Biology subjects

Hong, S.

Publications and source records attributed to Hong, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

EVscope: A Comprehensive Bioinformatics Pipeline for Accurate and Robust Analysis of Total RNA Sequencing from Extracellular Vesicles

MotivationExtracellular vesicle (EV) RNA sequencing has emerged as a powerful approach for studying RNA biomarkers and intercellular communication. Nevertheless, the extremely low abundance, fragmented nature and ubiquitous tissue origin of EV RNAs, alongside potential contamination from co-isolated materials, such as free DNA and bacterial RNA, pose substantial analytical challenges. These complexities highlight a pressing need for a standardized, computational workflow that ensures robust quality control and EV RNA characterization. ResultsHere, we present EVscope, an open-source bioinformatics pipeline designed specifically for processing EV RNA-seq datasets. EVscope employs an optimized genome-wide expectation-maximization (EM) algorithm that significantly improves multi-mapping read assignment at single-base resolution by effectively leveraging alignment scores (AS) and local read coverage, specifically tailored for fragmented and low-abundance EV RNAs. Notably, EVscope uniquely generates EM-based BigWig files for downstream analysis, a capability currently unavailable in existing EM-based BigWig quantification tools. The pipeline systematically integrates 27 major steps, including quality control, analysis of library structure, contamination assessment, read alignment, read strandedness detection, UMI-based deduplication, RNA quantification, genomic DNA (gDNA) contamination correction, cellular and tissue source inference and visualization with a comprehensive HTML report. EVscope incorporates a comprehensive, updated annotation covering 19 distinct RNA biotypes, encompassing protein-coding genes, lncRNAs, miRNAs, piRNAs, retrotransposons (LINEs, SINEs, ERVs), and additional non-coding RNAs (tRNAs, rRNAs, snoRNAs). Furthermore, it leverages two highly balanced circRNA detection algorithms for robust circular RNA identification. Notably, a downstream module enables the inference of the tissue/cellular origins of EV RNAs using bulk and single-cell RNA-seq reference datasets. EVscope is implemented as a convenient, single-command Bash pipeline leveraging Conda-managed standard software packages and custom scripts, ensuring reproducibility and straightforward deployment. Availability and implementationCode, documentation, and tutorials are available at GitHub (https://github.com/TheDongLab/EVscope) and archived on Zenodo (https://zenodo.org/records/15577789).

bioinformatics↗

bioRxiv2025

Multi-Level Regulation in RNA-Protein Hybrid Incoherent Feedforward Loop Circuits for Tunable Pulse Dynamics in Escherichia coli

Regulating gene expression with precision is essential for cellular engineering and biosensing applications, where rapid, programmable, and sensitive control is desired. Current approaches to regulatory circuit design often rely on control at a single regulatory level, primarily the transcriptional level, thereby limiting the capability of fine-tuning the regulatory dynamics in response to complex stimuli. To address this challenge, we developed four novel RNA-protein hybrid type-1 incoherent feed-forward loop (I1-FFL) circuits in Escherichia coli that integrate transcriptional and translational regulators to achieve multi-level control of gene expression. These hybrid circuits leverage the modularity and rapid dynamics of RNA-based activators alongside the versatile inhibition capabilities of the protein-based repressors, to endow tunable pulse dynamics through engineered delays that act as transient repressor decoys. By repurposing synthetic RNA regulators at multiple regulatory levels together with aptamer and RNA-binding proteins, we demonstrate previously unexplored circuits with tunable dynamics. Complementary simulation results highlighted the importance of the engineered delays in achieving tunable pulse dynamics in these circuits. Integrating modeling insights with experimental validation, we demonstrated the flexibility of designing the RNA-protein hybrid I1-FFL circuits, as well as the tunability of their dynamics, highlighting their suitability for applications in environmental monitoring, metabolic engineering, and other engineered biological systems, where precise temporal control and adaptable gene regulation are desired.

