bims-ershed 2021-12-26 papers

bims-ershed

Biomed News

on ER Stress in Health and Diseases

Issue of 2021–12–26
eight papers selected by
Matías Eduardo González Quiroz, Worker’s Hospital

Protein Aggregation in the ER: Calm behind the Storm.
Endoplasmic Reticulum Stress Promotes iNOS/NO and Influences Inflammation in the Development of Doxorubicin-Induced Cardiomyopathy.
Cellular Response to Unfolded Proteins in Depression.
A proximity labeling protocol to probe proximity interactions in C. elegans.
A detailed protocol for RNA cleavage assay in sympathetic neurons.
Identification of a novel signature based on unfolded protein response-related gene for predicting prognosis in bladder cancer.
Characterization of the AGR2 interactome uncovers new players of Protein Disulfide Isomerase network in cancer cells.
Protocol for cell type-specific labeling, enrichment, and proteomic profiling of plasma proteins in mice.

Cells. 2021 Nov 28. pii: 3337. [Epub ahead of print]10(12):

Protein Aggregation in the ER: Calm behind the Storm.

Haisen Li, Shengyi Sun.

  As one of the largest organelles in eukaryotic cells, the endoplasmic reticulum (ER) plays a vital role in the synthesis, folding, and assembly of secretory and membrane proteins. To maintain its homeostasis, the ER is equipped with an elaborate network of protein folding chaperones and multiple quality control pathways whose cooperative actions safeguard the fidelity of protein biogenesis. However, due to genetic abnormalities, the error-prone nature of protein folding and assembly, and/or defects or limited capacities of the protein quality control systems, nascent proteins may become misfolded and fail to exit the ER. If not cleared efficiently, the progressive accumulation of misfolded proteins within the ER may result in the formation of toxic protein aggregates, leading to the so-called "ER storage diseases". In this review, we first summarize our current understanding of the protein folding and quality control networks in the ER, including chaperones, unfolded protein response (UPR), ER-associated protein degradation (ERAD), and ER-selective autophagy (ER-phagy). We then survey recent research progress on a few ER storage diseases, with a focus on the role of ER quality control in the disease etiology, followed by a discussion on outstanding questions and emerging concepts in the field.

Keywords:  ER; ER storage disease; ER-associated protein degradation; ER-phagy; chaperone; protein aggregate; unfolded protein response

DOI:  https://doi.org/10.3390/cells10123337
Antioxidants (Basel). 2021 Nov 26. pii: 1897. [Epub ahead of print]10(12):

Endoplasmic Reticulum Stress Promotes iNOS/NO and Influences Inflammation in the Development of Doxorubicin-Induced Cardiomyopathy.

Ashim K Bagchi, Akshi Malik, Gauri Akolkar, Davinder S Jassal, Pawan K Singal.

  Doxorubicin (Dox) is known to cause heart failure in some cancer patients. Despite extensive studies over the past half century, the subcellular basis of Dox-induced cardiomyopathy (DIC) is still elusive. Earlier, we suggested that Dox causes a delayed activation of unfolded protein response (UPR) which may promote mitochondrial Bax activity leading to cardiomyocyte death. As a follow up, using NO donor, S-Nitroso-N-acetyl-d,l-penicillamine (SNAP), and/or NOS inhibitor, N(ω)-nitro-L-arginine methyl ester (L-NAME), we now show that endoplasmic reticulum (ER) stress promotes inflammation through iNOS/NO-induced TLR2 activation. In vivo Dox treatment increased mitochondrial iNOS to promote ER stress as there was an increase in Bip (Grp78) response, proapoptotic CHOP (DDIT3) and ER-mediated Caspase 12 activation. Increased iNOS activity is associated with an increase in TLR2 and TNF-α receptor associated factor 2 (TRAF2). These two together with NF-κB p105/50 expression and a synergistic support through ER stress, promote inflammatory response in the myocardium leading to cell death and ultimately fostering DIC conditions. In the presence of NOS inhibitor, such detrimental effects of Dox were inhibited, suggesting iNOS/NO as key mediators of Dox-induced inflammatory as well as apoptotic responses.

Keywords:  Dox-induced cardiomyopathy; ER stress; Toll-like receptor 2; apoptosis; inducible nitric oxide synthase

DOI:  https://doi.org/10.3390/antiox10121897
Life (Basel). 2021 Dec 10. pii: 1376. [Epub ahead of print]11(12):

Cellular Response to Unfolded Proteins in Depression.

