Biology subjects

Xie, J.

Publications and source records attributed to Xie, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Unwinding of RNA G-quadruplexes induces mouse and human totipotency

Totipotent stem cells (TotiSCs) have significant application prospects in regenerative medicine and assisted reproductive technologies. The mRNAs of totipotency-related genes are rich in G-quadruplex (G4) structures, while the G4 density of pluripotency-related genes mRNAs is relatively low, suggesting a potential functional link between RNA G4s and the totipotent state. Nevertheless, how G4s are involved in the establishment or maintenance of mouse and human totipotency remains poorly understood. Here, we demonstrate that FC3, a small-molecule RNA G4 unwinder, enables efficient induction and maintenance of mouse and human TotiSCs (mG4TotiSCs and hG4TotiSCs). These FC3-induced TotiSCs closely recapitulate the molecular features of 2-cell-stage blastomeres via transcriptomic and epigenomic profiling. Functionally, both mG4TotiSCs and hG4TotiSCs exhibit totipotent capacity: they differentiate into embryonic and extraembryonic lineages in vitro and in chimeric embryos; moreover, they autonomously self-organize into blastocyst-like structures without exogenous signalling. Mechanistically, we identify that Gata2 mRNA, a G4-containing transcript, is essential for FC3-mediated reprogramming. Genetic disruption of Gata2 would abolish totipotency induction. Collectively, RNA G4 unwinding is a new regulatory axis governing totipotency acquisition and maintenance, providing insight into the functional interplay between nucleic acid secondary structures and cell fate plasticity.

cell biology↗

bioRxiv2026

Harnessing Tumor-Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is refractory to immunotherapy due to its immunologically cold microenvironment and the scarcity of mutation-derived neoantigens. Here, we introduce NeoAPP, a computational tool designed to systematically decode neoantigens arising from tumor-specific transcripts (TSTs) generated by transcriptional dysregulation. Multi-cohort transcriptomic profiling of 413 PDAC samples using NeoAPP reveal a median of 351 neoantigens per sample derived from 56 neoantigen-encoding TSTs (neoTSTs), surpassing mutation-derived counterparts in both abundance and patient coverage. Mechanistic analyses show that non-canonical splicing junction and transposable element activation drive neoantigen generation, while FOXA2-regulated promoter usage constitutes a potential major source of neoTSTs. Tumor-derived neoTSTs are also detected in extracellular vesicles and cancer-associated fibroblasts, implicating stromal crosstalk in immune modulation. Vaccination with neoTSTs induce CD8+ T cell responses in HLA-A*02:01/A*11:01 transgenic mice and suppressed tumor growth in syngeneic PDAC models. Collectively, this work establishes TST-derived neoantigens as a dominant and therapeutically actionable antigen reservoir in PDAC, advancing a transcriptome-guided framework for neoantigen discovery with potential to overcome immune resistance in low-mutation cancers. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/705024v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@82ff31org.highwire.dtl.DTLVardef@401342org.highwire.dtl.DTLVardef@b0771corg.highwire.dtl.DTLVardef@15c03ef_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Single-Cell and Spatial Transcriptomics Integration Identifies Mural Cell Oxidative Stress Genes Clu and Gria2 as Key Biomarkers in Ischemic Stroke

Oxidative stress (OS) is a key factor in ischemic stroke (IS), but the characterization of OS-related genes in IS remains largely unexplored. Identifying key OS-associated genes could improve our understanding of OS in IS. We analysed single-cell RNA sequencing datasets and utilized AUCell, Ucell, singscore, ssgsea, and AddModuleScore algorithms, along with correlation analysis, identified 167 OS-related genes potentially linked to IS. Furthermore, we used seven machine learning algorithms, including least absolute shrinkage and selection operator, XGBoost, Boruta, random forest, gradient boosting machines, decision trees, and support vector machine recursive feature elimination, to identify the optimal feature genes: Clusterin (Clu) and Glutamate Ionotropic Receptor AMPA Type Subunit 2 (Gria2). Bulk RNA-sequencing showed that Clu expression was upregulated and Gria2 expression was downregulated in IS tissues. Single-cell analysis further revealed that these expression changes predominantly occurred in mural cells, emphasizing their cell-specific roles in IS. Subsequently, we validated these findings through spatial transcriptomics (ST) analysis and animal model experiments. These results suggest that Clu and Gria2 may participate in the progression of IS by altering the OS activity of mural cells. However, further research is needed to validate its clinical efficacy and ensure its application in the treatment of IS.