synthetic biology↗

bioRxiv2025

Periventricular Diffusivity Reflects APOE4-modulated Amyloid Accumulation and Cognitive Impairment in Alzheimers Continuum

BackgroundAltered glymphatic-related fluid dynamics are increasingly recognized as a key feature of Alzheimers disease (AD). We generalized an established diffusion imaging technique to estimate periventricular diffusivity (PVeD), hypothesizing that fast diffusion signals in the periventricular region can reflect amyloid-beta (A{beta}) deposition across the Alzheimers continuum. MethodsParticipants from two multi-site cohorts (n = 440 and 414), comprising cognitively unimpaired individuals, those with mild cognitive impairment, and patients with AD, were included. We tested and validated the association of PVeD with A{beta} burden and core AD characteristics. ResultsLower PVeD was extensively associated with greater A{beta} burden, neurodegeneration, cognitive impairment, and clinical severity. Importantly, the relationship between PVeD and A{beta} burden was significantly modulated by APOE4 status, with APOE4 carriers showing a stronger negative association. Baseline PVeD also predicted longitudinal cognitive decline. DiscussionThese findings suggest that periventricular fast diffusion signals can reflect APOE4-modulated A{beta} burden and cognitive decline in AD. Research-in-ContextO_ST_ABSSystematic reviewC_ST_ABSA comprehensive PubMed literature search indicates that fluid movement related to glymphatic activity assessed by diffusion tensor image analysis along the perivascular space (DTI-ALPS) is associated with amyloid-beta deposition in Alzheimers disease (AD). However, recent evidence underscores certain limitations of DTI-ALPS, suggesting that it may not fully capture the diffusion processes involved in amyloid clearance. Moreover, no previous studies have investigated the role of APOE4 in modulating the relationship between glymphatic-related fast diffusion signals and amyloid-beta deposition. InterpretationThe transverse diffusion process along the perivenous space in the periventricular region appears to reflect glymphatic-related dysfunction manifested by amyloid-beta deposition. Reduced periventricular diffusivity is associated with greater amyloid burden across the AD continuum. This association is notably enhanced in APOE4 carriers, who exhibit higher amyloid accumulation for a given reduction in the periventricular diffusivity. Besides, periventricular diffusivity is related to other pathological markers of AD, including clinical symptom severity and neurodegeneration, and may also predict subsequent cognitive decline. Future directionsAlthough diffusion-based neuroimaging metrics hold promise as surrogate imaging biomarkers for glymphatic-related activity, they do not comprehensively capture the complex fluid dynamics such as convective bulk flow within the glymphatic system. By leveraging multimodal neuroimaging techniques and advanced analytic approaches, future research can refine these metrics into more sensitive, non-invasive tools capable of evaluating fluid dynamics related to glymphatic dysfunction in AD.

neuroscience↗

bioRxiv2025

Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution

Systematic whole-proteome screening and comprehensive profiling of antigen-specific CD4+ T cells are crucial for advancing our understanding of CD4+ T cell immunity, yet such efforts remain technically challenging. Here, we present a high-throughput platform that employs large-scale class II single-chain trimer libraries to detect antigen-specific CD4+ T cells, while simultaneously profiling their antigen specificity, TCR/{beta} sequences, MHC restriction, whole transcriptomes, and patient/timepoint origins at single-cell resolution. We benchmarked SCTs against conventional pMHCs and validated the SCT library-based approach in direct ex vivo identification of antigen-specific CD4+ T cells in healthy donors. We then applied the platform to screen the entire SARS-CoV-2 receptor-binding domain in a longitudinal patient cohort, identifying 2,188 antigen-specific CD4+ T cells and revealing key features that define antigen immunogenicity. Extending to cancer, we performed whole-proteome screening of HPV-16 E6/E7 for TCR repertoire profiling in a precancerous cohort, uncovering functional heterogeneity of HPV-specific TCRs. By integrating high-throughput antigen screening with high-dimensional, multi-modal cellular characterization, our approach offers an unprecedented window into CD4+ T cell immunity across diverse disease contexts and empowers the development of new therapies.

