bims-cemest Biomed News
on Cell metabolism and stress
Issue of 2025–09–28
thirteen papers selected by
Jessica Rosarda, Uniformed Services University
  1. Hsp70 and Hsp90 post-translational modifications and translating the chaperone code.
  2. Decoding the Impact of Lipid Saturation on ER Signaling Networks, ERSU, UPR, and ERAD.
  3. Harnessing indole scaffolds to identify small-molecule IRE1α inhibitors modulating XBP1 mRNA splicing.
  4. Cross-Organ Mitochondrial Communication in Stress and Disease.
  5. PKR-driven ISR signaling controls synaptic translation and structural plasticity in an age-dependent manner.
  6. Ageing-related decline of translation as a consequence of transcription dysregulation.
  7. Time to Reset: The Interplay Between Circadian Rhythms and Redox Homeostasis in Skeletal Muscle Ageing and Systemic Health.
  8. Steric repulsion counteracts ER-to-lipid droplet protein movement.
  9. Intra-tumoral hypoxia promotes CD8+ T cell dysfunction via chronic activation of integrated stress response transcription factor ATF4.
  10. Targeting ATF6 reduces pathological neovascularization and improves visual outcomes in retinal disease models.
  11. Proteome analysis of puromycin-labeled nascent polypeptides.
  12. Chemical proteomic approaches to investigate S-prenylation.
  13. The Hidden Influences of Macromolecular Crowding: A New Frontier in Cellular Biology and Medicine.
  1. Cell Stress Chaperones. 2025 Sep 19. pii: S1355-8145(25)00063-X. [Epub ahead of print] 100118
    Hsp70 and Hsp90 post-translational modifications and translating the chaperone code.
    Sarah J Backe, Jennifer A Heritz, Mehdi Mollapour.
      Molecular chaperones maintain proteostasis by assisting protein folding, stability, and activity. Heat shock protein 70 (Hsp70) and Hsp90 are ATP-dependent chaperones essential for protein quality control, signaling, and stress adaptation. Their activities are controlled not only by co-chaperones but also by dynamic post-translational modifications (PTMs). The review dissects phosphorylation, acetylation, methylation, ubiquitination, glycosylation, and other PTMs of Hsp70 and Hsp90 across systems. These PTMs regulate the ATPase activity, localization, and interactions of the molecular chaperones with major implications in health and disease. The term 'chaperone code' describes the PTMs landscape that fine tunes the chaperone function. This code governs client fate, drug sensitivity, and stress responses. Importantly, combinatorial PTMs introduce regulatory complexity and flexibility, especially in cancer, neurodegeneration, and inflammation. The crosstalk between various PTMs and feedback loops add new regulatory layers to chaperone function. Additionally, these PTMs impact the function of the clients that are central in regulating a specific cellular processes or pathways such as transcription, autophagy, metabolism, and immune regulation. These pathways are usually affected in different maladies such cancer, neurodegenerative, infectious and chronic diseases. Unlocking the chaperone code is essential for directing chaperone activity toward therapeutic benefit. This can be achieved by targeting enzymes that write, erase, or read the chaperone code therefore offering new therapeutic strategies.
    Keywords:  Molecular chaperone; O-GlcNAcylation; acetylation; cancer; chaperone code; co-chaperone; heat shock protein 70 (Hsp70) post-translational modification (PTM); heat shock protein 90 (Hsp90); phosphorylation
    DOI:  https://doi.org/10.1016/j.cstres.2025.100118
  2. bioRxiv. 2025 Sep 17. pii: 2025.09.15.676312. [Epub ahead of print]
    Decoding the Impact of Lipid Saturation on ER Signaling Networks, ERSU, UPR, and ERAD.
    Xia Li, Maho Niwa.
      The faithful inheritance of a functional endoplasmic reticulum (ER) in Saccharomyces cerevisiae is safeguarded by the ER Stress Surveillance (ERSU) checkpoint, which delays cytokinesis when ER homeostasis is perturbed. Under stress, ER transmission to the daughter cell is halted, while in parallel-but through independent pathways-the Unfolded Protein Response (UPR) restores ER function and ER-associated degradation (ERAD) eliminates misfolded proteins, ultimately allowing cell cycle re-entry. ER stress also transiently stimulates sphingolipid biosynthesis, with the intermediate phytosphingosine (PHS) acting as a key activator of ERSU. Yet, how broader lipid parameters-such as membrane composition, saturation, and fluidity-reshape ER quality control and, in particular, govern ER inheritance during division remains poorly understood. To address this, we employed a tightly controlled experimental system to selectively alter lipid saturation and phospholipid composition while monitoring ER inheritance within the framework of ER homeostasis maintained by UPR and ERAD. Strikingly, we found that perturbations in lipid balance exerted specific effects on ER inheritance that were distinct from their impact on UPR and ERAD. These findings reveal lipid homeostasis as a critical integrator of ER functional regulation, linking ERSU, UPR, and ERAD into a unified adaptive network that ensures robust ER transmission and cellular resilience under stress.
