Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program

Rising data rates in macromolecular crystallography outpace multi-program pipelines on computing clusters. Rugnux, a single GPU-accelerated program, turns rotation or serial still diffraction images into merged data and an initial structure. At synchrotrons, results arrive seconds after the last image; on one workstation, 207 public datasets from 36 sources took a median of 15 s each, with deposition-quality. Serial XFEL data were processed faster than the collection rate, enabling real-time structure determination.

biophysics↗

bioRxiv2026

WRN deficiency generates oncogenic rearrangements at TA-rich tandem repeats

Werner syndrome, a premature-aging disorder caused by inherited loss of the WRN helicase, predisposes to a narrow set of cancers, including melanoma and sarcoma, through mechanisms that have been unclear. WRN resolves the secondary structures that TA-dinucleotide repeats form, a role established for the expanded repeats of mismatch-repair-deficient cancers. We show that WRN loss also destabilizes native, unexpanded TA-rich tandem repeats, which become fragile sites where chromosomes break and rearrange. In melanoma these rearrangements recurrently produce an identical 15.7Mb-long deletion that transcriptionally activates TERT, the earliest driver of these tumors, and separately disrupt tumor suppressors such as CDKN2A/B and NF1. The same class of rearrangement occurs in WRN-deficient cancers of other types. WRN deficiency is thus a source of instability at TA-rich tandem repeats that generates oncogenic rearrangements.

cancer biology↗

bioRxiv2026

The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures

Bile acids and related steroidal metabolites are among the most studied biomolecules, yet recent work has revealed far greater structural diversity than previously recognized, much of it shaped by the microbiome. We previously introduced a repository-scale bile acid MS/MS library built from queries targeting C24 bile acid fragmentation, limited to Orbitrap Q Exactive datasets within GNPS/MassIVE. Here we announce a major expansion of this library: a bile acid and steroidal MS/MS spectral library assembled across three major metabolomics repositories, now capturing C23, C24 (including alkamine), C26 (C-C bonded aceto derivatives), and C27 bile acids, as well as C28 bile alcohols. The expanded libraries comprise 640,141 unique MS/MS spectra, of which 120,293 (18.8%) match 2,529 reference spectra, leaving most of this steroidal chemical space structurally unassigned. Linked to harmonized pan-repository metadata, the library provides a starting point for classifying MS/MS spectra as likely bile acids or related steroids, with two example analyses illustrated here. This resource allows researchers to flag candidate bile acid and steroidal signatures in their own data for further characterization.

bioinformatics↗

bioRxiv2026

Astrocytes in the Dentate Gyrus Shift the Equilibrium from Pattern Separation to Pattern Completion and Inhibit Fear Extinction

Pattern separation and pattern completion are core hippocampal computations linked to memory interference and overgeneralization in many neuropsychiatric disorders and to mnemonic discrimination deficits in neurodegenerative conditions. Astrocytes are increasingly recognized as important integrators and modulators of neuronal activity as many studies have shown changes in animal behavior and neural circuits induced by manipulation of astrocytic activity. The role of astrocytes in the dentate gyrus for learning and memory is, however, largely unknown. To investigate the functional significance of astrocytic activity in the dentate gyrus, we expressed the calcium extruding pump hPMCA2w/b (CalEx), resulting in inhibition of astrocytic calcium activity, the Gq-coupled receptor hM3Dq, or the Gi-coupled receptor hM4Di, allowing chronic activation of Gq- and Gi-dependent pathways by a designer drug, in dentate gyrus astrocytes. Our main finding is that inhibition of astrocytic calcium activity by CalEx resulted in improved pattern separation and impaired pattern completion. In -vivo calcium imaging revealed that CalEx expression in astrocytes altered the neuronal activity pattern in dentate gyrus neurons with an overall inhibitory effect. This suggests that in the dentate gyrus astrocytes promote the activity of these neurons. Furthermore, chronic activation of hM4Di resulted in impaired between-session fear extinction while chronic activation of hM3Dq resulted in impaired within-session fear extinction and improved pattern separation learning over multiple days, suggesting that activation of astrocytic activity enhances mechanistically separable forms of fear extinction in a Gq- or Gi-pathway-specific manner. Our findings reveal that dentate gyrus astrocytic calcium shifts the balance between pattern separation and pattern completion towards pattern completion and thus modulates an essential neuronal functional output of the dentate gyrus. Chronic activation of astrocytes inhibits fear extinction, and thus also affects management of memory interference. Our findings imply that astrocytic modulation may be beneficial to treat cognitive deficits in disorders in which overgeneralization is a problem.

