scholarly journals Transcriptomic Changes of Murine Visceral Fat Exposed to Intermittent Hypoxia at Single Cell Resolution

2020 ◽  
Vol 22 (1) ◽  
pp. 261
Author(s):  
Abdelnaby Khalyfa ◽  
Wesley Warren ◽  
Jorge Andrade ◽  
Christopher A. Bottoms ◽  
Edward S. Rice ◽  
...  
Keyword(s):  
Intermittent Hypoxia ◽  
Cell Types ◽  
Cellular Level ◽  
Cellular Heterogeneity ◽  
Transcriptional Networks ◽  
Metabolic Dysfunction ◽  
Rna Seq ◽  
Obstructive Sleep ◽  
Differential Expressed Gene ◽  
Key Aspects

Intermittent hypoxia (IH) is a hallmark of obstructive sleep apnea (OSA) and induces metabolic dysfunction manifesting as inflammation, increased lipolysis and insulin resistance in visceral white adipose tissues (vWAT). However, the cell types and their corresponding transcriptional pathways underlying these functional perturbations are unknown. Here, we applied single nucleus RNA sequencing (snRNA-seq) coupled with aggregate RNA-seq methods to evaluate the cellular heterogeneity in vWAT following IH exposures mimicking OSA. C57BL/6 male mice were exposed to IH and room air (RA) for 6 weeks, and nuclei from vWAT were isolated and processed for snRNA-seq followed by differential expressed gene (DEGs) analyses by cell type, along with gene ontology and canonical pathways enrichment tests of significance. IH induced significant transcriptional changes compared to RA across 14 different cell types identified in vWAT. We identified cell-specific signature markers, transcriptional networks, metabolic signaling pathways, and cellular subpopulation enrichment in vWAT. Globally, we also identify 298 common regulated genes across multiple cellular types that are associated with metabolic pathways. Deconvolution of cell types in vWAT using global RNA-seq revealed that distinct adipocytes appear to be differentially implicated in key aspects of metabolic dysfunction. Thus, the heterogeneity of vWAT and its response to IH at the cellular level provides important insights into the metabolic morbidity of OSA and may possibly translate into therapeutic targets.

scholarly journals Effects of acute intermittent hypoxia on glucose metabolism in awake healthy volunteers

2009 ◽  
Vol 106 (5) ◽  
pp. 1538-1544 ◽  
Author(s):  
Mariam Louis ◽  
Naresh M. Punjabi
Keyword(s):  
Obstructive Sleep Apnea ◽  
Insulin Secretion ◽  
Sleep Apnea ◽  
Insulin Sensitivity ◽  
Glucose Metabolism ◽  
Healthy Volunteers ◽  
Intermittent Hypoxia ◽  
Metabolic Dysfunction ◽  
Glucose Effectiveness ◽  
Obstructive Sleep

Accumulating evidence suggests that obstructive sleep apnea is associated with alterations in glucose metabolism. Although the pathophysiology of metabolic dysfunction in obstructive sleep apnea is not well understood, studies of murine models indicate that intermittent hypoxemia has an important contribution. However, corroborating data on the metabolic effects of intermittent hypoxia on glucose metabolism in humans are not available. Thus the primary aim of this study was to characterize the acute effects of intermittent hypoxia on glucose metabolism. Thirteen healthy volunteers were subjected to 5 h of intermittent hypoxia or normoxia during wakefulness in a randomized order on two separate days. The intravenous glucose tolerance test (IVGTT) was used to assess insulin-dependent and insulin-independent measures of glucose disposal. The IVGTT data were analyzed using the minimal model to determine insulin sensitivity (SI) and glucose effectiveness (SG). Drops in oxyhemoglobin saturation were induced during wakefulness at an average rate of 24.3 events/h. Compared with the normoxia condition, intermittent hypoxia was associated with a decrease in SI [4.1 vs. 3.4 (mU/l)−1·min−1; P = 0.0179] and SG (1.9 vs. 1.3 min−1×10−2, P = 0.0065). Despite worsening insulin sensitivity with intermittent hypoxia, pancreatic insulin secretion was comparable between the two conditions. Heart rate variability analysis showed the intermittent hypoxia was associated with a shift in sympathovagal balance toward an increase in sympathetic nervous system activity. The average R-R interval on the electrocardiogram was 919.0 ms during the normoxia condition and 874.4 ms during the intermittent hypoxia condition ( P < 0.04). Serum cortisol levels after intermittent hypoxia and normoxia were similar. Hypoxic stress in obstructive sleep apnea may increase the predisposition for metabolic dysfunction by impairing insulin sensitivity, glucose effectiveness, and insulin secretion.