    DOI:  https://doi.org/10.1101/2025.09.15.676312
  3. Nat Commun. 2025 Sep 26. 16(1): 8531
    Harnessing indole scaffolds to identify small-molecule IRE1α inhibitors modulating XBP1 mRNA splicing.
    Yang Liu, Amrutha K Avathan Veettil, Raphael Gasper, Mao Jiang, Leon Wagner, Oguz Hastürk, Peng Wu.
      The inositol-requiring enzyme 1 alpha (IRE1α) is an important sensor protein with dual kinase and ribonuclease function. It induces X-box binding protein 1 (XBP1) mRNA splicing and mediates endoplasmic reticulum (ER) stress-triggered downstream unfolded protein response signaling pathways. The dysregulation of IRE1α has been associated with multiple human diseases, and thus IRE1α-targeting small molecules harbor great therapeutic potential. We herein report a series of substituted indoles as IRE1α inhibitors (such as IA107) of excellent potency and selectivity. We also report a resolved co-crystal structure that reveals a unique inhibition mode of IA107 that allosterically inhibits IRE1α RNase activity via binding to the IRE1α kinase domain but without inhibiting the IRE1α dimerization. The following cellular evaluation results demonstrate that IA107 concentration-dependently inhibits the cellular ER stress-induced XBP1 mRNA splicing, and the ester-containing prodrug exhibits a ~ 50-fold increase in cellular activity. Collectively, our results establish the indoles as a potent and selective IRE1α-inhibiting chemotype that modulates RNA splicing and expands the biological application potential associated with IRE1α targeting via small molecules.
    DOI:  https://doi.org/10.1038/s41467-025-64291-4
  4. Annu Rev Pharmacol Toxicol. 2025 Sep 22.
    Cross-Organ Mitochondrial Communication in Stress and Disease.
    Koning Shen, Jenni Durieux, Andrew Dillin.
      Growing evidence points to mitochondria as not just the "powerhouse of the cell" but as a major cellular hub for signaling. Mitochondria use signaling pathways to communicate with other organelles within the cell or organs within an organism to regulate stress response, metabolic, immune, and longevity pathways. These communication pathways are carried out by mitokine signaling molecules encompassing metabolites, lipids, proteins, and even whole mitochondrial organelles themselves. In this review, we focus on the communication pathways mitochondria use to communicate between different organs in invertebrates, mammalian models, and humans. We cover the molecular events that trigger communication, the signaling mechanisms themselves, and the impact this communication has on organismal health in the context of stress and disease. Further understanding of cross-organ mitochondrial communication pathways will inform the design of therapeutics that take advantage of their protective effects to treat diseases associated with mitochondrial dysfunction.
    DOI:  https://doi.org/10.1146/annurev-pharmtox-062124-024150
  5. Neurobiol Dis. 2025 Sep 19. pii: S0969-9961(25)00330-4. [Epub ahead of print] 107113
    PKR-driven ISR signaling controls synaptic translation and structural plasticity in an age-dependent manner.
    Nicolás W Martínez, Felipe Gómez, Ariel Tapia-Godoy, Juan Francisco Roa, Yuwei Liu, Claudia Jara, Cheril Tapia-Rojas, Iván Alfaro, Mauro Costa-Mattioli, Soledad Matus.