neuroscience↗

bioRxiv2026

mzQC: a versatile way to communicate quality information for biological mass spectrometry

Reliable quality control (QC) is essential for reproducible biological mass spectrometry, yet QC information is still typically stored in tool-specific, poorly interoperable formats that hinder comparison, reuse, and transparent reporting. We present mzQC, a community-developed standard from the HUPO Proteomics Standards Initiative for the compact, machine-readable representation of QC metrics and their associated metadata across mass spectrometry workflows. mzQC is implemented in JSON, organized to support both individual mass spectrometry acquisitions and collections thereof, with formal QC metrics definitions supported by controlled vocabularies to ensure unambiguous metric interpretation and semantic consistency. The format is supported by validation tools and reference libraries in Python, R, and Java, facilitating integration into existing software ecosystems. We demonstrate the utility of mzQC across diverse analytical modalities and QC settings, spanning longitudinal instrument monitoring, acquisition-method evaluation, study-level quality assessment, repository-scale data characterization, and spatially resolved mass spectrometry imaging. Together, these use cases show that mzQC provides not merely a file format, but a shared foundation for interoperable QC reporting, large-scale data assessment, and more rigorous, reproducible, and reusable mass spectrometry-based research.

bioinformatics↗

bioRxiv2026

Migrasomes May Originate from Cilia and Represent an Alternative Ciliary Form

Abstract Background Migrasomes, the newly discovered vesicular organelles, have long been speculated to originate from membrane dynamics during cell migration. Here we present integrated imaging and multi-omics evidence supporting a ciliary origin of migrasomes. The shared vesicular trafficking pathways between ciliogenesis and migrasome biogenesis (trans-Golgi/endosomal systems) prompted us to investigate their spatiotemporal coupling mechanism in disease models. Methods Using high-resolution SEM and fluorescence confocal microscopy (FCM), we visualized cilium-like structures with enlarged tips adjacent to migrasome-like vesicles across multiple cell types. TMT-based quantitative proteomics was used to identify proteins shared among migrasomes from different cell types and examine their associations with ciliary proteins. DMBA-induced breast cancer and femoral fracture models were used to investigate the cilia-migrasome association during tumor metastasis and fracture healing. Results Bioinformatics analysis showed a highly positive incidence correlation between cilia and migrasome genes in 31 types of 7858 human normal tissues and organs and various cell types. In 32 cancer tissues, cilia and migrasome genes were still strongly but abnormally correlated. Signaling enrichment by ARL13B and TSPAN4 showed that cilia-migrasome association is related to epithelial-mesenchymal transition (EMT). By analyzing the ARL13B and PIGK expression, we found the abnormal cilia-migrasome association in metastatic breast cancer and positive cilia-migrasome association in fracture healing bone. Conclusion Our findings support a ciliary origin of migrasomes, pointing to a previously unrecognized pathway of organelle biogenesis. Notably, the ciliary-migrasomal association correlates with two distinct pathological/physiological contexts: (1) aberrant epithelial-mesenchymal transition (EMT) in metastatic breast cancer, and (2) accelerated regeneration during fracture healing and tissue repair. This dual correlation not only establishes a mechanistic link between ciliary function and migrasome biogenesis but also highlights their divergent roles in disease progression versus tissue homeostasis. Investigating the spatiotemporal dynamics of this association may provide novel therapeutic targets for metastatic malignancies and regenerative medicine.

cell biology↗

bioRxiv2026

The Spliceosome Scaffold Component BCAS2 Promotes Pancreatic Cancer Progression through Weak 5 Splice Site Dependent Splicing Regulation

