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Moon, J.

Publications and source records attributed to Moon, J..

At least 19 recordsLinked to original sources
bioRxiv2026

Variant-Specific Rewiring of Lysosomal Positioning by STARD9 Produces Opposite Cholesterol Trafficking Outcomes

Residual cardiovascular risk persists despite lipid-lowering therapy, independent of LDL and Lp(a), reflecting cholesterol dysregulation. We identify STARD9, a lysosomal cholesterol-sensing kinesin, as a causal gene for divergent familial dyslipidemias and premature atherosclerosis. Its START domain binds cholesterol to govern lysosomal positioning. Rare variants segregate with autosomal dominant hypercholesterolemia and premature coronary disease, while common variants associate with reduced HDL and elevated triglycerides. Both converge on lysosomal cholesterol sequestration, ER depletion, mTORC1 SREBP2 activation, impaired autophagy, and NF-kB inflammation, yet diverge through opposite lysosomal positioning: the rare variant disperses lysosomes peripherally, phenocopying START domain loss across cholesterol sequestration, lysosomal positioning, and TFEB activation, triggering LDLR degradation and CASM/TFEB-dependent efflux that preserves HDL, whereas the common variant causes perinuclear retention that suppresses TFEB dependent lipid-handling transcripts, yielding hypertriglyceridemia and low HDL. In Stard9-knockout mice, enterocyte cholesterol sequestration drives SREBP2 dependent NPC1L1 upregulation and apical localization, increasing intestinal cholesterol absorption. These findings position lysosomal cholesterol trafficking as a targetable node in statin-refractory cardiovascular disease.

genetics↗
bioRxiv2026

Human meningiomas arise from developmental meningeal mosaicism

Meningioma is the most common primary intracranial tumour, yet its genetic origin and the temporal sequence of mutational events remain poorly defined. Here, we analysed 80 triple-matched tumour, histologically normal meninges, and blood samples from 22 patients. NF2 or TRAF7 driver mutations are detectable in phenotypically normal meninges in 81.8% of cases (95% CI: 59.7-94.8%; VAF [~]0.02%), corroborated by high-depth sequencing, single-cell cloning, and phylogenetic analysis. By distinguishing developmental mosaic mutations from postnatal tumour-private mutations, we revealed distinct mutational signatures and resolved the temporal sequence of meningioma evolution. The developmental origin was further underscored in patients with multiple meningiomas, where identical driver mutations were shared across genomically distinct tumours and meninges, and in intraventricular meningiomas (IVM), where driver mutations were detected in distant cranial dura. Reconstruction of mutational timing revealed lineage-specific trajectories, linking mosaicism to diverse disease presentations including solitary meningioma, IVM, meningiomatosis, and NF2-related schwannomatosis. Together, these findings reveal an early origin of human meningioma, in which developmental mosaicism establishes a pre-neoplastic field within the meninges, providing a developmental framework for adult tumourigenesis.

Cancer Biology↗
bioRxiv2026

Engineering tumor-homing bacteria as membrane-anchored immune checkpoint-blockade interfaces

Bacterial cancer therapies can exploit tumor tropism to localize immunomodulatory payloads, but most approaches rely on secretion or lysis-dependent release of soluble biologics that may diffuse beyond the tumor niche. Here, we engineer non-pathogenic, tumor-homing Escherichia coli strains as membrane-anchored immunotherapeutic interfaces, with individual strains displaying immune checkpoint-blocking nanobodies targeting CTLA-4 or PD-L1, either alone or in combination with a separate strain displaying murine decoy-resistant IL-18 (mDR18). By screening multiple bacterial outer-membrane proteins as scaffolds, we identified scaffold-dependent differences in display levels and target engagement, and YiaT as a functional platform for checkpoint nanobody presentation. Delivery of YiaT-displayed nanobodies in combination with OmpA-displayed mDR18 suppressed tumor growth in syngeneic mouse colon cancer and melanoma models in either local or systemic delivery. Upon systemic administration, the combined bacterial therapy preferentially accumulated in tumors, outperformed benchmark checkpoint antibody regimens combining CTLA-4 and PD-L1 under the tested conditions, and promoted tumor rejection and rechallenge resistance, without inducing broad systemic cytokine release. Further immune profiling showed that the combined treatment was associated with increased CD8 and effector-memory T-cell responses in tumors and spleens. This work establishes bacterial surface display as a modular strategy for localized cancer immunotherapy.