neuroscience↗

bioRxiv2026

PRISM: Niche-informed Deciphering of Incomplete Spatial Multi-Omics Data

Spatial multi-omics data, characterizing the knowledge of diverse molecular layers, have become indispensable for the in situ analysis of tissue architecture and complex biological processes. Nevertheless, current spatial multi-omics sequencing protocols are often hindered by incompatible protocols, resulting in incomplete spatial multi-omics pairing due to inconsistent field-of-view or spatial resolution. To address this, we present PRISM, a novel computational method tailored for this scenario. PRISM leverages a niche-informed graph to propagate information from paired to unpaired regions, jointly achieving the spatial domain identification and spatial omics imputation. Extensive benchmarking on five diverse simulated and real experimental datasets demonstrated that PRISM outperformed existing methods in spatial multi-omics analysis tasks. Application to the human Parkinsons disease data revealed that PRISM accurately recovered dopamine-associated spatial domains and metabolite distributions masked by incomplete data gaps. PRISM offers a robust solution for bridging the integration gap inherent in incompatible sequencing protocols, thereby facilitating more accurate downstream biological interpretation.

bioinformatics↗

bioRxiv2026

Intranasal Replicating Adenovirus type 4-SARS-CoV-2 Recombinants Induce Superior Immune Response Durability and Efficacy in Preclinical Testing Compared to Standard Intramuscular Vaccines

The portfolio of next generation COVID-19 vaccines would benefit from candidates that induce durable systemic and mucosal immune responses that would lessen person-to-person transmission. We constructed an intranasal (IN) replication-competent adenovirus type 4 recombinant platform to express SARS-CoV-2 Spike variants (Ad4-S) and assessed immunogenicity and efficacy in the Syrian hamster model. Although both IN Ad4-S and intramuscular (IM) vaccines (Ad26.CoV2.S and mRNA-1273) induced serum binding antibodies, only Ad4-S induced a robust mucosal response in the nasal cavity. IN Ad4-S vaccination induced serum neutralizing titers equivalent to or greater than IM vaccination but more durable up to 6 months. Upon challenge, IN immunization also resulted in less weight loss, greater breadth and durability of restriction of viral replication, and less lung pathology than IM immunization up to 268 days after immunization. These data support the potential of the IN Ad4 vaccine platform to reduce transmission of SARS-CoV-2 and other respiratory viruses with pandemic potential.

immunology↗

bioRxiv2026

Biocontrol efficacy of 2-pyrroldione-5-carboxylic acid (2Py-5CA), an antifungal bioactive macromolecule from the endophyte Penicillium oxalicum, against Ramularia collo-cygni in barley

