bims-unfpre 2025-09-07 papers

bims-unfpre

Biomed News

on Unfolded protein response

Issue of 2025–09–07
eight papers selected by
Susan Logue, University of Manitoba

Interleukin-6 Modulates Endoplasmic Reticulum Stress Signaling and Mitochondrial Protein Complexes in the Kidney Following Acute Exhaustive Exercise.
CerS2 is a druggable target in triple-negative breast cancer.
An Ex Vivo Protocol to Assess IRE1α-Dependent RNA Cleavage Using Total RNA Isolated from Mouse Tissues.
Involvement of Perk and ATF6 Signal Pathways in Indicating Unfolded Protein Response in Patients with Chronic Lymphocytic Leukaemia.
The Proteostasis Network in Proteinopathies: Mechanisms and Interconnections.
The endoplasmic reticulum autophagy receptor TEX264 drives epidermal differentiation and is dysregulated in Darier disease.
Nucleotide-dependent conformational changes direct peptide export by the transporter associated with antigen processing.
Therapeutic restoration of mitochondria-endoplasmic reticulum cross talk for osteoarthritis.

Cell Stress Chaperones. 2025 Sep 02. pii: S1355-8145(25)00056-2. [Epub ahead of print] 100111

Interleukin-6 Modulates Endoplasmic Reticulum Stress Signaling and Mitochondrial Protein Complexes in the Kidney Following Acute Exhaustive Exercise.

Adelino S R da Silva, Caroline M da Luz, Bruno B Marafon, Maria Eduarda A Tavares, Ivo Vieira de S Neto, Ruither O Gomes Carolino, Driele C da Silva Ferreira, Julia T Marinho, Giovana R Teixeira, Dennys E Cintra, José R Pauli, Eduardo R Ropelle, Ellen C de Freitas, Ana P Pinto.

  Endoplasmic Reticulum (ER) homeostasis is closely regulated by an adaptive signaling network identified as the unfolded protein response (UPR), which is tightly related to the inflammatory pathway. However, physical exercise increases plasma concentrations of interleukin-6 (IL-6), which exhibits both pro- and anti-inflammatory properties that mediate ER function and mitochondrial metabolism, making its investigation relevant in physiological and pathological contexts. In kidney diseases, the IL-6 levels are effective in predicting mortality risk. To elucidate the relationship between exercise-induced IL-6 elevation, ER stress, and renal physiology, we explored the impact of an acute exhaustive exercise on the ER stress-related proteins and mitochondrial respiratory chain targets in the kidneys of IL-6 knockout (KO) mice. WT and IL-6 KO mice were divided into two subgroups for each phenotype: sedentary (Sed) and 1hour (after 1hour of acute exercise; Ex-1h). The kidneys were removed and prepared for histological, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and immunoblotting analysis. In summary, IL-6 KO mice had lower degranulated mast cells in the kidney. IL-6 KO mice exhibited reduced exercise performance. The Hspa5 mRNA levels were significantly increased in response to acute exhaustive exercise in both WT and KO groups, but Il-10 increased only in response to exercise in the KO group. Additionally, Ddit3 expression was significantly lower in IL-6 KO mice post-exercise, suggesting a blunted ER stress response without IL-6. At the protein levels, ATF6α expression was notably elevated in IL-6 KO mice following exercise. Regarding mitochondrial protein complexes, we observed lower protein levels of mitochondrial complex IV and CII in the WT Ex-1h group than in the WT Sed. At the same time, the absence of IL-6 did not seem to modify the expression of most mitochondrial complexes in response to acute exercise. Also, publicly available gene expression datasets in humans support our findings, indicating the upregulation of IL-6 signaling and heat shock proteins (HSPs), while decreasing mitochondrial respiratory complex mRNA levels in white blood cells of humans following acute exhaustive exercise. The findings indicate that IL-6 may modulate specific components of ER stress and cytokine responses in the kidney after acute exercise.

Keywords:  IL-6; UPR; cytokines; kidney; mast cells; running exercise

DOI:  https://doi.org/10.1016/j.cstres.2025.100111
bioRxiv. 2025 Aug 21. pii: 2025.08.15.670525. [Epub ahead of print]

CerS2 is a druggable target in triple-negative breast cancer.

Hissah Alatawi, Haritha H Nair, Lingbao Ai, Iqbal Mahmud, Abhishek Gour, Amandeep Singh, Doohyun Baek, Bowen Yan, Chandra K Maharjan, Weizhou Zhang, Brian K Law, Maria Zajac-Kaye, Christopher Vulpe, Olga A Guryanova, Arun K Sharma, Timothy J Garrett, Abhisheak Sharma, Coy D Heldermon, Sukwon Hong, Satya Narayan.