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies. Dysregulated RNA splicing has emerged as a critical mechanism contributing to PDAC progression. However, whether structural components of the spliceosome regulate oncogenic alternative splicing was not known. Here, we identify the nineteen complex (NTC) component BCAS2/SPF27 as a critical regulator of PDAC progression. Elevated expression of BCAS2 in PDAC is associated with poor patient outcomes. Transcriptomic analyses revealed that BCAS2 specifically regulates alternative exons with weak splice sites. In particular, BCAS2 promotes SOS1 exon 21 inclusion and consequently RAC-signaling activation. Furthermore, splice-switching antisense oligonucleotide (ASO) mediated skipping of SOS1 exon 21 suppressed PDAC proliferation and migration. Our findings uncover a role of BCAS2 in the regulation of weak splice site usage and identify the BCAS2/SOS1/RAC signaling axis as a potential therapeutic vulnerability in pancreatic cancer.

cancer biology↗

bioRxiv2026

Epigenetic regulators partition the genome by evolutionary and developmental constraint

Many epigenetic regulators play essential roles in animal development, but precisely how they function across different cell types without clear sequence preferences remains a foundational challenge. Here, we employed single-cell RNA sequencing to survey the mutant phenotypes of 30 essential regulatory pathways across over 450 gastrulation stage mouse embryo replicates, including essential factors associated with repressive chromatin states, RNA surveillance/processing, and other genomic roles. We then use this integrated manifold to partition mutant responses into a developmentally-resolved interaction network, revealing a hierarchy of heterochromatin-associated interactions that act orthogonally to Polycomb Repressive Complex-mediated control of embryo patterning. Compared to the embryo proper, we find that the developing placenta and yolk sac can accommodate broad swings in repetitive element expression, a resilience in keeping with the relative evolutionary recency and phenotypic plasticity of these tissues. Dense temporal sampling of Human Silencing Hub (HUSH) mutant embryogenesis further supports the notion that the gastrulating embryo is particularly constrained and depends on multiple layers of insulation, including the need to suppress evolutionarily young genetic elements to stably license highly conserved, phylotypic programs. In combination, our work highlights the power of single cell-resolved developmental genetics to contextualize the roles of epigenetic regulators, which restrict genomic action to support robust cellular identities and embryological forms.

developmental biology↗

bioRxiv2026

An age-preserving neuronal iSpheroid platform for modeling human aging and Alzheimer disease

Aging is the strongest risk factor for Alzheimer disease (AD), yet existing human neuronal models either erase age-associated features during reprogramming or fail to recapitulate three-dimensional organization of human neuronal tissue. Here, we establish directly induced neuronal spheroids (iSpheroids), a scalable three-dimensional platform generated by direct conversion of primary fibroblasts without pluripotency. iSpheroids generate long-lived, electrophysiologically active neurons from young, unimpaired aged, and sporadic AD donors while preserving donor-specific epigenetic age. Single-nucleus RNA sequencing revealed approximately 96% of cells acquired a neuronal identity and were distributed across multiple neuronal states, including a diversity of neurons. The platform supports incorporation of astrocytes and microglia and generation from non-human primate fibroblasts. AD iSpheroids spontaneously recapitulated neuronal degeneration, amyloid-beta; accumulation, progressive Tau pathology, and metabolic dysfunction. Integrated proteomic, metabolomic, and lipidomic profiling distinguished physiological aging from AD and revealed disease-associated metabolic remodeling. Oxaliplatin shifted AD iSpheroids toward oxidative metabolism, whereas a multi-compound screen identified trametinib as a modulator of inflammatory and age-associated programs.

neuroscience↗

bioRxiv2026

Compartmentalized Nanozyme Transduction Enables Regenerative Molecular Amplification for Multiplexed miRNA-Based Prostate Cancer Stratification

