bims-unfpre 2025-04-13 papers

bims-unfpre

Biomed News

on Unfolded protein response

Issue of 2025–04–13
ten papers selected by
Susan Logue, University of Manitoba

Mutant p53 upregulates HDAC6 to resist ER stress and facilitates Ku70 deacetylation, which prevents its degradation and mitigates DNA damage in colon cancer cells.
MiR-204-5p mediates PERK inhibition to suppress growth and induce apoptosis in ovarian cancer through the eIF2α/ATF-4/CHOP pathway.
The PERK-ATF4 pathway is required for metabolic reprogramming and progressive lung fibrosis.
Cytosolic and endoplasmic reticulum chaperones inhibit wt-p53 to increase cancer cells' survival by refluxing ER-proteins to the cytosol.
Targeting the ER stress sensor IRE1 protects the liver from fibrosis through the downregulation of the proteostasis factor P4HB/PDIA1.
Dissecting Branch-Specific Unfolded Protein Response Activation in Drug-Tolerant BRAF-Mutant Melanoma using Data-Independent Acquisition Mass Spectrometry.
PRKCSH enhances colorectal cancer radioresistance via IRE1α/XBP1s-mediated DNA repair.
PERK's novel agonist protects against myocardial ischemia-reperfusion injury by modulating ER-mitochondria contacts and phosphatidic acid transport.
The mitochondrial unfolded protein response inhibits pluripotency acquisition and mesenchymal-to-epithelial transition in somatic cell reprogramming.
A nonenzymatic dependency on inositol-requiring enzyme 1 controls cancer cell cycle progression and tumor growth.

Cell Death Discov. 2025 Apr 10. 11(1): 162

Mutant p53 upregulates HDAC6 to resist ER stress and facilitates Ku70 deacetylation, which prevents its degradation and mitigates DNA damage in colon cancer cells.

Rossella Benedetti, Michele Di Crosta, Maria Saveria Gilardini Montani, Gabriella D'Orazi, Mara Cirone.

Cancer cells employ interconnected mechanisms to withstand intrinsic and extrinsic stress, with mutant p53 (mutp53) playing a key role in bolstering resistance to endoplasmic reticulum (ER) stress. In this study, we further investigated this phenomenon, focusing on the DNA damage triggered by ER stress. Our findings indicate that mutp53 mitigates ER stress-induced DNA damage by sustaining high levels of Ku70, a critical protein in DNA repair via the non-homologous end joining (NHEJ) pathway, which functions alongside Ku80. HDAC6 upregulation emerged as a crucial driver of this response. HDAC6 deacetylates Ku70, promoting its nuclear localization and protecting it from degradation. This mechanism ensures continuous activity of the NHEJ repair pathway, allowing mutp53-expressing cells to better manage DNA damage from ER stress, thus contributing to the genomic instability characteristic of cancer progression. Furthermore, HDAC6 maintains the activation of the ATF6 branch of the unfolded protein response (UPR), enhancing the ability of mutp53 cells to resist ER stress, as ATF6 supports cellular adaptation to misfolded proteins and stressful conditions. Since HDAC6 is central to this enhanced stress resistance and DNA repair, targeting it could disrupt these protective mechanisms, increasing the vulnerability of mutp53 cancer cells to ER stress and inhibiting cancer progression.

DOI: https://doi.org/10.1038/s41420-025-02433-9
Sci Rep. 2025 Apr 11. 15(1): 12435

MiR-204-5p mediates PERK inhibition to suppress growth and induce apoptosis in ovarian cancer through the eIF2α/ATF-4/CHOP pathway.

Faranak Fallahian, Seyedeh Sara Ghorbanhosseini, Shekufe Rezghi Barez, Mahmoud Aghaei.