      The integrated stress response (ISR) modulates protein homeostasis in response to both intracellular and extracellular signals. The four kinases involved in the ISR all phosphorylate the same target, the alpha subunit of eukaryotic initiation factor 2 (eIF2a), to integrate various stress signals, thereby regulating cell fate. The activation of the ISR reprograms the proteome by inhibiting general protein synthesis while increasing the translation of specific mRNAs. In the brain, the ISR regulates the type of synaptic plasticity necessary for forming long-term memory. More importantly, the activation of the ISR has emerged as a causal mechanism underlying cognitive decline associated with a wide range of neurological disorders, prompting several pharmaceutical companies to target the ISR to promote brain health. However, whether the ISR acts at specific localities within neurons, including synapses, remains unclear. Here, we examined the presence, activity, and spatial arrangement of the ISR branch driven by the double-stranded RNA-dependent protein kinase (PKR) (PKR-eIF2a axis) in synapses and assessed the role of PKR in maintaining synaptic proteostasis over time. Our findings demonstrate that both PKR and eIF2a are localized at synapses, where a dynamic PKR-eIF2a axis regulates synaptic size and the abundance of synaptic proteins in an age-dependent manner. Moreover, PKR deficiency leads to an increase in protein synthesis in synapse-enriched fractions. Thus, the PKR branch of the ISR serves as a new regulator of synaptic structural plasticity.
    Keywords:  Neurons; PKR; PSD95; Proteostasis; Synapsin; eIF2a
    DOI:  https://doi.org/10.1016/j.nbd.2025.107113
  6. J R Soc Interface. 2025 Sep;22(230): 20250323
    Ageing-related decline of translation as a consequence of transcription dysregulation.
    Sebastian Pechmann.
      The ageing-related decline of translational fidelity disrupts cellular protein homeostasis, thus contributing to the onset of cancer and neurodegeneration. However, it remains unclear what alters speed and accuracy of translation at advanced age. Here, I show that the shift in translation kinetics upon ageing is systematic and a direct consequence of transcription deregulation. Computational modelling of ageing yeast and worm Riboseq data demonstrates that the loss of translational fidelity is independent of codon identity, tRNA abundances or the specificities of anticodon-codon interactions at the ribosome. Instead, large-scale transcriptional changes during ageing perturb the codon usage of the transcriptome, which at the systems level induces a dramatic remodelling and increase in ribosome collisions and stalling. Ribosome collisions in turn reduce control over translation elongation and effect an assimilation of codon translation rates. The presented results thus explain the ageing-related decline of translational fidelity, and provide important insights towards a systems-level understanding of ageing-related human diseases linked to mistranslation and protein homeostasis failure that are especially prevalent in the brain.
    Keywords:  ageing; codon usage; computational biology; stochastic modelling; translational fidelity
    DOI:  https://doi.org/10.1098/rsif.2025.0323
  7. Antioxidants (Basel). 2025 Sep 18. pii: 1132. [Epub ahead of print]14(9):
    Time to Reset: The Interplay Between Circadian Rhythms and Redox Homeostasis in Skeletal Muscle Ageing and Systemic Health.
    Elizabeth Sutton, Vanja Pekovic-Vaughan.
      Skeletal muscle plays vital roles in locomotion, metabolic regulation and endocrine signalling. Critically, it undergoes structural and functional decline with age, leading to a progressive loss of muscle mass and strength (sarcopenia) and contributing to a systemic loss of tissue resilience to stressors of multiple tissue systems (frailty). Emerging evidence implicates misalignments in both the circadian molecular clock and redox homeostasis as major drivers of age-related skeletal muscle deterioration. The circadian molecular clock, through core clock components such as BMAL1 and CLOCK, orchestrates rhythmic gene, protein and myokine expression impacting diurnal regulation of skeletal muscle structure and metabolism, mitochondrial function, antioxidant defence, extracellular matrix organisation and systemic inter-tissue communication. In parallel, the master redox regulator, NRF2, maintains cellular antioxidant defence, tissue stress resistance and mitochondrial health. Disruption of either system impairs skeletal muscle contractility, metabolism, and regenerative capacity as well as systemic homeostasis. Notably, NRF2-mediated redox signalling is clock-regulated and, in turn, affects circadian clock regulation. Both systems are responsive to external cues such as exercise and hormones, yet studies do not consistently include circadian timing or biological sex as key methodological variables. Given that circadian regulation shifts with age and differs between sexes, aligning exercise interventions with one's own chronotype may enhance health benefits, reduce adverse side effects, and overcome anabolic resistance with ageing. This review highlights the essential interplay between circadian and redox systems in skeletal muscle homeostasis and systemic health and argues for incorporating personalised chrono-redox approaches and sex-specific considerations into future experimental research and clinical studies, aiming to improve functional outcomes in age-related sarcopenia and broader age-related metabolic and musculoskeletal conditions.
    Keywords:  NRF2; ageing; chronotherapy; chronotype; circadian rhythms; exercise; frailty; myokines; oxidative stress; redox homeostasis; sarcopenia; skeletal muscle
    DOI:  https://doi.org/10.3390/antiox14091132
  8. Sci Adv. 2025 Sep 26. 11(39): eadu6998
    Steric repulsion counteracts ER-to-lipid droplet protein movement.