bioengineering↗

bioRxiv2025

HUWE1 stimulates mTORC1 activity by enhancing Rheb interaction with mTORC1 and supports de novo pyrimidine synthesis

mTORC1 is a central regulator of cell growth that is directly activated by the small GTPase Rheb on the lysosomal membrane in response to growth factors. We recently reported that polyubiquitinated Rheb facilitates its interaction with mTORC1, leading to mTORC1 activation. However, the molecular mechanisms underlying the ubiquitination of Rheb and its interaction with mTORC1 for activation are not fully understood. In this study, we demonstrate that HUWE1, an E3 ubiquitin ligase, preferentially interacts with ubiquitinated Rheb and is essential for the interaction between Rheb and mTOR, as well as for mTORC1 activation. Additionally, HUWE1 is necessary for Rheb to interact with CAD, a crucial enzyme involved in de novo pyrimidine biosynthesis, and for its activation through the mTORC1-S6K1 pathway. Knocking down HUWE1 in cultured cells or in the liver tissues of mice inhibits mTORC1 activity without affecting the phosphorylation of Akt or TSC2, nor does it affect the lysosomal localization of TSC2 or mTORC1. Furthermore, HUWE1 specifically enhances the expression of CAD without influencing other enzymes involved in de novo pyrimidine synthesis and maintains UMP levels in the hepatocytes of liver tissues. These findings indicate that HUWE1 serves as a key organizer of the Rheb ubiquitin complex, amplifying mTORC1 activity and playing a vital role in stimulating de novo pyrimidine synthesis by enhancing CAD expression and activity. HighlightsO_LIHUWE1 and CAD preferentially interact with ubiquitinated Rheb. C_LIO_LIHUWE1 further ubiquitinates Rheb and supports Rheb interaction with mTORC1 and CAD. C_LIO_LIHUWE1 stimulates mTORC1 activity through its E3 ligase activity. C_LIO_LIHUWE1 also supports pyrimidine synthesis by enhancing CAD expression. C_LI

biochemistry↗

bioRxiv2025

The mitochondrial NAD transporter SLC25A51 is a modulator of beta cell senescence and type 2 diabetes

AbstractNicotinamide adenine dinucleotide (NAD+) is an essential redox cofactor and signaling molecule linked to age-dependent metabolic decline, with its compartmentalization regulated by the mitochondrial carrier SLC25A51. The mechanisms contributing to declining NAD+ levels during aging and the consequences of altered NAD+ homeostasis across tissues are poorly understood. Here, we show that SLC25A51 is upregulated in aging and aging-associated conditions, particularly in senescent cells. In a mouse model of beta-cell senescence, upregulated SLC25A51 was associated with beta-cell identity loss, senescence progression, and a reduced NAD+/NADH ratio. SLC25A51 was elevated following p16INK4a-, replicative-, irradiation-, and H2O2-induced senescence, with NRF2 implicated as a potential transcriptional regulator. Overexpression of SLC25A51, but not a transport-dead mutant, induced senescence factors, while its deletion prevented this effect. Beta-cell-specific deletion of SLC25A51 lowered p16INK4a levels in pancreatic islets, circulating insulin, and glucose levels, improving insulin sensitivity and indicating its role in cellular senescence and the metabolic control of beta-cell function.

cell biology↗

bioRxiv2025

AMPK is dispensable for physiological podocyte and glomerular functions but prevents glomerular fibrosis in experimental diabetes

