bims-cemest 2025-04-20 papers

bims-cemest

Biomed News

on Cell metabolism and stress

Issue of 2025–04–20
39 papers selected by
Jessica Rosarda, Uniformed Services University

Phenylhydrazone-based Endoplasmic Reticulum Proteostasis Regulator Compounds with Enhanced Biological Activity.
The unfolded protein response is a potential therapeutic target in pathogenic fungi.
Preliminary exploration of endoplasmic reticulum stress transmission in astrocytes and neurons, and its mediators.
Targeting ATF6α Attenuates UVB-Induced Senescence and Improves Skin Homeostasis by Regulating IL8 Expression.
The mitochondrial unfolded protein response: acting near and far.
The PERK-eIF2α-ATF4 Axis Is Involved in Mediating ER-Stress-Induced Ferroptosis via DDIT4-mTORC1 Inhibition and Acetaminophen-Induced Hepatotoxicity.
Emerging roles for microproteins as critical regulators of endoplasmic reticulum function and cellular homeostasis.
Mechanism of small heat shock protein client sequestration and induced polydispersity.
Integrator loss leads to dsRNA formation that triggers the integrated stress response.
Identification of novel small molecule chaperone activators for neurodegenerative disease treatment.
Lipid Droplet in Lipodystrophy and Neurodegeneration.
Single-molecule observations of human small heat shock proteins in complex with aggregation-prone client proteins.
Saturated Phosphatidic Acids Induce mTORC1-Driven Integrated Stress Response Contributing to Glucolipotoxicity in Hepatocytes.
Induced proximity to PML protects TDP-43 from aggregation via SUMO-ubiquitin networks.
Schwann Cell Protein Kinase RNA-like ER Kinase (PERK) Is Not Necessary for the Development of Diabetic Peripheral Neuropathy but Negates the Efficacy of Cemdomespib Therapy.
Genetically encoded tool for manipulation of ΔΨm identifies its role as the driver of ISR induced by ATP synthase dysfunction.
Inhibitor-based modulation of huntingtin aggregation mechanisms mitigates fibril-induced cellular stress.
Mechanism of client loading from BiP to Grp94 and its disruption by select inhibitors.
The Spectrum of Small Heat Shock Protein B8 (HSPB8)-Associated Neuromuscular Disorders.
The role of phospholipid saturation and composition in α-synuclein aggregation and toxicity: A dual in vitro and in vivo approach.
Modulators of the ubiquitin-proteasome system from natural products: chemical structures and their potential for drug discovery.
Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.
Left-handed conformations of glycyl residues may confer protection against protein aggregation.
Identification of a Selective Pharmacologic IRE1/XBP1s Activator with Enhanced Tissue Exposure.
Emerging mechanisms of human mitochondrial translation regulation.
The proteostasis burden of aneuploidy.
Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.
SPI1 activates mitochondrial unfolded response signaling to inhibit chondrocyte senescence and relieves osteoarthritis.
Active control of mitochondrial network morphology by metabolism-driven redox state.
Endoplasmic Reticulum Stress in Acute Myeloid Leukemia: Pathogenesis, Prognostic Implications, and Therapeutic Strategies.
Phosphatidate phosphatase Lipin1 alters mitochondria-associated endoplasmic reticulum membranes (MAMs) homeostasis: effects which contribute to the development of diabetic encephalopathy.
Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis.
Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.
Mitochondrial classic metabolism and its often-underappreciated facets.
Initiation of Translation in Bacteria and Chloroplasts.
Understanding the Link Between Sterol Regulatory Element Binding Protein (SREBPs) and Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD).
Comprehensive survey of disease-causing missense mutations of the cholesterol synthesis enzyme NSDHL: Low temperature and a chemical chaperone rescue low protein expression of select mutants.
Dynamic Lipidome Reorganization in Response to Heat Shock Stress.
Engineered depalmitoylases enable selective manipulation of protein localization and function.

bioRxiv. 2025 Apr 05. pii: 2025.04.04.646800. [Epub ahead of print]

Phenylhydrazone-based Endoplasmic Reticulum Proteostasis Regulator Compounds with Enhanced Biological Activity.

Gabriel M Kline, Lisa Boinon, Adrian Guerrero, Sergei Kutseikin, Gabrielle Cruz, Marnie P Williams, Ryan J Paxman, William E Balch, Jeffery W Kelly, Tingwei Mu, R Luke Wiseman.