Global crop production suffers significant losses (23%) due to disease caused by fungal pathogens. Biocontrol agents may be sustainable alternatives to fungicides for disease management. Ramularia leaf spot (RLS), caused by Ramularia collo-cygni (RCC), is a widespread disease of barley (Hordeum vulgare). Two Penicillium oxalicum isolates identified from a collection of endophytes from wild barley, suppress development of R. collo-cygni and exhibit functional plant growth attributes in vitro. Analysis of the P. oxalicum culture filtrate revealed antifungal activity common to both isolates. An untargeted metabolomics (LC-MS/MS) approach uncovered the secondary metabolite profile of the P. oxalicum endophytes including the identification of 2Py-5CA as an antifungal. AntiSMASH-based genome mining identified a non-ribosomal peptide synthetase (NRPSs) biosynthetic gene cluster in P. oxalicum responsible for producing paraherquamide and ultimately the antifungal 2Py-5CA. In vitro studies demonstrated that 2Py-5CA can also suppress growth of the cereal pathogens; Zymoseptoria tritici, Pyrenophora teres, Fusarium graminearum and the horticultural pathogen, Botrytis cinerea disrupting the growth of pathogenic fungal hyphae and spore structure development. Finally, 2Py-5CA reduced RLS symptoms when sprayed on barley seedlings. Therefore 2Py-5CA has potential as a biofungicide to combat fungal crop pathogens. Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=55 SRC="FIGDIR/small/701693v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@9d1bf2org.highwire.dtl.DTLVardef@95bc91org.highwire.dtl.DTLVardef@8f0313org.highwire.dtl.DTLVardef@1130b0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

TNFα and Endothelial IL-1 Receptor Signaling Drive Peritubular Capillary Regression and Fibrosis in Obstructive Kidney Injury

Capillary regression destabilizes tissue homeostasis and contributes to chronic organ dysfunction, yet the inflammatory pathways that drive pathological vessel loss remain incompletely defined. We previously identified the inflammatory cytokines TNF and IL-1 as conserved mediators of physiological vessel regression in the neonatal mouse eye, but whether these cytokines contribute to pathological capillary regression in adult mice is unknown. In this study, we investigated the capillary regression that occurs along with inflammation in murine kidneys following irreversible unilateral ureteral obstruction (UUO) surgical challenge. Mice lacking genes encoding global TNF, the endothelial IL-1 receptor IL-1R1, or both (double knockout, DKO) were examined at 10 days after UUO surgery. While loss of the individual genes did not affect peritubular capillary (PTC) regression, PTC regression was significantly reduced in DKO mice. This reduction in PTC regression correlated with less expression of the tubular epithelial injury marker KIM-1. DKO kidneys also displayed less fibrosis by Picrosirius Red and Massons trichrome staining. These findings demonstrate that TNF and endothelial IL-1R1 cooperatively drive pathological capillary regression in the irreversible UUO model of chronic kidney injury and that preservation of PTCs correlates with less renal tubular injury and fibrosis at 10 days after injury. NEW & NOTEWORTHYPathological PTC regression drives progressive kidney injury, but its inflammatory triggers are unclear. Using the UUO model, this study identifies cooperative TNF and endothelial IL-1R1 signaling as key drivers of capillary loss. While deletion of either pathway alone was insufficient, combined loss preserved PTCs, reduced tubular injury, and attenuated fibrosis. These findings highlight synergistic inflammatory signaling in microvascular loss and suggest dual targeting may help preserve PTC integrity in chronic kidney disease.

pathology↗

bioRxiv2025

Design, synthesis and profiling of highly potent antivirals targeting emerging drug-resistant HIV-1 variants

AbstractLenacapavir (LEN), the first-in-class HIV capsid inhibitor (CAI), is approved by FDA as a long acting injectable (LAI) for both treatment and pre-exposure prophylaxis (PrEP). Despite its exceptional potency and long pharmacokinetics (PK), a few major resistant mutations have been selected in LEN-treated patients, underscoring the need to develop second-generation LEN analogs to mitigate resistance. Particularly, the M66I mutation confers an extraordinarily high-level LEN resistance, essentially abrogating LEN potency. In this work, we have designed and synthesized LEN analogs featuring a cycloalkyl R2 in subunit B drastically different from known analogs. Against wild-type HIV-1, the potency of our analog 3 (EC50 = 0.073 nM) was 2.6-fold higher than LEN (EC50 = 0.19 nM). More importantly, against the M66I mutant, 3 (EC50 = 5.8 nM) was decisively more potent than LEN (EC50 > 15 M) or any known analogs. We have also shown that the size of the R2 cycloalkyl ring is a major pharmacophore factor as a smaller (cyclopropyl, analog 1) or bigger (cyclohexyl, analog 4) ring confers weaker antiviral potency against both WT HIV-1 and M66I. The vastly improved profile of our lead 3 against M66I was confirmed in the target binding thermal shift assay. These results strongly validate our design and may represent a breakthrough in LEN-based HIV therapy and prophylaxis.

