Biology subjects

Ma, X.

Publications and source records attributed to Ma, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Differential nucleosome organization in human interphase and metaphase chromosomes

DNA bendability plays a critical role in stabilizing nucleosome assembly, yet its contribution to nucleosome dynamics in vivo remains poorly understood. Here, we applied chemical mapping to generate high-resolution nucleosome positioning maps at single-base-pair resolution from human interphase and metaphase chromosomes, revealing distinct patterns of nucleosome organization between the two states. Notably, we observed a unifying pattern of nucleosome positioning near euchromatic landmarks, including promoters, enhancers, and insulators, during mitosis. Interphase nucleosomes exhibited extensive repositioning, marked by increased nucleosome density, reduced spacing between nucleosomes, and the appearance of additional fragile nucleosomes compared to metaphase. Furthermore, our results show that metaphase nucleosomes display significantly higher DNA cyclizability around the dyad axis, whereas interphase nucleosomes, particularly those near regulatory regions, tend to position DNA with greater cyclizability at the edges of the nucleosome. Together, these findings highlight a dynamic interplay between DNA mechanics and nucleosome organization during the cell cycle.

genomics↗

bioRxiv2025

Transcriptional control of meiotic recombination by the DREAM complex

Meiotic chromosome segregation and recombination, essential for sexual reproduction and evolution, require a specialized gene set. However, how meiotic gene expression is controlled remains largely unclear in multicellular eukaryotes. Here, we identify the DREAM complex as a transcriptional regulator of meiotic recombination in Arabidopsis. We show that the DREAM complex localizes to meiotic chromosomes, and that reduced DREAM function disrupts recombination and causes sterility. Meiocyte-specific transcriptomics combined with genome-wide binding analyses revealed that recombination genes, including the crossover-promoting helicase MER3, are direct DREAM targets. Notably, bypassing DREAM regulation of MER3 partially restores recombination in DREAM-deficient plants. Our findings establish the DREAM complex as a major meiotic regulator. Given that reduced DREAM function causes reproductive defects in species such as Drosophila and mice, this role may be conserved across multicellular eukaryotes.

cell biology↗

bioRxiv2025

Evidence for strong purifying selection of human 47S ribosomal RNA genes

The multicopy 47S ribosomal RNA (rRNA) genes are among the most highly expressed genes in the human genome, yet to-date essentially no disease-causing sequence variants have been identified. This lack of disease association is surprising, as defects in 47S rRNA transcription and changes in ribosomal protein dosage, as well as nucleotide changes in the mitochondrial rRNA, all result in disease. The failure to identify rRNA-associated diseases may thus primarily stem from the experimental challenges associated with analyzing this chromosomally isolated high-copy gene family. Here, we used an evolutionary approach to test whether mutations in the human 47S genes can have phenotypic consequences. By analyzing sequence variants among rRNA genes across >3,000 individuals from the high-coverage 1,000 Genomes Project, we demonstrate highly stratified variant abundance across the 47S rRNA genes. In individual genomes, novel variants were frequently amplified in the transcribed spacer sequences and the evolutionarily young expansion segments, but rarely across the conserved 18S, 5.8S, and 28S rRNA-encoding sequences. Variant numbers and amplification were lowest in evolutionarily highly constrained nucleotide elements that are identical across >90% of sequenced eukaryotes. These results indicate that strong purifying selection acts to suppress copy number expansion of deleterious variants among the hundreds of 47S rRNA copies and imply that deleterious variants in the 47S rRNA have the potential to cause phenotypic consequences at very low copy numbers. As low-copy variant calls are rarely considered in association studies, this may explain why disease associations with 47S rRNA variants have so far escaped detection. SIGNIFICANCE STATEMENTThe rRNA genes are the most highly expressed genes in the human genome but there are almost no known diseases linked to sequence variants in the rRNA. We describe over 14,000 sequence variants that coexist within and between individuals and uncover signatures of strong purifying selection against deleterious variants. Our data indicate that deleterious rRNA variants cause sufficient fitness costs (and by extension, disease phenotypes) to be detected even against a massive backdrop of functional copies. As current disease-mapping algorithms generally ignore sequence variants that are only observed in a small percentage of sequencing reads, our data provide an obvious reason for the lack of disease associations.