Synthetic Biology↗
bioRxiv2026

A new mRNA antigen vaccine induces potent B and T cell responses and in vivo protection against SARS-CoV-2

The SARS-CoV-2 mRNA vaccine provides effective protection against viral infection and severe disease by inducing efficient adaptive immunity. However, vaccine efficacy is decreased against emerging variants, and immune memory is relatively short-lived. Here, we added new T cell epitopes to the RBD (receptor-binding domain) mRNA vaccine and identified a SARS-CoV-2 membrane epitope that significantly improved vaccine-induced immunity and protection in vivo. That new vaccine, designated G1-C, induced 8.2-fold higher levels of RBD-specific antibodies than did RBD and enhanced spike-specific T cell and B cell responses. Remarkably, the G1-C modulated hematopoietic stem cell (HSC) differentiation and increased levels of B and NK cells by regulating multiple signaling pathways in bone marrow potentially via Fos, Klf4, and Klf6 transcription factors. Altogether, these findings identify a new vaccine candidate to control viral infection by affecting the lymphoid-myeloid lineage bias and suggest the potential role of T cell epitopes in vaccine design and development.

immunology↗
bioRxiv2025

The realized host specificity of Leptopilina japonica and Ganaspis kimorum, adventive larval parasitoids of the invasive Drosophila suzukii

The non-native larval parasitoid wasps Leptopilina japonica and Ganaspis kimorum (Hymenoptera: Figitidae), which attack larvae of the invasive pest Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), were unintentionally introduced to the Pacific Northwest of North America between 10 and 15 years ago, and are now well-established. Previous laboratory studies conducted to assess the ecological risk of classical biological control introductions suggested that G. kimorum is highly host-specific, whereas L. japonica can develop in several other drosophilid species. Information on realized host use of the parasitoids under field conditions in the context of host-parasitoid food webs in their non-native range is limited. A two-year field study in coastal British Columbia, Canada was conducted, using complementary sampling methods to document host-parasitoid associations and quantify parasitoid specificity with respect to drosophilid communities inhabiting ripe and rotting fruit. Consistent with previous laboratory findings, G. kimorum was reared exclusively from D. suzukii, while L. japonica emerged primarily from D. suzukii but also from D. melanogaster and, less frequently, from members of the D. obscura species group. Leptopilina japonica shared some host species with the resident parasitoid species L. heterotoma and Asobara cf. rufescens. A particularly striking result was the extent to which almost all drosophilid and parasitoid taxa in this studys host-parasitoid trophic webs were non-native, complicating the interpretation of non-target ecological effects of L. japonica. These results provide field-based evidence of realized host use by these two non-native larval parasitoids of D. suzukii that can inform their future use in classical and augmentative biological control programs.

ecology↗
bioRxiv2025

An introduced parasitoid facilitates host range expansion of a resident parasitoid

Invasive species can cause maladaptive behaviours in native consumers, with evolution of behavioural or physiological traits thought to be the main way out of these so-called evolutionary traps. However, shorter-term ecological processes resulting from biological invasions could provide other ways to escape evolutionary traps. Asobara cf. rufescens, a resident (i.e., possibly native or previously introduced) parasitoid of drosophilid fly larvae in North America, can rarely produce offspring on the invasive fruit pest Drosophila suzukii in the laboratory, but in often emerges from field-collected D. suzukii. We hypothesized that the successful development of A. cf. rufescens in D. suzukii in the field is facilitated by Leptopilina japonica, a recently introduced parasitoid of D. suzukii. In laboratory experiments, we found that A. cf. rufescens had more than 30-fold higher offspring emergence from D. suzukii when L. japonica was also present. This facilitation occurred most frequently when A. cf. rufescens parasitized D. suzukii after L. japonica, possibly because parasitism by L. japonica destroyed the hosts cellular immunity that would otherwise prevent A. cf. rufescens development. The recent arrival of L. japonica may have partially rescued A. cf. rufescens from the evolutionary trap set by D. suzukii and, consequently, resulted in an expansion of its host range.