microbiology↗

bioRxiv2025

Discovery and Characterization of a Hydroxypyridone-3-carboxamide Analog as an Antiviral Lead against Orthopoxviruses

Orthopoxviruses remain a persistent global health concern due to the ongoing circulation of mpox, the possibility of the re-emergence of smallpox, and the threats posed by many poxviruses that infect animals and/or humans. The limited availability of antiviral drugs, the unproven efficacy in humans, and the emergence of resistant mutants underscore the need for new and better therapeutics. In this study, we identify and characterize ZW-2038, a hydroxypyridone-3-carboxamide analog, as an antiviral compound against vaccinia virus (VACV), monkeypox virus (MPXV), and cowpox virus (CPXV). Discovered through a focused in-house small-molecule screen, ZW-2038 exhibited low micromolar potency and high selectivity in primary human fibroblasts. The compound also reduced viral replication under physiomimetic conditions including human and monkey intestinal organoids (enteroids) and ex vivo mouse lung tissue models. Mechanistically, ZW-2038 suppresses VACV DNA replication and downstream post-replicative gene expression, albeit without inhibiting MPXV resolvase (Mpr) in vitro. These findings, along with in vitro safety profiling and mice pharmacokinetics studies, characterize ZW-2038 as a promising yet suboptimal antiviral lead against orthopoxviruses warranting future development.

microbiology↗

bioRxiv2025

Rapid robust high-fidelity 3D neuronal extraction from multi-view projections

Recent developments in imaging facilitate large-scale three-dimensional (3D) neuronal recording. While these huge amounts of data shed new light on population-level neural coding, it is much harder to extract neuronal calcium dynamics from 3D volumes than 2D images with the existence of noise and scattering. Here, we presented DeepWonder3D, a general end-to- end pipeline for rapid and robust 3D neuronal extraction with high fidelity. Instead of processing voxel by voxel, DeepWonder3D works on the multi-view projections of 3D imaging data obtained either digitally or optically through specific point spread functions (PSFs) for general applicability to diverse techniques, including point-scanning microscopy, light- field microscopy, and two-photon synthetic aperture microscopy. Integrating denoising, resolution registration, background removal, neuronal extraction, and multi-view fusion into a unified pipeline tailored for large-scale high-resolution datasets contaminated by noise and scattering, DeepWonder3D outperforms state-of-the-art methods in 3D localization accuracy with a 10-fold reduction in computational costs, validated by numerical simulations and a hybrid two-photon/light-field imaging system. With the RUSH3D mesoscope, DeepWonder3D achieves rapid high-fidelity 3D calcium extraction of tens of thousands of neurons across the mouse cortex within hours.

neuroscience↗

bioRxiv2025

Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics

Mitochondrial DNA copy number (mtDNA-CN) is a metric of mitochondrial function that has been associated with a variety of diseases including cardiovascular disease and all-cause mortality. To investigate genes and pathways affected by mtDNA-CN variation, we perturbed HEK 293T cells with ethidium bromide to deplete mtDNA. Using RNASeq and methylation microarrays, we evaluated transcriptomic and methylomic changes in treated cell lines. We observed an 8-fold decrease in mtDNA-CN and compensatory shifts in mitochondrial transcription to support mtDNA replication. Nuclear transcriptomic and methylomic analysis highlighted changes in metabolic pathways, including oxidative phosphorylation and canonical glycolysis. Longitudinal analyses revealed that the identified genes and pathways have different response timing, with nuclear response lagging behind mitochondrial response. These findings further elucidate the mechanisms behind mtDNA maintenance and responses to cellular energetics as well as mitochondrial-nuclear crosstalk dynamics.