scholarly journals Integrated profiling of single cell epigenomic and transcriptomic landscape of Parkinson’s disease mouse brain

2020 ◽  
Author(s):  
Jixing Zhong ◽  
Gen Tang ◽  
Jiacheng Zhu ◽  
Xin Qiu ◽  
Weiying Wu ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Single Cell ◽  
Early Stage ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Rna Seq ◽  
Cell Level ◽  
Distinct Cell ◽  
Single Nucleus

AbstractParkinson’s disease (PD) is a neurodegenerative disease leading to the impairment of execution of movement. PD pathogenesis has been largely investigated, but either restricted in bulk level or at certain cell types, which failed to capture cellular heterogeneity and intrinsic interplays among distinct cell types. To overcome this, we applied single-nucleus RNA-seq and single cell ATAC-seq on cerebellum, midbrain and striatum of PD mouse and matched control. With 74,493 cells in total, we comprehensively depicted the dysfunctions under PD pathology covering proteostasis, neuroinflammation, calcium homeostasis and extracellular neurotransmitter homeostasis. Besides, by multi-omics approach, we identified putative biomarkers for early stage of PD, based on the relationships between transcriptomic and epigenetic profiles. We located certain cell types that primarily contribute to PD early pathology, narrowing the gap between genotypes and phenotypes. Taken together, our study provides a valuable resource to dissect the molecular mechanism of PD pathogenesis at single cell level, which could facilitate the development of novel methods regarding diagnosis, monitoring and practical therapies against PD at early stage.

scholarly journals Single-nucleus RNA-seq reveals dysregulation of striatal cell identity due to Huntington’s disease mutations

2020 ◽  
Author(s):  
Sonia Malaiya ◽  
Marcia Cortes-Gutierrez ◽  
Brian R. Herb ◽  
Sydney R. Coffey ◽  
Samuel R.W. Legg ◽  
...  
Keyword(s):  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Neurodegenerative Disorder ◽  
Cell Types ◽  
Transcriptional Networks ◽  
Rna Seq ◽  
Cell Type ◽  
Cell Identity ◽  
Transcriptional Changes ◽  
Cell Type Specific

ABSTRACTHuntington’s disease (HD) is a dominantly inherited neurodegenerative disorder caused by a trinucleotide expansion in exon 1 of the huntingtin (Htt) gene. Cell death in HD occurs primarily in striatal medium spiny neurons (MSNs), but the involvement of specific MSN subtypes and of other striatal cell types remains poorly understood. To gain insight into cell type-specific disease processes, we studied the nuclear transcriptomes of 4,524 cells from the striatum of a genetically precise knock-in mouse model of the HD mutation, HttQ175/+, and from wildtype controls. We used 14-15-month-old mice, a time point roughly equivalent to an early stage of symptomatic human disease. Cell type distributions indicated selective loss of D2 MSNs and increased microglia in aged HttQ175/+ mice. Thousands of differentially expressed genes were distributed across most striatal cell types, including transcriptional changes in glial populations that are not apparent from RNA-seq of bulk tissue. Reconstruction of cell typespecific transcriptional networks revealed a striking pattern of bidirectional dysregulation for many cell type-specific genes. Typically, these genes were repressed in their primary cell type, yet de-repressed in other striatal cell types. Integration with existing epigenomic and transcriptomic data suggest that partial loss-of-function of the Polycomb Repressive Complex 2 (PRC2) may underlie many of these transcriptional changes, leading to deficits in the maintenance of cell identity across virtually all cell types in the adult striatum.