Mateusz Kowalczyk, Edward Kowalczyk, Paweł Kwiatkowski, Łukasz Łopusiewicz, Monika Talarowska, Monika Sienkiewicz.

  Despite many scientific studies on depression, there is no clear conception explaining the causes and mechanisms of depression development. Research conducted in recent years has shown that there is a strong relationship between depression and the endoplasmic reticulum (ER) stress. In order to restore ER homeostasis, the adaptive unfolded protein response (UPR) mechanism is activated. Research suggests that ER stress response pathways are continuously activated in patients with major depressive disorders (MDD). Therefore, it seems that the recommended drugs should reduce ER stress. A search is currently underway for drugs that will be both effective in reducing ER stress and relieving symptoms of depression.

Keywords:  depression; endoplasmic reticulum stress; inflammation; unfolded protein response

DOI:  https://doi.org/10.3390/life11121376
STAR Protoc. 2021 Dec 17. 2(4): 100986

A proximity labeling protocol to probe proximity interactions in C. elegans.

Ariana D Sanchez, Jessica L Feldman.

  Enzyme-catalyzed proximity labeling (PL) has emerged as a critical approach for identifying protein-protein proximity interactions in cells; however, PL techniques were not historically practical in living multicellular organisms due to technical limitations. Here, we present a protocol for applying PL to living C. elegans using the biotin ligase mutant enzyme TurboID. We demonstrated PL in a tissue-specific and region-specific manner by focusing on non-centrosomal MTOCs (ncMTOCs) of intestinal cells. This protocol is useful for targeted in vivo protein network profiling. For complete details on the use and execution of this protocol, please refer to Sanchez et al. (2021).

Keywords:  Cell Biology; Developmental biology; Microscopy; Model Organisms; Molecular Biology; Molecular/Chemical Probes; Protein Biochemistry; Proteomics

DOI:  https://doi.org/10.1016/j.xpro.2021.100986
STAR Protoc. 2021 Dec 17. 2(4): 101001

A detailed protocol for RNA cleavage assay in sympathetic neurons.

Catia Andreassi, Antonella Riccio.

  This protocol illustrates the use of an in vitro assay to study the cleavage of the IMPA1 3'UTR by the endonuclease Ago2 in sympathetic neurons. The procedure includes the preparation of cytoplasmic protein extracts and also describes the synthesis and labeling of the RNA probe. The protocol can be applied to other cell systems, RNA transcripts, and endonucleases to confirm the role of known cleavage site(s) and cleavage proteins, or to investigate new ones. For complete details on the use and execution of this protocol, please refer to Andreassi et al. (2021).

Keywords:  Chemistry; Molecular Biology; Neuroscience

DOI:  https://doi.org/10.1016/j.xpro.2021.101001
Hum Genomics. 2021 Dec 20. 15(1): 73

Identification of a novel signature based on unfolded protein response-related gene for predicting prognosis in bladder cancer.

Ke Zhu, Liu Xiaoqiang, Wen Deng, Gongxian Wang, Bin Fu.

   BACKGROUND: The unfolded protein response (UPR) served as a vital role in the progression of tumors, but the molecule mechanisms of UPR in bladder cancer (BLCA) have been not fully investigated.
METHODS: We identified differentially expressed unfolded protein response-related genes (UPRRGs) between BLCA samples and normal bladder samples in the Cancer Genome Atlas (TCGA) database. Univariate Cox analysis and the least absolute shrinkage and selection operator penalized Cox regression analysis were used to construct a prognostic signature in the TCGA set. We implemented the validation of the prognostic signature in GSE13507 from the Gene Expression Omnibus database. The ESTIMATE, CIBERSORT, and ssGSEA algorithms were used to explore the correlation between the prognostic signature and immune cells infiltration as well as key immune checkpoints (PD-1, PD-L1, CTLA-4, and HAVCR2). GDSC database analyses were conducted to investigate the chemotherapy sensitivity among different groups. GSEA analysis was used to explore the potential mechanisms of UPR-based signature.
RESULTS: A prognostic signature comprising of seven genes (CALR, CRYAB, DNAJB4, KDELR3, CREB3L3, HSPB6, and FBXO6) was constructed to predict the outcome of BLCA. Based on the UPRRGs signature, the patients with BLCA could be classified into low-risk groups and high-risk groups. Patients with BLCA in the low-risk groups showed the more favorable outcomes than those in the high-risk groups, which was verified in GSE13507 set. This signature could serve as an autocephalous prognostic factor in BLCA. A nomogram based on risk score and clinical characteristics was established to predict the over survival of BLCA patients. Furthermore, the signature was closely related to immune checkpoints (PD-L1, CTLA-4, and HAVCR2) and immune cells infiltration including CD8+ T cells, follicular helper T cells, activated dendritic cells, and M2 macrophages. GSEA analysis indicated that immune and carcinogenic pathways were enriched in high-risk group.
CONCLUSIONS: We identified a novel unfolded protein response-related gene signature which could predict the over survival, immune microenvironment, and chemotherapy response of patients with bladder cancer.