Circulating microRNAs (miRNAs) have emerged as promising liquid biopsy markers; however, their clinical translation is restricted by low abundance, biological heterogeneity, and the complexity of multiplex profiling. Herein, we develop a targeted cycling-mediated duplex-specific nuclease (DSN)-nanozyme signal amplification platform (TC-DSN-Nano) that establishes a compartmentalized catalytic transduction strategy for multiplexed miRNA analysis. By encapsulating gold nanozymes within liposomal nanoreactors, this platform spatially separates molecular recognition from catalytic signal generation, preserving nanozyme activity during sensor construction. Upon target miRNA recognition, DSN-mediated recycling induces regenerative release of nanozyme-loaded liposomes from magnetic substrates, converting individual miRNA molecules into amplified catalytic outputs without conventional nucleic acid amplification. The platform enables programmable profiling of six prostate cancer (PCa) associated miRNAs in serum samples. Furthermore, machine learning-assisted integration of multiplexed miRNA signatures enables accurate discrimination among healthy donors, nonmetastatic PCa patients, and metastatic PCa patients, achieving an overall classification accuracy of 90.5%. This work establishes a general compartmentalized nanozyme transduction framework that integrates molecular recycling, catalytic amplification, and computational analysis for liquid biopsy-based cancer stratification.

bioengineering↗

bioRxiv2026

Multiplexed hormone immunoassays for women's health on a regenerable silicon photonic chip

Hormone dynamics are central to a multitude of conditions in women's health; however, limitations in the cost, convenience, and multiplexing capacity of current hormone assays preclude routine longitudinal hormone testing. This limitation severely restricts our understanding in this historically neglected field, presenting a need for improved bioanalytical tools to support hormone-informed care. Silicon photonic resonator sensors have excellent multiplexing capacity and scalable fabrication, and offer strong potential to meet this important need. Here we demonstrate, for the first time, multiplexed silicon photonic detection of two urinary hormone biomarkers, follicle-stimulating hormone (FSH) and pregnanediol-3-glucuronide (PdG), using sub-wavelength grating ring resonators and a polydopamine-based, regenerable surface chemistry. We combine a sandwich immunoassay for FSH and an antigen-down competitive immunoassay for PdG on the same chip, both amplified using a commercially available quantum-dot-streptavidin conjugate and with on-chip regeneration over multiple measurement cycles. In artificial urine, this proof-of-principle multiplexed assay achieves limits of detection of 0.594 ng/mL for FSH and 19.1 ng/mL for PdG. This architecture is inherently scalable to tens of hormone targets on a millimetre-scale chip (a >10x multiplexing improvement over typical lateral-flow immunoassays) enabling future low-cost, quantitative at-home hormone panels that could transform research, diagnostics, and treatment in women's health.

bioengineering↗

bioRxiv2026

Brain state shapes the polarity of pulsed infrared neural stimulation responses in individual cortical neurons

Pulsed infrared neural stimulation (INS, 1875nm the peak of energy absorption by water) is a non-viral method developed to activate single submillimeter sites in the brain. When used in ultrahigh-field fMRI, it reveals functionally specific brain-wide columnar networks comprising synaptically activated nodes. INS is non-damaging and effective for use in the human cortex and is useful for neural and behavioral neuromodulation in primates. To investigate how physiological state influences its cellular effects, we performed in vivo two-photon calcium imaging with GCaMP6s in mice and tracked identified cortical neurons in awake vs anesthetized states. Across the tested radiant exposures, INS-evoked responses differed markedly between states: under anesthesia, stimulation produced predominantly positive-going calcium responses, whereas during wakefulness the same identified neurons exhibited negative-going responses. Pharmacological manipulation of this baseline level by GABAergic signaling shifted response polarity in opposite directions: picrotoxin under anesthesia produced awake-like negative responses, whereas muscimol during wakefulness produced anesthetized-like positive responses. Trial-by-trial analyses further showed that the relationship between pre-stimulus baseline level and INS-evoked response depended on physiological state. Because INS relies on transient tissue heating, we also developed an in situ EGFP-based calibration approach to estimate temperature-related fluorescence changes. These fluoro-thermal contributions were modest at lower radiant exposures and became increasingly important at higher exposures, particularly near the fiber pathway. The low-intensity results are consistent with, but do not establish, a state-dependent feed-forward inhibitory framework. Together, these findings show that the neuronal response to focal INS is shaped by ongoing brain state and provide a practical framework for separating state-dependent calcium responses from temperature-related fluorescence effects, making INS a potentially versatile tool for neuroscience and clinical applications.

neuroscience↗

bioRxiv2026

USP20 Stabilizes FABP5 to Drive Macrophage Foam Cell Formation and Atherosclerosis

