scholarly journals High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

2021 ◽  
Author(s):  
Jamie L Marshall ◽  
Teia Noel ◽  
Qingbo S Wang ◽  
Silvana Bazua-Valenti ◽  
Haiqi Chen ◽  
...  
Keyword(s):  
High Resolution ◽  
Mouse Model ◽  
Human Kidney ◽  
Specific Cell ◽  
Unfolded Protein ◽  
Distinct Disease ◽  
A Cell ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Disease Specific

High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse and human kidneys, in healthy and in distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in human kidney by analyzing tissue from 9 distinct donors, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially-restricted kidney filter and blood flow regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially-restricted subpopulation of epithelial cells, we also found perturbations in 77 genes associated with the unfolded protein response (UPR). Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods.

scholarly journals A Role for the DnaJ Homologue Scj1p in Protein Folding in the Yeast Endoplasmic Reticulum

1998 ◽  
Vol 143 (4) ◽  
pp. 921-933 ◽  
Author(s):  
Susana Silberstein ◽  
Gabriel Schlenstedt ◽  
Pam A. Silver ◽  
Reid Gilmore
Keyword(s):  
Endoplasmic Reticulum ◽  
Unfolded Protein Response ◽  
Physiological Role ◽  
Carboxypeptidase Y ◽  
Reporter Protein ◽  
Unfolded Protein ◽  
A Cell ◽  
The Unfolded Protein Response ◽  
Protein Response

Members of the eukaryotic heat shock protein 70 family (Hsp70s) are regulated by protein cofactors that contain domains homologous to bacterial DnaJ. Of the three DnaJ homologues in the yeast rough endoplasmic reticulum (RER; Scj1p, Sec63p, and Jem1p), Scj1p is most closely related to DnaJ, hence it is a probable cofactor for Kar2p, the major Hsp70 in the yeast RER. However, the physiological role of Scj1p has remained obscure due to the lack of an obvious defect in Kar2p-mediated pathways in scj1 null mutants. Here, we show that the Δscj1 mutant is hypersensitive to tunicamycin or mutations that reduce N-linked glycosylation of proteins. Although maturation of glycosylated carboxypeptidase Y occurs with wild-type kinetics in Δscj1 cells, the transport rate for an unglycosylated mutant carboxypeptidase Y (CPY) is markedly reduced. Loss of Scj1p induces the unfolded protein response pathway, and results in a cell wall defect when combined with an oligosaccharyltransferase mutation. The combined loss of both Scj1p and Jem1p exaggerates the sensitivity to hypoglycosylation stress, leads to further induction of the unfolded protein response pathway, and drastically delays maturation of an unglycosylated reporter protein in the RER. We propose that the major role for Scj1p is to cooperate with Kar2p to mediate maturation of proteins in the RER lumen.

scholarly journals The Role of the ER-Induced UPR Pathway and the Efficacy of Its Inhibitors and Inducers in the Inhibition of Tumor Progression

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Anna Walczak ◽  
Kinga Gradzik ◽  
Jacek Kabzinski ◽  
Karolina Przybylowska-Sygut ◽  
Ireneusz Majsterek
Keyword(s):  
Er Stress ◽  
Molecular Mechanisms ◽  
Unfolded Proteins ◽  
Cell Protection ◽  
Protection Mechanism ◽  
Unfolded Protein ◽  
Er Stress Response ◽  
A Cell ◽  
The Unfolded Protein Response ◽  
Protein Response

Cancer is the second most frequent cause of death worldwide. It is considered to be one of the most dangerous diseases, and there is still no effective treatment for many types of cancer. Since cancerous cells have a high proliferation rate, it is pivotal for their proper functioning to have the well-functioning protein machinery. Correct protein processing and folding are crucial to maintain tumor homeostasis. Endoplasmic reticulum (ER) stress is one of the leading factors that cause disturbances in these processes. It is induced by impaired function of the ER and accumulation of unfolded proteins. Induction of ER stress affects many molecular pathways that cause the unfolded protein response (UPR). This is the way in which cells can adapt to the new conditions, but when ER stress cannot be resolved, the UPR induces cell death. The molecular mechanisms of this double-edged sword process are involved in the transition of the UPR either in a cell protection mechanism or in apoptosis. However, this process remains poorly understood but seems to be crucial in the treatment of many diseases that are related to ER stress. Hence, understanding the ER stress response, especially in the aspect of pathological consequences of UPR, has the potential to allow us to develop novel therapies and new diagnostic and prognostic markers for cancer.

