Biology subjects

Leung, J. M.

Publications and source records attributed to Leung, J. M..

14 recordsLinked to original sources

bioRxiv2026

Elexacaftor/tezacaftor/ivacaftor treatment is associated with epigenetic age deceleration in cystic fibrosis

Background: Cystic fibrosis (CF) is associated with chronic inflammation and progressive multisystem disease, which may contribute to accelerated biological aging. Elexacaftor/tezacaftor/ivacaftor (ETI) substantially improves clinical outcomes in people with CF (pwCF), but its effects on epigenetic aging and their relationship with inflammation remain poorly understood. Methods: We performed a pilot longitudinal study of 8 modulator-naive pwCF. Blood DNA methylation was profiled before ETI initiation and after 1 year of treatment. DNAmGrimAge2 age acceleration was calculated adjusting for chronological age and blood cell composition. Associations with inflammatory biomarkers and clinical measures were assessed using repeated measures correlation. Results: DNAmGrimAge2 was strongly correlated with chronological age at baseline and follow-up. DNAmGrimAge2 age acceleration decreased after ETI treatment, from a median of 1.92 years before treatment to -1.70 years after 1 year (p=0.008). Greater age acceleration was associated with higher IL-6, IL-1{beta}, and calprotectin concentrations. Higher FEV1pp was associated with lower age acceleration, whereas higher sweat chloride was associated with greater age acceleration. Conclusions: DNAmGrimAge2 age acceleration decreased following ETI initiation and was associated with markers of innate and neutrophilic inflammation and CF disease activity. These findings suggest that epigenetic aging in CF may be dynamic and responsive to improvements in CFTR function and inflammatory disease burden. Larger longitudinal studies are needed to validate these findings and determine their relationship with long-term clinical outcomes.

genetics↗

bioRxiv2026

Rapid Mechanistic Bridging of an Alzheimer's Disease Plasma Protein Staging Panel Across Brain Proteomics Cohorts

Background: Blood-based biomarkers are transforming Alzheimer's Disease (AD) diagnosis and staging. Recent multi-protein plasma panels accurately identify individuals with advanced Braak pathology, but whether these circulating biomarkers truly reflect the molecular remodeling underlying AD neuropathology remains unclear. Pre-existing datasets could answer such questions, but their reuse requires harmonized protein expression data, standardized sample annotations, and consistent study metadata. Methods: A recently reported seven-protein plasma staging panel was evaluated across multiple post-mortem proteomics brain cohorts using pre-structured datasets on the Tesorai platform. Five datasets with Braak stage data were identified and re-analyzed. A linear model was used to distinguish late (V-VI) from early Braak stage (0-IV). Because phosphorylated tau 217 (p-tau217) and amyloid beta 1-40 (A{beta}40) were not reported for any studies, raw spectra were reprocessed to quantify these proteoforms. Results: Across the cohorts, the plasma-derived biomarker panel consistently discriminated early from late disease despite heterogeneous protein coverage. Reprocessing of raw spectra recovered tau phosphopeptides absent from the original protein summaries, enabling inclusion of p-tau217, while A{beta}40 remained undetected. Together, these findings show that proteins comprising a recently proposed blood-based staging panel are associated with proteomic remodeling in the AD brain across independent cohorts. Conclusions: These findings provide biological validation for a recently proposed blood-based seven-protein staging panel by demonstrating that its constituent biomarkers are associated with disease-stage proteomic changes in AD brain tissue. More broadly, re-mining legacy mass spectrometry data for disease-relevant proteoforms, combined with pre-structured datasets, can accelerate evaluation of emerging blood-based biomarkers against neuropathological and molecular features of disease.

neuroscience↗

bioRxiv2026

Real-paired single-cell/bulk RNA-seq benchmark and a practical protocol for accurate cell-type deconvolution in human BAL samples