Pharmacological enhancement of endoplasmic reticulum (ER) proteostasis is an attractive strategy to mitigate pathology linked to etiologically-diverse protein misfolding diseases. However, despite this promise, few compounds have been identified that enhance ER proteostasis through defined mechanisms of action. We previously identified the phenylhydrazone-based compound AA263 as a compound that promotes adaptive ER proteostasis remodeling through mechanisms including activation of the ATF6 signaling arm of the unfolded protein response (UPR). However, the protein target(s) of AA263 and the potential for further development of this class of ER proteostasis regulators had not been previously explored. Here, we employ chemical proteomics to demonstrate that AA263 covalently targets a subset of ER protein disulfide isomerases, revealing a molecular mechanism for the activation of ATF6 afforded by this compound. We then use medicinal chemistry to establish next-generation AA263 analogs showing improved potency and efficacy for ATF6 activation, as compared to the parent compound. Finally, we show that treatment with these AA263 analogs enhances secretory pathway proteostasis to correct the pathologic protein misfolding and trafficking of both a destabilized, disease-associated α1-antitrypsin (A1AT) variant and an epilepsy-associated GABA A receptor variant. These results establish AA263 analogs with enhanced potential for correcting imbalanced ER proteostasis associated with etiologically-diverse protein misfolding disorders.

DOI: https://doi.org/10.1101/2025.04.04.646800
FEBS J. 2025 Apr 14.

The unfolded protein response is a potential therapeutic target in pathogenic fungi.

Hao Zhou, Jinping Zhang, Rong Wang, Ju Huang, Caiyan Xin, Zhangyong Song.

  Pathogenic fungal infections cause significant morbidity and mortality, particularly in immunocompromised patients. The frequent emergence of multidrug-resistant strains challenges existing antifungal therapies, driving the need to investigate novel antifungal agents that target new molecular moieties. Pathogenic fungi are subjected to various environmental stressors, including pH, temperature, and pharmacological agents, both in natural habitats and the host body. These stressors elevate the risk of misfolded or unfolded protein production within the endoplasmic reticulum (ER) which, if not promptly mitigated, can lead to the accumulation of these proteins in the ER lumen. This accumulation triggers an ER stress response, potentially jeopardizing fungal survival. The unfolded protein response (UPR) is a critical cellular defense mechanism activated by ER stress to restore the homeostasis of protein folding. In recent years, the regulatory role of the UPR in pathogenic fungi has garnered significant attention, particularly for its involvement in fungal adaptation, regulation of virulence, and drug resistance. In this review, we comparatively analyze the UPRs of fungi and mammals and examine the potential utility of the UPR as a molecular antifungal target in pathogenic fungi. By clarifying the specificity and regulatory functions of the UPR in pathogenic fungi, we highlight new avenues for identifying potential therapeutic targets for antifungal treatments.

Keywords:  cellular stress response; pathogenic fungus; regulatory function; unfolded protein response therapeutic target

DOI:  https://doi.org/10.1111/febs.70100
Mol Med Rep. 2025 06;pii: 167. [Epub ahead of print]31(6):

Preliminary exploration of endoplasmic reticulum stress transmission in astrocytes and neurons, and its mediators.

Yating Ling, Muhammad Abid Hayat, Xiaorui Lv, Dongdong Niu, Yu Zeng, Yun Qiu, Bo Chen, Jiabo Hu.

  Unfolded protein response (UPR) signaling in cells stimulates UPR signaling in adjacent cells, facilitating the progression of disease (such as diabetes)by upregulating UPR target genes; however, whether this dissemination occurs between nerve cells, and its molecular basis, is currently unclear. In the present study, the supernatant of endoplasmic reticulum (ER) stress‑induced rat astrocytes was prepared and used to treat rat adrenal pheochromocytoma cell to simulate the propagation of ER stress between nerve cells. Reverse transcription‑quantitative PCR and western blotting were performed to detect the expression levels of mRNAs and protein levels associated with ER stress in cells. The results revealed that ER stress may propagate between rat nerve cells, ultimately leading to apoptosis. Analysis also revealed that the mediators of ER stress transmission were non‑vesicular, oxidative molecules with molecular weights >100 kDa. In conclusion, ER stress propagation may have a role in neuronal death following ER stress in central nervous system diseases, presenting potential novel therapeutic targets for these conditions.