genetics↗

bioRxiv2025

MDFIC2 is a sensory neuron-specific PIEZO channel auxiliary subunit

PIEZO channels are critical for sensory mechanotransduction. While MyoD-family inhibitor proteins were identified as PIEZO1 auxiliary subunits, their broader regulatory roles, particularly in sensory cells, remained unclear. Here we demonstrate native MDFIC and MDFI regulate endogenous PIEZO channel currents in various non-sensory cell types. However, neither MDFIC nor MDFI are expressed in primary sensory neurons. In these cell types we identified an uncharacterised member of this family, Mdfic2/Gm765, that shares the ability to physically bind to PIEZO1 and PIEZO2. MDFIC2 is selectively expressed in subsets of mechanosensitive neurons, including dorsal root ganglia, trigeminal ganglia, and vagal sensory neurons. Like its paralogues, MDFIC2 alters PIEZO1/2 mechanosensitivity and inactivation kinetics, converting them into high-threshold slowly inactivating mechanoreceptors. Extensive cryo-EM reveals a conserved binding pocket for these auxiliary subunits in the pore modules of both PIEZO1 and PIEZO2 mediated by the post-translationally modified distal C-termini of MyoD-family inhibitor proteins. This provides a comprehensive structural and functional characterisation of MyoD-family inhibitor proteins as PIEZO1/2 channel regulators and offers new insights into sensory physiology and mechanical pain mechanisms.

biophysics↗

bioRxiv2025

Cross-Species Insights from ART-D to Uncover Evolutionarily Conserved Oncogenic Mechanisms

Cancer arises from oncogenic clones, yet the dynamic mechanisms governing their stepwise evolution toward malignancy remain incompletely understood. Here, we establish the Atlas of Ras-driven Tumors in Drosophila (ART-D), a systematic, cross-species platform that dissects the molecular and phenotypic trajectories of tumorigenesis through ten genetically defined RasV12-driven models. By integrating longitudinal phenotypic profiling, we define three conserved stages of tumor development--initiation, promotion, and progression--distinguished by dynamic changes in tumor burden and tumor-induced cachexia. Transcriptomic dynamics reveal stage-specific signaling rewiring: early tumorigenesis is marked by co-activation of JAK/STAT, NF-{kappa}B/Toll, and MAPK pathways, whereas malignant progression is driven by Notch hyperactivation and Hippo pathway inactivation. Through integrative multi-omics and machine learning, we uncover an evolutionarily conserved pathogenic network involving coordinated JNK, NF-{kappa}B/Toll, Notch, and Hippo signaling that is functionally validated across species. ART-D provides a transformative resource that bridges Drosophila genetics and human cancer biology, offering a framework for decoding conserved oncogenic principles and enabling precision targeting of stage-specific vulnerabilities in RAS-driven cancers.

genetics↗

bioRxiv2025

A Micro-Engineered Heart Tissue Model of Desmin-related Cardiomyopathy Caused by Mutant αB Crystalin

Protein quality control (PQC) is essential for maintaining sarcomere integrity in cardiomyocytes. Crystallin B chain (CRYAB) R120G mutation disrupts CRYABs chaperone activity, leading to aggregation of CRYAB and its client proteins (including Desmin), leading to Desmin-related cardiomyopathy (DRM). Prior experimental systems for modeling DRM linked to CRYAB require massive overexpression of CRYAB mutant isoforms, raising questions about translational relevance. Here, we establish the first model of CRYAB-linked DRM that uses genome-edited hiPSC together with isogenic controls, allowing us to study the impact of mutant CRYAB expressed at near endogenous levels. Within micro-engineered heart tissues (HT), CRYAB-R120G mutant hiPSC-derived cardiomyocytes recapitulated key DRM hallmarks, including Desmin and CRYAB aggregation, contractile dysfunction, and increased vulnerability to PQC pathway inhibition. CRYAB-R120G mutant HT also exhibited dysfunctional calcium-contraction coupling, which exacerbated contractile deficits at higher pacing frequencies. JAK1 inhibition with Itacitinib partially restored contractile function at higher pacing frequencies, suggesting JAK1 inhibition as a viable therapeutic strategy. By preserving human-specific structural and functional features, our {micro}HT platform enables mechanistic characterization of proteotoxic cardiomyopathies and offers a scalable system for targeted drug screening.