genetics↗

bioRxiv2025

Seipin mediates Perilipin-1 recruitment to lipid droplets to preserve human adipocyte identity

Congenital generalized lipodystrophy type 2 (CGL2) is caused by mutations in the BSCL2 gene, which encodes the protein seipin. However, how seipin loss causes adipose tissue failure remains unclear. Using human adipocyte progenitor cells capable of robust differentiation in vitro and in vivo, we reveal two unexpected findings that redefine CGL2 pathogenesis. First, seipin is dispensable for lipid droplet biogenesis but essential for recruiting the major adipocyte scaffold protein Perilipin 1 (PLIN1) to the lipid droplet surface. Second, we discover that the integrity of the lipid droplet serves as an organelle to nucleus quality control checkpoint enforcing adipocyte identity. Without seipin-dependent PLIN1 recruitment, adipocytes exhibit enhanced lipolysis and ceramide accumulation, triggering an unexpected cellular response of de-differentiation into a progenitor-like state. From this de-differentiated state, cells can undergo additional cycles of differentiation and de-differentiation upon repeated adipogenic stimuli. However, some cells escape de-differentiation, instead forming a single large droplet and displaying severe cellular structural abnormalities. Consistent with this model, we find functional adipose tissue can form in vivo from seipin-deficient cells, yet ultimately fails. These findings resolve conflicting models of CGL2 pathogenesis by reframing seipin as a regulator of PLIN1 recruitment, rather than droplet formation per se, and reveal the fundamental role of lipid droplet integrity in the development of functional human adipocytes.

cell biology↗

bioRxiv2025

Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach

Understanding how distinct neuronal subtypes contribute to Alzheimers disease (AD) pathology remains a major challenge. Patient-derived induced pluripotent stem cell (iPSC) studies have shown neuronal subtype-specific molecular and pathological signatures, yet the underlying metabolic shifts driving this selective vulnerability are not completely understood. Here we present iNeuron-GEM, the first manually curated, genome-scale metabolic network of human neurons that integrates transcriptomic and metabolic knowledge to resolve subtype-specific metabolic states. By coupling iNeuron-GEM with single nucleus RNA sequencing data from post-mortem human cohort studies, ROSMAP and SEA-AD, we capture neuronal subtype-specific metabolic features and fluxes and identify perturbations in lipid and energy metabolism across excitatory and inhibitory neurons. Integrative analysis with NPS-AD data shows overlapping metabolic disruptions in AD and schizophrenia (SCZ), suggesting shared molecular vulnerabilities between neurodegenerative and neuropsychiatric disorders. We also developed a computational pipeline to infer transcriptional regulation of metabolic pathways and identify NR6A1 and NR3C1 as important regulators of lipid dysregulation in AD neurons. Our study establishes iNeuron-GEM as a framework to identify neuronal subtype-specific metabolic vulnerabilities in complex brain disorders.

systems biology↗

bioRxiv2025

Endoplasmic reticulum-mitochondrion disconnection promotesmetabolic reprogramming and cystogenesis in polycystic kidneydisease