Triple-negative breast cancer (TNBC) remains a significant clinical challenge due to its aggressive nature and lack of effective targeted therapies. The enzyme ceramide synthase 2 (CerS2), which synthesizes pro-apoptotic very long-chain ceramides (VLCCs), represents a promising therapeutic target. Here, we identify and characterize DH20931, a novel, first-in-class small-molecule agonist of CerS2. We demonstrate that DH20931 directly activates CerS2 with nanomolar potency, leading to significant VLCC accumulation in breast cancer cells. This lipotoxic event induces endoplasmic reticulum (ER) stress and triggers apoptosis via the canonical ATF4/CHOP/PUMA signaling pathway. Mechanistically, we uncover a novel interaction between CerS2 and the ER calcium channel, Inositol 1,4,5-trisphosphate receptor 1 (IP3R1). We demonstrate that DH20931 promotes this interaction, enhancing ER-mitochondria proximity and facilitating a CerS2-dependent flux of calcium (Ca²⁺) from the ER into mitochondria. This subsequent mitochondrial Ca²⁺ overload serves as a critical trigger for apoptosis. In preclinical evaluations, DH20931 potently inhibited the growth of TNBC cells in 2D and 3D cultures and significantly suppressed tumor progression in orthotopic and patient-derived xenograft (PDX) models, all while exhibiting a favorable safety profile. Our findings validate CerS2 as a druggable target in TNBC and establish a novel therapeutic strategy that leverages a coordinated attack on cancer cells through ER stress and calcium-mediated mitochondrial dysfunction.
Highlights: DH20931 is a first-in-class, potent agonist of Ceramide Synthase 2 (CerS2).CerS2 activation induces ER stress and engages the ATF4/CHOP/PUMA apoptotic pathway.DH20931 promotes a novel CerS2-IP3R1 interaction, causing lethal mitochondrial calcium overload.Targeting CerS2 shows significant preclinical efficacy against triple-negative breast cancer.

DOI: https://doi.org/10.1101/2025.08.15.670525
Bio Protoc. 2025 Aug 20. 15(16): e5414

An Ex Vivo Protocol to Assess IRE1α-Dependent RNA Cleavage Using Total RNA Isolated from Mouse Tissues.

Mohammad Mamun Ur Rashid, So-Young Rah, Se-Woong Ko, Han-Jung Chae.

  Regulated IRE1-dependent decay (RIDD) is a critical cellular mechanism mediated by the endoplasmic reticulum (ER) stress sensor IRE1α, which cleaves a variety of RNA targets to regulate ER homeostasis. Current in vitro assays to study IRE1α activity largely rely on synthetic or in vitro transcribed RNA substrates, which may not fully replicate the physiological complexities of native RNA molecules. Here, we present a comprehensive protocol to assess IRE1α-dependent RNA cleavage activity using total RNA isolated directly from mouse tissues. This protocol provides a step-by-step guide for tissue collection, RNA isolation, an ex vivo RIDD assay, cDNA synthesis, and subsequent RT-PCR analysis of target mRNA cleavage products. Key reagents include active IRE1α protein, the RIDD-specific inhibitor 4μ8C, and target-specific primers for RIDD-regulated genes such as Bloc1s1 and Col6a1. Quantitative assessment is achieved using agarose gel electrophoresis and imaging software. This methodology enables the study of IRE1α's RNA cleavage activity under conditions that closely mimic in vivo environments, providing a more physiologically relevant approach to understanding the role of RIDD in cellular and tissue-specific contexts. Key features • Uses total RNA from mouse tissues instead of synthetic RNA to better reflect in vivo conditions. • Includes RIDD-specific controls such as IRE1α inhibitor (4μ8C) and RNase A to confirm targeted RNA cleavage. • Combines agarose gel electrophoresis and ImageJ quantification for both qualitative and statistical validation. • Allows comparative studies of IRE1α activity across multiple mouse tissues in different biological contexts.

Keywords:  ER stress; Endoplasmic reticulum; Ex vivo; IRE1α; RIDD; RNA Cleavage

DOI:  https://doi.org/10.21769/BioProtoc.5414
Biomarkers. 2025 Aug 29. 1-12

Involvement of Perk and ATF6 Signal Pathways in Indicating Unfolded Protein Response in Patients with Chronic Lymphocytic Leukaemia.

