Biology subjects

Do, A.

Publications and source records attributed to Do, A..

9 recordsLinked to original sources

bioRxiv2026

Large-scale meta-analysis of over one million individuals reveals the genetic architecture of 127 complex traits in East Asian populations

Genome-wide association studies (GWASs) have disproportionately focused on European (EUR) populations, limiting the characterization of genetic architecture in other ancestries. To address this imbalance, we integrated large-scale biobanks from Japan, Korea, Taiwan, and China to perform the largest phenome-wide meta-analysis to date in East Asian (EAS) populations, encompassing over one million individuals across 127 complex traits. We identified 8,010 previously unreported associations and observed substantial genetic sharing across EAS subpopulations, while also detecting cohort-specific heterogeneity within the broader EAS context. Transethnic analyses revealed moderate genetic correlations between EAS and EUR populations, indicating both shared and ancestry-specific components of disease risk. Pleiotropy analyses highlighted prominent signals within the HLA region, supported by protein-protein interaction connectivity and immune-related pathway enrichment. Decomposition of genome-wide association matrices further uncovered structured cross-trait architectures, revealing a predominantly shared polygenic backbone driven by metabolic, biochemical, and anthropometric traits, together with two discrete latent components enriched for immune-related processes. Together, our findings refine the genetic architecture of complex traits in East Asian populations at unprecedented scale and clarify the balance between shared and population-specific determinants of human diseases.

genetics↗

bioRxiv2025

Alpha Parvin Promotes Glucose Uptake and Metabolism in Skeletal Muscle with Minimal Influence on Hepatic Insulin Sensitivity

Skeletal muscle and liver insulin resistance are early features in the sequelae of type 2 diabetes. Integrins are extracellular matrix receptors expressed on skeletal muscle cells and hepatocytes and have been implicated in modulating obesity-associated insulin resistance. Integrins regulate cell function through intracellular proteins including the ILK-PINCH-Parvin (IPP) complex. ILK promotes skeletal muscle and liver insulin resistance in diet-induced obesity in mice but the role of Parvin is unexplored. Here we demonstrate that hepatocyte specific deletion of -Parvin had only minimal influence on endogenous glucose production or whole-body insulin sensitivity. In contrast, deletion of -Parvin in skeletal muscle caused a striking reduction in muscle glucose uptake during an insulin clamp in lean mice which was not exacerbated by diet-induced obesity. Insulin-mediated GLUT4 membrane recruitment was impaired in mutant muscles which displayed significant morphological abnormalities due to actin cytoskeleton dysfunction. Consistent with severe muscular dysfunction, mitochondrial oxidative capacity and aerobic exercise capacity were blunted in muscle -Parvin-null mice. Thus, -Parvin has a minor role in liver insulin action but is required for insulin-stimulated glucose uptake in skeletal muscle due to its role in actin cytoskeleton regulation. These data suggest that individual IPP complex proteins link cell structure to metabolism via distinct mechanisms in a tissue-specific fashion.

physiology↗

bioRxiv2024

B cells targeting parasites capture spatially linked antigens to secure T cell help

Our understanding of T-cell-dependent humoral responses has been largely shaped by studies involving model antigens such as recombinant proteins and viruses 1,2. In these contexts, B cells internalize the entire antigen or pathogen, and present a range of antigens to helper CD4+ T cells to initiate the humoral response. However, this model does not account for large pathogens (such as parasites) that are too large to be taken up by individual B cells, and the mechanisms by which B cells acquire and present antigens from large complex pathogens to T cells remain poorly understood. Here we used Plasmodium, the causative parasite of malaria, as a model to investigate the requirements for T cell help for B cells targeting the Plasmodium surface circumsporozoite protein (CSP). Upon Plasmodium sporozoite (SPZ) immunization, CSP-specific B cells can form a synapse-like structure with SPZs and take up CSP and non-CSP surface antigens. As a result, CSP-specific B cells can receive help from CD4+ T cells specific to antigens that are located on the surface but not cytosol of the Plasmodium SPZ. Therefore, B cells can obtain help, not only from T cells with the same protein specificity, but also from T cells specific for spatially linked antigens. This flexibility in T cell help may enhance the initiation and maintenance of humoral immune responses to complex pathogens.

immunology↗

bioRxiv2024

Claustrum projections to the anterior cingulate modulate nociceptive and pain-associated behaviour

The anterior cingulate cortex (ACC) processes nociceptive information and pain unpleasantness. The claustrum is a subcortical region that provides robust feed-forward inhibition onto the ACC, suggesting this circuit could play a role in modulating pathological states such as pain. However, the function of this circuit in the context of acute and chronic inflammatory pain is unclear. Here, we show that claustrocingulate neurons exhibit a bimodal pattern of activation following acute pain but are suppressed during states of chronic inflammatory pain. Molecular lesion and chemogenetic suppression of claustrocingulate neurons increased acute nociception but interfered with pain learning. Activation of this pathway rescued mechanical allodynia associated with chronic pain. Together, these results suggest claustrocingulate neurons are a critical component of the pain neuromatrix, and dysregulation of this connection may contribute to chronic pain.

neuroscience↗

bioRxiv2023

Harmonization of CSF and imaging biomarkers for Alzheimer's disease biomarkers: need and practical applications for genetics studies and preclinicalclassification

