Biology subjects

Zhu, M.

Publications and source records attributed to Zhu, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Spatial profiling of protein-DNA interactions is essential for understanding gene regulatory processes, but current methods suffer from low sensitivity, limited resolution, and complex workflows. Here we introduce Super-CUT&Tag (Solid-phase interface embedded with an Ultra-dense DNA barcode array to Profile Epigenomic landscapes for spatially Resolved CUT&Tag), a robust spatial epigenomic method that directly transfers in situ protein-DNA interactions from tissue sections onto a pre-fabricated spatially barcoded array. Incorporating 3D polyamidoamine (PAMAM) dendrimers markedly improves chromatin capture efficiency, achieving several-fold higher sensitivity compared to current spatial CUT&Tag approaches. Using Super-CUT&Tag, we profile H3K27ac spatial landscape and uncover previously hidden active-chromatin heterogeneity across mouse embryonic tissues and stages. Integration with spatial transcriptomics further reveals spatiotemporal enhancer regulation dynamics of Neurod2 during corticogenesis. By overcoming key bottlenecks in sensitivity, resolution and usability, Super-CUT&Tag establishes a powerful platform for spatial epigenomic profiling in complex tissues.

genetics↗

bioRxiv2025

Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation

Despite recent advances in technology to map RNA chemical modifications transcriptome-wide, the distribution of N{superscript 1}-methyladenosine (m{superscript 1}A) in mRNA remains contested, hindering a clear understanding of its function. Additionally, the enzyme(s) that installs the majority of reported mRNA m1A sites has yet to be identified. In this study, we characterized TRMT61B, an m1A methyltransferase known to methylate mitochondrial RNAs, but whose sequence preferences have been underexplored. By integrating cellular overexpression of TRMT61B and in vitro methylation of a synthetic pool of diverse human RNA sequences, we identified a preference for a YMRA consensus motif in single stranded RNA regions. In these experiments, TRMT61B methylated thousands of novel human mRNA sites, revealing activity on cytosolic mRNAs. We used these novel m1A-modifiable sequences to test the effects of m1A on translation of luciferase reporters and on ribosome recruitment to modified transcripts in the pool. We found that m1A addition can significantly affect translation and ribosome recruitment, but that these effects are vary by transcript. Taken together, our results can inform future studies of TRMT61B and mRNA, and emphasize that studies of m1A regulation of mRNA must be carried out and interpreted in a highly context-aware manner.

biochemistry↗

bioRxiv2025

Exploring the potential value of aloe active components in inhibiting non-small cell lung cancer through network pharmacology

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide, and its management is challenged by profound molecular heterogeneity and inevitable resistance to targeted therapies. Natural products offer a valuable reservoir for anticancer drug discovery, yet the therapeutic potential of Aloe vera--a medicinal plant rich in structurally diverse bioactive compounds--remains insufficiently characterised in the context of NSCLC. Here, we employed an integrated strategy combining network pharmacology, protein-protein interaction analysis, Gene Ontology and KEGG enrichment, molecular docking, and 100-ns molecular dynamics simulations to comprehensively elucidate the multi-target and multi-pathway regulatory mechanisms of Aloe vera active constituents against NSCLC. We identified 369 aloe-derived targets and 5519 NSCLC-related genes, with 268 overlapping targets enriched in pathways involving EGFR signalling, PI3K/AKT/mTOR activation, p53 regulation, inflammation, apoptosis, and drug-resistance networks. Core hub genes included TP53, EGFR, AKT1, and STAT3. Molecular docking demonstrated strong spontaneous binding between key aloe compounds (such as aloe-emodin, aloeresin C, quercetin and sitosterols) and wild-type EGFR, mutant EGFR T790M/C797S, AKT1, and p53. Molecular dynamics simulations confirmed stable ligand-protein interactions, favourable hydrogen-bonding networks, and energetically favourable binding free energies. Collectively, our findings reveal a systematic, multi-level regulatory landscape through which Aloe vera may exert anti-NSCLC effects and highlight several candidate molecules with potential to enhance therapeutic efficacy or overcome EGFR-TKI resistance. This study provides a solid theoretical framework for subsequent experimental validation and the development of novel aloe-derived anticancer agents with low toxicity.