Keywords:  astrocytes; endoplasmic reticulum stress; endoplasmic reticulum stress propagation; mediators; neurons

DOI:  https://doi.org/10.3892/mmr.2025.13532
Aging Cell. 2025 Apr 16. e70024

Targeting ATF6α Attenuates UVB-Induced Senescence and Improves Skin Homeostasis by Regulating IL8 Expression.

Joëlle Giroud, Pauline Delvaux, Laura Carlier, Clémentine De Schutter, Nathalie Martin, Raphaël Rouget, Ayeh Bolouki, Valérie De Glas, Inès Bouriez, Florent Bourdoux, Sophie Burteau, Julien Théry, Gauthier Decanter, Nicolas Penel, Yvan de Launoit, Benjamin Ledoux, Corinne Abbadie, Yves Poumay, Olivier Pluquet, Florence Debacq-Chainiaux.

  Skin aging is influenced by both intrinsic and extrinsic factors, particularly UV radiation, and is characterized by an accumulation of senescent cells. Remarkably, exposure to UV can trigger senescence in different skin cell types, including dermal fibroblasts. However, the molecular mechanisms underlying UV-induced senescence and the impact of the related senescence-associated secretory phenotype (SASP) on the homeostasis of the overlying epidermis remain poorly understood. Here, we identified that both chronological aging and photoaging induce the unfolded protein response (UPR) in human dermal samples. We demonstrated that silencing ATF6α disrupts the establishment of the UVB-induced senescent phenotype by preventing the onset of several senescent biomarkers and alters the composition of the SASP, consequently affecting its impact on the increased proliferation of keratinocytes embedded in reconstructed human epidermis. Moreover, we found that ATF6α partially mediates IL8 expression involved in the hyperproliferation of cultured keratinocytes. Together, our findings highlight the importance of the ATF6α/IL8 axis in regulating the homeostasis of neighboring cells during skin photoaging, thus suggesting ATF6α as a potentially promising target for senotherapeutic interventions.

Keywords:  ATF6α; UPR; UVB‐induced senescence; normal human dermal fibroblasts; skin

DOI:  https://doi.org/10.1111/acel.70024
Biol Chem. 2025 Apr 17.

The mitochondrial unfolded protein response: acting near and far.

Nikolaos Charmpilas, Qiaochu Li, Thorsten Hoppe.

  Mitochondria are central hubs of cellular metabolism and their dysfunction has been implicated in a variety of human pathologies and the onset of aging. To ensure proper mitochondrial function under misfolding stress, a retrograde mitochondrial signaling pathway known as UPRmt is activated. The UPRmt ensures that mitochondrial stress is communicated to the nucleus, where gene expression for several mitochondrial proteases and chaperones is induced, forming a protective mechanism to restore mitochondrial proteostasis and function. Importantly, the UPRmt not only acts within cells, but also exhibits a conserved cell-nonautonomous activation across species, where mitochondrial stress in a defined tissue triggers a systemic response that affects distant organs. Here, we summarize the molecular basis of the UPRmt in the invertebrate model organism Caenorhabditis elegans and in mammals. We also describe recent findings on cell-nonautonomous activation of the UPRmt in worms, flies and mice, and how UPRmt activation in specific tissues affects organismal metabolism and longevity.

Keywords:  cell-nonautonomous regulation; integrated stress response; mitochondria; mitochondrial unfolded protein response; stress signaling

DOI:  https://doi.org/10.1515/hsz-2025-0107
Antioxidants (Basel). 2025 Mar 03. pii: 307. [Epub ahead of print]14(3):

The PERK-eIF2α-ATF4 Axis Is Involved in Mediating ER-Stress-Induced Ferroptosis via DDIT4-mTORC1 Inhibition and Acetaminophen-Induced Hepatotoxicity.

Thu-Hang Thi Nghiem, Kim Anh Nguyen, Fedho Kusuma, Soyoung Park, Jeongmin Park, Yeonsoo Joe, Jaeseok Han, Hun Taeg Chung.

