Biology subjects

Kim, D. W.

Publications and source records attributed to Kim, D. W..

42 records · Page 3Linked to original sources

bioRxiv2019

A single cell transcriptional atlas of early synovial joint development

Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 6,202 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and functional analysis of prospectively isolated populations, we have inferred the underlying transcriptional networks of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.

developmental biology↗

bioRxiv2019

Single cell RNA-Seq analysis identifies molecular mechanisms controlling hypothalamic patterning and differentiation.

The hypothalamus is a central regulator of many innate behaviors essential for survival, but the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control hypothalamic development, we have used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across 12 developmental time points between embryonic day 10 and postnatal day 45. This identified genes that delineated clear developmental trajectories for all major hypothalamic cell types, and readily distinguished major regional subdivisions of the developing hypothalamus. By using our developmental dataset, we were able to rapidly annotate previously unidentified clusters from existing scRNA-Seq datasets collected during development, and to identify the developmental origins of major neuronal populations of the ventromedial hypothalamus. We further show that our approach can rapidly and comprehensively characterize mutants that have altered hypothalamic patterning, identifying Nkx2.1 as a negative regulator of prethalamic identity. These data serve as a resource for further studies of hypothalamic development, physiology and dysfunction.

neuroscience↗

bioRxiv2019

PanoView: An iterative clustering for single-cell RNA sequencing data

Single-cell RNA-sequencing (scRNA-seq) provides new opportunities to gain a mechanistic understanding of many biological processes. Current approaches for single cell clustering are often sensitive to the input parameters and have difficulty dealing with cell types with different densities. Here, we present Panoramic View (PanoView), an iterative method integrated with a novel density-based clustering, Ordering Local Maximum by Convex hull (OLMC), that uses a heuristic approach to estimate the required parameters based on the input data structures. In each iteration, PanoView will identify the most confident cell clusters and repeat the clustering with the remaining cells in a new PCA space. Without adjusting any parameter in PanoView, we demonstrated that PanoView was able to detect major and rare cell types simultaneously and outperformed other existing methods in both simulated datasets and published single-cell RNA-sequencing datasets. Finally, we conducted scRNA-Seq analysis of embryonic mouse hypothalamus, and PanoView was able to reveal known cell types and several rare cell subpopulations.\n\nAuthor summaryOne of the important tasks in analyzing single-cell transcriptomics data is to classify cell subpopulations. Most computational methods require users to input parameters and sometimes the proper parameters are not intuitive to users. Hence, a robust but easy-to-use method is of great interest. We proposed PanoView algorithm that utilizes an iterative approach to search cell clusters in an evolving three-dimension PCA space. The goal is to identify the cell cluster with the most confidence in each iteration and repeat the clustering algorithm with the remaining cells in a new PCA space. To cluster cells in a given PCA space, we also developed OLMC clustering to deal with clusters with varying densities. We examined the performance of PanoView in comparison to other existing methods using ten published single-cell datasets and simulated datasets as the ground truth. The results showed that PanoView is an easy-to-use and reliable tool and can be applied to diverse types of single-cell RNA-sequencing datasets.

bioinformatics↗

bioRxiv2019

Tanycyte-independent control of hypothalamic leptin signaling

Leptin is secreted by adipocytes to regulate appetite and body weight. Recent studies have reported that tanycytes actively transport circulating leptin across the brain barrier into the hypothalamus, and are required for normal levels of hypothalamic leptin signaling. However, direct evidence for leptin receptor (LepR) expression is lacking, and the effect of tanycyte-specific deletion of LepR has not been investigated. In this study, we analyze the expression and function of the tanycytic LepR in mice. Using single-molecule fluorescent in situ hybridization (smfISH), RT-qPCR, single-cell RNA sequencing (scRNA-Seq), and selective deletion of the LepR in tanycytes, we are unable to detect expression of LepR in the tanycytes. Tanycyte-specific deletion of LepR likewise did not affect leptin-induced pSTAT3 expression in hypothalamic neurons, regardless of whether leptin was delivered by intraperitoneal or intracerebroventricular injection. Finally, we use activity-regulated scRNA-Seq (act-Seq) to comprehensively profile leptin-induced changes in gene expression in all cell types in mediobasal hypothalamus. Clear evidence for leptin signaling is only seen in endothelial cells and subsets of neurons, although virtually all cell types show leptin-induced changes in gene expression. We thus conclude that LepR expression in tanycytes is either absent or undetectably low, that tanycytes do not directly regulate hypothalamic leptin signaling through a LepR-dependent mechanism, and that leptin regulates gene expression in diverse hypothalamic cell types through both direct and indirect mechanisms.