AMP-activated protein kinase (AMPK) has been postulated to be crucial in regulating various renal physiology and pathophysiology processes, including energy metabolism, ion and water transport, inflammation, and hypertrophy. However, the specific roles of AMPK in the podocyte, a cell critical for maintaining glomerular filtration, have not been fully explored using genetic model animals. In this study, we generated mice lacking both AMPK 1 and 2 catalytic subunits in glomerular podocytes (pmut). Our findings revealed that, surprisingly, AMPK is dispensable for normal podocyte function. These knockout mice could live as long as their wild-type littermates without showing any pathological alterations in their glomeruli or glomerular function at two years of age. However, under type 1 diabetic conditions, the diabetic pmut mice exhibited increased lipid and collagen accumulation and an elevated expression of mesenchymal proteins in their glomeruli. They also showed more significant albuminuria compared to control diabetic mice. Under high glucose culture conditions, glomeruli isolated from pmut mice demonstrated a reduced expression of mitochondrial genes (e.g., Ndufv2) and increased leakage of mitochondrial components. Additionally, there was heightened expression of genes associated with nucleotide sensing and pro-inflammatory pathways (including mb21d2, IL-1 beta, and NF-kB). These observations suggest that while AMPK is not necessary for podocyte function in healthy kidneys, it is crucial for preventing glomerular fibrosis resulting from lipotoxicity and inflammation under diabetic conditions.

cell biology↗

bioRxiv2025

Topoisomerase IIα orchestrates secretion of IL-6 and IL-8 with human papillomavirus replication

High-risk human papillomavirus (HPV) replication requires deregulation of host DNA damage response (DDR) and inflammatory pathways. DNA topoisomerase 2{beta} (Top2{beta}) was previously shown to promote HPV replication, while the function of its paralog Top2 in the viral life cycle remains unknown. Elevated levels of Top2 are consistently observed in cervical intraepithelial lesions and the related carcinomas, as well as in HPV-positive cell lines. Silencing Top2 with shRNA severely suppresses HPV genome maintenance and amplification, but in a DDR-independent manner. Instead, Top2 facilitates secretion of interleukin (IL)-6 and IL-8, which are necessary for HPV replication. Mechanistically, this manipulation is regulated by toll-like receptor 4 (TLR4). Top2 binds to the TLR4 promoter to transcriptionally induce TLR4 expression. Blockade of TLR4 signaling by the specific inhibitor TAK-242 significantly reduces the secreted IL-6/IL-8 levels and HPV replication. Overall, our results reveal a novel role of Top2 to shape the inflammatory microenvironment that benefits HPV replication, making it a promising therapeutic target for HPV-associated diseases. IMPORTANCEHuman papillomaviruses (HPVs) are oncogenic pathogens responsible for many HPV-related diseases such as cervical cancer. HPV replication depends on the subversion of host cellular machineries, particularly pathways governing DNA damage response (DDR) and inflammation. However, the roles of enzymes that directly introduce DNA nicks or mediate strand rejoining remain poorly characterized. Here we highlight a novel role of DNA topoisomerase 2 (Top2) in promoting HPV genome maintenance and amplification but in a DDR-independent manner. Unlike its previously studied paralog Top2{beta}, Top2 supports HPV replication by driving the secretion of inflammatory molecules interleukin (IL)-6 and IL-8, which are critical for the viral genome persistence and copy number expansion. To our knowledge, this is the first evidence that a DDR-associated protein manipulates cytokine secretion, rather than expression, to support HPV replication. Furthermore, blocking toll-like receptor 4 (TLR4) activities significantly reduced Top2-dependent IL-6/IL-8 secretion and impaired HPV replication. These findings establish Top2 as a crucial player in HPV pathogenesis, with a therapeutic potential for treating HPV-associated malignancies.

microbiology↗

bioRxiv2025

Synthesis, anticancer properties, and biological profiling of synthetic glycan analogs of proscillaridin A

