standard treatment drugs. High concordance was observed between the drug responses of patients and those observed in the CLOs, with specific sensitivity to ibrutinib and methotrexate and resistance to dexamethasone and rituximab. Taken together, these results emphasize that CLOs can effectively emulate the key characteristics of PCNSL, enhancing the understanding of the genetic landscape of this complex disease. CLOs provide a rapid and reliable platform for exploring individualized treatment strategies, potentially accelerating the transition of research findings to clinical practice.

cancer biology↗

bioRxiv2024

Parameter-free clear image deconvolution (CLID) technique for single-frame live-cell super-resolution imaging

Advancing single-frame imaging techniques beyond the diffraction limit and upgrading traditional wide-field or confocal microscopes to super-resolution (SR) capabilities are greatly sought after by biologists. While enhancing image resolution by deconvolving noise-free images is beneficial, achieving a noise-free image that maintains the distribution of signal intensity poses a challenge. We first developed a denoising method utilizing reversibly switchable fluorescent proteins through synchronized signal switching (3S). Additionally, we introduced a denoising neural network technique, 3Snet, which combines supervised and self-supervised learning using 3S denoised images as the ground truth. These approaches effectively eliminate noise while maintaining fluorescence signal distribution across camera pixels. We then implemented clear image deconvolution (CLID) on both 3S and 3Snet denoised images to develop SR techniques, named 3S-CLID and 3Snet-CLID. Notably, 3Snet-CLID boosts the resolution of single fluorescence images from wide-field and spinning-disk confocal microscopies by up to 3.9 times, achieving a spatial resolution of 65 nm, the highest in such imaging scenarios without an additional SR module and complex parameter setting. 3Snet-CLID enables dual-color single-frame live-cell imaging of various subcellular structures labeled with conventional fluorescent proteins and/or dyes, allowing observations of dynamic cellular processes. We expect that these advancements will drive innovation and uncover new insights in biology.

biophysics↗

bioRxiv2024

Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements

The co-evolution of prokaryotes, phages, and mobile genetic elements (MGEs) over the past billions of years has driven the emergence and diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse functional domains, sequences, and are typically small, creating a challenge to detect anti-defense homologs across the prokaryotic genomes. To date, no tools comprehensively annotate anti-defense proteins within a desired genome or MGE. Here, we developed "AntiDefenseFinder" - a free open-source tool and web service that detects 156 anti-defense systems (of one or more proteins) in any genomic sequence. Using this dataset, we identified 47,981 anti-defense systems distributed across prokaryotes, phage, and MGEs. We found that some genes co-localize in "anti-defense islands", including E. coli T4 and Lambda phages, although many are standalone. Out of the 112 systems detected in bacteria, 100 systems localize only or preferentially in prophages, plasmids, phage satellites, integrons, and integrative and conjugative elements. However, over 80% of anti-Pycsar protein 1 (Apyc1) resides in non-mobile regions of bacteria. Evolutionary and functional analyses revealed that Apyc1 likely originated in bacteria to regulate cNMP signaling, but was co-opted multiple times by phages to overcome cNMP-utilizing defenses. With the AntiDefenseFinder tool, we hope to facilitate the identification of the full repertoire of anti-defense systems in MGEs, the discovery of new protein functions, and a deeper understanding of host-pathogen arms race.

microbiology↗

bioRxiv2024

CaMutQC: An R Package for Integrative Quality Control of Cancer Somatic Mutations

The quality control and filtration of cancer somatic mutations (CAMs), including the elimination of false positives resulting from technical bias and the selection of key mutation candidates, is crucial for downstream analysis in cancer genomics. Due to diverse needs and the absence of standardized filtering criteria, the filtering strategies employed vary from study to study, often leading to reduced efficiency, accuracy, and comparability across similar analyses. Here we present CaMutQC, a heuristic quality control and soft-filtering R/Bioconductor package for CAMs. With CaMutQC, the removal of false positives, selection of potential mutation candidates, and Tumor Mutation Burden estimation can be executed in a single line of code, using default or customized parameters. A filter report and a code log generated after the filtration process assist with recording and comparison. The application of CaMutQC on a Whole-exome Sequencing (WES) benchmark dataset demonstrated its impressive capability by eliminating 85.55% of false positive mutations while retaining 90.72% of true positive mutations. Additionally, an extra 11.56% of true positive mutations were recused by the union strategy embedded in CaMutQC. CaMutQC is now available through Bioconductor at https://bioconductor.org/packages/CaMutQC/ under the GPL v3 license, and it will be updated regularly to incorporate top filtration strategy and parameter sets shared within the community.

bioinformatics↗

bioRxiv2024

Phase transition of WTAP regulates m6A modification of interferon-stimulated genes

N6-methyladenosine (m6A) is the most prevalent modification of mRNA which controls diverse physiological processes. Although m6A modification has been reported to regulate type I interferon (IFN) responses by targeting the mRNA of IFN-{beta} and the interferon stimulated genes (ISGs), the detailed mechanism of how m6A methyltransferase complex (MTC) rapidly responds to conduct the modification on nascent mRNA during IFN-{beta} stimulation remains largely unclear. Here, we demonstrate that WTAP, the adaptor protein of m6A MTC, undergoes dephosphorylation-regulated phase transition from aggregates to liquid-like condensates under IFN-{beta} stimulation, thereby mediates m6A modification of a subset of ISG mRNAs to restrict their expression. The phase transition of WTAP promotes the interaction with nucleus-translocated transcription factor STAT1, which recruits MTC to the promoter regions of ISGs and directing the co-transcriptional m6A modification on ISG mRNAs. Collectively, our findings reveal a novel regulatory role of WTAP phase transition in manipulating signaling pathways and fine-tuning immune response by orchestrating dynamic m6A modification through the cooperation of transcription factors and MTC.

immunology↗