bioinformatics↗

bioRxiv2025

Hidden-driver inference reveals synergistic brain-penetrant therapies for medulloblastoma

Effective therapies for high-risk medulloblastoma (MB), particularly MYC-driven Group 3 (G3) MB, remain elusive due to limited druggable mutations, poor blood-brain barrier (BBB) penetration, and rapid resistance. We developed SINBA (Synergy Inference by Data-driven Network-Based Bayesian Analysis), a systems biology framework that computationally prioritizes synergistic, BBB-permeable drug combinations by identifying hidden drivers sustaining oncogenic programs. Integrating MB-specific networks, transcriptomic data, and drug-gene interactions, SINBA nominated 32 candidates, of which 19 were experimentally validated as synergistic. Through iterative prioritization and experimental refinement, the MEK inhibitor mirdametinib and p38 inhibitor regorafenib emerged as the top brain-penetrant pair, suppressing G3 MB progression and extending survival in xenograft and immunocompetent models, with efficacy enhanced by low-dose radiation. Single-cell analysis revealed selective targeting of developmental origins and immune reprogramming. These findings establish SINBA as a computationally assisted discovery framework for clinically actionable combinations in high-risk MB.

cancer biology↗

bioRxiv2025

Optimization of fermentation conditions for Metarhizium robertsii and its effect on rice growth

Metarhizium robertsii is an important entomopathogenic fungus and plant endophyte, possessing dual functionality as both an insecticide and a plant growth promoter, which has led to its widespread application in agriculture. However, the effects and underlying mechanisms of M. robertsii (MAA)in promoting rice growth remain poorly understood. This study confirmed the growth-promoting effects of MAA and its fermentation supernatant on rice. Based on single-factor and response surface methodology experiments, the fermentation conditions of MAA were subsequently optimized using rice root length as a key indicator, and the potential mechanisms behind this growth promotion were preliminarily investigated. The results demonstrated that both MAA and its fermentation supernatant exerted significant growth-promoting effects on rice. Sucrose and peptone were identified as the optimal carbon and nitrogen sources, respectively. The most pronounced effect was observed when the fermentation supernatant, produced under the conditions of pH 6.0, 0.2% {beta}-Ala, and 100 mol/L Al2(SO4)3, was applied, resulting in a 21.7% increase in rice root length compared to the control group. Furthermore, significant enhancements in chlorophyll content and denser root hairs were recorded in rice treated with the MAA fermentation supernatant, with the chlorophyll content increasing by 28.17% compared to the control. These findings provide a theoretical basis for the development and application of green and efficient bio-inoculants. IMPORTANCEMetarhizium robertsii is an endogenous plant fungus that can be effective for efficient insect control, but the plant-promoting effect of this fungus and its related studies are less reported. The colonization ability and growth promotion effect of Metarhizium robertsii on different crops vary. In this study, a sterile hydroponic system for rice was established. The research found that Metarhizium robertsii can colonize the root system of rice, significantly promoting rice growth, and its growtion-promoting effect is affected by the differences in its fermentation products. After the optimization of the response surface of the fermentation conditions of Metarhizium robertsii, its growth-promoting ability increased by 21.7%. Developing microbial biofertilizers/biopesticides as a basis for reducing chemical inputs in rice cultivation.

microbiology↗

bioRxiv2025

Anatomical integrity of the human cochlea estimated with optical coherence tomography for future clinical application