ecology↗
bioRxiv2025

Cas9-enriched nanopore sequencing enables comprehensive and multiplexed detection of repeat expansions

Short tandem repeat (STR) expansion is a major genetic mechanism underlying numerous neurogenetic disorders. However, traditional PCR amplification and short-read next-generation sequencing (NGS)-based methods often fail to detect complex and large expansions including methylation information. Here, we modified an amplification-free nanopore Cas9-targeted sequencing (nCATS) platform and developed a dedicated analysis algorithm, STRiker, for the simultaneous assessment of all currently defined STR loci (56 sites) using a single test with genomic DNA from patient-derived blood cells. We ultimately identified pathogenic repeat expansions in 12 of 37 patients (32.4%) with cerebellar ataxia who remained genetically undiagnosed despite extensive prior genetic testing, in FGF14 (n=4), ATXN8OS, NOP56, RFC1 (n=2 each), and PRNP and NOTCH2NLC (n=1 each). Additionally, family-based cascade screening revealed six relatives with repeat expansions in five families. These results demonstrated a broader diversity of pathogenic repeat structures, particularly in FGF14, and illustrated that CpG methylation can mitigate the pathogenic effects of repeat expansions. This approach offers a powerful strategy for improving the diagnosis of STR-related neurogenetic diseases, for cerebellar ataxia and other STR-related diseases in the future. One Sentence SummaryImproved nanopore Cas9-targeted sequencing with STRiker enhances diagnosis of STR- related neurogenetic diseases and offers broader molecular insights.

bioengineering↗
bioRxiv2025

Translating clinical gene sequencing into a foundational representation of tumor subtype

While gene sequencing is routine in cancer care, translating sequences into treatment decisions remains a challenge. Here we introduce MutationProjector, an AI foundation model that transforms tumor mutation profiles into a compact representation of cancer subtype, with broad implications for diagnosis and therapy. MutationProjector is pre-trained by integrating genomic alterations from >30,000 tumors with extensive molecular knowledge, yielding a model that accurately reconstructs held-out genetic profiles (demonstrating strong generalization) and determines subtype representations from altered molecular pathways (enabling model interpretability). We evaluate MutationProjector in independent tasks related to prediction of immunotherapy response, prediction of chemotherapy response, and classification of metastasis, recording leading performance in all areas. Each task identifies key biomarkers of interest, including KMT2A and KRAS-STK11 alterations which govern immunotherapy response.

systems biology↗
bioRxiv2025

Mechanism of PMC (2,2,5,7,8-pentamethyl-6-chromanol), a sterically hindered phenol antioxidant, in rescuing oxidized low-density lipoprotein-induced cytotoxicity in human retinal pigment epithelial cells