  The unfolded protein response (UPR) is crucial in maintaining cell survival during stressful conditions, but prolonged ER stress can lead to apoptosis. Based on the evidence acquired, it has been suggested that inhibiting the protein kinase RNA-like ER kinase (PERK) pathway, which constitutes an adaptive branch of UPR, may represent a viable approach for impeding the proliferation of neoplastic cells. This study assesses the influence of PERK inhibition mediated by miR-204-5p on the growth of ovarian cancer cell lines, OVCAR3 and SKOV3. We demonstrated that miR-204-5p significantly downregulated the expression of PERK at the RNA and protein levels. The suppression of PERK, mediated by miR-204-5p, significantly diminished cellular viability and enhanced apoptotic cell death in cells exposed to Tunicamycin (Tm). We ascertained that the inhibition of PERK by miR-204-5p decreased eukaryotic initiation factor 2alpha (eIF2α) phosphorylation. Moreover, activating transcription factor 4 (ATF4) and CCAAT-enhancer-binding homologous protein (CHOP) expression levels were notably elevated in response to miR-204-5p. The expression of Bax and caspase-12 was found to be upregulated, while the expression of Bcl-2 was reduced. This study is the first to demonstrate that silencing the PERK gene through miR-204-5p significantly inhibits cell growth and promotes ER-stress-induced apoptosis in ovarian cancer cells.

Keywords:  Apoptosis; ER stress; MiR-204-5p; MicroRNA; Ovarian cancer; PERK

DOI:  https://doi.org/10.1038/s41598-025-95883-1
JCI Insight. 2025 Apr 10. pii: e189330. [Epub ahead of print]

The PERK-ATF4 pathway is required for metabolic reprogramming and progressive lung fibrosis.

Jyotsana Pandey, Jennifer L Larson-Casey, Mallikarjun H Patil, Chao He, Nisarat Pinthong, A Brent Carter.

  Asbestosis is a prototypical type of fibrosis that is progressive and does not resolve. ER stress is increased in multiple cell types that contribute to fibrosis; however, the mechanism(s) by which ER stress in lung macrophages contributes to fibrosis is poorly understood. Here, we show that ER stress resulted in PERK activation in human subjects with asbestosis. Similar results were seen in asbestos-injured mice. Mice harboring a conditional deletion of Eif2ak3 were protected from fibrosis. Lung macrophages from asbestosis subjects had evidence of metabolic reprogramming to fatty acid oxidation (FAO). Eif2ak3fl/fl mice had increased oxygen consumption rate (OCR), whereas OCR in Eif2ak3-/-Lyz2-cre mice was reduced to control levels. PERK increased Atf4 expression, and ATF4 bound to the Ppargc1a promoter to increase its expression. GSK2656157, a PERK-specific inhibitor, reduced FAO, Ppargc1a, and Aft4 in lung macrophages and reversed established fibrosis in mice. These observations suggest that PERK is a unique therapeutic target to reverse established fibrosis.

Keywords:  Fatty acid oxidation; Fibrosis; Immunology; Macrophages; Pulmonology

DOI:  https://doi.org/10.1172/jci.insight.189330
Elife. 2025 Apr 09. pii: e102658. [Epub ahead of print]14

Cytosolic and endoplasmic reticulum chaperones inhibit wt-p53 to increase cancer cells' survival by refluxing ER-proteins to the cytosol.

Salam Dabsan, Gali Zur, Naim Abu-Freha, Shahar Sofer, Iris Grossman-Haham, Ayelet Gilad, Aeid Igbaria.

  The endoplasmic reticulum (ER) is an essential sensing organelle responsible for the folding and secretion of almost one-third of eukaryotic cells' total proteins. However, environmental, chemical, and genetic insults often lead to protein misfolding in the ER, accumulating misfolded proteins, and causing ER stress. To solve this, several mechanisms were reported to relieve ER stress by decreasing the ER protein load. Recently, we reported a novel ER surveillance mechanism by which proteins from the secretory pathway are refluxed to the cytosol to relieve the ER of its content. The refluxed proteins gain new prosurvival functions in cancer cells, thereby increasing cancer cell fitness. We termed this phenomenon ER to CYtosol Signaling (or 'ERCYS'). Here, we found that in mammalian cells, ERCYS is regulated by DNAJB12, DNAJB14, and the HSC70 cochaperone SGTA. Mechanistically, DNAJB12 and DNAJB14 bind HSC70 and SGTA - through their cytosolically localized J-domains to facilitate ER-protein reflux. DNAJB12 is necessary and sufficient to drive this phenomenon to increase AGR2 reflux and inhibit wt-p53 during ER stress. Mutations in DNAJB12/14 J-domain prevent the inhibitory interaction between AGR2-wt-p53. Thus, targeting the DNAJB12/14-HSC70/SGTA axis is a promising strategy to inhibit ERCYS and impair cancer cell fitness.