BackgroundPseudo-bulk RNA-seq, generated by aggregating single-cell profiles, is widely used for benchmarking deconvolution methods because it globally approximates bulk transcriptomes and provides known cell-type proportions as ground truth. However, pseudo-bulk inherits single-cell specific measurement properties, and the extent to which these differ from real bulk RNA-seq remains difficult to quantify in the absence of paired data. In practice, deconvolution studies also commonly rely on large external single-cell references, yet the value of small, protocol-matched in-study references has not been systematically evaluated under real bulk conditions. These gaps motivate a paired benchmark that jointly examines pseudo-bulk fidelity, reference design, and their consequences for deconvolution accuracy. ResultsWe establish a fully paired benchmarking framework using split-sample, donor-matched bulk and single-cell RNA-seq (scRNA-seq) from human bronchoalveolar lavage (BAL). Embedded within a reverse five-fold cross-validation design and evaluated on real bulk RNA-seq data, this framework benchmarks 15 deconvolution algorithms published in 2013-2025 across 3 cell-type resolutions and 5 single-cell references, including three published BAL datasets, a harmonized lung BAL atlas, and an in-study reference derived from paired aliquots. We show that real bulk and matched pseudo-bulk profiles exhibit systematic gene-level differences, identifying 557 reproducibly discordant genes (|log2 FC| > 1, FDR< 0.05 by LIMMA), including cell-type informative features. These discrepancies reflect technology-specific effects and violate the linear mixing assumption underlying most deconvolution methods. We demonstrate that a protocol-matched in-study reference constructed from only six donors consistently outperforms substantially larger external references, with the advantage that increases at finer cell-type resolution. Moreover, paired samples enable the identification and selective removal of discordant genes, which further improves deconvolution accuracy for many algorithms, particularly in high-resolution settings. These findings are robust across methods, references, and evaluation criteria and extend beyond compositional accuracy to improving recovery of disease-associated cell-type differences in clinical applications. ConclusionsOur study provides the first fully paired benchmark of transcriptomic deconvolution on real bulk RNA-seq data of human BAL samples and demonstrates that reference design and data compatibility are as influential as algorithm choice. Beyond benchmarking, we introduce a practical and cost-effective protocol for deconvolution studies: generate single-cell data for a minimal subset of bulk samples (pilot pairing), use these data to construct an in-study reference and identify discordant genes, and apply the resulting insights to the full cohort. This strategy requires limited additional experimental effort yet yields substantial gains in accuracy and stability, offering actionable guidance for future bulk RNA-seq deconvolution studies across tissues and platforms. One-sentence summarySystematic benchmarking reveals pseudo-bulk biases and provides practical fixes for accurate RNA deconvolution.

bioinformatics↗

bioRxiv2026

A standardized atlas of human bronchoalveolar lavage cells built using scalable ensemble annotation and cross-study robust markers

BackgroundBronchoalveolar lavage (BAL) single-cell RNA sequencing (scRNA-seq) offers rich insights into pulmonary immune dynamics, yet consistent cell-type annotation remains elusive. Existing methods often rely on a single reference, risking inconsistency and domain shift across datasets. A BAL-specific, high-resolution annotation framework is critically needed. MethodsWe developed BAL-EA (BAL Ensemble Annotation), a BAL-centric automated annotation framework that integrates robust, cross-study marker discovery with ensemble machine learning. BAL-EA harmonizes BAL cell identities into a three-tier taxonomy (11 major lineages, 13 refined classes, 21 fine-grained subtypes) compatible with the Human Lung Cell Atlas (HLCA) while capturing lavage-enriched biology. Marker catalogues were derived via reproducibility-guided differential expression across at least 10 independent sub-studies, ensuring resilience to dataset-specific bias. Comparative benchmarking was performed against six leading annotation tools using independent BAL datasets. ResultsWe assembled the largest BAL scRNA-seq atlas to date, integrating more than 347,333 lung cells from HLCA, multiple public BAL datasets, and the largest inhouse BAL cohort ever reported (241,924 cells from 30 individuals). BAL-EA outperformed existing annotation tools, achieving balanced macro-F1 scores over 0.95 for key lineages such as alveolar macrophages (AM), non-alveolar macrophages, and epithelial cells. Application to Chronic Obstructive Pulmonary Disease (COPD) BAL samples revealed reproducible disease-associated shifts, including increased neutrophils and CCL2-positive macrophages alongside reduced AM in COPD patients, findings validated in independent COVID-19 BAL datasets. The released atlas includes harmonized multi-resolution annotations, robust marker panels, pretrained models. ConclusionsThis work contributes the most comprehensive BAL scRNA-seq atlas, introduces a novel BAL-specific annotation framework (BAL-EA), standardizes BAL taxonomy at three resolutions, and provides rigorously validated marker gene resources. Together, these advances deliver a powerful reference for reproducible BAL scRNA-seq analysis and lay the foundation for clinical and translational applications in respiratory disease research.

