Biology subjects

Ryu, D.

Publications and source records attributed to Ryu, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Syndecan-4 exerts canonical heparan sulfate-dependent and noncanonical heparan sulfate-independent functions that regulate Aβ amyloid homeostasis

Background Heparan sulfate (HS) and heparan sulfate proteoglycans (HSPGs) are components of the amyloid deposits in Alzheimers disease (AD) and other amyloidoses. HS and HSPGs are canonically thought to facilitate amyloid deposition by accelerating the aggregation of amyloidogenic proteins and impairing their clearance in a HS-dependent manner. Methods Leveraging insights from large-scale proteomic data, we focused on Syndecan-4 (Sdc4), the most increased transmembrane HSPG in the AD brain and in the brain of A{beta} amyloid depositing mice. We used proximity ligation assays (PLA) to evaluate the association of Sdc4 with A{beta} in situ and assessed the impacts of the Sdc4 ectodomain on A{beta} aggregation in vitro. Overexpression studies in cells, hiPSC-derived neurons, and mouse organotypic brain slice cultures (OBSCs) coupled with structure-function studies were used to investigate impacts on A{beta} production and APP processing. Finally, effects of overexpression of Sdc4 in vivo in the CRND8 amyloid deposition model were evaluated. Results Consistent with canonical roles, PLA demonstrated a spatial association of Sdc4 with amyloid deposits, and in vitro, the Sdc4 ectodomain accelerated A{beta} fibril formation in a HS-dependent manner. Unexpectedly, Sdc4 overexpression reduced A{beta} production in CHO cells, hiPSC-derived neurons, and OBSCs. These effects were accompanied by dramatic decreases in the levels of sAPP and C83 and increased immature APP in the cell. Sdc4 promoted altered APP localization into detergent resistant membrane domains and increased APP association with ATG5+/LC3+/Cathepsin D+ vesicles. Structure-function studies revealed that the transmembrane region mediates these effects in a glycosaminoglycan-independent manner. Sdc4 overexpression in the brain of APP mice significantly reduced amyloid deposition at an early age. Conclusions Sdc4 exerts paradoxical and mechanistically distinct effects that could impact AD pathogenesis differentially, potentially promoting A{beta} fibrillization extracellularly while suppressing APP processing and A{beta} production. Such data challenge the prevailing view that increased levels of HSPGs in AD are always pro-amyloidogenic and identify Sdc4 as a previously unrecognized regulator of amyloid homeostasis in AD.