The human cochlea is encased within the otic capsule, the densest bone in the body, posing significant challenges for anatomical imaging of cochlear structures. Because of difficult access and fragility of cochlear structures, our understanding of intracochlear anatomy has historically relied on postmortem histology. We thus have a limited understanding of human cochlear anatomy in its native, unfixed state. Clinical diagnostics for hearing loss, such as audiometry and otoacoustic emissions, offer functional assessments but fail to elucidate the often diverse underlying structural pathologies with any degree of precision. To address the critical need for assessing the human cochlear anatomy and associated pathologies without the risk of traumatizing cochlear structures, we imaged fresh cochleae in situ soon after death through the intact round window membrane with Optical Coherence Tomography (OCT) without inserting instruments inside or opening the cochlea. Micron-resolution OCT cross-sectional images of the human intracochlear structures were acquired and compared with corresponding histology systematically to aid in the identification of fine structural features and possible pathologies. With OCT imaging, we observed varied anatomy of the organ of Corti, and developed a cochlear "integrity" rating system to differentiate healthy appearing cochleae from various pathological states. These results demonstrate the capability of OCT to non-traumatically visualize cochlear integrity, highlighting its potential as a diagnostic tool. This work shows promise in translating the ability to determine the likelihood of existing or lack of hair cells and supporting cells in live patients, which would enable appropriate targeted treatments.

physiology↗

bioRxiv2025

A paradigm shift of SERPINA3N in neurobehavioral development and brain injury

Murine serine protease inhibitor clade A member 3N (SERPINA3N) and its human ortholog SERPINA3 are dysregulated in neurological disorders. SERPINA3N has been proposed as a protective factor, enhancing neurobehavioral development under homeostasis and mitigating neuronal/glial and vascular damage under neurological conditions. Here, we employed powerful, non-invasive genetic tools to revisit the concept of SERPINA3N in brain development and injury. Brain-specific SERPINA3N overexpression neither alters neuronal or glial development nor improves cognitive ability under homeostasis. In stark contrast, SERPINA3N drives a pro-inflammatory response to brain injury and exacerbates blood-brain barrier dysfunction. Its overexpression promotes neurodegeneration through apoptosis-mediated neuronal loss and disrupts oligodendroglial differentiation and myelination following neonatal brain injury. Collectively, our findings challenge the prevailing paradigm of SERPINA3N in neurodevelopment and injury, revealing that while SERPINA3N is dispensable for neurobehavioral development, it aggravates neural injury and vascular damage under pathological conditions.

neuroscience↗

bioRxiv2025

The abscisic acid could reverse the cuproptosis in sepsis-associated acute kidney injury through the inhibition of ferredoxin-1

Sepsis-associated acute kidney injury (S-AKI) is a grave clinical condition with a poor prognosis. Prior studies have observed a potential correlation between copper (Cu) and S-AKI, though the underlying mechanisms remain to be fully elucidated. The present study aims to investigate the underlying mechanism between Cu and renal dysfunction under sepsis conditions. Utilizing a cecal ligation and puncture (CLP) murine model, we observed a substantial upregulation of inflammatory factors and deteriorated renal function (p<0.05), concomitant with an augmented mortality rate (p<0..05). Concurrently, the renal tissue exhibited a series of pathological manifestations, including fibrosis and cell death. Concurrently, the expression of the cuproptosis-regulating protein FDX-1 (p<0.05) was found to be elevated in CLP mice. Collectively, these data indicated the activation of cuproptosis in CLP-induced S-AKI. Intriguingly, the application of abscisic acid (ABA), a FDX-1 inhibitor, led to a substantial alleviation of mortality rate and inflammatory factor level (p<0.05). Furthermore, a significant alleviation was observed in renal pathology and biofunction (p<0.05). Collectively, these observations suggest that ABA exerts a protective effect on renal function during cuproptosis promoted S-AKI. Consequently, it can be concluded that ABA has the potential to reverse cuproptosis in S-AKI by inhibiting FDX-1.

molecular biology↗

bioRxiv2025

Integrated Histology and Molecular Profiling of Postmortem Human Auditory and Vestibular Organs via a Poly(Methyl Methacrylate)-Based Workflow