neuroscience↗

bioRxiv2018

Human pathogenic bacterium Shigella infects Arabidopsis plants using type-III effectors that suppress conserved MAP kinase signaling

Originality-significance statementIncreased incidence of food-borne disease outbreaks caused by fresh produce contaminated with Escherichia coli O157:H7 and Salmonella spp. has prompted researchers to examine the interaction between these bacteria and various plant species under different environmental conditions. Although studies show that human enteropathogenic bacteria survive both on the surface of and inside plants, little is known about the molecular mechanism underlying plant invasion and colonization. Here, we examined the interaction between the human pathogenic bacterium Shigella and the model plant Arabidopsis. We found that four Shigella spp. strains proliferated successfully in Arabidopsis, causing symptom-like lesions in tissues. Using mutants lacking T3S effectors (i.e., noninvasive human strains), we demonstrated that effectors regulating pathogenesis of shigellosis in humans also play a central role in bacteria-plant interactions. To the best of our knowledge, this is the first study to examine Shigella-mediated virulence and host immune suppression in a plant host at a molecular level.\n\nSummaryAlthough there is debate about whether human intestinal pathogenic bacteria are also plant pathogens, it is clear that these bacteria use plants as an alternative host. Shigella, which infects primates, is reportedly transmitted by fresh vegetables; however, its molecular interactions with plants have not been extensively studied. Here, we show that four Shigella strains, S. boydii (S. b), S. sonnei (S. s), S. flexneri 2a (S. f 2a), and S. flexneri 5a (S. f 5a), proliferated at different levels in Arabidopsis thaliana. Microscopic studies revealed that these bacteria were present inside leaves and damaged plant cells. GFP-labeled S. b, S. f 2a, and S. f 5a entered plants via guard cells, and S. f 2a infiltrated root tissues and colonized roots. Using mutants lacking type III secretion systems (T3SS), we found that T3SS of Shigella that regulate the pathogenesis of shigellosis in humans also play a central role in attachment and multiplication in Arabidopsis. Furthermore, the immunosuppressive activity of two T3S effectors, OspF and OspG, were needed for the proliferation of Shigella in Arabidopsis. These findings demonstrate that Shigella-mediated virulence determinants are expressed, and pathogenic symptoms are observed, in model plants.

microbiology↗

bioRxiv2017

Disruption of the interfacial membrane leads to Magnaporthe oryzae effector re-location and lifestyle switch during rice blast disease

The hemibiotrophic fungus Magnaporthe oryzae produces invasive hyphae enclosed in a plant-derived interfacial membrane, known as the extra-invasive hyphal membrane (EIHM), in living rice cells. Little is known about when the EIHM is disrupted and how the disruption contributes to blast disease. Here we show that EIHM disruption correlates with the hyphal growth stage in first-invaded susceptible rice cells. Our approach utilized GFP secreted from invasive hyphae as an EIHM integrity reporter. Secreted-GFP accumulated in the EIHM compartment but appeared in the rice cytoplasm when the EIHM integrity was compromised. Live-cell imaging of secreted-GFP and various fluorescent reporters revealed that EIHM disruption led to rice vacuole rupture and cell death limited to the invaded cell with closed plasmodesmata. We report that EIHM disruption and host cell death are landmarks delineating three distinct infection phases (early biotrophic, late biotrophic, and transient necrotrophic phases) within the first-invaded cell before reestablishment of biotrophy in second-invaded cells. M. oryzae effectors exhibited phase-specific localizations, including entry of the apoplastic effector Bas4 into the rice cytoplasm during the late biotrophic phase. Understanding how the phase-specific dynamics are regulated and linked to host susceptibility will offer potential targets that can be exploited to control blast disease.

cell biology↗