genomics↗

bioRxiv2023

N4-Hydroxycytidine/Molnupiravir Inhibits RNA-Virus Induced Encephalitis by Producing Mutated Viruses with Reduced Fitness

A diverse group of RNA viruses including Rabies, Polio, La Crosse, West Nile, Zika, Nipah, Eastern and Western equine encephalitis, Venezuelan equine encephalitis, Japanese encephalitis, and tick-borne encephalitis viruses have the ability to gain access to and replicate in the central nervous system (CNS), causing severe neurological disease. Current treatment for these patients is generally limited to supportive care. To address the need for a generalizable antiviral, we utilized a strategy of mutagenesis to limit virus replication. We evaluated ribavirin (RBV), favipiravir (FAV) and N4-hydroxycytidine (NHC) against La Crosse virus (LACV) which is the primary cause of pediatric arboviral encephalitis cases in North America. NHC was more potent than RBV or FAV in neuronal cells. Oral administration of molnupiravir (MOV), the 5-isobutyryl prodrug of NHC, decreased neurological disease development by 32% following intraperitoneal (IP) infection of LACV. MOV also reduced disease by 23% when virus was administered intranasally (IN). NHC and MOV produced less fit viruses by incorporating predominantly G-to-A or C-to-U mutations. Furthermore, NHC also inhibited two other orthobunyaviruses, Jamestown Canyon virus and Cache Valley virus. Collectively, these studies indicate that NHC/MOV has therapeutic potential to inhibit virus replication and subsequent neurological disease caused by this neurotropic RNA virus.

microbiology↗

bioRxiv2023

LPATH: A semi-automated Python tool for clustering molecular pathways

The pathways by which a molecular process transitions to a target state are highly sought-after as direct views of a transition mechanism. While great strides have been made in the physics-based simulation of such pathways, the analysis of these pathways can be a major challenge due to their diversity and variable lengths. Here we present the LPATH Python tool, which implements a semi-automated method for linguistics-assisted clustering of pathways into distinct classes (or routes). This method involves three steps: 1) discretizing the configurational space into key states, 2) extracting a text-string sequence of key visited states for each pathway, and 3) pairwise matching of pathways based on a text-string similarity score. To circumvent the prohibitive memory requirements of the first step, we have implemented a general two-stage method for clustering conformational states that exploits machine learning. LPATH is primarily designed for use with the WESTPA software for weighted ensemble simulations; however, the tool can also be applied to conventional simulations. As demonstrated for the C7eq to C7ax conformational transition of alanine dipeptide, LPATH provides physically reasonable classes of pathways and corresponding probabilities. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/553774v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@14eed4corg.highwire.dtl.DTLVardef@bd1f67org.highwire.dtl.DTLVardef@58c04borg.highwire.dtl.DTLVardef@b88034_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a rapid response by the scientific community to further understand and combat its associated pathologic etiology. A focal point has been on the immune responses mounted during the acute and post-acute phases of infection, but the immediate post-diagnosis phase remains relatively understudied. We sought to better understand the immediate post-diagnosis phase by collecting blood from study participants soon after a positive test and identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. Additionally, in the lymphocyte compartment, CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. Importantly, the identification of these cellular and molecular immune changes occurred at the early stages of COVID-19 disease. These observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. One Sentence SummaryImmunological changes associated with COVID-19 progression can be detected during the early stages of infection.

immunology↗

bioRxiv2023

Single-cell RNA-sequencing of bronchoscopy specimens: development of a rapid, minimal-handling protocol

Single-cell RNA-sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airways diseases. Currently, the majority of scRNA-seq studies in airways diseases have used invasive methods (airway biopsy, surgical resection) which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we are describing the development of a rapid and minimal-handling protocol for preparing single cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximises cell recovery and cell quality, and may facilitate large-scale profiling of the airway transcriptome at single cell resolution. Lay abstractSingle-cell RNA-sequencing (scRNA-seq) measures the gene expression of individual cells, and may be useful for understanding disease processes. scRNA-seq may be used to investigate lung diseases, but using invasive methods such as biopsy or surgery limits our ability to conduct large research studies. Bronchial brushing, where a soft brush is used to collect cells from inside the lungs, is a safer method but we need a better way to isolate individual cells from the brush specimens. We developed a method that is faster and involves less handling of the specimens compared to other published methods. Our method may therefore be useful for conducting large scRNA-seq studies in lung diseases.