INTRODUCTIONIn Alzheimers disease (AD) research, cerebrospinal fluid (CSF) Amyloid beta (A{beta}), Tau and pTau are the most accepted and well validated biomarkers. Several methods and platforms exist to measure those biomarkers which leads to challenges in combining data across studies. Thus, there is a need to identify methods that harmonize and standardize these values. METHODSWe used a Z-score based approach to harmonize CSF and amyloid imaging data from multiple cohorts and compared GWAS result using this method with currently accepted methods. We also used a generalized mixture modelling to calculate the threshold for biomarker-positivity. RESULTSZ-scores method performed as well as meta-analysis and did not lead to any spurious results. Cutoffs calculated with this approach were found to be very similar to those reported previously. DISCUSSIONThis approach can be applied to heterogeneous platforms and provides biomarker cut-offs consistent with the classical approaches without requiring any additional data.

bioinformatics↗

bioRxiv2022

Combined loss of obscurin and obscurin-like 1 in murine hearts results in impaired diastolic dysfunction, altered metabolism and deregulated mitophagy.

Muscle proteins of the obscurin protein family play important roles in sarcomere organization, sarcoplasmic reticulum (SR) and T-tubule architecture and function. However, their precise molecular functions and redundancies between protein family members as well as their involvement in cardiac diseases remain to be fully understood. To investigate the functional roles of obscurin and its close homologue obscurin-like 1 (Obsl1) in the heart, we generated and analyzed knockout mice for obscurin, Obsl1, as well as obscurin/Obsl1 double-knockouts (dKO). We show that dKO mice are viable but show postnatal deficits in cardiac muscle SR and mitochondrial architecture and function at the microscopic, biochemical and cellular level. Altered SR structure resulted in perturbed calcium cycling, while mitochondrial ultrastructure deficits were linked to decreased levels of Chchd3, a Micos complex protein. Hearts of dKO mice also show increased expression of Atg4d, a novel Obsl1 interacting protein, resulting in abnormal mitophagy and increased unfolded protein response. At the physiological level, loss of obscurin and Obsl1 resulted in a profound delay of cardiac relaxation, associated with metabolic signs of heart failure. Taken together, our data suggest that obscurin and Obsl1 play crucial roles in cardiac SR structure, calcium cycling, mitochondrial function, turnover and metabolism.

cell biology↗

bioRxiv2021

StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritise potentially pathogenic genetic variation

SummaryMissense mutations that change protein stability are strongly associated with human inherited genetic disease. With the recent availability of predicted structures for all human proteins generated using the AlphaFold2 prediction model, genome-wide assessment of the stability effects of genetic variation can, for the first time, be easily performed. This facilitates the interrogation of personal genetic variation for potentially pathogenic effects through the application of stability metrics. Here, we present a novel algorithm to prioritise variants predicted to strongly destabilise essential proteins, available as both a standalone software package and a web-based tool. We demonstrate the utility of this tool by showing that at values of the Stability Sort Z-score above 1.6, pathogenic, protein-destabilising variants from ClinVar are detected at a 58% enrichment, over and above the destabilising (but presumably non-pathogenic) variation already present in the HapMap NA12878 genome. Availability and ImplementationStabilitySort is available as both a web service (http://130.56.244.113/StabilitySort/) and can be deployed as a standalone system (https://gitlab.com/baaron/StabilitySort). ContactDan.Andrews@anu.edu.au

bioinformatics↗

bioRxiv2021

Structural and functional analysis of lorlatinib analogs reveals roadmap for targeting diverse compound resistance mutations in ALK-positive lung cancer

The treatment approach to advanced, ALK-positive non-small cell lung cancer (NSCLC) utilizing sequential ALK tyrosine kinase inhibitors (TKIs) represents a paradigm of precision oncology. Lorlatinib is currently the most advanced, potent and selective ALK tyrosine kinase inhibitor (TKI) in the clinic. However, tumors invariably acquire resistance to lorlatinib, and after sequential ALK TKIs culminating with lorlatinib, diverse refractory compound ALK mutations can emerge. Here, we determine the spectrum of lorlatinib-resistant compound ALK mutations identified in patients after treatment with lorlatinib, the majority of which involve ALK G1202R or I1171N/S/T. By assessing a panel of lorlatinib analogs against compound ALK mutant in vitro and in vivo models, we identify structurally diverse lorlatinib analogs that harbor differential selective profiles against G1202R- versus I1171N/S/T-based compound ALK mutations. Structural analysis revealed that increased potency against compound mutations was achieved primarily through two different mechanisms of improved targeting of either G1202R- or I1171N/S/T-mutant kinases. Based on these results, we propose a classification of heterogenous ALK compound mutations designed to focus the development of distinct therapeutic strategies for precision targeting of compound resistance mutations following sequential TKIs.

cancer biology↗

bioRxiv2019

LITE-1 Mediates X-ray Avoidance Response in C. elegans

We report the finding that C. elegans display X-ray avoidance behavior at high but well tolerated doses, and that this behavior appears to require LITE-1, a gustatory receptor that has been implicated in UV avoidance behavior. We recorded acute behavioral responses of wildtype worms to increasing intensities of X-ray stimulation and found a positive stimulation-response relationship. Mutant strains of worms with dysfunctional photoreceptor proteins LITE-1 and GUR-3 were assayed, and the X-ray avoidance response was found to be nearly absent in LITE-1 mutants but not GUR-3 mutants, suggesting a prominent role for LITE-1 in the detection of X-rays. These findings may be important for developing optogenetics tools to stimulate cells in deep tissue using X-rays, for understanding the mechanism of LITE-1 signaling, and for understanding how organisms may respond to radiation.

neuroscience↗