Keywords:  Biomarker; Bladder cancer; Prognostic; Unfolded protein response

DOI:  https://doi.org/10.1186/s40246-021-00372-x
Mol Cell Proteomics. 2021 Dec 17. pii: S1535-9476(21)00160-2. [Epub ahead of print] 100188

Characterization of the AGR2 interactome uncovers new players of Protein Disulfide Isomerase network in cancer cells.

Pavla Bouchalova, Lucia Sommerova, David Potesil, Andrea Martisova, Petr Lapcik, Veronika Koci, Alex Scherl, Petr Vonka, Joan Planas-Iglesias, Eric Chevet, Pavel Bouchal, Roman Hrstka.

  AGR2 is an endoplasmic reticulum (ER)-resident protein disulfide isomerase (PDI) known to be overexpressed in many human epithelial cancers, and is involved in cell migration, cellular transformation, angiogenesis, and metastasis. This protein inhibits the activity of the tumor suppressor p53 and its expression levels can be used to predict cancer patient outcome. However, the precise network of AGR2-interacting partners and clients remains to be fully characterized. Herein, we used label-free quantification and also SILAC-based LC-MS/MS analyses to identify proteins interacting with AGR2. Functional annotation confirmed that AGR2 and its interaction partners are associated with processes in the ER that maintain intracellular metabolic homeostasis and participate in the unfolded protein response, including those associated with changes in cellular metabolism, energy, and redox states in response to ER stress. As a proof of concept, the interaction between AGR2 and PDIA3, another ER resident PDI, was studied in more detail. Pathway analysis revealed that AGR2 and PDIA3 play roles in protein folding in ER, including posttranslational modification and in cellular response to stress. We confirmed the AGR2-PDIA3 complex formation in cancer cells, which was enhanced in response to ER stress. Accordingly, molecular docking characterized potential quaternary structure of this complex, however, it remains to be elucidated whether (i) AGR2 rather contributes to PDIA3 maturation in ER, (ii) the complex directly acts in cellular signaling, or (iii) mediates AGR2 secretion. Our study provides a comprehensive insight into the protein-protein interaction network of AGR2 by identifying functionally relevant proteins and related cellular and biochemical pathways associated with the role of AGR2 in cancer cells.

Keywords:  anterior gradient protein 2; mass spectrometry; protein disulfide isomerase; protein-protein interactions; secretory pathway

DOI:  https://doi.org/10.1016/j.mcpro.2021.100188
STAR Protoc. 2021 Dec 17. 2(4): 101014

Protocol for cell type-specific labeling, enrichment, and proteomic profiling of plasma proteins in mice.

Wei Wei, Nicholas M Riley, Xuchao Lyu, Carolyn R Bertozzi, Jonathan Z Long.

  Secreted polypeptides represent a fundamental axis of intercellular communication. Here, we present a protocol for the cell type-specific biotinylation, enrichment, and proteomic profiling of secreted plasma proteins directly in mice. This protocol uses conditional "turn-on" adeno-associated viruses expressing an endoplasmic reticulum-targeted biotin ligase to globally biotinylate proteins of the secretory pathway in a cell type-specific manner. Biotinylated secreted proteins can be directly purified from blood plasma and analyzed by SDS-PAGE gel or shotgun proteomics. For complete information on the generation and use of this protocol, please refer to Wei et al. (2021).

Keywords:  Biotechnology and bioengineering; Cell Biology; Mass Spectrometry; Model Organisms; Protein Biochemistry; Proteomics; Systems biology

DOI:  https://doi.org/10.1016/j.xpro.2021.101014