neuroscience↗

bioRxiv2025

Urolithin A Restores Mitochondrial Function and Reverses Cardiac Remodeling in Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) accounts for nearly half of all heart failure cases; however, mechanism-based therapies targeting cellular dysfunction remain absent. Emerging evidence suggests that mitochondrial dysfunction and impaired quality control, particularly defective mitophagy, are central to the pathogenesis of HFpEF. Urolithin A (UA), a gut microbiome-derived postbiotic metabolite, has shown promise as a mitophagy activator in preclinical models; however, its therapeutic efficacy in HFpEF remains unknown. MethodsWe used a clinically relevant two-hit HFpEF mouse model (high-fat diet (HFD) plus N{omega}-nitro-L-arginine methyl ester (L-NAME)) and co-administered UA during disease progression. The cardiac structure and function were assessed using echocardiography, histology, and transmission electron microscopy. Mitochondrial bioenergetics were evaluated using Seahorse-based respirometry. Mitophagy flux was monitored using mt-Keima assays in H9c2 cells and human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Mechanistic insights were obtained using immunoblotting, integrated shotgun metagenomic and lipidomic profiling, and single-nucleus RNA sequencing (snRNA-seq). ResultsUA treatment significantly attenuated cardiac remodeling and fibrosis in HFpEF mice while improving diastolic function parameters. Transmission electron microscopy revealed restoration of the mitochondrial ultrastructure, and mitochondrial stress tests demonstrated enhanced oxidative phosphorylation capacity and glycolytic reserves. Immunoblot assays revealed that UA treatment recovered PINK1/Parkin-mediated mitophagy markers (reduced LC3-II and p62/SQSTM1). Mt-Keima assays confirmed enhanced mitophagic flux in H9c2 cells under HFpEF-like stress conditions. Integrated metagenomics and lipidomics revealed significant reductions in cardiovascular risk-associated ceramides. snRNA-seq demonstrated that HFpEF-like stress downregulated contractile, calcium-handling, and mitochondrial mitophagy gene programs. UA treatment restored the mitochondrial quality control signatures and normalized profibrotic and conduction-type cell populations. ConclusionsUrolithin A restored mitochondrial quality control through the activation of mitophagy and reversed cardiac remodeling in HFpEF. These findings establish UA as a mitochondria-targeted therapeutic candidate for HFpEF. Novelty and SignificanceO_ST_ABSWhat is known?C_ST_ABS{checkmark} Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome driven by metabolic stress and myocardial remodeling, for which effective disease-modifying therapies are lacking. {checkmark}Mitochondrial dysfunction and impaired mitophagy have been implicated in HFpEF, but their roles in cardiomyocyte state remodeling and fibrosis remain incompletely defined. {checkmark}Urolithin A, a gut microbiome-derived metabolite, enhances mitophagy in aging and metabolic tissues, but its relevance to HFpEF has not been established. What new information does this article contribute?{checkmark} Urolithin A restores mitochondrial quality control and mitophagic flux in cardiomyocytes, improving diastolic function and attenuating cardiac remodeling in a two-hit HFpEF model. {checkmark}Integrated metagenomic and lipidomic analyses identify suppression of gut microbiome-associated ceramide biosynthesis as a systemic mechanism linked to Urolithin A-mediated cardioprotection. {checkmark}Single-nucleus RNA sequencing reveals that Urolithin A reverses maladaptive cardiomyocyte transcriptional state transitions toward fibrogenic and conduction-like programs.

molecular biology↗

bioRxiv2023

Spatial dissection of cellular heterogeneity and functional crosstalk in the tumor microenvironments of gastric cancers

Spatial transcriptomics offers unprecedented challenges in characterizing tumor ecosystems, encompassing tumor cells and their surrounding tumor microenvironments (TME) along with cellular interactions therein. Here, we conducted Visium-based spatial transcriptomics on nine primary gastric cancers (GC) to translate the spatial organization of GC ecosystems into the functional landscape of cellular crosstalk across malignant, stromal and immune cells. We identified three distinct GC subtypes of 3 immunogenic, 3 epithelial and 3 stromal GCs with elevated infiltration of immune, malignant cells and fibroblasts reflecting the heterogeneity of the cell types and their interactions in GC TME. GC spatial architecture was further delineated into 6 regional compartments with varying degree of TME infiltration, among which the fibroblast-enriched TME was associated with the upregulation of epithelial-to-mesenchymal transformation (EMT) and immune response in malignant and immune cells, respectively. Cell type-specific transcriptional dynamics representing cellular crosstalk between TME cells were further identified, e.g., the infiltration of malignant and endothelial cells promote the cellular proliferations of TME cells whereas the fibroblasts and immune cells are associated with pro-cancer and anti-cancer immunity, respectively. Ligand-receptor analysis further revealed that CCL2-expressing fibroblasts promote the pro-cancer signaling of immune cells including JAK-STAT3 signaling and inflammatory response in tumor-infiltration macrophages. The CCL2+fibroblasts and macrophages with activated JAK-STAT3 signals are co-localized in spatial GC architecture and their co-abundance was associated with unfavorable clinical outcomes. Taken together, GC spatial transcriptomes can be regionally and functionally delineated into functional cellular crosstalk involving multiple cell types with potential clinical relevance, particularly the interaction between CCL2+ fibroblasts and JAK-STAT3+macrophages contributing to cancer-favoring immune contexture in GC TME.