scholarly journals Loss of αA or αB-Crystallin Accelerates Photoreceptor Cell Death in a Mouse Model of P23H Autosomal Dominant Retinitis Pigmentosa

2021 ◽  
Vol 23 (1) ◽  
pp. 70
Author(s):  
Tiantian Wang ◽  
Jingyu Yao ◽  
Lin Jia ◽  
Patrice E. Fort ◽  
David N. Zacks
Keyword(s):  
Cell Death ◽  
Mouse Model ◽  
Unfolded Protein ◽  
Retinal Degenerations ◽  
Light Sensing ◽  
Cell Death Pathways ◽  
Αb Crystallin ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Photoreceptor Death

Inherited retinal degenerations (IRD) are a leading cause of visual impairment and can result from mutations in any one of a multitude of genes. Mutations in the light-sensing protein rhodopsin (RHO) is a leading cause of IRD with the most common of those being a missense mutation that results in substitution of proline-23 with histidine. This variant, also known as P23H-RHO, results in rhodopsin misfolding, initiation of endoplasmic reticulum stress, the unfolded protein response, and activation of cell death pathways. In this study, we investigate the effect of α-crystallins on photoreceptor survival in a mouse model of IRD secondary to P23H-RHO. We find that knockout of either αA- or αB-crystallin results in increased intraretinal inflammation, activation of apoptosis and necroptosis, and photoreceptor death. Our data suggest an important role for the ⍺-crystallins in regulating photoreceptor survival in the P23H-RHO mouse model of IRD.

scholarly journals The stem/progenitor landscape is reshaped in a mouse model of essential thrombocythemia and causes excess megakaryocyte production

2020 ◽  
Vol 6 (48) ◽  
pp. eabd3139
Author(s):  
Daniel Prins ◽  
Hyun Jung Park ◽  
Sam Watcham ◽  
Juan Li ◽  
Michele Vacca ◽  
...  
Keyword(s):  
Mouse Model ◽  
Essential Thrombocythemia ◽  
Cholesterol Biosynthesis ◽  
Wild Type ◽  
Cell Compartment ◽  
Hematopoietic Stem ◽  
Unfolded Protein ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Transcriptomic Changes

Frameshift mutations in CALR (calreticulin) are associated with essential thrombocythemia (ET), but the stages at and mechanisms by which mutant CALR drives transformation remain incompletely defined. Here, we use single-cell approaches to examine the hematopoietic stem/progenitor cell landscape in a mouse model of mutant CALR-driven ET. We identify a trajectory linking hematopoietic stem cells (HSCs) with megakaryocytes and prospectively identify a previously unknown intermediate population that is overrepresented in the disease state. We also show that mutant CALR drives transformation primarily from the earliest stem cell compartment, with some contribution from megakaryocyte progenitors. Last, relative to wild-type HSCs, mutant CALR HSCs show increases in JAK-STAT signaling, the unfolded protein response, cell cycle, and a previously undescribed up-regulation of cholesterol biosynthesis. Overall, we have identified a novel megakaryocyte-biased cell population that is increased in a mouse model of ET and described transcriptomic changes linking CALR mutations to increased HSC proliferation and megakaryopoiesis.

scholarly journals Walking Along the Serendipitous Path of Discovery

2010 ◽  
Vol 21 (1) ◽  
pp. 15-17 ◽  
Author(s):  
Peter Walter
Keyword(s):  
Gene Expression ◽  
Protein Folding ◽  
Scientific Discovery ◽  
Molecular Machines ◽  
Unfolded Protein ◽  
Folding Defect ◽  
A Cell ◽  
Folded Proteins ◽  
The Unfolded Protein Response ◽  
Protein Response

Deciphering of the molecular mechanism of the “unfolded protein response” (UPR) provides a wonderful example of how serendipity can shape scientific discovery. Secretory and membrane proteins begin their journey to the cell surface in the endoplasmic reticulum (ER). Before leaving the organelle, proteins are quality-controlled, and only properly folded proteins are transported onwards. The UPR detects an insufficiency in the protein-folding capacity in the ER and in the ways of a finely tuned homeostat adjusts organelle abundance according to need. If the protein-folding defect in the ER cannot be corrected, the UPR switches from a cell-protective to a cell-destructive mode and activates apoptosis in metazoan cells. Such life or death decisions position the UPR in the center of numerous pathologies, including viral infection, protein-folding diseases, diabetes, and cancer. The UPR proved to be a rich field for serendipitous discovery because the molecular machines that transmit information about insufficient protein folding and activate appropriate gene expression programs function in unusual, unprecedented ways. A key regulatory switch in the UPR, for example, is a cytoplasmic, nonconventional mRNA spicing reaction, initiated by a bifunctional transmembrane kinase/endoribonuclease.