bioengineering↗

bioRxiv2025

PPP1R3G Deletion Blocks RIPK1-Mediated Apoptosis and Necroptosis in Doxorubicin-Induced Cardiotoxicity

Cardiotoxicity is a major limitation of cancer chemotherapy, exemplified by doxorubicin (DOX), yet its underlying mechanisms remain incompletely defined. Here, we identify Protein Phosphatase 1 Regulatory Subunit 3G (PPP1R3G) as a critical amplifier of DOX-induced cardiotoxicity. We show that DOX activates both apoptosis and necroptosis in vitro. Mechanistically, DOX first induces p38-dependent inhibitory phosphorylation of receptor-interacting protein kinase 1 (RIPK1), providing a transient brake on cell death. PPP1R3G facilitates the removal of inhibitory phosphorylation, thereby permitting RIPK1 activation, oligomerization, and downstream apoptotic signaling. Activated RIPK1 further promotes mitochondrial DNA (mtDNA) release, which induces IFN-{beta}-mediated ZBP1 expression and establishes a positive feedback loop that amplifies late-stage necroptosis. Genetic ablation of Ppp1r3g suppresses both apoptosis and necroptosis in cardiomyocytes, attenuates inflammatory cytokine production, and protects mice from DOX-induced cardiac injury and mortality. These findings delineate a PPP1R3G-RIPK1 axis that converts an early protective phosphorylation checkpoint into sustained death signaling and identify PPP1R3G as a potential therapeutic target for cardioprotection.

molecular biology↗

bioRxiv2025

A Multi-Layered Atlas of Spatial Regulatory Programs and Therapeutic Vulnerabilities in Glioblastoma

Glioblastoma (GBM) is marked by profound spatial heterogeneity. This complexity fuels tumor progression and therapy resistance. Although recent spatial transcriptomics (ST) studies have defined transcriptional niches, or metaprograms, the systems level regulatory logic linking upstream signaling, transcriptional programs, and therapeutic vulnerabilities remains unresolved. Here, we introduce an integrated, multi layered framework that unifies transcription factor and pathway activity inference (STAN and SPAN) with ligand/receptor and drug target mapping, thereby constructing a systems-level regulatory atlas of GBM across 26 tumors. This atlas uncovers spatial niches organized around transcriptional hubs and signaling programs, including hypoxic mesenchymal regions coordinated by HIF1A and SOX2 with mTORC1 signaling, macrophage rich areas driven by STAT3 mediated immune modulation, and astrocyte-like states shaped by lipid metabolic regulators such as SREBF2. By coupling this regulatory atlas to drug target predictions, we identify niche specific therapeutic vulnerabilities, such as VEGF blockade in HIF1A high regions and MAO-B inhibition in mesenchymal states. Finally, we provide an open, interactive web resource to make these data broadly accessible. This work provides a generalizable blueprint for linking spatial regulation to therapeutic hypotheses across diverse human diseases.

bioinformatics↗

bioRxiv2025

Reference-Informed Spatial Domain Detection Using Weak Supervision for Spatial Transcriptomics