cancer biology↗

bioRxiv2023

Aβ Amyloid Scaffolds the Accumulation of Matrisome and Additional Proteins in Alzheimer's Disease

We report a highly significant correlation between human Alzheimers disease (AD) brain proteome changes and those in CRND8 APP695NL/F transgenic mice. Comparing protein changes observed in the CRND8 mice with co-expression networks derived from human Alzheimers disease (AD), reveals both conserved and divergent module changes. Many proteins in the most highly conserved module (M42, matrisome) accumulate in plaques, cerebrovascular amyloid (CAA), dystrophic neuronal processes, or a combination thereof. Overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), in CRND8 mice brains leads to increased accumulation of A{beta} in plaques and in blood vessels; further, recombinant MDK and PTN enhance A{beta} aggregation into amyloid structures. Multiple M42 proteins bind to fibrillar A{beta}42 and a non-human amyloid fibril in vitro. Supporting this binding data, MDK and PTN co-accumulate with transthyretin (TTR) amyloid in the heart. Notably, our findings establish that proteomic changes in modules observed in human AD brains define an A{beta} amyloid "responsome" that is well conserved from mouse models to humans. Further, distinct amyloid structures appear to serve as scaffolds, facilitating the co-accumulation of proteins with signaling functions, and this co-accumulation may contribute to downstream pathological sequalae. Overall, this contextualized understanding of proteomic changes and their interplay with amyloid deposition provides valuable insights into the complexity of AD pathogenesis and potential biomarkers and therapeutic targets.

neuroscience↗

bioRxiv2023

3-phenyllactic acid promotes healthspan through SKN-1/ATFS-1-mediated mitochondrial activation and stress resilience

The mechanisms underlying the impact of probiotic supplementation on health remain largely elusive. While previous studies have primarily focused on the discovery of novel bioactive bacteria and alterations in the microbiome environment to explain potential probiotic effects, our research delves into the role of living lactic acid bacteria (LAB) and their conditioned media, highlighting that only the former, not dead bacteria, enhance the healthspan of Caenorhabditis elegans. To elucidate the underlying mechanisms, we conducted transcriptomic profiling through RNA-seq analysis in C. elegans exposed to LAB or 3-phenyllactic acid (PLA), mimicking the presence of key candidate metabolites of LAB and evaluating healthspan. Our findings reveal that PLA treatment significantly extends the healthspan of C. elegans by promoting energy metabolism and stress resilience in a SKN-1/ATFS-1-dependent manner. Moreover, PLA-mediated longevity is associated with a novel age-related parameter, the Healthy Aging Index (HAI), introduced in this study, which comprises healthspan-related factors such as motility, oxygen consumption rate (OCR), and ATP levels. Extending the relevance of our work to humans, we observed an inverse correlation between blood PLA levels and physical performance in patients with sarcopenia, when compared to age-matched non-sarcopenic controls. Our investigation thus sheds light on the pivotal role of the metabolite PLA in probiotics-mediated enhancement of organismal healthspan, and also hints at its potential involvement in age-related sarcopenia. These findings warrant further investigation to delineate PLAs role in mitigating age-related declines in healthspan and resilience to external stressors. HighlightsO_LIMetabolites Produced by Lactic Acid Bacteria Function as Mediators of Longevity in C. elegans C_LIO_LI3-Phenyllactic Acid (PLA) Augmented Lifespan Extension and Elevated the Healthy Aging Index (HAI) C_LIO_LIPLA Facilitated Healthy Aging by Inducing Mitochondrial Activation and Stress Resistance Dependent on SKN-1/ATFS-1 C_LIO_LIPatients with Sarcopenia and Symptoms of Frailty Exhibited Reduced Blood PLA Levels. C_LI

molecular biology↗

bioRxiv2023

Granulins rescue inflammation, lysosome dysfunction, and neuropathology in a mouse model of progranulin deficiency.