  Ferroptosis, a regulated form of cell death characterized by lipid peroxidation and iron accumulation, is increasingly recognized for its role in disease pathogenesis. The unfolded protein response (UPR) has been implicated in both endoplasmic reticulum (ER) stress and ferroptosis-mediated cell fate decisions; yet, the specific mechanism remains poorly understood. In this study, we demonstrated that ER stress induced by tunicamycin and ferroptosis triggered by erastin both activate the UPR, leading to the induction of ferroptotic cell death. This cell death was mitigated by the application of chemical chaperones and a ferroptosis inhibitor. Among the three arms of the UPR, the PERK-eIF2α-ATF4 signaling axis was identified as a crucial mediator in this process. Mechanistically, the ATF4-driven induction of DDIT4 plays a pivotal role, facilitating ferroptosis via the inhibition of the mTORC1 pathway. Furthermore, acetaminophen (APAP)-induced hepatotoxicity was investigated as a model of eIF2α-ATF4-mediated ferroptosis. Our findings reveal that the inhibition of eIF2α-ATF4 or ferroptosis protects against APAP-induced liver damage, underscoring the therapeutic potential of targeting these pathways. Overall, this study not only clarifies the intricate role of the PERK-eIF2α-ATF4 axis in ER-stress-and erastin-induced ferroptosis but also extends these findings to a clinically relevant model, providing a foundation for potential therapeutic interventions in conditions characterized by dysregulated ferroptosis and ER stress.

Keywords:  DDIT4; ER stress; GPX4; PERK; ferroptosis; unfolded protein response

DOI:  https://doi.org/10.3390/antiox14030307
Semin Cell Dev Biol. 2025 Apr 16. pii: S1084-9521(25)00018-7. [Epub ahead of print]170 103608

Emerging roles for microproteins as critical regulators of endoplasmic reticulum function and cellular homeostasis.

Taylor M Coughlin, Catherine A Makarewich.

  The endoplasmic reticulum (ER) is a multifunctional organelle essential for key cellular processes including protein synthesis, calcium homeostasis, and the cellular stress response. It is composed of distinct domains, such as the rough and smooth ER, as well as membrane regions that facilitate direct communication with other organelles, enabling its diverse functions. While many well-characterized ER proteins contribute to these processes, recent studies have revealed a previously underappreciated class of small proteins that play critical regulatory roles. Microproteins, typically under 100 amino acids in length, were historically overlooked due to size-based biases in genome annotation and often misannotated as noncoding RNAs. Advances in ribosome profiling, mass spectrometry, and computational approaches have now enabled the discovery of numerous previously unrecognized microproteins, significantly expanding our understanding of the proteome. While some ER-associated microproteins, such as phospholamban and sarcolipin, were identified decades ago, newly discovered microproteins share similar fundamental characteristics, underscoring the need to refine our understanding of the coding potential of the genome. Molecular studies have demonstrated that ER microproteins play essential roles in calcium regulation, ER stress response, organelle communication, and protein translocation. Moreover, growing evidence suggests that ER microproteins contribute to cellular homeostasis and are implicated in disease processes, including cardiovascular disease and cancer. This review examines the shared and unique functions of ER microproteins, their implications for health and disease, and their potential as therapeutic targets for conditions associated with ER dysfunction.

Keywords:  Calcium; Cellular stress response; Endoplasmic reticulum; Micropeptide; Microprotein; sORF

DOI:  https://doi.org/10.1016/j.semcdb.2025.103608
Nat Commun. 2025 Apr 16. 16(1): 3635

Mechanism of small heat shock protein client sequestration and induced polydispersity.

Adam P Miller, Steve L Reichow.

Small heat shock proteins (sHSPs) act as first responders during cellular stress, sequestering destabilized proteins (clients) to prevent aggregation and facilitate refolding or degradation. This critical function, conserved across all life, is linked to proteostasis and protein misfolding diseases. However, the extreme molecular plasticity of sHSP/client complexes has limited mechanistic understanding. Here, we present high-resolution cryo-EM structures of Methanocaldococcus jannaschii sHSP (mjHSP16.5) in apo and multiple client-bound states. The ensemble reveals molecular mechanisms of client sequestration, highlighting cooperative chaperone-client interactions. Client engagement polarizes scaffold stability, promoting higher-order assembly and enhanced sequestration. Higher-order states suggest multiple sHSP/client assembly pathways, including subunit insertion at destabilized geometrical features. These findings provide critical insights into sHSP chaperone function and the interplay between polydispersity and client handling under stress.