Geographic atrophy or late stage dry age-related macular degeneration (AMD) is characterized by drusen deposition and progressive retinal pigment epithelium (RPE) degeneration, leading to irreversible vision loss. The formation of drusen leads to dyshomeostasis, oxidative stress and irreversible damage to RPE. In this study, we used an in vitro model of oxidized-low density lipoproteins (ox-LDL) induced human RPE damage/death model to investigate the mechanism whereby a sterically hindered phenol antioxidant compound, PMC (2,2,5,7,8-pentamethyl-6-chromanol) protects RPE against ox-LDL-induced damage. We show that PMC exerts its protective effect by preventing the upregulation of stress-responsive heme oxygenase-1 (HMOX1/HO-1) and NAD(P)H:quinone oxidoreductase (NQO1) at mRNA and protein levels. This effect was due to PMCs blockade of ROS generation, which in turn blocked nuclear translocation of the Nuclear factor erythroid 2-related factor 2 (Nrf2) transcription factor, ultimately preventing the upregulation of antioxidant response elements (ARE), including HMOX1 and NQO1. A key role for HO-1 was demonstrated when the protective effect of PMC was inhibited by the knockdown of HMOX1. Additionally, treatment of PMC under different experimental conditions and time points revealed that the continuous presence of PMC is required for optimal protection against ox-LDL-induced cytotoxicity, defining the cellular pharmacokinetics of the molecule. Our data demonstrate the involvement of a key antioxidant pathway through which PMC mitigates oxidative stress induced by ox-LDL and provides a potential therapeutic strategy to suppress RPE degeneration/damage during AMD progression.

molecular biology↗
bioRxiv2025

Inflamed Microglia like Macrophages in the Central Nervous System of Prodromal Parkinson's Disease

We hypothesized that prodromal Parkinsons Disease (PD), characterized by REM Sleep Behavior Disorder and hyposmia, is an inflammatory disorder initiated in the gut that evolves into a neurodegenerative process manifest as classical PD. To test this hypothesis, we performed single-cell RNAseq analysis of cerebrospinal fluid (CSF) and blood from 118 individuals, comparing healthy subjects with prodromal PD and manifest PD to patients with the central nervous system (CNS) autoimmune disease, multiple sclerosis (MS). Surprisingly, we identified increased numbers of immune cells in the CSF of patients with prodromal PD. Single-cell RNA sequencing revealed increases in CSF-specific microglia-like macrophages with enhanced JAK-STAT and TNF signaling signatures in prodromal PD. CSF macrophages exhibited similar transcriptional profiles to dural macrophages and gut muscularis macrophages from -synuclein-expressing PD model mice. Finally, shared memory T cell clones were found in humans between gut and CSF T cells. These findings uncover a myeloid-mediated TNF inflammatory process in the CNS of patients with prodromal PD, with an immunological linkage between the gut and the CNS.

immunology↗
bioRxiv2025

InferPloidy: A fast ploidy inference tool accurately classifies cells with abnormal CNVs in large single-cell RNA-seq datasets

BackgroundAccurate inference of copy number variation (CNV) and ploidy from single-cell RNA-seq data is essential for resolving tumor heterogeneity and identifying malignant cells, yet existing tools such as CopyKat and SCEVAN are limited by long runtimes and reduced accuracy in large or heterogeneous datasets. ResultsHere, we present InferPloidy, a high-speed and robust ploidy inference method built on InferCNV that combines graph-based cell-grouping with iterative Gaussian mixture modeling. Across multiple cancer types--breast cancer, non-small cell lung cancer, pancreatic ductal adenocarcinoma, and colorectal cancer--InferPloidy achieved up to two orders of magnitude faster runtimes than existing tools, while maintaining superior classification accuracy. This accurate separation of aneuploid tumor cells enabled the discovery of subtype-specific therapeutic targets, including ERBB2, ESR1, EGFR, and MET, as well as recurrent surfaceome markers such as CD82, F11R, SLC2A1, TM9SF2, CXADR, and PLPP2, several of which have preclinical or clinical relevance. ConclusionThese results establish InferPloidy as a scalable platform for CNV-guided tumor cell identification and surfaceome-based biomarker discovery, offering broad utility for precision oncology and translational research.

bioinformatics↗
bioRxiv2024

SOX2-induced IL-1alpha-mediated immune suppression drives epithelial dysplasia malignant transformation