Progranulin (PGRN) deficiency is linked to neurodegenerative diseases including frontotemporal dementia, Alzheimers disease, Parkinsons disease, and neuronal ceroid lipofuscinosis. Proper PGRN levels are critical to maintain brain health and neuronal survival, however the function of PGRN is not well understood. PGRN is composed of 7.5 tandem repeat domains, called granulins, and is proteolytically processed into individual granulins inside the lysosome. The neuroprotective effects of full-length PGRN are well-documented, but the role of granulins is still unclear. Here we report, for the first time, that expression of single granulins is sufficient to rescue the full spectrum of disease pathology in mice with complete PGRN deficiency (Grn-/-). Specifically, rAAV delivery of either human granulin-2 or granulin-4 to Grn-/- mouse brain ameliorates lysosome dysfunction, lipid dysregulation, microgliosis, and lipofuscinosis similar to full-length PGRN. These findings support the idea that individual granulins are the functional units of PGRN, likely mediate neuroprotection within the lysosome, and highlight their importance for developing therapeutics to treat FTD-GRN and other neurodegenerative diseases.

neuroscience↗

bioRxiv2023

Loss-of-SIRT7 sensitizes hepatocellular carcinoma to sorafenib through the regulation of ERK Phosphorylation

The FDA-approved oral multi-kinase inhibitor, sorafenib (BAY 43-9006, Nexavar), is the first approved systemic therapy for patients with unresectable hepatocellular carcinoma (HCC). Although it has been shown to significantly improve the overall survival of patients with HCC, drug resistance limits the response rate to this therapeutic. Here, we report that acquired sorafenib resistance is associated with overexpression of the deacetylase, SIRT7, and a high level of ERK phosphorylation. Further, we identify that the hyperactivation of ERK is controlled by SIRT7-mediated deacetylation of DDX3X. The inhibition of SIRT7 combined with sorafenib resulted in a marked reduction of cell viability in vitro and of tumor growth in vivo. It seems plausible that SIRT7 is responsible for the acquired sorafenib resistance and its inhibition is most likely beneficial together in conjunction with sorafenib by suppressing ERK signaling. HighlightsO_LISorafenib resistance in HCC is associated with SIRT7 and ERK hyperactivation. C_LIO_LISuppression of SIRT7 combined with sorafenib restores sensitivity to sorafenib. C_LIO_LISIRT7 controls sorafenib resistance through ERK activation by mediating DDX3X deacetylation. C_LI

cancer biology↗

bioRxiv2023

Label-free histological analysis of retrieved thrombi in acute ischemic stroke using optical diffraction tomography and deep learning

For patients with acute ischemic stroke, histological quantification of thrombus composition provides evidence for determining appropriate treatment. However, the traditional manual segmentation of stained thrombi is laborious and inconsistent. In this study, we propose a label-free method that combines optical diffraction tomography (ODT) and deep learning (DL) to automate the histological quantification process. The DL model classifies ODT image patches with 95% accuracy, and the collective prediction generates a whole-slide map of red blood cells and fibrin. The resulting whole-slide composition displays an average error of 1.1% and does not experience staining variability, facilitating faster analysis with reduced labor. The present approach will enable rapid and quantitative evaluation of blood clot composition, expediting the preclinical research and diagnosis of cardiovascular diseases.

bioengineering↗

bioRxiv2022

Inhibition of GCN5 decreases skeletal muscle fat metabolism during high fat diet feeding