One of the key objectives in spatial transcriptomics (ST) studies is to map the complex organization and functions of tissues. We introduce GraphScrDom, a reference-informed and weakly supervised contrastive learning model that uniquely integrates expert-provided manual annotations (i.e., scribbles) on spatial grids or histology images with cell type-specific gene expression profiles derived from reference single-cell RNA-seq data to perform tissue segmentation. With only limited scribble annotations, GraphScrDom consistently outperforms existing methods across various ST platforms and at both bulk and single-cell resolutions, as evaluated by six widely used metrics, demonstrating strong generalizability and robustness. Additionally, we have developed an integrative software toolkit that includes an interactive annotation interface and a model training module for spatial domain detection, providing a unified and user-friendly framework to facilitate spatial domain analysis.

bioinformatics↗

bioRxiv2025

Real-Time Viability Assessment of Ex Vivo Mouse Kidneys for Transplant Applications Using Dynamic Optical Coherence Tomography

Kidney transplantation remains the preferred treatment for patients with end-stage kidney disease. However, the ongoing shortage of donor organs continues to limit the availability of transplant treatments. Existing evaluation methods, such as the kidney donor profile index (KDPI) and pre-transplant donor biopsy (PTDB), have various limitations, including low discriminative power, invasiveness, and sampling errors, which reduce their effectiveness in organ quality assessment and contribute to the risk of unnecessary organ discard. In this study, we explored the dynamic optical coherence tomography (DOCT) as a real-time, non-invasive approach to monitor the viability of ex vivo mouse kidneys during static cold storage over 48 hours. The dynamic metrics logarithmic intensity variance (LIV), early OCT correlation decay speed (OCDSe), and late OCT correlation decay speed (OCDSl) were extracted from OCT signal fluctuations to quantify temporal and spatial tissue activity and deterioration. Our results demonstrate that DOCT provides complementary functional information to morphological assessment offered by conventional OCT imaging, showing potential to improve pre-transplant organ evaluation and clinic decision-making.

bioengineering↗

bioRxiv2025

An Objective Detection Method for Tinnitus using Memristors

Approximately 10-20% of the world population experiences tinnitus, which is increased with age and comorbid with frustration, annoyance, anxiety, depression, cognitive dysfunction, insomnia and stress. The underlying mechanisms of tinnitus remain largely unknown and there are no quantifiable biomarkers, making this prevalent disorder a global burden. There are no FDA-approved therapeutics and the current assessment mainly relies on self-reports (e.g., questionnaires), which underscore the need for diagnostic tools for tinnitus. Memristors, nanoscale electronic components mimicking synaptic plasticity, can monitor and control neuronal activity, hold transformative potential for detecting and characterizing tinnitus objectively. Here, we harvested the blood from human and mice with tinnitus, and engineered memristors via magnetron sputtering and made the functional layer with serum. Its core mechanism lies in regulating the reversible formation and rupture of conductive filaments which is formed by utilizing abnormally elevated glutamate concentrations in serum assisted Ag+ ions. This serum-based memristor achieves unprecedented discrimination between tinnitus and non-tinnitus individuals. Furthermore, this platform provides mechanistic insights into tinnitus pathogenesis, with potential implications in other neurological disorders.

pathology↗

bioRxiv2025

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

DNA abnormalities characterized by cytogenetic imaging at the single cell resolution, i.e. karyotyping, have long served as cancer diagnostic and prognostic biomarkers. To enable in-silico karyotyping using unpaired whole-genome sequencing data, we developed Seq2Karyotype (S2K), a tool that fits karyotype models with clonality estimation based on read-depth and allelic imbalance in a bulk sample and supports visualization-guided refinement. Analysis on 19 adult and pediatric cancer cell lines revealed unexpected intratumoral heterogeneity involving multiple copy number variation (CNV) states including whole-genome duplication, which were validated by imaging and single-cell omics profiling. Analyses on patient samples showed high concordance with clinical cytogenetic reports for acute myeloid leukemia, and revealed evolutionary trajectories from multi-region metastatic neuroblastomas implicating reversion. These findings highlight extensive and dynamic intratumoral heterogeneity contributed by CNV in both cell line models and patient samples, which may inform future research on tumor evolution under selective pressure such as drug exposure.