genomics↗

bioRxiv2022

HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy

The lung is an understudied site of HIV persistence. We isolated 882 subgenomic proviral sequences by single-genome approaches from blood and lung from nine individuals on long-term suppressive antiretroviral therapy (ART), and characterized genetic diversity and compartmentalization using formal tests. Consistent with clonal expansion as a driver of HIV persistence, identical sequences comprised between 9% to 86% of within-host datasets, though their location (blood vs. lung) followed no consistent pattern. The majority (77%) of participants harbored at least one sequence shared across blood and lung, supporting the migration of clonally-expanded cells between sites. No participant exhibited genetic compartmentalization so obvious that it was visually apparent in a phylogeny. When formal tests were applied however, two (22%) participants showed modest yet significant support for compartmentalization when analysis was restricted to distinct proviruses per site. This increased to four participants (44%) when considering all within-host sequences. Thus, while a minority of individuals harbor somewhat distinctive proviral populations in blood and lung, these can simply be due to unequal distributions of clonally-expanded sequences. Importantly, the extent of lung proviral diversity on ART strongly reflected that in blood (Spearman {rho} = 0.98, p < 0.0001), confirming blood as a strong indicator of total body proviral diversity. Analysis of on-ART proviral diversity in context of pre-therapy viral diversity in two participants revealed marked differences in proviral longevity and dynamics. Whereas one participants proviral pool was rich in ancestral sequences that recapitulated more of HIVs within-host evolutionary history, the others largely comprised more contemporary sequences, including ones that re-seeded the reservoir during a three-year treatment interruption. Results highlight the genetic complexity of proviruses persisting in lung and blood during ART, and the uniqueness of each individuals proviral composition. Individualized HIV remission and cure strategies may be needed to overcome these challenges. Author SummaryHIV persists in the body despite long-term suppressive antiretroviral therapy. Much of our knowledge about the HIV reservoir comes from studying proviruses in blood, but a fundamental question is whether these are distinct from those in tissues. The lung could theoretically engender genetically distinctive HIV populations, but this remains understudied. Our analysis of nearly 900 proviral sequences from blood and lung of nine individuals with HIV receiving long-term therapy revealed substantial within-host heterogeneity, yet some common patterns. Identical sequences (consistent with clonal expansion of infected cells) were observed in everyone, though at different (9-86%) frequencies. Recovery of shared sequences across blood and lung was common (77% of participants). Fewer than half of participants exhibited blood-lung genetic compartmentalization, and only modestly so. Moreover, when present, compartmentalization was often attributable to differential distribution of identical sequences, not the presence of genetically distinctive populations, across sites. Results also revealed marked inter-individual differences in proviral dynamics, as evidenced by the proportion of persisting proviruses that represented ancestral versus more recently-circulating viral sequences. Critically, the extent of within-host proviral diversity in blood correlated strongly with that in lung, indicating that despite inter-individual heterogeneity, blood is a strong indicator of proviral diversity elsewhere in the body.

molecular biology↗

bioRxiv2019

Housing laboratory mice in a natural environment uncovers genetic and environmental contributions to immune variation.

The relative contributions of genetic and environmental factors to variation in immune responses are still poorly understood. Here, we performed a deep phenotypic analysis of immunological parameters of laboratory mice released into an outdoor enclosure, carrying susceptibility genes (Nod2 and Atg16l1) implicated in the development of inflammatory bowel diseases. Variations of immune cell populations were largely driven by environment, whereas cytokine production in response to stimulation was affected more by genetic mutations. Multi-omic models identified transcriptional signatures associated with differences in T cell populations. Subnetworks associated with responses against Clostridium perfringens, Candida albicans and Bacteroides vulgatus were also coupled with rewilding. Hence, exposing laboratory mice carrying different genetic mutations to a natural environment uncovered important contributors to immune variation. One sentence summaryNatural environment exposure in laboratory mice primarily promotes variation in population frequencies of immune cells, whereas cytokine responses to stimulation are affected more by genetic susceptibility to inflammatory bowel disease.

immunology↗

bioRxiv2019

Altered immunity of laboratory mice in the natural environment is associated with fungal colonization