IntroductionGCN5 (Kat2a) is a lysine acetyl transferase capable of acetylating and inhibiting PGC-1 activity. As such, it is described as a negative regulator of PGC-1 and subsequently restricts mitochondrial content. However, elimination of GCN5 in skeletal muscle does not increase mitochondrial content or alter lipid metabolism under normal metabolic conditions. GCN5 levels increase with high-fat diet (HFD) feeding in rodents. Additionally, the GCN5 homolog, PCAF, has previously been shown to also acetylate and inhibit PGC-1 and therefore may possibly compensate for loss of GCN5. ObjectiveThe objective of this study was to examine if with HFD feeding that elimination of GCN5 (Kat2a gene) from skeletal muscle would elicit improvements in mitochondrial and metabolic markers. MethodsSkeletal muscle specific GCN5 knockouts (Gcn5 skm-/-) were fed an HFD. Body composition, cardio-metabolic and physical fitness outcomes were monitored. Additionally, cultured myotubes were treated with a pan-GCN5/PCAF inhibitor and examined for changes in mitochondrial markers. ResultsElimination of skeletal muscle GCN5 did not alter body composition, tissue masses, energy intake, or energy expenditure measurements of mice fed an HFD. Furthermore, whole body glucose homeostasis and cardiac measurements were not altered. There were few differences in lipid metabolism genes, relatively more glucose oxidation versus Gcn5 skm+/+ (wildtype) mice, and a reduction in Pdk4 expression. Exercise capacity and mitochondrial content levels were not altered in Gcn5 skm-/- mice. Further, elimination of GCN5 in skeletal muscle increased Kat2b (PCAF) mRNA expression; however, inhibition of GCN5/PCAF bromodomains in cultured myotubes did not increase oxidative metabolism genes and decreased expression of some mitochondrial genes and Pdk4 mRNA. ConclusionsNeither elimination of GCN5, nor simultaneous inhibition of GCN5 and its homolog PCAF improved skeletal muscle mitochondrial content under normal or HFD-fed conditions. Despite this, GCN5 may play a role in regulating macronutrient preference by regulating Pdk4 content. Thus, HFD/macronutrient excess revealed novel roles of GCN5 in skeletal muscle. Highlights- Skeletal muscle specific elimination of Gcn5/Kat2a decreases fat oxidation without 1) preventing high-fat diet induced weight gain, 2) improving whole body glucose handling, or 3) improving skeletal muscle mitochondrial content. - Inhibition of the GCN5 and PCAF bromodomains and Gcn5 ablation decreases expression of Pdk4. - Expression of Kat2b increases with Gcn5 elimination in skeletal muscle. - Inhibition of the GCN5 and PCAF bromodomains do not result in increased skeletal muscle mitochondrial content.

physiology↗

bioRxiv2022

L-threonine mediated DAF-16/HSF-1 activation inhibits ferroptosis and increases healthspan

The pathways that impact longevity in the wake of dietary restriction (DR) pathway remain still ill-defined. Most studies have focused on nutrient limitation and perturbations of energy metabolism to explain the beneficial effects of DR. We showed that the essential amino acid L-threonine was elevated in Caenorhabditis elegans under DR, and that L-threonine supplementation increased its healthspan. To elucidate the underlying mechanism, we conducted metabolic and transcriptomic profiling using LC-MS/MS and RNA-seq analyses in worms that were fed with RNAi to induce loss of function of key candidate mediators and evaluated healthspan. L-threonine supplementation and loss-of-threonine dehydrogenase, which govern L-threonine metabolism, increased the healthspan of C. elegans by attenuating ferroptosis in a ferritin-dependent manner. Tran-scriptomic analysis of C. elegans supplemented with L-threonine showed that FTN-1 encoding ferritin was elevated, implying FTN-1 is an essential mediator of longevity promotion through L-threonine. Organismal ferritin levels were positively correlated with chronological aging and L-thre-onine supplementation further increased ferritin levels, which protected against age-associated ferroptosis through the DAF-16 and HSF-1 pathways. Our investigation uncovered the role of a distinct and universal metabolite, L-threonine, in DR-mediated improvement in organismal healthspan, suggesting it could be an effective intervention for preventing senescence progression and age-induced ferroptosis.