Background: Macrophage foam cell formation is a central event in atherosclerosis. Although protein ubiquitination is increasingly recognized as a regulator of macrophage lipid handling, whether deubiquitinating enzymes directly control lipid uptake and metabolic remodeling during atherogenesis remains unclear. Methods and Results: Here, transcriptomic profiling identified ubiquitin-specific protease 20 (USP20) as a previously unrecognized regulator of macrophage foam cell formation. Genetic and pharmacological studies demonstrated that USP20 promoted macrophage lipid accumulation and foam cell formation, whereas macrophage-specific Usp20 deficiency markedly attenuated atherosclerotic lesion formation, lipid deposition, and macrophage accumulation in mice. To elucidate the underlying mechanism, integrative analysis of USP20-interacting proteins and proteomic alterations in Usp20-deficient macrophages identified fatty acid-binding protein 5 (FABP5) as a substrate of USP20. Mechanistically, USP20 interacted with FABP5 and stabilized its protein abundance by preventing ubiquitin-dependent proteasomal degradation. Consequently, USP20-mediated stabilization of FABP5 enhanced PPAR{gamma} occupancy at the Cd36 promoter, thereby increasing Cd36 transcription, ox-LDL uptake, and foam cell formation. Accordingly, Fabp5 knockdown abolished USP20-induced CD36 expression, ox-LDL uptake, and foam cell formation, whereas pharmacological activation of PPAR{gamma} restored CD36 expression in Fabp5-deficient macrophages. Finally, macrophage-targeted delivery of the USP20 inhibitor GSK2643943A markedly reduced atherosclerotic burden without evident systemic toxicity, supporting the therapeutic potential of targeting USP20 in atherosclerosis. Conclusions: USP20 promotes macrophage foam cell formation by stabilizing FABP5 and enhancing PPAR{gamma}-dependent Cd36 transcription. Targeting the USP20-FABP5-PPAR{gamma}-CD36 axis may represent a therapeutic strategy to limit macrophage lipid accumulation, metabolic dysfunction, and atherosclerosis progression.

cell biology↗

bioRxiv2026

A brain locus for viable gestation

The expectant mother's body is systemically remodeled by her hormones to weather the physiological vicissitudes of pregnancy. In contrast to other reproductive organs, how the expectant mother's brain promotes these system-wide changes is largely unexplored. Here we show that pregnancy induces profound changes in gene expression and identity of hormone-sensitive neurons and report a previously unknown class of such cells that is required for viable pregnancy. We performed RNA sequencing from late mid-gestation mice of four estrogen receptor alpha-expressing populations from hypothalamus and amygdala that regulate reproductive behaviors altered during gestation. Each of these populations undergoes such large, specific transcriptional shifts during pregnancy that these changes even exceed their transcriptional differences between the sexes. The gene expression changes during pregnancy also imbue particular transcriptomically-defined neuronal types within these four populations with new molecular identities. Targeted ablation of one such neuronal type, POANpy2r cells, precludes implantation and abrogates viable pregnancy. Taken together, we have uncovered an essential role of hormone-sensitive neurons in the brain in sustaining pregnancy. The etiology of spontaneous gestational loss, which afflicts ~15% of human pregnancies, remains idiopathic in many cases, and our findings suggest a brain-based mechanism that contributes to such events. More broadly, we provide a molecular and cellular foundation to study gestational processes in health and disease from the perspective of the pregnant brain-body axis.

neuroscience↗

bioRxiv2026

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

Despite long-standing epidemiological associations, the mechanism linking folate availability to gestational neural tube defects remains unclear, partly because measuring and interpreting metabolic activity in dynamic biological systems remains challenging. Here, we apply a deep-learning-based graph-guided variational autoencoder (MeRN; Metabolic Representation Network) to infer single-cell metabolic activity and states from scRNA-seq data of mouse embryogenesis. By analyzing folate-deficient embryogenesis from E7.0 to E9.0, we identify a transient state within the nascent neural lineage that is acutely sensitive to folate availability, leading to an interconnected disruption between key bioenergetic pathways and de novo purine biosynthesis. Moreover, metabolically induced growth defects lead to permanent morphological disruptions along the dorsal-ventral axis, which we confirm by generating whole-embryo fate maps using a prime-editing-based lineage recorder (PEtracer). Collectively, our results establish a highly scalable framework for interpreting dynamic changes in embryonic metabolism and elucidating the mechanistic bases underlying environmentally linked congenital disorders.