scholarly journals Bulk Tissue Cell Type Deconvolution with Multi-Subject Single-Cell Expression Reference

2018 ◽  
Author(s):  
Xuran Wang ◽  
Jihwan Park ◽  
Katalin Susztak ◽  
Nancy R. Zhang ◽  
Mingyao Li
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Tissue Cell ◽  
Specific Gene ◽  
Rna Seq ◽  
Cell Type ◽  
Cell Type Specific ◽  
Cell Expression

AbstractWe present MuSiC, a method that utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. When applied to pancreatic islet and whole kidney expression data in human, mouse, and rats, MuSiC outperformed existing methods, especially for tissues with closely related cell types. MuSiC enables characterization of cellular heterogeneity of complex tissues for identification of disease mechanisms.

scholarly journals Meta-Analysis of cortical inhibitory interneurons markers landscape and their performances in scRNA-seq studies.

2021 ◽  
Author(s):  
Lorenzo Martini ◽  
Roberta Bardini ◽  
Stefano Di Carlo
Keyword(s):  
Single Cell ◽  
Meta Analysis ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Marker Genes ◽  
Inhibitory Interneurons ◽  
Rna Seq ◽  
Circuit Function ◽  
The Brain

The mammalian cortex contains a great variety of neuronal cells. In particular, GABAergic interneurons, which play a major role in neuronal circuit function, exhibit an extraordinary diversity of cell types. In this regard, single-cell RNA-seq analysis is crucial to study cellular heterogeneity. To identify and analyze rare cell types, it is necessary to reliably label cells through known markers. In this way, all the related studies are dependent on the quality of the employed marker genes. Therefore, in this work, we investigate how a set of chosen inhibitory interneurons markers perform. The gene set consists of both immunohistochemistry-derived genes and single-cell RNA-seq taxonomy ones. We employed various human and mouse datasets of the brain cortex, consequently processed with the Monocle3 pipeline. We defined metrics based on the relations between unsupervised cluster results and the marker expression. Specifically, we calculated the specificity, the fraction of cells expressing, and some metrics derived from decision tree analysis like entropy gain and impurity reduction. The results highlighted the strong reliability of some markers but also the low quality of others. More interestingly, though, a correlation emerges between the general performances of the genes set and the experimental quality of the datasets. Therefore, the proposed method allows evaluating the quality of a dataset in relation to its reliability regarding the inhibitory interneurons cellular heterogeneity study.

scholarly journals Single-Cell RNA-Seq of Cisplatin-Treated Adult Stria Vascularis Identifies Cell Type-Specific Regulatory Networks and Novel Therapeutic Gene Targets

2021 ◽  
Vol 14 ◽  
Author(s):  
Ian A. Taukulis ◽  
Rafal T. Olszewski ◽  
Soumya Korrapati ◽  
Katharine A. Fernandez ◽  
Erich T. Boger ◽  
...  
Keyword(s):  
Single Cell ◽  
Regulatory Networks ◽  
Stria Vascularis ◽  
Cell Types ◽  
Cellular Level ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Transcriptional Responses ◽  
Transcriptional Changes ◽  
Cell Type Specific

The endocochlear potential (EP) generated by the stria vascularis (SV) is necessary for hair cell mechanotransduction in the mammalian cochlea. We sought to create a model of EP dysfunction for the purposes of transcriptional analysis and treatment testing. By administering a single dose of cisplatin, a commonly prescribed cancer treatment drug with ototoxic side effects, to the adult mouse, we acutely disrupt EP generation. By combining these data with single cell RNA-sequencing findings, we identify transcriptional changes induced by cisplatin exposure, and by extension transcriptional changes accompanying EP reduction, in the major cell types of the SV. We use these data to identify gene regulatory networks unique to cisplatin treated SV, as well as the differentially expressed and druggable gene targets within those networks. Our results reconstruct transcriptional responses that occur in gene expression on the cellular level while identifying possible targets for interventions not only in cisplatin ototoxicity but also in EP dysfunction.