Hearing and balance disorders are the most prevalent sensory impairments, affecting hundreds of millions worldwide, yet their underlying cellular and molecular pathologies remain poorly understood. This knowledge gap stems from the inaccessibility of the ears sensory organs--embedded within the temporal bone (TB), the hardest bone in the body--which cannot be biopsied in living patients without causing irreversible damage. Conventional histopathology workflows rely on postmortem en bloc extraction of TBs, followed by lengthy decalcification, celloidin embedding, and manual serial sectioning of these large specimens--a process that takes one to two years, is labor- and cost-intensive, and lacks compatibility with most modern protein, DNA, and RNA assays. Here, we present a rapid, reversible polymethyl methacrylate (rPMMA) workflow that enables advanced molecular histopathology studies on formalin-fixed, calcified TBs. Our protocol uses low-temperature (-40 {degrees}C to +4 {degrees}C) resin embedding, precision near-serial sectioning (10-50 {micro}m) via femtosecond laser microtomy or precision diamond wire sawing, and subsequent deacrylation to fully restore tissue accessibility for high-fidelity histomorphology, multiplexed immunofluorescence, whole-genome sequencing, and in situ mRNA detection (RNAscope) assays. Compared to the gold-standard celloidin workflow, our method reduces processing time and costs by approximately 90% while integrating equivalent histomorphology with advanced molecular assays, providing a new benchmark for multidimensional studies in human hearing and balance pathologies.

pathology↗

bioRxiv2025

Development and application of a genotyping by target sequencing SNP array panel in Salix suchowensis

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a genotyping by target sequencing SNP array panel to facilitate efficient genotyping. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.

genetics↗

bioRxiv2025

Gut Microbiota Dysbiosis and Short-chain Fatty Acid alterations in Pediatric New-Onset Type 1 diabetes with Ketoacidosis

ObjectiveDiabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication with a relatively high mortality rate among children diagnosed with type 1 diabetes (T1D). Previous studies have shed light on gut dysbiosis in newly-onset T1D children, but research targeting the gut microbiota and microbial metabolites in patients with DKA remains scarce. MethodsShotgun metagenomic analysis was conducted on fecal samples from 96 newly diagnosed T1D children, including 32 patients who presented with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative analyses were performed on the gut microbiome and SCFA levels between DKA and non-DKA subgroups. ResultsGut microbiota composition differed between DKA and non-DKA groups. While alpha-diversity remained consistent, beta-diversity showed marked differences between the two groups, and the phyla Firmicutes and Bacteroidetes exhibited predominance in the DKA group. DKA was associated with increased potential pathogens and a significant depletion of SCFA-producing genera (Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus), accompanied by reduced SCFA levels. Further correlation analysis revealed strong associations between SCFAs, SCFA-producing microbiota, and disease severity indicators. Propionic acid and butyric acid mediated the association between SCFA-producing bacteria and DKA. ConclusionThis study first reported reductions in SCFAs and SCFA-producing bacteria in the fecal samples of T1D children at DKA onset. Our findings highlight SCFAs and their producers as protective biomarkers of DKA and suggest that targeting gut microbiota and SCFA metabolism may offer a potential therapeutic strategy for DKA. ImportanceWhile gut microbiota imbalances have been linked to type 1 diabetes (T1D), little is known about the role of gut microbes and their metabolites during acute diabetic ketoacidosis (DKA), an acute and life-threatening complication. This study examined the gut microbiome and levels of short-chain fatty acids (SCFAs) in fecal samples from children with new-onset T1D with and without DKA. DKA was characterized by distinct microbial signatures, including increased potential pathogens, a loss of beneficial SCFA-producing bacteria, and consistently lower SCFA levels. These changes closely correlated with indicators of disease severity, and further mediation analysis revealed the role of SCFAs in linking gut microbiota to DKA. These findings suggest that SCFAs and their producers may serve as protective markers for DKA, highlighting the potential of microbiome-based interventions to improve outcomes in children facing this critical complication.

microbiology↗

bioRxiv2025

Dysregulated Proline Metabolism Contributes to Subretinal Fibrosis in Neovascular AMD: Therapeutic Potential of Prolyl-4-Hydroxylase Inhibition