DOI: https://doi.org/10.1038/s41467-025-58964-3
Cell. 2025 Apr 10. pii: S0092-8674(25)00343-5. [Epub ahead of print]

Integrator loss leads to dsRNA formation that triggers the integrated stress response.

Apoorva Baluapuri, Nicole ChenCheng Zhao, Ryan J Marina, Kai-Lieh Huang, Anastasia Kuzkina, Maria E Amodeo, Chad B Stein, Lucie Y Ahn, Jordan S Farr, Ashleigh E Schaffer, Vikram Khurana, Eric J Wagner, Karen Adelman.

  Integrator (INT) is a metazoan-specific complex that targets promoter-proximally paused RNA polymerase II (RNAPII) for termination, preventing immature RNAPII from entering gene bodies and functionally attenuating transcription of stress-responsive genes. Mutations in INT subunits are associated with many human diseases, including cancer, ciliopathies, and neurodevelopmental disorders, but how reduced INT activity contributes to disease is unknown. Here, we demonstrate that the loss of INT-mediated termination in human cells triggers the integrated stress response (ISR). INT depletion causes upregulation of short genes such as the ISR transcription factor activating transcription factor 3 (ATF3). Further, immature RNAPII that escapes into genes upon INT depletion is prone to premature termination, generating incomplete pre-mRNAs with retained introns. Retroelements within retained introns form double-stranded RNA (dsRNA) that is recognized by protein kinase R (PKR), which drives ATF4 activation and prolonged ISR. Critically, patient cells with INT mutations exhibit dsRNA accumulation and ISR activation, thereby implicating chronic ISR in diseases caused by INT deficiency.

Keywords:  IR-Alu; Integrator; RNA polymerase II pausing; double-stranded RNA; gene regulation; integrated stress response; premature cleavage and polyadenylation; premature termination; protein kinase R

DOI:  https://doi.org/10.1016/j.cell.2025.03.025
Biomed Pharmacother. 2025 Apr 15. pii: S0753-3322(25)00243-4. [Epub ahead of print]187 118049

Identification of novel small molecule chaperone activators for neurodegenerative disease treatment.

Anita K Ho, Fiona Jeganathan, Magda Bictash, Han-Jou Chen.

  A pathological hallmark of neurodegenerative disease is the accumulation of aberrant protein aggregates which contribute to the cytotoxicity and are therefore a target for therapy development. One key mechanism to manage cellular protein homeostasis is heat shock proteins (HSPs), protein chaperones which are known to target aberrant protein accumulation. Activation of HSPs target aberrant TDP-43, tau and amyloid to rescue neurodegenerative disease. As an attempt to target HSP activation for neurodegeneration therapy, we here develop a drug screening assay to identify compounds that will activate the master regulator of HSPs, the transcription factor heat shock factor 1 (HSF1). As HSF1 is bound by HSP90 which prevents its activation, we developed a NanoBRET assay, which allows us to monitor and quantify the HSF1-HSP90 interaction in living cells to screen for compounds disrupting this interaction and thereby releasing HSF1 for activation. After the optimisation and validation of the assay, a two thousand compound library was screened which produced 10 hits including two known HSP90 inhibitors. Follow-up functional study showed that one of the hits oxyphenbutazone (OPB) significantly reduces the accumulation of insoluble TDP-43 in a cell model, eliciting no signs of stress or toxicity. Overall, this study demonstrates a viable strategy for new drug discovery in targeting aberrant proteins and identifies potential candidates for translation into neurodegenerative disease treatment.

Keywords:  Chaperones; Drug screening; HSF1; Neurodegenerative disease; TDP-43

DOI:  https://doi.org/10.1016/j.biopha.2025.118049
Biol Cell. 2025 Apr;117(4): e70009

Lipid Droplet in Lipodystrophy and Neurodegeneration.

Priyatama Behera, Monalisa Mishra.