    Alicia Damm, Mohyeddine Omrane, Ozren Stojanović, Bianca M Esch, Mehdi Zouiouich, Maxime Carpentier, Robin Klemm, Florian Fröhlich, Lionel Forêt, Abdou Rachid Thiam.
      Lipid droplets (LDs) are organelles with a neutral lipid core surrounded by a phospholipid monolayer, which is continuous with the cytoplasmic leaflet of the endoplasmic reticulum (ER). LD function depends on a highly dynamic LD surface proteome. Key proteins continuously exchange between the ER and LDs; however, the mechanisms governing the interorganelle movement and accumulation on the LD surface remain poorly understood. Here, we developed an ex cellulo tool introducing a classification of ER-derived proteins based on their different affinity for LDs. We find that proteins with higher LD affinity can effectively displace those with lower affinity from the LD surface, identifying steric hindrance as a key mechanism in regulating ER-to-LD protein transfer. Consistent with this model, we show that, during adipocyte differentiation Plin1-an adipocyte-specific high-affinity LD protein-reduces the recruitment of ER proteins with lower affinity by displacing them from the LD surface. These findings highlight lateral protein-protein exclusion as a fundamental mechanism in shaping the LD proteome.
    DOI:  https://doi.org/10.1126/sciadv.adu6998
  9. Immunity. 2025 Sep 25. pii: S1074-7613(25)00414-5. [Epub ahead of print]
    Intra-tumoral hypoxia promotes CD8+ T cell dysfunction via chronic activation of integrated stress response transcription factor ATF4.
    Coral Del Mar Alicea Pauneto, Brian P Riesenberg, Evelyn J Gandy, Andrew S Kennedy, Genevieve T Clutton, Jessica W Hem, Katie E Hurst, Elizabeth G Hunt, Jarred M Green, Brian C Miller, Steven P Angus, Gary L Johnson, Robert J Esther, Jennifer L Guerriero, Peng Gao, David R Soto-Pantoja, Robert L Ferris, Jennifer L Modliszewski, Michael F Coleman, H Kay Chung, J Justin Milner, Stergios J Moschos, R Luke Wiseman, Jessica E Thaxton.
      Metabolic stress in the tumor microenvironment (TME) promotes T cell dysfunction and immune checkpoint inhibitor (ICI) resistance. We examined the contribution of activating transcription factor 4 (ATF4), the central node of the integrated stress response (ISR), to T cell dysfunction in tumors. CD8+ tumor-infiltrating lymphocytes (TILs) in patient samples exhibited chronic ATF4 activity, which was reflected across various tumor models. Hypoxia in the TME imposed chronic ATF4 activity via the ISR kinases. ATF4 overexpression in CD8+ T cells induced metabolic polarity, mitochondrial oxidative stress, and cell death, impairing antitumor immunity. Chronic ATF4 transcriptional activity replicated the terminal exhaustion CD8+ T cell state independent of T cell receptor (TCR) stimulation. Genetic or pharmacologic attenuation of ATF4 reduced mitochondrial oxidative stress and promoted CD8+ TIL viability, enabling response to programmed cell death protein-1 (PD-1) inhibitor therapy and conferring protection from re-emergent disease. Thus, the ISR converges on chronic ATF4 activity in CD8+ TILs as a barrier to ICI response, positioning ISR therapeutics as candidates for immunotherapy.
    Keywords:  ATF4; T cell; hypoxia; immunotherapy; integrated stress response; metabolism; mitochondria; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.immuni.2025.09.003
  10. Sci Rep. 2025 Sep 26. 15(1): 33070
    Targeting ATF6 reduces pathological neovascularization and improves visual outcomes in retinal disease models.
    Allyssa Bradley, Soyoung Park, Soyeon Park, Kyle Kim, Angela Galdamez, Hyejung Min, Monica Sophia Diaz-Aguilar, M Elizabeth Hartnett, Eun-Jin Lee, Jonathan H Lin.