Subretinal fibrosis, a major cause of irreversible vision loss in neovascular age-related macular degeneration (nAMD), is driven by excessive deposition of extracellular matrix such as collagens. While proline metabolism is known to play a critical role in collagen biosynthesis and fibrosis, its involvement in subretinal fibrosis remains unclear. Here, we characterized the progression of fibrovascular lesions in JR5558 mice, observing significant molecular alterations as early as 4 weeks of age and phenotypic changes by 8 weeks. Transcriptomic and metabolomic analyses revealed elevated levels of 4-hydroxyproline, an essential component of collagen, alongside significant alterations of other fibrosis-related pathways. P4HA1, a catalytic subunit of prolyl-4-hydroxylase essential for 4-hydroxyproline biosynthesis, was prominently expressed in fibrotic lesions in retinas of JR5558 and two-stage laser-induced murine models, as well as human eyes with nAMD. Targeting P4HA1 with the small-molecule inhibitor diethyl pythiDC significantly attenuated fibrovascular lesion growth in the JR5558 murine models and reduced collagen turnover in human retinal pigment epithelium cells. Combining diethyl pythiDC with aflibercept had a stronger antifibrotic effect than monotherapies in JR5558 mice. These findings suggest a key contribution of proline metabolism, particularly proline hydroxylation, in subretinal fibrosis. Inhibiting P4HA1 with diethyl pythiDC inhibited fibrosis in the models we studied, offering a novel therapeutic strategy. Further research is warranted to explore the potential benefits of combining existing anti-angiogenic therapies with drugs that inhibit proline metabolism for the management of nAMD-associated fibrosis.

neuroscience↗

bioRxiv2025

Single-Cell eQTL Mapping Reveals Cell Type-Specific Genetic Regulation in Lung Cancer

Genome-wide association studies (GWAS) have identified over 50 lung cancer risk loci; however, the precise cellular context of these genetic mechanisms remains unclear due to limitations in bulk tissue eQTL analyses. Here, we present the largest single-cell eQTL atlas of human lung tissue to date, profiling 222 donors using multiplexed scRNA-seq. We identified 16,785 eQTLs across 17 cell types, with over 90% of sc-eQTLs and 59% eGene being cell-type-specific, and fewer than 23% were detectable in paired bulk datasets. Integration with GWAS for non-small cell lung cancer highlighted epithelial and immune cells as key contributors to genetic susceptibility, identifying 28 candidate genes within known risk loci and 24 in novel regions. Notably, 47% of established NSCLC susceptibility loci exhibited cell-type-specific pleiotropic genetic regulation. This study provides a valuable resource of lung sc-eQTLs and illuminates how genetic variation modulates gene expression in a cell-type-specific fashion, contributing to lung cancer susceptibility.

genetics↗

bioRxiv2025

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most significant diseases affecting global wheat production. Breeding for disease resistance (R) genes against Bgt often follows a boom-bust cycles, where cultivars with effective resistance are widely deployed on an expanding area until virulence emerges in the avirulence (Avr) pathogen population. While extensive effort has been devoted to identifying and cloning R genes, Avr genes remain relatively understudied, limiting our understanding of R-Avr interactions. That said, understanding R-Avr interactions is crucial for developing durable resistance strategies. ResultsWe conducted whole genome sequencing on 245 Bgt isolates collected from major wheat-growing regions in China, identifying 120 genetically unique isolates. Each of these unique isolates was inoculated and phenotyped on a diverse panel of wheat germplasm. Through Genome-Wide Association Analysis (GWAS) in both Bgt and wheat, we identified 65 Avr loci and 251 R loci overlapping with nine and eight cloned Avr or R genes, respectively. On average, each isolate carries eight Avr alleles, ranging from one to 17. Little geographical preference for Avr alleles or their combinations was observed, suggesting that disease resistance breeding against this pathogen should be coordinated at the national level. The level of resistance level is positively correlated with the number of R alleles carried by a wheat line, and the average frequency of an R allele is 2% among the wheat panel, indicating the potential for accumulating R alleles in breeding programs. We mapped 212 R-Avr interactions based on joint GWAS using both plant and pathogen genomes and cross-species epistasis, where a network of interactions was formed between wheat and Bgt. These interactions indicate that pyramiding five major R loci has the potential to confer resistance to half of the Avr loci. As a proof of concept, we successfully verified two previously described R-Avr pairs using tobacco experiments. Furthermore, we provided molecular validation evidence for three new Avr genes, including Bgt-50651, BgtE-5826 and BgtE-20009, and two new R-Avr interactions. Among them, Bgt-50651 interacts with Pm1a, Pm2a, and another unidentified R gene located near the Pm6/Pm52 interval. ConclusionOur study provides a framework for understanding the genetic interaction between plants and pathogens. The discovery of novel R/Avr loci and their complex interaction network underscores the need to integrate crop and pathogen genetic background, particularly the R/Avr allele composition, into breeding program design. These findings have significant implications for developing durable resistance strategies in wheat alongside offering valuable insights into the broader dynamics of plant-pathogen interactions.

