scholarly journals Fast, sensitive, and accurate integration of single cell data with Harmony

2018 ◽  
Author(s):  
Ilya Korsunsky ◽  
Jean Fan ◽  
Kamil Slowikowski ◽  
Fan Zhang ◽  
Kevin Wei ◽  
...  
Keyword(s):  
Stress Response ◽  
Er Stress ◽  
Single Cell ◽  
Islet Cells ◽  
Superior Performance ◽  
Joint Analysis ◽  
Cell Type ◽  
Integration Algorithm ◽  
Fine Grained ◽  
Er Stress Response

AbstractThe rapidly emerging diversity of single cell RNAseq datasets allows us to characterize the transcriptional behavior of cell types across a wide variety of biological and clinical conditions. With this comprehensive breadth comes a major analytical challenge. The same cell type across tissues, from different donors, or in different disease states, may appear to express different genes. A joint analysis of multiple datasets requires the integration of cells across diverse conditions. This is particularly challenging when datasets are assayed with different technologies in which real biological differences are interspersed with technical differences. We present Harmony, an algorithm that projects cells into a shared embedding in which cells group by cell type rather than dataset-specific conditions. Unlike available single-cell integration methods, Harmony can simultaneously account for multiple experimental and biological factors. We develop objective metrics to evaluate the quality of data integration. In four separate analyses, we demonstrate the superior performance of Harmony to four single-cell-specific integration algorithms. Moreover, we show that Harmony requires dramatically fewer computational resources. It is the only available algorithm that makes the integration of ∼ 106 cells feasible on a personal computer. We demonstrate that Harmony identifies both broad populations and fine-grained subpopulations of PBMCs from datasets with large experimental differences. In a meta-analysis of 14,746 cells from 5 studies of human pancreatic islet cells, Harmony accounts for variation among technologies and donors to successfully align several rare subpopulations. In the resulting integrated embedding, we identify a previously unidentified population of potentially dysfunctional alpha islet cells, enriched for genes active in the Endoplasmic Reticulum (ER) stress response. The abundance of these alpha cells correlates across donors with the proportion of dysfunctional beta cells also enriched in ER stress response genes. Harmony is a fast and flexible general purpose integration algorithm that enables the identification of shared fine-grained subpopulations across a variety of experimental and biological conditions.

Endoplasmic reticulum accumulation of Kir6.2 without activation of ER stress response in islet cells from adult Sur1 knockout mice

2010 ◽  
Vol 340 (2) ◽  
pp. 335-346 ◽  
Author(s):  
Ihsane Marhfour ◽  
Jean-Christophe Jonas ◽  
Joëlle Marchandise ◽  
Alberte Lefevre ◽  
Jacques Rahier ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Stress Response ◽  
Er Stress ◽  
Knockout Mice ◽  
Islet Cells ◽  
Er Stress Response ◽  
Sur1 Knockout Mice

Targeted regulation of lymphocytic ER stress response with an overall immunosuppression to alleviate allograft rejection

Biomaterials ◽  
2021 ◽  
pp. 120757
Author(s):  
Yingying Shi ◽  
Yichao Lu ◽  
Chunqi Zhu ◽  
Zhenyu Luo ◽  
Xiang Li ◽  
...  
Keyword(s):  
Stress Response ◽  
Er Stress ◽  
Allograft Rejection ◽  
Er Stress Response

scholarly journals Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 255
Author(s):  
Katharina F. Witting ◽  
Monique P.C. Mulder
Keyword(s):  
Dna Repair ◽  
Stress Response ◽  
Embryonic Development ◽  
Er Stress ◽  
Unmet Needs ◽  
Biological Function ◽  
Post Translational Modification ◽  
Er Stress Response ◽  
Cellular Events ◽  
Complex Signaling

Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.

Abstract 292: The Role of the ATF6 Branch of the ER Stress Response in the Endocrine Heart

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Erik A Blackwood ◽  
Christopher C Glembotski
Keyword(s):  
Stress Response ◽  
Er Stress ◽  
Knockout Mice ◽  
Ex Vivo ◽  
Proteolytic Cleavage ◽  
Isolated Perfused Heart ◽  
Wild Type ◽  
Atrial Myocytes ◽  
Perfused Heart ◽  
Er Stress Response

Rationale: Atrial natriuretic peptide (ANP) is stored in the heart in large dense core granules of atrial myocytes as a biologically inactive precursor, pro-ANP. Hemodynamic stress and atrial stretch stimulate coordinate secretion and proteolytic cleavage of pro-ANP to its bioactive form, ANP, which promotes renal salt excretion and vasodilation, which, together contribute to decreasing blood pressure. While the ATF6 branch of the ER stress response has been studied in ventricular tissue mouse models of myocardial ischemia and pathological hypertrophy, roles for ATF6 and ER stress on the endocrine function of atrial myocytes have not been studied. Objective/Methods: To address this gap in our knowledge, we knocked down ATF6 in primary cultured neonatal rat atrial myocytes (NRAMs) using a chemical inhibitor of the proteolytic cleavage site enabling ATF6 activation and siRNA and measured ANP expression and secretion basally and in response to alpha- adrenergic agonist stimulation using phenylephrine. We also compared the ANP secretion from wild- type mice and ATF6 knockout mice in an ex vivo Langendorff model of the isolated perfused heart. Results: ATF6 knockdown in NRAMs significantly impaired basal and phenylephrine-stimulated ANP secretion. ATF6 knockout mice displayed lower levels of ANP in atrial tissue at baseline as well as after phenylephrine treatment. Similarly, in the ex vivo isolated perfused heart model, less ANP was detected in effluent of ATF6 knockout hearts compared to wild-type hearts. Conclusions: The ATF6 branch of the ER stress response is necessary for efficient co-secretional processing of pro-ANP to ANP and for agonist-stimulated ANP secretion from atrial myocytes. As ANP is secreted in a regulated manner in response to a stimulus and pro-ANP is synthesized and packaged through the classical secretory pathway, we posit that ATF6 is required for adequate expression, folding, trafficking, processing and secretion of biologically active ANP from the endocrine heart.