Nergiz Erkut, Merve Kestane, Selim Demir, Ahmet Mentese, Ozlen Balta, Mehmet Sonmez.

   INTRODUCTION: PERK, ATF6, and IRE1α signalling pathways are unfolded protein response (UPR) signalling pathways. In this study, we evaluated the effect of PERK and ATF6 signalling pathways, which are UPR signalling pathways, in chronic lymphocytic leukaemia (CLL) patients.
METHODS: ELISA was performed on peripheral blood plasma samples from CLL patients and the control group for the markers eIF2AK3, GRP78, ATF6, CHOP, HIF-1α and caspase 3.
RESULTS: In this study, the levels of eIF2AK3, GRP78, ATF6 and CHOP were higher in the CLL group than in the control group (p = <0.001, p = <0.001, p = <0.001, p = <0.001, respectively). While no difference was observed between the CLL group and the control group in terms of HIF-1α level, caspase 3 level was higher in the CLL group (p = <0.001). There was a positive relationship between the level of HIF-1α and the levels of ATF6 and CHOP (r = 0.648, p = <0.001; r = 0.727, p = <0.001, respectively). Also, a positive correlation was observed between caspase 3 level and ATF6 level (r = 0.301, p = 0.030).
DISCUSSION: In this study, markers associated with PERK and ATF6 signalling pathways were higher in CLL patients.

Keywords:  ATF6 signaling pathway; Endoplasmic reticulum stress; PERK signaling pathway; apoptosis; hypoxia

DOI:  https://doi.org/10.1080/1354750X.2025.2553628
Am J Pathol. 2025 Aug 26. pii: S0002-9440(25)00300-1. [Epub ahead of print]

The Proteostasis Network in Proteinopathies: Mechanisms and Interconnections.

Dariusz Pytel, Jody Fromm Longo.

  Proteinopathies are neurodegenerative disorders that are characterized by accumulation of misfolded toxic protein aggregates that lead to synaptic and neuronal dysfunction. Though genetically, clinically and pathologically distinct, a common feature of these diseases is disruption of protein homeostasis (proteostasis), which causes accumulation of misfolded proteins. The machinery mediating proteostasis exquisitely balances and interlaces protein synthesis, protein folding and trafficking, and protein degradation processes within the proteostasis network to maintain homeostasis. The proteostasis network governs a functional and dynamic proteome by modulating the timing, location, and stoichiometry of protein expression, surveillance and maintenance of protein folding and removal of misfolded or excess proteins. Although a functional proteome is essential for the health of all cell types, this is especially true for neurons which are prone to enhanced cellular stress. Aging is the most important risk factor for proteostasis decline and the development of proteinopathies. However, germline and somatic mutations can also functionally impair components of the proteostasis network. Post-mitotic cells, particularly neurons, are rendered further susceptible to proteostasis dysfunction due to their extended lifespan. This review discusses the interconnections between the functional components mediating proteostasis in neuronal cells and how aberrations in proteostasis contribute to neuronal dysfunction and disease.

Keywords:  Alzheimer’s Disease; Amyotrophic Lateral Sclerosis; ER stress; ERAD; Frontotemporal Dementia; Huntington’s Disease; Parkinson’s Disease; UPR; aggregates; autophagy; protein homeostasis; proteinopathies

DOI:  https://doi.org/10.1016/j.ajpath.2025.07.011
bioRxiv. 2025 Aug 07. pii: 2025.08.05.668774. [Epub ahead of print]

The endoplasmic reticulum autophagy receptor TEX264 drives epidermal differentiation and is dysregulated in Darier disease.

Christopher J Johnson, Afua Tiwaa, Arti Parihar, Edwin Antonio, Brooke D Lorenz, Reeteka Kudallur, Aaron Ramonett, Anthony Coon, Mrinal K Sarkar, Johann E Gudjonsson, Cory L Simpson.