Mutations in PKD1 and PKD2 cause autosomal-dominant polycystic kidney disease (ADPKD), characterized by fluid-filled cysts, aberrant cell proliferation, and widespread genetic and epigenetic remodeling. While mitochondrial dysfunction and metabolic shifts are central to disease progression, the mechanisms linking PKD mutations to these changes remain unclear. Here, we demonstrate that ER-mitochondria connectivity was disrupted in Pkd1- and Pkd2-deleted mice, preceding cyst formation. This disconnection induces mitochondrial stress, triggering epigenetic remodeling and transcriptional activation of pathways driving proliferation and metabolic reprogramming. Remarkably, restoring PKD function in the ER or pharmacologically enhancing ER-mitochondria connection ameliorates mitochondrial dysfunction, epigenetic shifts, and cystogenesis. These findings reveal a critical role for ER-localized PKD in maintaining mitochondrial integrity and transcriptional homeostasis. Mitochondrial dysfunction resulting from ER-mitochondria uncoupling emerges as a key driver of cystogenesis in ADPKD, and correcting this defect may offer a promising therapeutic strategy. SignificanceAutosomal dominant polycystic kidney disease (ADPKD) is the most prevalent monogenic cause of kidney failure, marked by fluid-filled cysts, aberrant cell proliferation, metabolic reprogramming, and extensive genetic and epigenetic alterations. The mechanisms by which loss-of-function mutations in PKD1 and PKD2 drive disease progression remain poorly understood. Here, we demonstrate that ER-mitochondria contacts are disrupted in Pkd-mutant mice prior to cyst formation. This disconnection induces mitochondrial dysfunction and epigenetic remodeling, which in turn promote metabolic reprogramming and cystogenesis. Restoration of PKD function in the ER or pharmacological enhancement of ER-mitochondria coupling mitigates these pathological changes. Our findings uncover a critical role for ER-mitochondria crosstalk in suppressing cystogenesis and identify a promising therapeutic target for ADPKD.

molecular biology↗

bioRxiv2025

Development of a High-Throughput Screening Method for Anti-NNV Drugs

Nervous necrosis virus (NNV) is an infectious pathogen, characterized by rapid infection and high mortality, commonly encountered in the aquaculture industry. Therefore, there is an urgent need to develop effective antiviral drugs against NNV, which is crucial for targeted treatment strategies, pathogen control, and loss reduction. Screening of effective antiviral active compounds, namely drug precursors, is key to developing highly efficient drugs against NNV. Reverse transcription-quantitative real-time PCR (RT-qPCR) is widely applied to screen and evaluate various substances to prevent and control virus infection. However, RT-qPCR is a cumbersome procedure and not suitable for high-throughput rapid screening. The aptamer TNA1c, which specifically binds to NNV-infected cells, was used to construct a target-driven activatable aptamer probe (TAA). Then, the TAA probe was applied to establish a high-throughput screening (TAA-HTS) method for efficient evaluation of substances against NNV infection. TAA-HTS technology achieved rapid, sensitive, and specific screening of bioactive substances with significant anti-NNV effects. As compared to commonly used analytical methods, such as RT-qPCR, TAA-HTS has the advantages of easy operation and high sensitivity and specificity. The findings of this study provide data support and a theoretical basis for the development of effective antivirus preparations. IMPORTANCEIn this study, a target-driven activatable aptamer probe was employed to establish a high-throughput screening method for anti-NNV drugs. This method enables rapid, sensitive, and specific screening of anti-NNV compounds while reducing background interference. Although RT-qPCR is currently the most widely used technique for antiviral drug screening and validation, the screening approach developed in this study significantly shortens screening time while achieving results consistent with those of RT-qPCR. This demonstrates that the screening method presented here has the potential to become a universal strategy for future drug screening against viral diseases. Moreover, this study not only provides a novel technical solution for NNV control but also demonstrates the potential of aptamer-based probes in high-throughput antiviral screening, serving as a model for combating viral pathogens in aquaculture and other fields.

pathology↗

bioRxiv2025

From Correlation to Causation: Cell-Type-Specific Gene Regulatory Networks in Alzheimer's Disease

INTRODUCTIONAlzheimers disease (AD) involves complex regulatory disruptions across multiple brain cell types, yet a comprehensive understanding of the intracellular causal mechanisms remains unclear. METHODSWe presented an integrative analysis framework using single-nucleus transcriptomic with matched subject-level genotype data from 272 human AD in the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP) study, and constructed causality-based, cell-type-specific gene regulatory networks (GRNs). RESULTSOur method identifies regulatory genes from both transcription factors (TFs) and non-TFs, thereby capturing a complete and accurate causal regulatory map across different brain cell types. This work revealed both established and novel regulations, pathways, and cell-type-unique hub genes in AD. Beyond constructing transcriptome-wide GRNs, we quantitatively assessed hub genes and distinguished those with regulatory or responsive roles. DISCUSSIONOur study provides a comprehensive mapping of cell-type-specific causal GRNs in AD, providing a powerful resource for dynamic pathway exploration, hypothesis generation, and functional interpretation.