genomics↗

bioRxiv2025

Mechanistic basis for protection against fatty liver disease by CIDEB loss-of-function mutations

Background & AimsSomatic and germline CIDEB mutations are associated with protection from chronic liver diseases. The mechanistic basis and whether CIDEB suppression would be an effective therapy against fatty liver disease remain unclear. Methods21 CIDEB somatic mutations were introduced into cells to assess functionality. In vivo screening was used to trace Cideb mutant clones in mice fed normal chow, western (WD), and choline-deficient, L-amino acid-defined, high-fat (CDA-HFD) diets. Constitutive and conditional Cideb knockout mice were generated to study Cideb in liver disease. Isotope tracing was used to evaluate fatty acid oxidation and de novo lipogenesis. Transcriptomics, lipidomics, and metabolic analyses were utilized to explore molecular mechanisms. Double knockout models (Cideb/Atgl and Cideb/Ppara) tested mechanisms underlying Cideb loss. ResultsMost CIDEB mutations showed that they impair function, and lineage-tracing showed that loss-of-function clones were positively selected with some, but not all fatty liver inducing diets. Cideb KO mice were protected from WD, CDA-HFD, and alcohol diets, but had the greatest impact on CDA-HFD induced liver disease. Hepatocyte-specific Cideb deletion could ameliorate disease after MASLD establishment, modeling the impact of therapeutic siRNAs. Cideb loss protected livers via increased {beta}-oxidation, specifically through ATGL and PPARa activation. ConclusionsCideb deletion is more protective in some types of fatty liver disease. {beta}-oxidation is an important component of the Cideb protective mechanism. CIDEB inhibition represents a promising approach, and somatic mutations in CIDEB might predict the patient populations that might benefit the most.

physiology↗

bioRxiv2025

RAMA: an Integrative Approach to Identify Hot Spots and Guide the Directed Evolution of High Molecular Weight Enzyme

Directed evolution has revolutionized enzyme engineering but remains challenging for large, multidomain proteins due to their complex dynamics and vast combinatorial sequence space. Traditional NMR spectroscopy, while powerful for identifying functional residues, is limited by the requirement for complete resonance assignments that become intractable in high molecular weight systems. Here, we present a hybrid NMR-computational framework that integrates chemical shift perturbation mapping with AlphaFold3-docked distance constraints, enabling the identification and assignment of ligand-proximal hotspots without the need for full resonance assignment. By analyzing side chain 1H-13C correlation spectra, probabilistic amino acid typing, and structural proximity filtering, we mapped functional hotspots in the [~]90 kDa Pyrococcus furiosus DNA polymerase. Targeted saturation mutagenesis of these sites resulted in variants exhibiting multi-fold increases in catalytic efficiency while sampling less than 0.6% of total residues. The identified hotspots revealed spatially distinct yet cooperative contributions to catalysis, as further supported by combinatorial mutagenesis and kinetic analyses. This hybrid strategy provides a practical pipeline for narrowing mutagenesis targets in large enzymes under catalytic conditions, overcoming the size, assignment, and screening limitations of conventional NMR-guided evolution, offering a powerful route toward efficient biocatalyst optimization by prioritizing high-probability target residues.