Several cardiac glycosides, including digoxin, digitoxin, and proscillaridin A, have been originally identified as cardiomyocyte modulators and are currently being investigated for their anticancer properties. These cardiac glycosides are generally classified into cardenolides and bufadienolides, which bear butenolide and pyrone D-ring functionality, respectively, and have exhibited remarkable in vitro toxicity in various cancerous cell lines. As simple modifications on steroidal small molecules have demonstrated success in augmenting bioavailability or enhancing downstream biological activities, we sought to prepare synthetic analogs of proscillaridin A, a bufadienolide isolated from the genus Scilla. We synthesized two novel analogs of proscillaridin A bearing acetate esters or a dimethyl ketal to investigate how strategies of ketalization or acetylation of the A-ring allylic glycoside might alter its anticancer properties. The antiproliferative activity of these compounds was evaluated alongside proscillaridin A and two model cardiac glycosides, digoxin and digitoxin, across several colorectal and liver cancer cell lines. Through a diverse panel of cell viability and cytotoxicity experiments, reporter assays, and cell cycle and protein marker analysis by flow cytometry, we find that ketalization of the glycan of proscillaridin A provides similar, and in some cases enhanced, in vitro potency. This study establishes the foundation for current and further in vitro and in vivo evaluation of glycan analogs of proscillaridin A.

cancer biology↗

bioRxiv2025

The B. subtilis replicative polymerases bind the sliding clamp with different strengths to tune replication processivity and fidelity

Ring-shaped sliding clamp proteins are essential components of the replication machinery, the replisome, across all domains of life. In bacteria, DNA polymerases bind the sliding clamp, DnaN, through conserved short peptide sequences called clamp-binding motifs. Clamp binding increases the processivity and rate of DNA synthesis and is generally required for polymerase activity. The current understanding of clamp-polymerase interactions was elucidated in the model bacterium Escherichia coli, which has a single replicative polymerase, Pol III. However, many bacteria have two essential replicative polymerases, such as PolC and DnaE in Bacillus subtilis. PolC performs the bulk of DNA synthesis whereas the error-prone DnaE only synthesizes short stretches of DNA on the lagging strand. How the clamp interacts with the two polymerases and coordinates their activity is unknown. We investigated this question by combining in vivo single-molecule fluorescence microscopy with biochemical and microbiological assays. We found that PolC-DnaN binding is essential for replication, although weakening the interaction is tolerated with only minimal effects. In contrast, the DnaE-DnaN interaction is dispensable for replication. Altering the clamp-binding strength of DnaE produces only subtle effects on DnaE cellular localization and dynamics, but it has a substantial impact on mutagenesis. Our results support a model in which DnaE acts distributively during replication but can be stabilized on the DNA template by clamp binding. This study provides new insights into the coordination of multiple replicative polymerases in bacteria and the role of the clamp in polymerase processivity, fidelity, and exchange.

biochemistry↗

bioRxiv2025

Anti-Parasitics with a Triple Threat: Targeting Parasite Enzymes, the Proton Motive Force, and Host Cell-Mediated Killing

We investigated the effects of the tuberculosis drug candidate SQ109 (8a) and of its analog MeSQ109 (8b) against Leishmania mexicana in promastigote and amastigote forms, as well as against host cell macrophages finding potent activity (1.7 nM) for MeSQ109 against the intracellular forms, as well as low toxicity ([~]61 {micro}M) to host cells, resulting in a selectivity index of [~]36,000. We then investigated the mechanism of action of MeSQ109 finding that it targeted parasite mitochondria, collapsing the proton motive force, as well as targeting acidocalcisomes, rapidly increasing the intracellular Ca2+ concentration. Using an E. coli inverted membrane vesicle assay, we investigated the pH gradient collapse for SQ109 and 17 analogs finding that there was a significant correlation (on average R=0.67, p[~]0.008) between pH gradient collapse and cell growth inhibition in Trypanosoma brucei, T. cruzi, L. donovani and Plasmodium falciparum. We also investigated pH gradient collapse with other anti-leishmanial agents: azoles, antimonials, benzofurans, amphotericin B and miltefosine. The enhanced activity against intracellular trypanosomatids is seen with Leishmania spp. grown in macrophages but not with Trypanosoma cruzi in epithelial cells and is proposed to be due in part to host-based killing, based on the recent observation that SQ109 is known to convert macrophages to a pro-inflammatory (M1) phenotype.