scholarly journals The Unfolded Protein Response in Breast Cancer

Cancers ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 344 ◽  
Author(s):  
Eoghan McGrath ◽  
Susan Logue ◽  
Katarzyna Mnich ◽  
Shane Deegan ◽  
Richard Jäger ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Unfolded Protein Response ◽  
Therapy Resistance ◽  
Breast Cancers ◽  
Unfolded Protein ◽  
Promising Target ◽  
A Cell ◽  
The Unfolded Protein Response ◽  
Cell Stress Response ◽  
Protein Response

In 2018, in the US alone, it is estimated that 268,670 people will be diagnosed with breast cancer, and that 41,400 will die from it. Since breast cancers often become resistant to therapies, and certain breast cancers lack therapeutic targets, new approaches are urgently required. A cell-stress response pathway, the unfolded protein response (UPR), has emerged as a promising target for the development of novel breast cancer treatments. This pathway is activated in response to a disturbance in endoplasmic reticulum (ER) homeostasis but has diverse physiological and disease-specific functions. In breast cancer, UPR signalling promotes a malignant phenotype and can confer tumours with resistance to widely used therapies. Here, we review several roles for UPR signalling in breast cancer, highlighting UPR-mediated therapy resistance and the potential for targeting the UPR alone or in combination with existing therapies.

scholarly journals The inositol-requiring enzyme 1 (IRE1α) RNAse inhibitor, 4µ8C, is also a potent cellular antioxidant

2018 ◽  
Vol 475 (5) ◽  
pp. 923-929 ◽  
Author(s):  
Stanley M.H. Chan ◽  
Mark P. Lowe ◽  
Ashton Bernard ◽  
Alyson A. Miller ◽  
Terence P. Herbert
Keyword(s):  
Er Stress ◽  
Cultured Cells ◽  
Specific Inhibitor ◽  
Unfolded Protein ◽  
Ic50 Values ◽  
A Cell ◽  
Target Effect ◽  
The Unfolded Protein Response ◽  
Protein Response

Inositol-requiring enzyme 1 alpha (IRE1α) is an endoplasmic reticulum (ER)-transmembrane endonuclease that is activated in response to ER stress as part of the unfolded protein response (UPR). Chronic activation of the UPR has been implicated in the pathogenesis of many common diseases including diabetes, cancer, and neurological pathologies such as Huntington's and Alzheimer's disease. 7-Hydroxy-4-methyl-2-oxo-2H-chromene-8-carbaldehyde (4µ8C) is widely used as a specific inhibitor of IRE1α ribonuclease activity (IC50 of 6.89 µM in cultured cells). However, in this paper, we demonstrate that 4µ8C acts as a potent reactive oxygen species (ROS) scavenger, both in a cell-free assay and in cultured cells, at concentrations lower than that widely used to inhibit IRE1α activity. In vitro we show that, 4µ8C effectively decreases xanthine/xanthine oxidase catalysed superoxide production with an IC50 of 0.2 µM whereas in cultured endothelial and clonal pancreatic β-cells, 4µ8C inhibits angiotensin II-induced ROS production with IC50 values of 1.92 and 0.29 µM, respectively. In light of this discovery, conclusions reached using 4µ8C as an inhibitor of IRE1α should be carefully evaluated. However, this unexpected off-target effect of 4µ8C may prove therapeutically advantageous for the treatment of pathologies that are thought to be caused by, or exacerbated by, both oxidative and ER stress such as endothelial dysfunction and/or diabetes.

scholarly journals Probiotics Supplements Reduce ER Stress and Gut Inflammation Associated with Gliadin Intake in a Mouse Model of Gluten Sensitivity

Nutrients ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 1221
Author(s):  
Eleonora Ferrari ◽  
Romina Monzani ◽  
Valentina Saverio ◽  
Mara Gagliardi ◽  
Elżbieta Pańczyszyn ◽  
...  
Keyword(s):  
Mouse Model ◽  
Er Stress ◽  
Human Leukocyte ◽  
Gut Inflammation ◽  
Leukocyte Antigen ◽  
Unfolded Protein ◽  
Worldwide Population ◽  
The Unfolded Protein Response ◽  
Protein Response