molecular biology↗

bioRxiv2025

Genome-Wide CRISPR Screening Identifies Cellular Factors Controlling Nonviral Genome Editing Efficiency

After administering genome editors, their efficiency is limited by a multi-step process involving cellular uptake, trafficking, and nuclear import of the vector and its payload. These processes vary widely across cell types and differ depending on the nature and structure of the vector, whether it is a lipid nanoparticle or a different synthetic material. We developed a novel genome-wide CRISPR screening strategy to better understand these limitations within human cells to identify genes modulating cellular uptake, payload delivery, and gene editing efficiency. Our screen interrogates the cellular processes controlling genome editing by Cas-based nuclease and base editing strategies in human cells. We designed a genome-wide screen targeting 19,114 genes in HEK293 cells, and we identified six genes whose knockout increased nonviral editing efficiency in human cells by up to five-fold. Further validation through arrayed knockouts of the top hits from our screen boosted the editing efficiency from 5% to 50% when Cas9 was delivered via lipid-based nanoparticles. By designing the guides to target the screen library cassette, we could accurately track the library sgRNA identity and the editing outcome on the same amplicon via short-read sequencing, enabling the identification of rare outcomes via computationally sorting edited from unedited cells within a heterogenous pool of >200M cells. In patient-derived human retinal pigment epithelium cells derived from pluripotent stem cells, BET1L, GJB2, and MS4A13 gene knockouts increased targeted genome editing by over five-fold. We anticipate that this high-throughput screening approach will facilitate the systematic engineering of novel nonviral genome editing delivery methods, where the identified novel gene hits can be further used to increase editing efficiency for other therapeutically relevant cell types.

genomics↗

bioRxiv2025

Hyperplastic Growth, Not Hydrostatic Distension, in Endolymphatic Hydrops in Humans Challenges the Classic View of Meniere's Disease

Menieres disease (MD), a degenerative inner ear disorder, is characterized by debilitating episodic vertigo "attacks" and hearing fluctuations, progressing to permanent sensory impairment. The prevailing dogma attributes these symptoms to an abnormal inner ear fluid buildup--known as endolymphatic hydrops (EH)--with concomitant rise of fluid pressure and repetitive microtrauma to sensory epithelia. However, this pressure-based mechanism lacks direct experimental evidence and fails to explain key clinical aspects of MD--exposing a critical gap in our disease understanding. To revisit the fundamental nature of EH, we performed 3D reconstructive, machine-learning-enhanced histological analyses and immunohistochemistry on human postmortem inner ear specimens. Contrary to the classic theory, EH-affected epithelia showed no signs of pressure-induced change. Instead, we observed an up to four-to seven-fold increase in epithelial cell number (hyperplasia) in both early and advanced EH stages. Quantification of the hyperplastic epithelial surface area, as well as immunohistochemical localization of key fluid homeostasis-associated proteins in the hyperplastic epithelium suggest this epithelial hyperplasia may actively compensate for cell loss in the endolymphatic sac, a key site of MD pathology. These findings challenge the conventional view of EH as solely a pathological pressure phenomenon, instead revealing an unexpected massive cellular expansion of these epithelia, consistent with a coordinated compensatory cellular response aimed at preserving inner ear fluid homeostasis and function in a compromised environment. This paradigm shift introduces dual beneficial and detrimental roles for EH, and suggests new therapeutic avenues for MD focused on promoting compensatory tissue repair while preventing maladaptive remodeling. Significance StatementFor over a century, the leading explanation for Menieres disease--a debilitating inner ear disorder causing vertigo and hearing loss--has been a buildup of fluid and pressure in the inner ear, analogous to conditions like glaucoma. However, this long-held theory has never been directly proven, and treatments based on reducing this supposed pressure have shown limited success. Our research challenges this traditional view, revealing that the expansion of endolymphatic spaces is not primarily a fluid pressure problem, but secondary to a complex cellular response. This fundamental shift in understanding Menieres disease opens new avenues for developing effective therapies to prevent and treat hearing loss and vertigo attacks.

neuroscience↗