microbiology↗

bioRxiv2025

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Elucidating the relationships between a class I peptide antigen, a CD8 T cell receptor (TCR) specific to that antigen, and the T cell phenotype that emerges following antigen stimulation, remains a mostly unsolved problem, largely due to the lack of large data sets that can be mined to resolve such relationships. Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. We leverage this unique, comprehensive dataset to integrate with peptide antigen properties, TCR CDR3 sequences, and T cell phenotypes to show that distinct physicochemical features of the antigen-TCR pairs strongly associate with both T cell phenotype and T cell persistence. This analysis suggests that CD8+ T cell phenotype following antigen stimulation is at least partially deterministic, rather than the result of stochastic biological properties.

immunology↗

bioRxiv2025

Mesoscale landscaping of the TRIM protein family reveals a novel human condensatopathy

The mesoscale organization of cells is central to cellular physiology and pathology. Cellular condensates often form via biomolecular phase separation, mediated by intrinsically disordered regions (IDRs) and represent a key mechanism for mesoscale organization. The TRI-partite Motif (TRIM) family of ubiquitin ligases is implicated in diverse cellular functions and disease, yet the role of biomolecular condensation in TRIM family organization remains understudied. Here, we systematically investigate the mesoscale localization of 72 TRIM proteins, revealing that a majority form condensates in distinct cellular compartments. IDR content correlates with dynamic condensate formation, suggesting a critical role in mesoscale organization. Focusing on TRIM8, associated with a neuro-renal disorder, we demonstrate that disease-causing truncations of the TRIM8 C-terminal IDR result in a condensatopathy, characterized by disrupted condensation, proteasomal regulation, and TAK1/NF{kappa}B signaling. Functional assays in cellular and animal models link these disruptions to podocyte dysfunction and impaired response to injury. Our findings establish a framework for understanding condensatopathies and the mesoscale principles governing TRIM family organization and function.

cell biology↗

bioRxiv2024

Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

C1q and immunoglobulins mediate activity-dependent synapse loss in the adult brain

C1q, the initiating protein of the classical complement cascade, mediates synapse loss in development and disease. In various mouse models of neurologic diseases, including Alzheimer's disease, C1q, which is secreted by microglia, the brain's resident macrophages, is found deposited on synapses in vulnerable brain regions. However, what underlies C1q deposition on synapses in the adult brain is unclear. Using in vivo chemogenetics, we demonstrate that neuronal hyperactivity acts as a trigger for region-specific deposition of C1q, which is required for activity-dependent synapse loss. Further, using spatial transcriptomics, live cell tracking, super-resolution microscopy and other molecular and cellular tools, we report a role for B lymphocyte lineage cells and immunoglobulins in the activity-dependent C1q deposition and synapse loss. Overall, our work suggests a link between neuronal hyperactivity and C1q-mediated synapse loss in the adult brain and introduces immunoglobulins as players in this process.

neuroscience↗

bioRxiv2024

Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation

Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. Long-read sequencing (LRS) enhances our ability to detect disease-associated and functionally relevant structural variants; however, its application in large-scale genomic studies has been limited by challenges in sample preparation and high costs. Here, we leverage a new scalable wet-lab protocol and computational pipeline for whole-genome Oxford Nanopore Technologies sequencing and apply it to neurologically normal control samples from the North American Brain Expression Consortium (NABEC) (European ancestry) and Human Brain Collection Core (HBCC) (African or African admixed ancestry) cohorts. Through this work, we present a publicly available long-read resource from 351 human brain samples (median N50: 27 Kbp and at an average depth of ~40x genome coverage). We discover approximately 234,905 SVs and produce locally phased assemblies that cover 95% of all protein-coding genes in GRCh38. To resolve cis-regulatory effects, we develop ASM-LR, a method for allele-specific methylation analysis from long-read data, revealing both strong and subtle regulatory effects, including numerous novel methylation QTLs masked in unphased models. Our results highlight the power of haplotype-resolved methylation to uncover regulatory mechanisms and establish a foundational resource for exploring how genetic variation shapes gene expression and epigenetic architecture across diverse ancestries.