Keywords:  DNAJB12; ER stress; ERCYS; UPR; cancer biology; cell biology; chaperones; none; reflux

DOI:  https://doi.org/10.7554/eLife.102658
Hepatology. 2025 Apr 09.

Targeting the ER stress sensor IRE1 protects the liver from fibrosis through the downregulation of the proteostasis factor P4HB/PDIA1.

Younis Hazari, Lama Habbouche, Valeria A Garcia Lopez, Hery Urra, Javier Diaz, Giovanni Tamburini, Mateus Milani, Sylvere Durand, Fanny Aprahamian, Reese Baxter, Menghao Huang, X Charlie Dong, Luis Gonzalez-Rojas, Juan Francisco Silva, Ignacio Tapia-Dufey, Helena Vihinen, Vlad Ratziu, Fabienne Foufelle, Jan G Hengstler, Eija Jokitalo, Jessica L Maiers, Lars Plate, Guido Kroemer, Beatrice Bailly-Maitre, Claudio Hetz.

  Collagen is the main cargo of the secretory pathway, contributing to hepatic fibrogenesis due to extensive accumulation of extracellular matrix. An excess of collagen deposition is a characteristic feature of several chronic liver diseases. Collagen overproduction imposes pressure on the secretory pathway, altering endoplasmic reticulum (ER) proteostasis. Here we investigated the possible contribution of the unfolded protein response UPR, the main adaptive pathway that monitors and adjusts protein production capacity at the ER, to collagen biogenesis and liver disease. Genetic ablation of the ER stress sensor IRE1 in the liver using conditional knockout mice reduced liver damage and collagen deposition in models of fibrosis, steatosis, and acute hepatotoxicity. Proteomic profiling identified the prolyl 4-hydroxylase (P4HB, also known as PDIA1) as a major IRE1-regulated gene, a critical factor involved in collagen maturation. Cell culture studies demonstrated that IRE1 deficiency results in collagen retention at the ER, reducing its secretion, and this phenotype is rescued by P4HB/PDIA1 overexpression. Analyses of human MASH samples revealed a positive correlation between IRE1 signaling and P4HB/PDIA1 expression as well as the severity of the disease. Altogether, our results establish a role of the IRE1/P4HB axis in the regulation of collagen production and support its implication in the pathogenesis of liver fibrosis.

Keywords:  IRE1; PDIA1/ P4HB; UPR; collagen; endoplasmic reticulum; liver fibrosis

DOI:  https://doi.org/10.1097/HEP.0000000000001335
bioRxiv. 2025 Mar 24. pii: 2025.03.20.644425. [Epub ahead of print]

Dissecting Branch-Specific Unfolded Protein Response Activation in Drug-Tolerant BRAF-Mutant Melanoma using Data-Independent Acquisition Mass Spectrometry.

Lea A Barny, Jake N Hermanson, Sarah K Garcia, Philip E Stauffer, Lars Plate.

Cells rely on the Unfolded Protein Response (UPR) to maintain ER protein homeostasis (proteostasis) when faced with elevated levels of misfolded and aggregated proteins. The UPR is comprised of three main branches-ATF6, IRE1, and PERK-that coordinate the synthesis of proteins involved in folding, trafficking, and degradation of nascent proteins to restore ER function. Dysregulation of the UPR is linked to numerous diseases, including neurodegenerative disorders, cancer, and diabetes. Despite its importance, identifying UPR targets has been challenging due to their heterogeneous induction, which varies by cell type and tissue. Additionally, defining the magnitude and range of UPR-regulated genes is difficult because of intricate temporal regulation, feedback between UPR branches, and extensive cross-talk with other stress-signaling pathways. To comprehensively identify UPR-regulated proteins and determine their branch specificity, we developed a data-independent acquisition (DIA) liquid-chromatography mass spectrometry (LC-MS) pipeline. Our optimized workflow improved identifications of low-abundant UPR proteins and leveraged an automated SP3-based protocol on the Biomek i5 liquid handler for label-free peptide preparation. Using engineered stable cell lines that enable selective pharmacological activation of each UPR branch without triggering global UPR activation, we identified branch-specific UPR proteomic targets. These targets were subsequently applied to investigate proteomic changes in multiple patient-derived BRAF-mutant melanoma cell lines treated with a BRAF inhibitor (PLX4720, i.e., vemurafenib). Our findings revealed differential regulation of the XBP1s branch of the UPR in the BRAF-mutant melanoma cell lines after PLX4720 treatment, likely due to calcium activation, suggesting that the UPR plays a role as a non-genetic mechanism of drug tolerance in melanoma. In conclusion, the validated branch-specific UPR proteomic targets identified in this study provide a robust framework for investigating this pathway across different cell types, drug treatments, and disease conditions in a high-throughput manner.