      Pathological retinal neovascularization is a cause of vision loss in diseases including retinopathy of prematurity (ROP), wet age-related macular degeneration (AMD), and diabetic retinopathy. The Unfolded Protein Response (UPR) is an intracellular signal transduction mechanism that is activated by ER stress and upregulates many proteins, including angiogenesis factors like VEGF and HIF-1α. This suggests that UPR genes and pathways may drive retinal angiogenesis. Here, we tested the role of the UPR regulator Activating Transcription Factor 6 (ATF6) in pathological and developmental retinal angiogenesis. We induced pathological retinal neovascularization in Atf6-/- mice using the oxygen-induced retinopathy (OIR) model and found significantly preserved visual function, accompanied by decreased retinal neovascularization, endothelial cell proliferation, and UPR transcriptional program induction. When we chemically blocked ATF6 signaling by intraocular injection of the small molecule Ceapin-A7, we also saw suppressed retinal expression of UPR genes. Additionally, in postnatal day 7 Atf6-/- mice when the retinal vasculature is developing in response to physiologic intraocular hypoxia, there was a transient but significant defect in pruning and retinal blood vessel extension. Together, our results demonstrate ATF6's causal role in developmental and pathological retinal angiogenesis and highlight its potential as a therapeutic target to preserve vision in retinal neovascularization diseases.
    DOI:  https://doi.org/10.1038/s41598-025-15393-y
  11. Methods Enzymol. 2025 ;pii: S0076-6879(25)00226-5. [Epub ahead of print]719 1-23
    Proteome analysis of puromycin-labeled nascent polypeptides.
    Koshi Imami.
      Emerging nascent polypeptides from ribosomes and their protein N-termini have significant impact on protein stability, folding, interaction and subcellular targeting. To profile elongating nascent polypeptides on a proteome-wide scale, here we present a streamlined protocol that combined a biochemical enrichment of puromycin-labeled nascent polypeptides and mass spectrometry-based quantitative proteomics. This chapter includes the detailed protocol for metabolic pulse labeling with puromycin and SILAC amino acids, immunoprecipitation for nascent polypeptides, fractionation and enrichment of N-terminal acetylated peptides as well as MS and data analysis. These protocols are illustrated using HeLa cells treated with cycloheximide, a protein synthesis inhibitor, but can be broadly applied to any cell culture systems, including primary cultures, or any treatments (e.g., drugs).
    Keywords:  Mass spectrometry; Nascent polypeptide; Protein N-terminal acetylation; Puromycin; Ribosome
    DOI:  https://doi.org/10.1016/bs.mie.2025.06.018
  12. Methods Enzymol. 2025 ;pii: S0076-6879(25)00220-4. [Epub ahead of print]719 299-316
    Chemical proteomic approaches to investigate S-prenylation.
    Sarah Hassan, James Zhang, Wouter Kallemeijn, Edward W Tate.
      Protein S-prenylation is a post-translational lipid modification that occurs at C-terminal cysteines. While S-prenylation has been widely studied in the context of disease biology and drug discovery, only in the last decade have robust proteomic techniques emerged to study the complex dynamics between different classes of protein prenyltransferases, significantly aiding the development and application of tools and inhibitors. Herein, we describe the use of S-prenylation probes as a chemical proteomic technique to interrogate S-geranylgeranylation and S-farnesylation, the two classes of protein prenylation, from sample preparation to mass spectrometry analysis.
    Keywords:  Chemical probes; Chemical proteomics; Lipidation; Post-translational modifications; Prenylation
    DOI:  https://doi.org/10.1016/bs.mie.2025.06.012
  13. Subcell Biochem. 2025 ;109 531-542
    The Hidden Influences of Macromolecular Crowding: A New Frontier in Cellular Biology and Medicine.
    Isabella V Gimón, Conner Sandefur, Santiago Schnell.
      Macromolecular crowding, the dense packing of macromolecules within cells, significantly influences enzyme kinetics, cell signaling, liquid-liquid phase separation, and disease progression. This review explores the multifaceted effects of crowding on osmotic balance, intracellular compartmentalization, and metabolic efficiency. We highlight the exclusion volume effect's role in protein folding, stability, and osmotic homeostasis. Crowding also modulates enzyme activity and kinetics, contributing to metabolic regulation, and plays a crucial role in forming membraneless organelles. Dysregulation of macromolecular crowding is implicated in neurodegenerative diseases, cancer, and type 2 diabetes, highlighting its importance for therapeutic development. Future research should focus on elucidating crowding mechanisms, developing in vivo models, and exploring therapeutic interventions targeting macromolecular crowding.
    Keywords:  Cell biology; Cell signaling; Disease; Enzyme kinetics; Liquid-liquid phase separation; Macromolecular crowding; Protein aggregation; Therapeutics
    DOI:  https://doi.org/10.1007/978-3-032-03370-3_23
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