cell biology↗

bioRxiv2021

Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways

The S209F variant of Abelson Interactor Protein 3 (ABI3) increases risk for Alzheimers disease (AD), but little is known about ABI3 function. RNAscope showed Abi3 is expressed in microglial and non-microglial cells, though its increased expression appears to be driven in plaque-associated microglia. Here, we evaluated Abi3-/- mice and document that both Abi3 and its overlapping gene, Gngt2, are disrupted in these mice. Expression of Abi3 and Gngt2 are tightly correlated, and elevated, in rodent models of AD. RNA-seq of the Abi3-Gngt2-/- mice revealed robust induction of an AD-associated neurodegenerative signature, including upregulation of Trem2, Plcg2 and Tyrobp. In APP mice, loss of Abi3-Gngt2 resulted in a gene dose- and age-dependent reduction in A{beta} deposition. Additionally, in Abi3-Gngt2-/- mice, expression of a pro-aggregant form of human tau exacerbated tauopathy and astrocytosis. Further, the AD-associated S209F mutation alters the extent of ABI3 phosphorylation. These data provide an important experimental framework for understanding the role of Abi3-Gngt2 function in AD. Our studies also demonstrate that manipulation of glial function could have opposing effects on amyloid and tau pathology, highlighting the unpredictability of targeting such pathways in AD.

neuroscience↗

bioRxiv2021

Synthetic glabridin derivatives mitigate steatohepatitis in a diet-induced biopsy-confirmed non-alcoholic steatosis hepatitis mouse model through paraoxonase-2

Limited therapeutic agents have been developed for non-alcoholic steatohepatitis (NASH), a common immunometabolic disease that can progress to hepatic cirrhosis and cancer. Glabridin and its derivatives are potential therapeutics for some metabolic diseases. However, the therapeutic effects of glabridin and its derivatives on NASH and their biological functions are unclear. This study demonstrated the role of synthetic glabridin derivatives (SGDs) in alleviating hepatic steatosis and inflammation in a biopsy-confirmed rodent NASH model. SGDs exerted therapeutic effects by activating autophagy and the antioxidant defense system, which mitigate NASH pathogenesis. The cellular target of HSG4112, an SGD, was paraoxonase 2. These findings will enable the development of novel therapeutics for NASH in the future.

pharmacology and toxicology↗

bioRxiv2021

Reagent- and actuator-free analysis of individual erythrocytes using three-dimensional quantitative phase imaging and capillary microfluidics

Histopathological examination of blood cells plays a crucial role in the diagnosis of various diseases. However, it involves time-consuming and laborious staining procedures required for microscopic review by medical experts and is not directly applicable for point-of-care diagnosis in resource-limited locations. This study reports a dilution-, actuation- and label-free method for the analysis of individual red blood cells (RBCs) using a capillary microfluidic device and quantitative phase imaging. Blood, without any sample treatment, is directly loaded into a micrometer-thick channel such that it forms a quasi-monolayer inside the channel. The morphological and biochemical properties of RBCs, including hemoglobin concentration, hemoglobin content, and corpuscular volume, were retrieved using the refractive index tomograms of individual RBCs measured using 3D quantitative phase imaging. The deformability of individual RBCs was also obtained by measuring the dynamic membrane fluctuations. The proposed framework applies to other imaging modalities and biomedical applications, facilitating rapid and cost-effective diagnosis and prognosis of diseases.

bioengineering↗

bioRxiv2021

GCN5 Maintains Muscle Integrity by Acetylating YY1 to Promote Dystrophin Expression

This work identifies a novel role for the acetyltransferase GCN5 in regulating muscle integrity through inhibition of DNA binding activity of the transcriptional repressor YY1. Here we report that in mice a muscle-specific knockout of GCN5 (Gcn5skm-/-) reduces the expression of key structural muscle proteins, including dystrophin, resulting in myopathy. Supporting our observation, a meta-analysis between the differential transcriptome of Gcn5skm-/- muscle and all available open-access data sets identified top correlations with musculoskeletal diseases in humans. GCN5 was found to acetylate YY1 at two residues (K392 and K393), which disrupts the interaction between the YY1 zinc-finger region and DNA. De/acetylation mimics for these YY1 post-translational modifications modulated muscle structural gene expression and DNA binding. Analysis of human GTEx data also found positive and negative correlations between fiber diameter and GCN5 and YY1 respectively. Collectively, our results demonstrate that GCN5 acetyltransferase activity regulates YY1 DNA binding and expression of dystrophin to modulate muscle integrity.