genomics↗

bioRxiv2026

Hierarchical chromatin polyvalency governs robust gene regulation and organogenesis

Precise temporal control of gene expression is fundamental for embryonic development, yet the epigenetic and chromatin basis governing transcriptional timing remain poorly understood. The bivalency model, characterized by coexistence of H3K4me3 and H3K27me3, has been proposed to mark a poised state ready for activation. However, this model has been challenged by lacking of rapid gene activation in response to H3K27me3 depletion, suggesting that the H3K27me3 mark is not responsible for the silencing. Here, through temporal epigenomic profiling of post-implantation mouse embryos and use of the protein degradation tag (dTAG) system, we demonstrate that H2Aub, but not H3K27me3, functions as the major repressor. We further reveal a hierarchical repression architecture in which H2Aub is responsible for transcriptional silencing, while H3K27me3 and H3K9me3 serve to reinforce the silencing state in post-implantation embryos. Functionally, disruption of this H2Aub-centered hierarchy perturbs temporal control of polyvalent gene activation, leading to severe organogenesis defects. Mechanistically, acute loss of H2Aub disrupts retinoic acid-FGF signaling pathway, causing somitogenesis arrest. Together, our findings establish chromatin polyvalency model as a multi-layered, hierarchical repression mechanism that governs temporal control of gene expression during embryogenesis.

genetics↗

bioRxiv2026

Widespread detection of Polyethylene glycol reveals chronic human exposure through pharmaceutical drugs

Polyethylene glycol (PEG) is a synthetic polymer ubiquitous in pharmaceuticals, personal care products, food additives, and industrial manufacturing. Despite its widespread use and potential importance as an exposure chemical, the prevalence of PEG exposure and its excretion in human populations remain largely uncharacterized. Moreover, PEG detected in human biofluids is frequently assumed to arise from analytical contamination during sample preparation, potentially obscuring its contribution to the human exposome and confounding metabolic phenotyping studies. Here, we show that PEG is as component of the human xenobiotic exposome and is further metabolized into PEG hydoxy acid and diacid metabolites in humans. We further find that PEG exposure is associated with alterations in microbiome composition and short-chain fatty acid metabolism, suggesting its biological impact of its exposure. We identify PEG exposure in approximately 2.3% of publicly available metabolomics data files and provide a reusable 85,484 candidate PEG and PEGylated MS/MS spectral library for future use for the metabolomic community. Together, these findings establish PEG signal in human biofluids can reflect genuine exposure, and that PEG exposure is neither metabolically inert nor biologically silent.

biochemistry↗

bioRxiv2026

A Hybrid Residual-Swin Transformer Design with Attention for Prostate Cancer Segmentation

Prostate cancer, a leading cause of cancer-related deaths among men globally, necessitates the development of precise diagnostic and treatment strategies. Accurate segmentation of prostate cancer in medical imaging, particularly in MRI scans, is crucial for early diagnosis and clinical decisions. Traditional manual segmentation techniques, while efficient, are labor-intensive and necessitate significant expertise, resulting in an increasing demand for automated alternatives. The RSAUNet is a novel deep learning architecture designed to improve prostate cancer segmentation. It incorporates essential components, including Residual Blocks, Swin Transformer Blocks, and Attention Mechanisms within a U-Net architecture. This markedly enhances the model's capacity to discern complex anatomical features and accurately segment malignant tissues. Using sophisticated deep Learning methods, RSAUNet addresses the complexities of prostate imaging, delivering reliable, consistent segmentation results. The model was evaluated against various cutting-edge techniques on extensive multi-parametric MRI datasets, attaining an impressive Dice coefficient (DC) of 0.998 and a Jaccard Index (IoU) of 0.965. These findings highlight the innovative characteristics of RSAUNet and its capacity to transform prostate cancer diagnosis and treatment strategies. The proposed model surpasses current methods and shows potential for practical clinical applications, providing an efficient, precise, and scalable solution for automated prostate cancer segmentation and fostering optimism for the future of medical imaging and diagnosis.

cancer biology↗