The immune systems of free-living mammals such as humans and wild mice display a heightened degree of activation compared with laboratory mice maintained under artificial conditions. Here, we demonstrate that releasing inbred laboratory mice into an outdoor enclosure to mimic life in a natural environment alters the state of immunity. In addition to enhancing the differentiation of T cell populations previously associated with pathogen exposure, we found that outdoor release of mice led to an increase in circulating granulocytes. However, rewilded mice were not infected by pathogens previously implicated in immune activation. Rather, changes to the immune system were associated with an altered composition of the microbiota, and fungi isolated from rewilded mice were sufficient to increase circulating granulocytes. These findings establish an experimental procedure to investigate the impact of the natural environment on immune development and identify a role for sustained fungal exposure in determining granulocyte numbers.

immunology↗

bioRxiv2019

A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers

TgDCX is a doublecortin-domain protein associated with the conoid fibers, a set of strongly curved non-tubular tubulin-polymers in Toxoplasma. TgDCX deletion impairs conoid structure and parasite invasion. TgDCX contains two tubulin-binding domains: a partial P25-alpha and the DCX/doublecortin domain. Orthologues are found in apicomplexans and their free-living relatives Chromera and Vitrella. We report that isolated TgDCX-containing conoid fibers retain their pronounced curvature, but loss of TgDCX destabilizes the fibers. We crystallized and determined the 3D-structure of the DCX-domain, which is similar to those of human doublecortin and well-conserved among TgDCX orthologues. However, the orthologues vary widely in targeting to the conoid in Toxoplasma and in modulating microtubule organization in Xenopus cells. Several orthologues bind to microtubules in Xenopus cells, but only TgDCX generates short, strongly curved microtubule arcs. EM analysis shows microtubules decorated with TgDCX bundled into rafts, often bordered on one edge by a "C"-shaped incomplete tube. A Chromera orthologue closely mimics TgDCX targeting in Toxoplasma and binds to microtubules in Xenopus cells, but does not generate arcs or "C"-shaped tubes, and fails to rescue the defects of the TgDCX-knockout parasite. These observations suggest that species-specific features of TgDCX enable it to generate strongly curved tubulin-polymers to support efficient host-cell invasion.

cell biology↗

bioRxiv2018

TgCentrin2 is required for invasion and replication in the human parasite Toxoplasma gondii

Centrins are EF-hand containing proteins ubiquitously found in eukaryotes and are key components of centrioles/basal bodies as well as certain contractile fibers. We previously identified three centrins in the human parasite Toxoplasma gondii, all of which localized to the centrioles. However, one of them, TgCentrin2 (CEN2), is also targeted to ring-shaped structures at the apical and basal ends of the parasite, as well as to multiple annuli at the junction between the apical cap and the rest of the membrane cortex. The role(s) that TgCentrin2 plays in these locations was unknown. Here we report the functional characterization of TgCentrin2 in the parasite lytic cycle. After multiple unsuccessful attempts to knock out or knock down the TgCentrin2 gene with existing tools, we designed a new conditional knockdown method that combines transcriptional and protein stability control to achieve tight regulation of TgCentrin2 levels in the parasite. We discovered that under knockdown conditions, there was an ordered loss of TgCentrin2 from its four compartments, due to differences in incorporation kinetics and structural inheritance over successive generations. This was correlated with the development of major invasion deficiency at early stages of CEN2 knockdown, and replication defects at later stages. These results indicate that TgCentrin2 is incorporated into multiple cytoskeletal structures to serve distinct functions in T. gondii that are required for parasite survival.

cell biology↗

bioRxiv2017

Stability and function of a putative microtubule organizing center in the human parasite Toxoplasma gondii

The organization of the microtubule cytoskeleton is dictated by microtubule nucleators or organizing centers. Toxoplasma gondii, an important human parasite, has an array of 22 regularly spaced cortical microtubules stemming from a hypothesized organizing center, the apical polar ring. Here, we examine the functions of the apical polar ring by characterizing two of its components, KinesinA and APR1, and discovered that its putative role in templating can be separated from its mechanical stability. Parasites that lack both KinesinA and APR1 ({Delta}kinesinA{Delta}apr1) are capable of generating 22 cortical microtubules. However, the apical polar ring is fragmented in live{Delta} kinesinA{Delta}apr1 parasites, and is undetectable by electron microscopy after detergent extraction. Disintegration of the apical polar ring results in the detachment of groups of microtubules from the apical end of the parasite. These structural defects are linked to a diminished ability of the parasite to move and to invade host cells, as well as decreased secretion of effectors important for these processes. Together, the findings demonstrate the importance of the structural integrity of the apical polar ring and the microtubule array in the Toxoplasma lytic cycle, which is responsible for massive tissue destruction in acute toxoplasmosis.

cell biology↗