cell biology↗

bioRxiv2020

Label-free bone marrow white blood cell classification using refractive index tomograms and deep learning

In this study, we report a label-free bone marrow white blood cell classification framework that captures the three-dimensional (3D) refractive index (RI) distributions of individual cells and analyzes with deep learning. Without using labeling or staining processes, 3D RI distributions of individual white blood cells were exploited for accurate profiling of their subtypes. Powered by deep learning, our method used the high-dimensional information of the WBC RI tomogram voxels and achieved high accuracy. The results show >99 % accuracy for the binary classification of myeloids and lymphoids and >96 % accuracy for the four-type classification of B, T lymphocytes, monocytes, and myelocytes. Furthermore, the feature learning of our approach was visualized via an unsupervised dimension reduction technique. We envision that this framework can be integrated into existing workflows for blood cell investigation, thereby providing cost-effective and rapid diagnosis of hematologic malignancy.

bioengineering↗

bioRxiv2020

Data-driven multiplexed microtomography of endogenous subcellular dynamics

Simultaneous imaging of various facets of intact biological systems across multiple spatiotemporal scales would be an invaluable tool in biomedicine. However, conventional imaging modalities have stark tradeoffs precluding the fulfilment of all functional requirements. Here we propose the refractive index (RI), an intrinsic quantity governing light-matter interaction, as a means for such measurement. We show that major endogenous subcellular structures, which are conventionally accessed via exogenous fluorescence labeling, are encoded in 3D RI tomograms. We decode this information in a data-driven manner, thereby achieving multiplexed microtomography. This approach inherits the advantages of both high-specificity fluorescence imaging and label-free RI imaging. The performance, reliability, and scalability of this technology have been extensively characterized, and its application within single-cell profiling at unprecedented scales has been demonstrated.

bioengineering↗

bioRxiv2019

Rapid and label-free identification of individual bacterial pathogens exploiting three-dimensional quantitative phase imaging and deep learning

The healthcare industry is in dire need for rapid microbial identification techniques. Microbial infection is a major healthcare issue with significant prevalence and mortality, which can be treated effectively during the early stages using appropriate antibiotics. However, determining the appropriate antibiotics for the treatment of the early stages of infection remains a challenge, mainly due to the lack of rapid microbial identification techniques. Conventional culture-based identification and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy are the gold standard methods, but the sample amplification process is extremely time-consuming. Here, we propose an identification framework that can be used to measure minute quantities of microbes by incorporating artificial neural networks with three-dimensional quantitative phase imaging. We aimed to accurately identify the species of bacterial bloodstream infection pathogens based on a single colony-forming unit of the bacteria. The successful distinction between a total of 19 species, with the accuracy of 99.9% when ten bacteria were measured, suggests that our framework can serve as an effective advisory tool for clinicians during the initial antibiotic prescription. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/596486v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@786668org.highwire.dtl.DTLVardef@8b4eb4org.highwire.dtl.DTLVardef@1dc2452org.highwire.dtl.DTLVardef@1d4888c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

JuLI: accurate detection of DNA fusions in clinical sequencing for precision oncology

Accurate detection of genomic fusions by high-throughput sequencing in clinical samples with inadequate tumor purity and formalin-fixed paraffin embedded (FFPE) tissue is an essential task in precise oncology. We developed the fusion detection algorithm Junction Location Identifier (JuLI) for optimization of high-depth clinical sequencing. We implemented novel filtering steps to minimize false positives and a joint calling function to increase sensitivity in clinical setting. We comprehensively validated the algorithm using high-depth sequencing data from cancer cell lines and clinical samples and whole genome sequencing data from NA12878. We showed that JuLI outperformed state-of-the-art fusion callers in cases with high-depth clinical sequencing and rescued a driver fusion from false negative in plasma cell-free DNA. JuLI is freely available via GitHub (https://github.com/sgilab/JuLI).

bioinformatics↗