Squamous cell carcinomas (SCC) are often preceded by potentially malignant precursor lesions, most of which remain benign. The terminal exhaustion phenotypes of effector T-cells and the accumulation of myeloid-derived suppressor cells (MDSC) have been thoroughly characterized in established SCC. However, it is unclear what precancerous lesions harbor a bona fide high risk for malignant transformation and how precancerous epithelial dysplasia drives the immune system to the point of no return. Here we show that expression of SRY-box transcription factor 2 (SOX2) in precancerous lesions imparts an irreversible risk that recruits suppressive myeloid cells by promoting the release of CCL2. We developed a unique genetically engineered mouse model (GEMM) to recapitulate the malignant transformation of epithelial dysplasia to SCC in the oral mucosa with high histologic and phenotypic fidelity. Using a combination of longitudinal human specimens and the Sox2-GEMM, we found that the myeloid cells in precancerous epithelial dysplasia exhibit a distinctive dichotomous profile featuring high levels of IL-1-SLC2A1 and low levels of type-I interferon (IFN-I) signatures, which occurs before SCC emerges histologically. Brief priming of myeloid cells with IL-1 desensitizes them to IFN-I agonists and makes myeloid-derived suppressor cells (MDSC) even more suppressive of T-cell activation. Mechanistically, IL-1 activation represses the expression of DHHC3/7 enzymes, which are responsible for the palmitoylation of stimulator of interferon genes (STING). Early blockade of IL1 signaling using pharmacologic and genetic approaches similarly reduces MDSC and SLC2A1high myeloid cells, suppresses epithelial dysplasia transformation, and extends survival. This work establishes a previously unrecognized SOX2-CCL2-IL1 pathway that leads to irreversible immune escape when precancerous epithelial lesions transform.

cancer biology↗
bioRxiv2024

Local Haplotype Classifiers enable Efficient, Flexible, and Secure Genotype Imputation and Downstream Analyses

The decreasing cost of genotyping technologies led to abundant availability and usage of genetic data. Although it offers many potentials for improving health and curing diseases, genetic data is highly intrusive in many aspects of individual privacy. Secure genotype analysis methods have been developed to perform numerous tasks such as genome-wide association studies, meta-analysis, kinship inference, and genotype imputation outsourcing. Here we present a new approach for using lightweight haplotype classifier models to use predicted haplotype information in a flexible privacy-preserving framework to perform genotype imputation and downstream tasks. Compared to the previous secure methods that rely main on linear models, our approach utilizes efficient models that rely on utilizing haplotypic information, which improves accuracy and increases the throughput of imputation by performing multiple imputations per model evaluation.

bioinformatics↗
bioRxiv2024

Endomucin regulates the endothelial cytoskeleton independent of VEGF

The endothelial glycocalyx, lining the apical surface of the endothelium, is involved in a host of vascular processes. The layer contains a network of membrane-bound proteoglycans and glycoproteins. One such glycoprotein is endomucin (EMCN), which our lab has revealed is a modulator of VEGFR2 function. Intravitreal injection of siEMCN into the eyes of P5 mice impairs vascular development. In vitro silencing of EMCN suppresses VEGF-induced proliferation and migration. Signaling pathways that drive cell migration converge on cytoskeletal remodeling. By coupling co-immunoprecipitation with liquid chromatography/mass spectrometry, we identified interactions between EMCN, and proteins associated with actin cytoskeleton organization. The aim of the study was to investigate the influence of EMCN on cytoskeleton dynamics in angiogenesis. EMCN depletion resulted in reduction of F-actin levels, whereas overexpression of EMCN induced membrane protrusions in cells that were rich in stress fibers. The reorganization of the actin filaments did not depend on VEGFR2 signaling, suggesting that EMCN is a potential connection between the cytoskeleton and the glycocalyx.