scholarly journals Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Gang Wu ◽  
Yin Yeng Lee ◽  
Evelyn M Gulla ◽  
Andrew Potter ◽  
Joseph Kitzmiller ◽  
...  
Keyword(s):  
Intermittent Hypoxia ◽  
Hypoxia Inducible Factor ◽  
Cell Types ◽  
Short Term Exposure ◽  
Obstructive Sleep ◽  
Chronic Pulmonary Diseases ◽  
Transcriptional Changes ◽  
Expression Pathways ◽  
Health Complications ◽  
Upregulated Genes

Obstructive sleep apnea (OSA) results from episodes of airway collapse and intermittent hypoxia (IH) and is associated with a host of health complications. Although the lung is the first organ to sense changes in oxygen levels, little is known about the consequences of IH to the lung hypoxia-inducible factor-responsive pathways. We hypothesized that exposure to IH would lead to cell-specific up- and downregulation of diverse expression pathways. We identified changes in circadian and immune pathways in lungs from mice exposed to IH. Among all cell types, endothelial cells showed the most prominent transcriptional changes. Upregulated genes in myofibroblast cells were enriched for genes associated with pulmonary hypertension and included targets of several drugs currently used to treat chronic pulmonary diseases. A better understanding of the pathophysiologic mechanisms underlying diseases associated with OSA could improve our therapeutic approaches, directing therapies to the most relevant cells and molecular pathways.

scholarly journals A 2020 view of tension-based cortical morphogenesis

2020 ◽  
Vol 117 (52) ◽  
pp. 32868-32879
Author(s):  
David C. Van Essen
Keyword(s):  
Cell Types ◽  
Tissue Level ◽  
Cellular Level ◽  
General Hypothesis ◽  
Cortical Gray Matter ◽  
Level I ◽  
Key Aspects ◽  
Des Model

Mechanical tension along the length of axons, dendrites, and glial processes has been proposed as a major contributor to morphogenesis throughout the nervous system [D. C. Van Essen, Nature 385, 313–318 (1997)]. Tension-based morphogenesis (TBM) is a conceptually simple and general hypothesis based on physical forces that help shape all living things. Moreover, if each axon and dendrite strive to shorten while preserving connectivity, aggregate wiring length would remain low. TBM can explain key aspects of how the cerebral and cerebellar cortices remain thin, expand in surface area, and acquire their distinctive folds. This article reviews progress since 1997 relevant to TBM and other candidate morphogenetic mechanisms. At a cellular level, studies of diverse cell types in vitro and in vivo demonstrate that tension plays a major role in many developmental events. At a tissue level, I propose a differential expansion sandwich plus (DES+) revision to the original TBM model for cerebral cortical expansion and folding. It invokes tangential tension and “sulcal zipping” forces along the outer cortical margin as well as tension in the white matter core, together competing against radially biased tension in the cortical gray matter. Evidence for and against the DES+ model is discussed, and experiments are proposed to address key tenets of the DES+ model. For cerebellar cortex, a cerebellar multilayer sandwich (CMS) model is proposed that can account for many distinctive features, including its unique, accordion-like folding in the adult, and experiments are proposed to address its specific tenets.

scholarly journals Exosome and Macrophage Crosstalk in Sleep-Disordered Breathing-Induced Metabolic Dysfunction

2018 ◽  
Vol 19 (11) ◽  
pp. 3383 ◽  
Author(s):  
Abdelnaby Khalyfa ◽  
Leila Kheirandish-Gozal ◽  
David Gozal
Keyword(s):  
Critical Role ◽  
Adaptive Immune Response ◽  
Upper Airway ◽  
Public Health Problem ◽  
Cell Types ◽  
Low Grade ◽  
Metabolic Dysfunction ◽  
Bodily Fluids ◽  
Exosome Biogenesis ◽  
Obstructive Sleep