neuroscience↗

bioRxiv2025

The use of Artificial Intelligence in Magnetic Resonance Imaging of Epilepsy: A Systematic Review and Meta-Analysis

BackgroundThe application of artificial intelligence (AI)/machine learning (ML) to MRI can be a powerful tool to streamline clinical decision-making, yet variability amongst MRI sequences and algorithms have hindered appropriate assessment of reliability and generalizability. MethodsWe conducted a systematic review and meta-analysis of the ability of current AI/ML models operating on MRI data for: 1) epilepsy diagnosis, 2) temporal lobe epilepsy lateralization, 3) lesion localization, and 4) post-surgical outcome prediction. Searches were conducted across PubMed, Medline, and Embase databases from inception until January 1, 2025. We selected studies that employed AI/ML models trained on any MRI modality to classify at least ten patients across the four main objectives for qualitative assessment, and further included in the meta-analysis if they reported an accuracy rate. The primary outcome of the meta-analysis was the overall accuracy of AI/ML models trained on MRI data. The secondary outcome was the concomitant risk of bias evaluation using PROBAST. FindingsWe identified 158 studies for qualitative evaluation and 127 studies for inclusion in the meta-analysis. AI/ML on multimodal MRI could accurately distinguish epilepsy patients from healthy controls (overall accuracy: 88% [85-90]), lateralize temporal lobe epilepsy (90% [87-93]), localize epileptogenic lesions (82% [74-88]), and predict post-surgical seizure-freedom (83% [78-87]). Overall, a high risk of bias remains in the literature; participant bias remained high across all outcomes (64-87%), as well as predictor (88-100%) and analysis (83-100%) bias. Outcome bias was low only for AI/ML studies predicting post-surgical outcomes. InterpretationOur results support promising accuracy of AI/ML models in epilepsy diagnostics and prognostics but remain highly susceptible to bias in participants, predictors, outcome, and analysis domains which limits current translation to routine clinical practice. We encourage closer interdisciplinary collaboration between clinical and scientific groups to improve validation studies based on thorough study design, analysis, and reporting.

neuroscience↗

bioRxiv2025

A Mammalian Genomic Signature Shaped by Single Nucleotide Variants Controlling Transcriptome Integrity and Diversity

BackgroundMany functional features of mammalian genomic sequences remain poorly defined, especially how sequence motifs and genetic variants within non-coding regions (NCRs) regulate transcriptome integrity and diversity. We have shown that G-tracts unusually positioned between the polypyrimidine tract and 3' AG repress usage of the AG and are enriched at cryptic splice sites in cancer cells but their broader role across the extensive NCRs of mammalian genomes is unknown. ResultsHere, we identify a widely evolved genomic signature, G-tract-AG motifs consisting of guanine tracts closely upstream of AG dinucleotides, which is significantly associated with single-nucleotide variants (SNVs) identified in genome-wide association studies, particularly within NCRs. Approximately 9,000 such G-tracts within human genes are disrupted by variants of the cis-splicing quantitative trait loci in the Genotype-Tissue Expression project. Functionally, G-tracts repress splicing at the adjacent 3' AG, primarily by stalling the second transesterification step. Disruption of G-tracts by SNVs relieves this repression, enabling splicing and generating novel transcript isoforms. These G-tract-disrupting SNVs are in cis across the majority of protein-coding genes and are among thousands of rare variants causing genetic diseases. ConclusionsG-tract-AG signatures are widespread bipartite motifs with dual functions: G-tracts repress AG usage to safeguard transcriptome integrity, while SNV-induced disruption releases AGs for splicing to promote transcriptome diversity. Our findings provide mechanistic insights into the regulation of transcriptome integrity and diversity by a mammalian genomic signature, particularly for NCR SNVs associated with diverse traits and a new framework for their functional annotation.

genetics↗