bioinformatics↗

bioRxiv2025

HP1β and densely packed chromatin form separate microdomains in mouse ES cells, which are reconfigured upon exit from naive pluripotency

Heterochromatin proteins play a key role in establishing local chromatin structure to control the transcription of target genes. Here we uncover a surprising segregation between regions of high DNA- and high heterochromatin protein 1{beta} (HP1{beta})-density in mouse ES cells. DNA-low/HP1{beta}-high foci retain freely diffusing HP1{beta}, and form via condensation through a multitude of weak interactions on top of HP1{beta} that is bound stably to chromatin. DNA-high/HP1{beta}-low foci exclude freely diffusing HP1{beta} and display reduced chromatin mobility, suggesting a higher degree of chromatin self-interaction and a more repressive environment. Finally, the two types of environments are intertwined in DNA-high/HP1{beta}-high foci, where HP1{beta} maintains heterochromatin in a more compact yet dynamic chromatin state. During the exit from naive pluripotency HP1{beta} is lost from regions of high DNA density as cells transition through the formative state, which might facilitate the reconfiguration of genome structure accompanying a change in cell state that we observed previously. Subsequently, as cells enter primed pluripotency, canonical heterochromatin is established.

molecular biology↗

bioRxiv2025

High-throughput 3D super-resolution ultrasound imaging

Capturing fast hemodynamics in deep organs is essential for understanding microvascular regulation of organ responses to physiological demands and pathological stress. However, non-invasive three-dimensional (3D) imaging of these microscale processes remains challenging due to trade-offs between spatial resolution, imaging speed, and penetration depth. Here, we present fluctuation-based high-order super-resolution acoustic microscope (FLAME), a tracking-free 3D ultrasound imaging technology capable of fast microvascular angiography and flow measurement. Using as few as 30 volumes, FLAME improves 3D ultrasound resolution by 8-fold ([~]50 m) and shortens data acquisition time by over two orders of magnitude, from tens of seconds to tens of milliseconds, compared with conventional tracking-based super-resolution approaches1-6. This high-throughput capability supports high-fidelity imaging of tissue functions under flexible experimental settings. FLAME achieves an unprecedented 3D super-resolution frame rate of [~]40 Hz, capturing transient hemodynamic responses to various physiological and pathological stimuli in different mouse organs, from the microvascular level to the whole-body scale. With open-sourced implementation, FLAME provides an accessible platform for real-time, in-depth hemodynamic monitoring across diverse biomedical applications and clinical translation.

bioengineering↗

bioRxiv2025

CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies

Cancer subtype classification is critical for precision therapy and there is a growing trend of augmenting histopathology testing procedures with omics-based machine learning classifiers. However, analytical challenges remain for pediatric cancer on the scope and precision of the current classifiers as well as the evolving subtype standardization. To address these challenges, we built Cancer Identification or CanID, a stacked ensemble machine learning classification scheme, using the transcriptomic features derived from gene-level RNA sequencing count data as the sole input. CanID was developed primarily from 3203 pediatric cancer samples of 13 solid tumor subtypes and 38 hematologic malignancy subtypes with subtype labels curated without the use of RNA-seq data. The accuracies of independent testing in three independent or external data sets for Solid Tumor and Hematologic Malignancy are 99% and 92-93%, respectively. Notably, CanID was able to classify subtypes challenging for clinical histology evaluation and was robust to both biological and technical challenges, including differences in data collection protocols, class imbalance, potential mislabeled training samples and classes unobserved in training. The high accuracy, robustness, biological interpretability of this transcriptome-based classification scheme represents a valuable approach to advance tumor diagnosis and clinically meaningful stratification of tumor types. CanID can be accessed on GitHub at https://github.com/chenlab-sj/CanID.