Differentiating keratinocytes break down their organelles and nuclei to become the compacted cornified layers of the epidermal barrier in a poorly understood catabolic process. Live confocal imaging of stratified human organotypic epidermis revealed endoplasmic reticulum (ER) fragmentation and lysosomal engulfment in the cornifying layers, where we found up-regulation of TEX264, a receptor that mediates selective autophagy of the ER (reticulophagy). TEX264 expression was increased by ER stress, which caused precocious cornification of organotypic epidermis. In undifferentiated keratinocytes, ectopic TEX264 was sufficient to fragment the ER, while in highly differentiated keratinocytes, it accelerated ER elimination and induced nuclear shrinkage; these effects were abolished by mutating the LC3 interacting region required for its autophagic function. Knockout of TEX264 or inhibiting its activation disrupted maturation of organotypic cultures, pointing to a critical role for reticulophagy in cornification. Finally, in patient biopsies and an organotypic model of Darier disease, a genetic cornification disorder linked to ER dysfunction, we found increased TEX264 in areas of premature cornification (dyskeratosis). Our results identified TEX264 as a key driver of epidermal differentiation and led us to propose a novel model of cornification in which keratinocytes activate selective autophagy receptors to orchestrate orderly organelle elimination during cutaneous barrier formation.
GRAPHICAL ABSTRACT:

DOI: https://doi.org/10.1101/2025.08.05.668774
Immunity. 2025 Aug 23. pii: S1074-7613(25)00366-8. [Epub ahead of print]

Nucleotide-dependent conformational changes direct peptide export by the transporter associated with antigen processing.

James Lee, Victor Manon, Jue Chen.

  The transporter associated with antigen processing (TAP) delivers peptide antigens from the cytoplasm into the endoplasmic reticulum (ER) for loading onto major histocompatibility complex class I (MHC-I) molecules. To examine the mechanisms of peptide transport and release into the ER, we determined cryo-electron microscopy structures of the human TAP heterodimer in multiple functional states along the transport cycle. In the inward-facing conformation, when the peptide translocation cavity within the TAP heterodimer is exposed to the cytosol, ATP binding strengthened intradomain assembly. Transition to the outward-facing conformation, when the transporter opens to the ER lumen, led to a complete reconfiguration of the peptide-binding site, facilitating peptide release. ATP hydrolysis opened the catalytically active nucleotide-binding consensus site, and the subsequent separation of the nucleotide-binding domains reset the transport cycle. These findings establish a comprehensive structural framework for understanding unilateral peptide transport, vanadate trapping, and trans-inhibition-an internal feedback mechanism that prevents excessive peptide accumulation and activation of the ER stress response.

Keywords:  ABC transporter; MHC-I; adaptive immunity; antigen presentation; nucleotide-binding domain; transporter associated with antigen processing

DOI:  https://doi.org/10.1016/j.immuni.2025.08.003
Proc Natl Acad Sci U S A. 2025 Sep 09. 122(36): e2426992122

Therapeutic restoration of mitochondria-endoplasmic reticulum cross talk for osteoarthritis.

Mingzhuang Hou, Yifan Ma, Yaoge Deng, Yubin Wu, Yanrun Zhu, Yang Liu, Xiaoping Li, Lili Yu, Zirui He, Yifan Wang, Shiyan Dong, Xiaowei Xia, Jianfeng Yu, Chenqi Yu, Kang Kang, Yingjie Lu, Lili Sun, Betty Y S Kim, Yuan Yuan, Yijian Zhang, Wen Jiang, Xuesong Zhu.

  Osteoarthritis is a prevalent joint disease in the aging population. The hallmark of osteoarthritis is the degeneration of the joint cartilage, characterized by changes in chondrocytes including mitochondrial dysfunction. However, the precise mechanisms of how this affects chondrocyte homeostasis and whether such processes can be explored as therapeutic targets for osteoarthritis remain unclear. Here, we show that impaired mitochondrial function and disrupted cartilage matrix metabolism due to loss of mitofusin-2 (MFN2) expression in chondrocytes leads to the development of osteoarthritis. Sirtuin-3 (SIRT3), a key regulator of mitochondrial function, plays a critical role in modulating MFN2 to restore mitochondrial dynamics, reduce fragmentation, and preserve mitochondrial function in chondrocytes. Specifically, SIRT3 directly deacetylates and indirectly deubiquitinates MFN2, preventing its degradation. MFN2-mediated mitochondrial-endoplasmic reticulum (ER) junctions support cellular homeostasis, alleviate ER stress, and maintain mitochondrial calcium ion balance, which collectively mitigate chondrocyte senescence. Extracellular vesicles engineered with MFN2 mRNA effectively prevented cartilage degeneration and restored mobility in osteoarthritic mice. These findings suggest that targeting MFN2 is a promising strategy to prevent cartilage degeneration and alleviate progression of osteoarthritis.

Keywords:  endoplasmic reticulum; extracellular vesicles; mitochondrial dynamics; osteoarthritis; posttranslational modifications

DOI:  https://doi.org/10.1073/pnas.2426992122