Exposure to gluten, a protein present in wheat rye and barley, is the major inducer for human Celiac Disease (CD), a chronic autoimmune enteropathy. CD occurs in about 1% worldwide population, in genetically predisposed individuals bearing human leukocyte antigen (HLA) DQ2/DQ8. Gut epithelial cell stress and the innate immune activation are responsible for the breaking oral tolerance to gliadin, a gluten component. To date, the only treatment available for CD is a long-term gluten-free diet. Several studies have shown that an altered composition of the intestinal microbiota (dysbiosis) could play a key role in the pathogenesis of CD through the modulation of intestinal permeability and the regulation of the immune system. Here, we show that gliadin induces a chronic endoplasmic reticulum (ER) stress condition in the small intestine of a gluten-sensitive mouse model and that the coadministration of probiotics efficiently attenuates both the unfolded protein response (UPR) and gut inflammation. Moreover, the composition of probiotics formulations might differ in their activity at molecular level, especially toward the three axes of the UPR. Therefore, probiotics administration might potentially represent a new valuable strategy to treat gluten-sensitive patients, such as those affected by CD.

scholarly journals The Endoplasmic Reticulum Role in the Plant Response to Abiotic Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Sofía Reyes-Impellizzeri ◽  
Adrian A. Moreno
Keyword(s):  
Endoplasmic Reticulum ◽  
Plant Response ◽  
Er Quality Control ◽  
Unfolded Protein ◽  
A Cell ◽  
Client Proteins ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
The Impact ◽  
S Proteins

The endoplasmic reticulum (ER) is the organelle where one third of the proteins of a cell are synthetized. Several of these proteins participate in the signaling and response of cells, tissues, or from the organism to the environment. To secure the proper synthesis and folding of these proteins, or the disposal of unfolded or misfolded proteins, the ER has different mechanisms that interact and regulate each other. These mechanisms are known as the ER quality control (ERQC), ER-associated degradation (ERAD) and the unfolded protein response (UPR), all three participants of the maintenance of ER protein homeostasis or proteostasis. Given the importance of the client proteins of these ER mechanisms in the plant response to the environment, it is expected that changes or alterations on their components have an impact on the plant response to environmental cues or stresses. In this mini review, we focus on the impact of the alteration of components of ERQC, ERAD and UPR in the plant response to abiotic stresses such as drought, heat, osmotic, salt and irradiation. Also, we summarize findings from recent publications looking for a connection between these processes and their possible client(s) proteins. From this, we observed that a clear connection has been established between the ERAD and UPR mechanisms, but evidence that connects ERQC components to these both processes or their possible client(s) proteins is still lacking. As a proposal, we suggest the use of proteomics approaches to uncover the identity of these proteins and their connection with ER proteostasis.

scholarly journals Pathogenic tau does not drive activation of the unfolded protein response

2019 ◽  
Vol 294 (25) ◽  
pp. 9679-9688 ◽  
Author(s):  
Aleksandra P. Pitera ◽  
Ayodeji A. Asuni ◽  
Vincent O'Connor ◽  
Katrin Deinhardt
Keyword(s):  
Endoplasmic Reticulum ◽  
Mouse Model ◽  
Neurodegenerative Diseases ◽  
Unfolded Protein Response ◽  
Neuronal Cultures ◽  
Critical Determinant ◽  
Unfolded Protein ◽  
The Unfolded Protein Response ◽  
Protein Response

The unfolded protein response (UPR) is commonly associated with a range of neurodegenerative diseases, and targeting UPR components has been suggested as a therapeutic strategy. The UPR surveys protein folding within the endoplasmic reticulum. However, many of the misfolded proteins that accumulate in neurodegeneration are localized so that they do not directly cause endoplasmic reticulum triggers that activate this pathway. Here, using a transgenic mouse model and primary cell cultures along with quantitative PCR, immunoblotting, and immunohistochemistry, we tested whether the UPR is induced in in vivo and in vitro murine models of tauopathy that are based on expression of mutant tauP301L. We found no evidence for the UPR in the rTg4510 mouse model, in which mutant tau is transgenically expressed under the control of tetracycline-controlled transactivator protein. This observation was supported by results from acute experiments in which neuronal cultures expressed mutant tau and accumulated misfolded cytoplasmic tau aggregates but exhibited no UPR activation. These results suggest that the UPR is not induced as a response to tau misfolding and aggregation despite clear evidence for progressive cellular dysfunction and degeneration. We propose that caution is needed when evaluating the implied significance of the UPR as a critical determinant across major neurodegenerative diseases.

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