genomics↗

bioRxiv2024

CNV-Finder: Streamlining Copy Number Variation Discovery

Copy Number Variations (CNVs) play pivotal roles in the etiology of complex diseases and are variable across diverse populations. Understanding the association between CNVs and disease susceptibility is significant in disease genetics research and often requires analysis of large sample sizes. One of the most cost-effective and scalable methods for detecting CNVs is based on normalized signal intensity values, such as Log R Ratio (LRR) and B Allele Frequency (BAF), from Illumina genotyping arrays. In this study, we present CNV-Finder, a novel pipeline integrating deep learning techniques on array data, specifically a Long Short-Term Memory (LSTM) network, to expedite the large-scale identification of CNVs within predefined genomic regions. This facilitates efficient prioritization of samples for time-consuming or costly subsequent analyses such as Multiplex Ligation-dependent Probe Amplification (MLPA), short-read, and long-read whole genome sequencing. We incorporate four genes to establish our methods--Parkin (PRKN), Leucine Rich Repeat And Ig Domain Containing 2 (LINGO2), Microtubule Associated Protein Tau (MAPT), and alpha-Synuclein (SNCA)--which may be relevant to neurological diseases such as Alzheimers disease (AD), Parkinsons disease (PD), Progressive Supranuclear Palsy (PSP), or related disorders such as essential tremor (ET). By training our models on expert-annotated samples and validating them across diverse cohorts, including those from the Global Parkinsons Genetics Program (GP2) and additional dementia-specific databases, we demonstrate the efficacy of CNV-Finder in accurately detecting deletions and duplications. Our pipeline outputs app-compatible files for visualization within CNV-Finders interactive web application. This interface enables researchers to review predictions and filter displayed samples by model prediction values, LRR range, and variant count in order to explore or confirm results. Our pipeline integrates this human feedback to enhance model performance and reduce false positive rates. Through a series of comprehensive analyses and validations using visual inspection, MLPA, short-read, and long-read sequencing data, we demonstrate the robustness and adaptability of CNV-Finder in identifying CNVs with regions of varied size, probe density, and noise. Our findings highlight the significance of contextual understanding and human expertise in enhancing the precision of CNV identification, particularly in complex genomic regions like 17q21.31. The CNV-Finder pipeline is a scalable, publicly available resource for the scientific community, available on GitHub (https://github.com/GP2code/CNV-Finder; DOI 10.5281/zenodo.14182563). CNV-Finder not only expedites accurate candidate identification but also significantly reduces the manual workload for researchers, enabling future targeted validation and downstream analyses in regions or phenotypes of interest.

bioinformatics↗

bioRxiv2024

Human Stem Cell-derived Kidney Collecting Duct Model via Epithelial Microphysiological Analysis Platform: Epi-MAP

The kidney epitheliums pivotal role in molecular filtration, metabolism, and excretion highlights the crucial importance of understanding kidney physiology in drug development. However, our knowledge is largely derived from non-human or non-physiological models, potentially limiting its applicability to humans. To address this significant gap, we have pioneered a human kidney epithelial microphysiological analysis platform (Epi-MAP) designed to establish, mature, and monitor renal functions of the human collecting epithelium within a physiologically relevant microenvironment. We first demonstrate the highly mature collecting duct physiology derived from human stem cells, enabled by the Epi-MAPs microenvironments that recapitulate in vivo asymmetries in fluidic and biochemical conditions. The integrated biosensors of the Epi-MAP provide long-term, time-resolved epithelial maturation trajectories, revealing advanced integrity and functional maturity with transepithelial metrics. Furthermore, Epi-MAPs electrophysiological analytics for measuring water flux, in conjunction with transepithelial potential and resistance, allow for real-time decoding of intricate epithelial responses to substance stimulation, showcasing its effectiveness as a robust pharmacological test model. This human cell-derived, physiologically advanced model on a chip stands as a robust in vitro tool, offering comprehensive insights into human kidney biology and significantly enhancing drug discovery process based on human physiology.

bioengineering↗