Biology subjects

Luo, O.

Publications and source records attributed to Luo, O..

4 recordsLinked to original sources

bioRxiv2026

An Integrated Pipeline for Cell-Type Annotation, Metabolic Profiling, and Spatial Communication Analysis in the Liver using Spatial Transcriptomics

The liver acts as a central metabolic hub, integrating systemic signals through a spatially organized pattern known as zonation, driven by the coordinated activity of diverse cell types including hepatocytes, stellate cells, Kupffer cells, endothelial cells, and immune populations. Spatial transcriptomics (ST) enables the profiling of thousands of cells with spatial resolution in a single experiment, facilitating the identification of novel gene markers, cell types, cellular states, and tissue neighborhoods across diverse tissues and organisms. By simultaneously capturing transcriptional and spatial heterogeneity, ST has become a powerful tool for understanding cellular and tissue biology. Given its advantages, there is growing demand for applying ST to uncover novel biological insights in the liver under various physiological and pathological conditions including obesity, diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD). However, to date no comprehensive and practical protocols currently exist for analyzing ST data specifically in the context of liver metabolism. Herein, we present a systematic and detailed protocol for ST data analysis using liver tissues from MASLD mouse models. This guide offers practical support for metabolic based researchers without advanced expertise in coding, mathematics and statistics enabling single-cell RNA-seq referencing for deconvolution-based annotation, curated liver cell type markers for manual annotation, and a GMT file of metabolic gene sets and flux balance analysis to analyze liver metabolic activity. This framework and integrated computational resources for decoding metabolic reprogramming and cellular heterogeneity will empower researchers to uncover novel biological pathways regulating liver metabolism in health and disease.

bioinformatics↗

bioRxiv2019

VariantSpark, A Random Forest Machine Learning Implementation for Ultra High Dimensional Data

The demands on machine learning methods to cater for ultra high dimensional datasets, datasets with millions of features, have been increasing in domains like life sciences and the Internet of Things (IoT). While Random Forests are suitable for \"wide\" datasets, current implementations such as Googles PLANET lack the ability to scale to such dimensions. Recent improvements by Yggdrasil begin to address these limitations but do not extend to Random Forest. This paper introduces CursedForest, a novel Random Forest implementation on top of Apache Spark and part of the VariantSpark platform, which parallelises processing of all nodes over the entire forest. CursedForest is 9 and up to 89 times faster than Googles PLANET and Yggdrasil, respectively, and is the first method capable of scaling to millions of features.

bioinformatics↗

bioRxiv2019

Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and - independent phagosomal signals that contribute to phagocytosis and inflammation

Lyme disease is a tick-borne illness caused by the spirochete Borrelia burgdorferi (Bb). It is believed that the robust inflammatory response induced by the hosts innate immune system is responsible for the clinical manifestations associated with Bb infection. The macrophage plays a central role in the immune response to many bacterial infections and is thought to play a central role in activation of the innate immune response to Bb. Previous studies have shown that following phagocytosis of spirochetes by macrophages, phagosome maturation results in degradation of Bb and liberation of bacterial lipoproteins and nucleic acids, which are recognized by TLR2 and TLR8, respectively, and elicit MyD88-mediated phagosome signaling cascades. Bone marrow-derived macrophages (BMDMs) from MyD88-/- mice show significantly reduced spirochete uptake and inflammatory cytokine production when incubated with Bb ex vivo. Paradoxically, additional studies revealed that Bb-infected MyD88-/- mice exhibit inflammation in joint and heart tissues. To determine the contribution of MyD88 to macrophage-mediated spirochete clearance, we compared wildtype (WT) and MyD88-/- mice using a murine model of Lyme disease. MyD88-/- mice showed increased Bb burdens in hearts 28 days post infection, while H&E staining and immunohistochemistry showed significantly increased inflammation and greater macrophage infiltrate in the hearts of MyD88-/- mice. This suggests that Bb triggers MyD88-independent inflammatory pathways in macrophages to facilitate cell recruitment to tissues. Upon stimulation with Bb ex vivo, WT and MyD88-/- BMDMs exhibit significant differences in bacteria uptake, suggesting that MyD88 signaling mediates cytoskeleton remodeling and the formation of membrane protrusions to enhance bacteria phagocytosis. A comprehensive transcriptome comparison in Bb-infected WT and MyD88-/- BMDMs identified a large cohort of MyD88-dependent genes that are differentially expressed in response to Bb, including genes involved in actin and cytoskeleton organization (Daam1, Fmnl1). We also identified a cohort of differentially-expressed MyD88-independent chemokines (Cxcl2, Ccl9) known to recruit macrophages. We identified master regulators and generated networks which model potential signaling pathways that mediate both phagocytosis and the inflammatory response. These data provide strong evidence that MyD88-dependent and -independent phagosomal signaling cascades in macrophages play significant roles in the ability of these cells to phagocytose Bb and mediate infection.\n\nAUTHOR SUMMARYMacrophages play prominent roles in bacteria recognition and clearance, including Borrelia burgdorferi (Bb), the Lyme disease spirochete. To elucidate mechanisms by which MyD88/TLR signaling enhances clearance of Bb by macrophages, we studied Bb-infected wildtype (WT) and MyD88-/- mice and Bb-stimulated bone marrow-derived macrophages (BMDMs). Bb-infected MyD88-/- mice show increased bacterial burdens, macrophage infiltration and altered gene expression in inflamed heart tissue. MyD88-/- BMDMs exhibit impaired uptake of spirochetes but comparable maturation of phagosomes following internalization of spirochetes. RNA-sequencing of infected WT and MyD88-/- BMDMs identified a large cohort of differentially expressed MyD88-dependent genes involved in re-organization of actin and cytoskeleton during phagocytosis along with several MyD88-independent chemokines involved in inflammatory cell recruitment. We computationally generated networks which identified several MyD88-independent master regulators (Cxcl2 and Vcam1) and MyD88-dependent intermediate proteins (Rhoq and Cyfip1) that are known to mediate inflammation and phagocytosis respectively. These results provide mechanistic insights into MyD88-mediated phagosomal signaling enhancing Bb uptake and clearance.

immunology↗

bioRxiv2018

EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and function

EndoC-{beta}H1 is emerging as a critical human beta cell model to study the genetic and environmental etiologies of beta cell function, especially in the context of diabetes. Comprehensive knowledge of its molecular landscape is lacking yet required to fully take advantage of this model. Here, we report extensive chromosomal (spectral karyotyping), genetic (genotyping), epigenetic (ChIP-seq, ATAC-seq), chromatin interaction (Hi-C, Pol2 ChIA-PET), and transcriptomic (RNA-seq, miRNA-seq) maps of this cell model. Integrated analyses of these maps define known (e.g., PDX1, ISL1) and putative (e.g., PCSK1, mir-375) beta cell-specific chromatin interactions and transcriptional cis-regulatory networks, and identify allelic effects on cis-regulatory element use and expression.\n\nImportantly, comparative analyses with maps generated in primary human islets/beta cells indicate substantial preservation of chromatin looping, but also highlight chromosomal heterogeneity and fetal genomic signatures in EndoC-{beta}H1. Together, these maps, and an interactive web application we have created for their exploration, provide important tools for the broad community in the design and success of experiments to probe and manipulate the genetic programs governing beta cell identity and (dys)function in diabetes.

genomics↗