bioinformatics↗

bioRxiv2025

Translational control of innate barrier defense by the gut microbiota

The intestinal epithelium is protected by a mucus barrier, infused with antimicrobial proteins, that restricts microbial access to host tissue. Because assembling this barrier is energetically costly, its production must be tightly regulated. Here, we show that the microbiota regulates the translation of key mucus barrier components, including the structural glycoprotein mucin 2 and the antimicrobial enzyme lysozyme. This process is initiated by microbial induction of histone deacetylase 5 (HDAC5) in secretory epithelial cells of the intestine. HDAC5 promotes deacetylation of 14-3-3 proteins, enabling activation of the energy sensing kinase mTOR which enhances translation of mucus and antimicrobial proteins. These findings reveal a mechanism by which the microbiota controls barrier immunity at the level of protein synthesis and suggest that the HDAC5-mTOR axis integrates microbial and energetic signals to regulate intestinal defense. One sentence summaryThe gut microbiota enhances translation of innate barrier defense proteins through HDAC5-mediated activation of mTORC1 signaling.

immunology↗

bioRxiv2025

Retinal pigment epithelium-derived PD-L1 reprograms microglial cells and protects against retinal degeneration in mouse models of experimental AMD and genetic retinitis pigmentosa

Retinal degeneration is a leading cause of blindness and a significant health burden during aging worldwide. Because of its complex pathogenic mechanisms, however, effective interventions applicable to multiple retinal degenerations remain limited. Excessive microglia-mediated inflammation is a common pathological feature of different retinal degenerative diseases, and inhibiting these overactive inflammatory responses by reprogramming microglia may provide a therapeutic strategy with broad-spectrum potential. Here, we uncover a novel retinal pigment epithelium (RPE) homeostatic signal, PD-L1, that drives the reprogramming of activated microglial toward a retinal-protective phenotype. Using multiple analyses, including gene expression profiling bioinformatics, adeno-associated virus-mediated RPE-specific gene overexpression, pharmacological, and genetic manipulations, we show that RPE cells upregulate the expression of PD-L1 to modulate microglia for protection against retinal degeneration in an experimental dry AMD mouse model. Bioinformatics enrichment analysis of the high-expression gene signatures of subretinal microglia in AMD patients, combined with pharmacological blocking of NF-{kappa}B activity or using Nlrp3 knockout mice, show that PD-L1/PD-1 signaling suppresses NF-{kappa}B activation in microglia, thereby inhibiting NLRP3 inflammasome priming and attenuating microglia-mediated excessive inflammation. Furthermore, the overexpression of PD-L1 by the AAV8 virus exerts similar microglial reprogramming and retinal protective effects to alleviate retinal degeneration in a preclinical model of retinitis pigmentosa. These findings reveal that RPE-derived PD-L1 suppresses inflammatory reprogramming of subretinal microglia and mitigates retinal degeneration, highlighting a promising proof of concept for PD-L1 as a potential therapeutic target for the broad treatment of retinal degenerative diseases.

genetics↗

bioRxiv2025

Biosynthesis of lavandulol and lavandulyl acetate in Escherichia coli

Lavandulol and its ester derivative, lavandulyl acetate, are key fragrance constituents of lavender essential oil with widespread applications in cosmetics, perfumery, and food. However, traditional plant extraction suffers from low yield and unsustainable practices, and chemical synthesis relies on petrochemical feedstocks. Here, we report the first de novo microbial biosynthesis of lavandulol and lavandulyl acetate in Escherichia coli through modular pathway engineering. By screening 13 pyrophosphatases from E. coli, we identified RdgB as an efficient pyrophosphatase catalyzing the conversion of lavandulyl diphosphate into lavandulol, enabling its production at 24.9 mg/L. Building on this, we established a three-plasmid expression system and introduced a lavender-derived alcohol acyltransferase, LiAAT4, to achieve the biosynthesis of lavandulyl acetate at 42.4 mg/L. This study establishes the biosynthetic route to lavandulol in E. coli, demonstrating a viable and sustainable microbial platform for producing significant natural components of lavender oil. Our work provides the basis for future strain optimization and industrial-scale biomanufacturing of high-value monoterpene fragrance molecules.

synthetic biology↗