Obstructive sleep apnea (OSA) is a highly prevalent worldwide public health problem that is characterized by repetitive upper airway collapse leading to intermittent hypoxia, pronounced negative intrathoracic pressures, and recurrent arousals resulting in sleep fragmentation. Obesity is a major risk factor of OSA and both of these two closely intertwined conditions result in increased sympathetic activity, oxidative stress, and chronic low-grade inflammation, which ultimately contribute, among other morbidities, to metabolic dysfunction, as reflected by visceral white adipose tissue (VWAT) insulin resistance (IR). Circulating extracellular vesicles (EVs), including exosomes, are released by most cell types and their cargos vary greatly and reflect underlying changes in cellular homeostasis. Thus, exosomes can provide insights into how cells and systems cope with physiological perturbations by virtue of the identity and abundance of miRNAs, mRNAs, proteins, and lipids that are packaged in the EVs cargo, and are secreted from the cells into bodily fluids under normal as well as diseased states. Accordingly, exosomes represent a novel pathway via which a cohort of biomolecules can travel long distances and result in the modulation of gene expression in selected and targeted recipient cells. For example, exosomes secreted from macrophages play a critical role in innate immunity and also initiate the adaptive immune response within specific metabolic tissues such as VWAT. Under normal conditions, phagocyte-derived exosomes represent a large portion of circulating EVs in blood, and carry a protective signature against IR that is altered when secreting cells are exposed to altered physiological conditions such as those elicited by OSA, leading to emergence of IR within VWAT compartment. Consequently, increased understanding of exosome biogenesis and biology should lead to development of new diagnostic biomarker assays and personalized therapeutic approaches. Here, the evidence on the major biological functions of macrophages and exosomes as pathophysiological effectors of OSA-induced metabolic dysfunction is discussed.

scholarly journals Cell-Selective Altered Cargo Properties of Extracellular Vesicles Following In Vitro Exposures to Intermittent Hypoxia

2021 ◽  
Vol 22 (11) ◽  
pp. 5604
Author(s):  
David Sanz-Rubio ◽  
Abdelnaby Khalyfa ◽  
Zhuanhong Qiao ◽  
Jorge Ullate ◽  
José M. Marin ◽  
...  
Keyword(s):  
Insulin Sensitivity ◽  
Extracellular Vesicles ◽  
Intermittent Hypoxia ◽  
Adverse Outcomes ◽  
Metabolic Dysfunction ◽  
Cellular Effects ◽  
Obstructive Sleep ◽  
Cell Sources

Intermittent hypoxia (IH), a hallmark of obstructive sleep apnea (OSA), is associated with cardiovascular and metabolic dysfunction. However, the mechanisms underlying these morbidities remain poorly delineated. Extracellular vesicles (EVs) mediate intercellular communications, play pivotal roles in a multitude of physiological and pathological processes, and could mediate IH-induced cellular effects. Here, the effects of IH on human primary cells and the release of EVs were examined. Microvascular endothelial cells (HMVEC-d), THP1 monocytes, THP1 macrophages M0, THP1 macrophages M1, THP1 macrophages M2, pre-adipocytes, and differentiated adipocytes (HAd) were exposed to either room air (RA) or IH for 24 h. Secreted EVs were isolated and characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blotting. The effects of each of the cell-derived EVs on endothelial cell (EC) monolayer barrier integrity, on naïve THP1 macrophage polarity, and on adipocyte insulin sensitivity were also evaluated. IH did not alter EVs cell quantal release, but IH-EVs derived from HMVEC-d (p < 0.01), THP1 M0 (p < 0.01) and HAd (p < 0.05) significantly disrupted HMVEC-d monolayer integrity, particularly after H2O2 pre-conditioning. IH-EVs from HMVEC-d and THP1 M0 elicited M2-polarity changes did not alter insulin sensitivity responses. IH induces cell-selective changes in EVs cargo, which primarily seem to target the emergence of endothelial dysfunction. Thus, changes in EVs cargo from selected cell sources in vivo may play causal roles in some of the adverse outcomes associated with OSA.

Sign in / Sign up

Export Citation Format

Share Document