DOI: https://doi.org/10.1101/2025.03.20.644425
Cell Death Dis. 2025 Apr 06. 16(1): 258

PRKCSH enhances colorectal cancer radioresistance via IRE1α/XBP1s-mediated DNA repair.

Hui Shen, Jing Jin, Nanxi Yu, Tingting Liu, Yongzhan Nie, Zhijie Wan, Yuanyuan Chen, Kun Cao, Ying Xu, Yijuan Huang, Chao Feng, Ruixue Huang, Yanyong Yang, Fu Gao.

Neoadjuvant radiotherapy is the standard treatment for locally advanced rectal cancer, but resistance to this therapy remains a significant clinical challenge. Understanding the molecular mechanisms of radioresistance and developing strategies to enhance radiosensitivity are crucial for improving treatment outcomes. This study investigated the role of PRKCSH in colorectal cancer radioresistance and its underlying mechanisms. Our results demonstrate that PRKCSH is upregulated in colorectal cancer cells following ionizing radiation. Inhibiting PRKCSH sensitized these cells to radiation by reducing clonogenic survival, promoting apoptosis, and impairing DNA damage repair. Mechanistically, PRKCSH inhibition reduced p53 ubiquitination and degradation by activating the ER stress IRE1α/XBP1s pathway after radiation exposure, which enhanced DNA repair and contributed to radioresistance. In preclinical CRC models, PRKCSH depletion suppressed tumor growth and increased radiosensitivity. Similarly, in patient-derived organoid models, PRKCSH knockdown reduced organoid growth post-radiotherapy. In rectal cancer patients receiving neoadjuvant radiotherapy, higher PRKCSH expression in post-treatment samples correlated with reduced tumor regression. These findings suggest that targeting PRKCSH diminishes radioresistance by impairing DNA repair through the modulation of ER stress. Furthermore, PRKCSH expression may serve as a biomarker for evaluating radiotherapy efficacy and clinical outcomes in rectal cancer patients undergoing neoadjuvant therapy.

DOI: https://doi.org/10.1038/s41419-025-07582-4
Int J Cardiol. 2025 Apr 04. pii: S0167-5273(25)00265-7. [Epub ahead of print] 133222

PERK's novel agonist protects against myocardial ischemia-reperfusion injury by modulating ER-mitochondria contacts and phosphatidic acid transport.

Zeyu Li, Suiqing Huang, Huayang Li, Quan Liu, Jing Lu, Peiqing Liu, Zhongkai Wu.

  The role of PERK in maintaining the homeostasis of MAM is believed to exert a significant impact on mitochondrial energy metabolism and structural morphology. However, there exists controversy regarding the therapeutic effect of PERK activation on ischemia-reperfusion injury. We have discovered a novel agonist for PERK named ZY341. ZY341 interacts with the active pocket of PERK through π-π stacking interactions, and surface plasmon resonance experiments have confirmed its exceptional potency as an agonist with a Kd value of 17.5 μM. This study provides initial evidence that ZY341 exhibits potent activity as a PERK agonist, effectively activating the PERK/eIF2α pathway in a mouse model of ischemia-reperfusion and demonstrating significant anti-apoptotic effects on cardiomyocytes. Ischemia-reperfusion not only induces cardiomyocyte apoptosis but also leads to substantial increases in MAM-mediated mitochondrial calcium overload, resulting in severe damage to mitochondrial structure and function. ZY341 significantly protects cardiac myocytes' respiratory capacity and improves heart function. Mechanistically, through PERK activation, ZY341 inhibits abnormal binding between VAPB-PTPIP51 complex in OGD/R models, regulates MAM-mediated calcium ion and phosphatidic acid transport homeostasis, suppresses mitochondrial fragmentation thereby significantly enhancing cardiac function. In conclusion, this study unveils new avenues for targeting PERK as a therapeutic strategy for myocardial ischemia-reperfusion treatment.