Abstract 415: Cardioprotective Effects of Interleukin-15 in Immortalized Human Ventricular Cardiomyocytes

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Marin Jane McBride ◽  
Kristina Durham ◽  
Bernardo L Trigatti
Keyword(s):  
Stress Response ◽  
Er Stress ◽  
Interleukin 2 ◽  
Cell Types ◽  
Human Cardiomyocytes ◽  
Er Stress Response ◽  
Distinct Cell ◽  
Receptor Chain ◽  
Interleukin 15 ◽  
Receptor Beta

Interleukin-15 (IL-15) is a pleotropic cytokine that has a profound effect on the proliferation, survival and differentiation of many distinct cell types. The IL-15 receptor complex has 3 subunits: the unique receptor chain IL-15 receptor alpha (IL-15Rα), and two receptor chains shared with interleukin-2 (IL-2) and/or other cytokines, referred to as IL-2 receptor beta (IL-2Rβ) and IL-2 receptor gamma/gamma common chain (IL-2Rγ/γc), respectively. To our knowledge, this is the first study to examine the effects of IL-15 in immortalized human cardiomyocytes. Data collected by RT-PCR shows mRNA expression of IL-15Rα, IL-2Rβ and IL-2 Rγ/γc in these cells. Additionally, western blotting for IL-15Rα, IL-2Rβ and IL-2 Rγ/γc confirms the presence of all three IL-15 receptors. Early experiments examining the effect of IL-15 on cardiomyocyte cell survival show a statistically significant protective effect of IL-15 on the survival of cells exposed to tunicamycin, a pharamacological endoplasmic reticulum (ER) stress inducing agent. These findings suggest that IL-15 signaling may be an important cardioprotective pathway that is involved in the cardiac ER stress response. As ER stress is a major component of multiple different cardiac pathologies, such as myocardial infarction, heart failure and diabetes, uncovering the molecular mechanism by which IL-15 protects the heart will allow for deeper understanding of the cardiac ER stress response.

scholarly journals C. sakazakii activates AIM2 pathway accompanying with excessive ER stress response in mammalian mammary gland epithelium

2020 ◽  
Vol 25 (2) ◽  
pp. 223-233 ◽  
Author(s):  
Wenjuan Song ◽  
Le Sheng ◽  
Fanghui Chen ◽  
Yu Tian ◽  
Lian Li ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Stress Response ◽  
Er Stress ◽  
Er Stress Response

scholarly journals Constitutive Photomorphogenic 1 Enhances ER Stress Tolerance in Arabidopsis

2021 ◽  
Vol 22 (19) ◽  
pp. 10772
Author(s):  
Chang Ho Kang ◽  
Eun Seon Lee ◽  
Ganesh M. Nawkar ◽  
Joung Hun Park ◽  
Seong Dong Wi ◽  
...  
Keyword(s):  
Stress Response ◽  
Er Stress ◽  
Stress Conditions ◽  
Negative Regulator ◽  
Light Signaling ◽  
Dependent Manner ◽  
Wild Type ◽  
Er Stress Response ◽  
The Unfolded Protein Response ◽  
Mutant Locus

Interaction between light signaling and stress response has been recently reported in plants. Here, we investigated the role of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a key regulator of light signaling, in endoplasmic reticulum (ER) stress response in Arabidopsis. The cop1-4 mutant Arabidopsis plants were highly sensitive to ER stress induced by treatment with tunicarmycin (Tm). Interestingly, the abundance of nuclear-localized COP1 increased under ER stress conditions. Complementation of cop1-4 mutant plants with the wild-type or variant types of COP1 revealed that the nuclear localization and dimerization of COP1 are essential for its function in plant ER stress response. Moreover, the protein amount of ELONGATED HYPOCOTYL 5 (HY5), which inhibits bZIP28 to activate the unfolded protein response (UPR), decreased under ER stress conditions in a COP1-dependent manner. Accordingly, the binding of bZIP28 to the BIP3 promoter was reduced in cop1-4 plants and increased in hy5 plants compared with the wild type. Furthermore, introduction of the hy5 mutant locus into the cop1-4 mutant background rescued its ER stress-sensitive phenotype. Altogether, our results suggest that COP1, a negative regulator of light signaling, positively controls ER stress response by partially degrading HY5 in the nucleus.

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