cell biology↗
bioRxiv2024

Systematic Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis

Multiple sclerosis (MS) is a complex genetically mediated autoimmune disease of the central nervous system where anti-CD20-mediated B cell depletion is remarkably effective in the treatment of early disease. While previous studies investigated the effect of B cell depletion on select immune cell subsets using flow cytometry-based methods, the therapeutic impact on patient immune landscape is unknown. In this study, we explored how a therapy-driven "in vivo perturbation" modulates the diverse immune landscape by measuring transcriptomic granularity with single-cell RNA sequencing (scRNAseq). We demonstrate that B cell depletion leads to cell type-specific changes in the abundance and function of CSF macrophages and peripheral blood monocytes. Specifically, a CSF-specific macrophage population with an anti-inflammatory transcriptomic signature and peripheral CD16+ monocytes increased in frequency post-B cell depletion. This was accompanied by increases in TNF messenger RNA and protein in monocytes post-B cell depletion, consistent with the finding that anti-TNF treatment exacerbates autoimmune activity in MS. In parallel, B cell depletion induced changes in peripheral CD4+ T cell populations, including increases in the frequency of TIGIT+ regulatory T cells and marked decreases in the frequency of myelin peptide loaded-tetramer binding CD4+ T cells. Collectively, this study provides an exhaustive transcriptomic map of immunological changes, revealing different mechanisms of action contributing to the high efficacy in B cell depletion treatment of MS.

immunology↗
bioRxiv2024

Treatment of a genetic liver disease in mice through transient prime editor expression

Prime editing is a versatile genome editing technology that does not rely on DNA double-strand break formation and homology-directed repair (HDR). This makes it a promising tool for correcting pathogenic mutations in tissues consisting predominantly of postmitotic cells, such as the liver. While recent studies have already demonstrated proof-of-concept for in vivo prime editing, the use of viral delivery vectors resulted in prolonged prime editor (PE) expression, posing challenges for clinical application. Here, we developed an in vivo prime editing approach where we delivered the pegRNA using self-complementary adeno-associated viral (scAAV) vectors and the prime editor using nucleoside-modified mRNA encapsulated in lipid nanoparticles (LNPs). This methodology led to transient expression of the PE for 48h and 26% editing at the Dnmt1 locus using AAV doses of 2.5x1013 vector genomes (vg)/kg and a single dose of 3mg/kg mRNA-LNP. When targeting the pathogenic mutation in the Pahenu2 mouse model of phenylketonuria (PKU), we achieved 4.3% gene correction using an AAV dose of 2.5x1013 vg/kg and three doses of 2 mg/kg mRNA-LNP. Editing was specific to the liver and the intended locus, and was sufficient to reduce blood L-phenylalanine (Phe) levels from over 1500 {micro}mol/l to below the therapeutic threshold of 600 {micro}mol/l. Our study demonstrates the feasibility of in vivo gene correction in the liver with transient PE expression, bringing prime editing closer to clinical application.

bioengineering↗
bioRxiv2023

Early viral infection of cyanobacteria drives bacterial chemotaxis in the oceans

Interactions among marine microbes primarily occur through exudation and sensing of dissolved chemical compounds, which ultimately control ecosystem-scale processes such as biomass production, nutrient cycling, carbon fixation, and remineralization. Prior to lysis, viruses alter host metabolism, stimulating the release of dissolved chemical cues from intact plankton. However, the nature and degree of interactions between prelysis, virus-infected cells and neighbouring microbes remain unquantified. Here, we determine the impact of viral infection on dissolved metabolite pools from the marine cyanobacterium Synechococcus and the subsequent chemotactic response of heterotrophic bacteria using time-resolved metabolomics and microfluidics. Metabolites released from intact, virus-infected Synechococcus elicited vigorous chemoattractive responses from heterotrophic bacteria (Vibrio alginolyticus and Pseudoalteromonas haloplanktis), with the strongest responses occurring in the early infection stages and following cell lysis. We provide the first experimental observations of sustained chemotaxis towards live, infected Synechococcus, which is contrasted by no discernible chemotaxis toward uninfected Synechococcus. Finally, metabolite compounds and concentrations driving chemotactic responses were identified using a novel high-throughput microfluidic device. Our findings establish that prior to cell lysis, virus-infected picophytoplankton release compounds that significantly attract motile heterotrophic bacteria, illustrating a viable mechanism for resource transfer to chemotactic bacteria with implications for our understanding of carbon and nutrient flux across trophic levels.

biophysics↗