Keywords:  ER stress; Mitochondria; Mitochondria-associated membranes; Myocardial ischemia/reperfusion; PERK

DOI:  https://doi.org/10.1016/j.ijcard.2025.133222
Nat Metab. 2025 Apr 09.

The mitochondrial unfolded protein response inhibits pluripotency acquisition and mesenchymal-to-epithelial transition in somatic cell reprogramming.

Zhongfu Ying, Yanmin Xin, Zihuang Liu, Tianxin Tan, Yile Huang, Yingzhe Ding, Xuejun Hong, Qiuzhi Li, Chong Li, Jingyi Guo, Gaoshen Liu, Qi Meng, Shihe Zhou, Wenxin Li, Yao Yao, Ge Xiang, Linpeng Li, Yi Wu, Yang Liu, Miaohui Mu, Zifeng Ruan, Wenxi Liang, Junwei Wang, Yaofeng Wang, Baojian Liao, Yang Liu, Wuming Wang, Gang Lu, Dajiang Qin, Duanqing Pei, Wai-Yee Chan, Xingguo Liu.

The mitochondrial unfolded protein response (UPRmt), a mitochondria-to-nucleus retrograde pathway that promotes the maintenance of mitochondrial function in response to stress, plays an important role in promoting lifespan extension in Caenorhabditis elegans1,2. However, its role in mammals, including its contributions to development or cell fate decisions, remains largely unexplored. Here, we show that transient UPRmt activation occurs during somatic reprogramming in mouse embryonic fibroblasts. We observe a c-Myc-dependent, transient decrease in mitochondrial proteolysis, accompanied by UPRmt activation at the early phase of pluripotency acquisition. UPRmt impedes the mesenchymal-to-epithelial transition (MET) through c-Jun, thereby inhibiting pluripotency acquisition. Mechanistically, c-Jun enhances the expression of acetyl-CoA metabolic enzymes and reduces acetyl-CoA levels, thereby affecting levels of H3K9Ac, linking mitochondrial signalling to the epigenetic state of the cell and cell fate decisions. c-Jun also decreases the occupancy of H3K9Ac at MET genes, further inhibiting MET. Our findings reveal the crucial role of mitochondrial UPR-modulated MET in pluripotent stem cell plasticity. Additionally, we demonstrate that the UPRmt promotes cancer cell migration and invasion by enhancing epithelial-to-mesenchymal transition (EMT). Given the crucial role of EMT in tumour metastasis3,4, our findings on the connection between the UPRmt and EMT have important pathological implications and reveal potential targets for tumour treatment.

DOI: https://doi.org/10.1038/s42255-025-01261-6
PLoS Biol. 2025 Apr 10. 23(4): e3003086

A nonenzymatic dependency on inositol-requiring enzyme 1 controls cancer cell cycle progression and tumor growth.

Iratxe Zuazo-Gaztelu, David Lawrence, Ioanna Oikonomidi, Scot Marsters, Ximo Pechuan-Jorge, Catarina J Gaspar, David Kan, Ehud Segal, Kevin Clark, Maureen Beresini, Marie-Gabrielle Braun, Joachim Rudolph, Zora Modrusan, Meena Choi, Wendy Sandoval, Mike Reichelt, David C DeWitt, Pekka Kujala, Suzanne van Dijk, Judith Klumperman, Avi Ashkenazi.

Endoplasmic-reticulum resident inositol-requiring enzyme 1α (IRE1) supports protein homeostasis via its cytoplasmic kinase-RNase module. Known cancer dependency on IRE1 entails its enzymatic activation of the transcription factor XBP1s and regulated RNA decay. We discovered that some cancer cells surprisingly require IRE1 but not its enzymatic activity. IRE1 knockdown but not enzymatic IRE1 inhibition or XBP1 disruption attenuated cell cycle progression and tumor growth. IRE1 silencing led to activation of TP53 and CDKN1A/p21 in conjunction with increased DNA damage and chromosome instability, while decreasing heterochromatin as well as DNA and histone H3K9me3 methylation. Immunoelectron microscopy detected endogenous IRE1 at the nuclear envelope. Thus, cancer cells co-opt IRE1 either enzymatically or nonenzymatically, which has significant implications for IRE1's biological role and therapeutic targeting.

DOI: https://doi.org/10.1371/journal.pbio.3003086