  Lipid droplets are ubiquitous yet distinct intracellular organelles that are gaining attention for their uses outside of energy storage. Their formation, role in the physiological function, and the onset of the pathology have been gaining attention recently. Their structure, synthesis, and turnover play dynamic roles in both lipodystrophy and neurodegeneration. Factors like development, aging, inflammation, and cellular stress regulate the synthesis of lipid droplets. The biogenesis of lipid droplets has a critical role in reducing cellular stress. Lipid droplets, in response to stress, sequester hazardous lipids into their neutral lipid core, preserving energy and redox balance while guarding against lipotoxicity. Thus, the maintenance of lipid droplet homeostasis in adipose tissue, CNS, and other body tissues is essential for maintaining organismal health. Insulin resistance, hypertriglyceridemia, and lipid droplet accumulation are the severe metabolic abnormalities that accompany lipodystrophy-related fat deficit. Accumulation of lipid droplets is detected in almost all neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Hereditary spastic paraplegia. Hence, the regulation of lipid droplets can be used as an alternative approach to the treatment of several diseases. The current review summarizes the structure, composition, biogenesis, and turnover of lipid droplets, with an emphasis on the factors responsible for the accumulation and importance of lipid droplets in lipodystrophy and neurodegenerative disease.

Keywords:  cellular stress; lipid droplet; lipodystrophy; neurodegenerative diseases

DOI:  https://doi.org/10.1111/boc.70009
Biochem J. 2025 Apr 09. pii: BCJ20240473. [Epub ahead of print]

Single-molecule observations of human small heat shock proteins in complex with aggregation-prone client proteins.

Lauren Rice, Nicholas Marzano, Dezerae Cox, Bailey Skewes, Antoine van Oijen, Heath Ecroyd.

  Small heat shock proteins (sHsps) are molecular chaperones that act to prevent the aberrant aggregation of misfolded proteins. Whilst it is suggested that sHsps prevent aggregation by binding to misfolded client proteins, the dynamic and heterogeneous nature of sHsps has hindered attempts to establish the mechanistic details of how sHsp-client protein complexes form. Single-molecule approaches have emerged as a powerful tool to investigate dynamic and heterogeneous interactions such as those that can occur between sHsps and their client proteins. Here, we use total internal reflection fluorescence microscopy to observe and characterise the complexes formed between model aggregation-prone client proteins [firefly luciferase (FLUC), rhodanese, and chloride intracellular channel 1 protein (CLIC)], and the human sHsps αB-crystallin (αB-c; HSPB5) and Hsp27 (HSPB1). We show that small (monomeric or dimeric) forms of both αB-c and Hsp27 bind to misfolded or oligomeric forms of the client proteins at early stages of aggregation, resulting in the formation of soluble sHsp-client complexes. Stoichiometric analysis of these complexes revealed that additional αB-c subunits accumulate onto pre-existing sHsp-client complexes to form larger species - this does not occur to the same extent for Hsp27. Instead, Hsp27-client interactions tend to be more transient than those of αB-c. Elucidating these mechanisms of sHsp function is crucial to our understanding of how these molecular chaperones act to inhibit protein aggregation and maintain cellular proteostasis.

Keywords:  Hsp27; molecular chaperones; photobleaching; proteostasis; single-molecule fluorescence; αB-crystallin

DOI:  https://doi.org/10.1042/BCJ20240473
Am J Physiol Gastrointest Liver Physiol. 2025 Apr 17.

Saturated Phosphatidic Acids Induce mTORC1-Driven Integrated Stress Response Contributing to Glucolipotoxicity in Hepatocytes.

Rui Guo, Yanhui Li, Yuwei Jiang, Md Wasim Khan, Brian T Layden, Zhenyuan Song.

  Hepatic glucolipotoxicity, characterized by the synergistic detrimental effects of elevated glucose levels combined with excessive lipid accumulation in hepatocytes, plays a central role in the pathogenesis of various metabolic liver diseases. Despite recent advancements, the precise mechanisms underlying this process remain unclear. Employing cultured AML12 and HepG2 cells exposed to excess palmitate, with and without high glucose, as an in vitro model, we aimed to elucidate the cellular and molecular mechanisms underlying hepatic glucolipotoxicity. Our data showed that palmitate exposure induced the integrated stress response (ISR) in hepatocytes, evidenced by increased eIF2α phosphorylation (serine 51) and upregulated ATF4 expression. Moreover, we identified mTORC1 as a novel upstream kinase responsible for palmitate-triggered ISR induction. Furthermore, we showed that either mTORC1 inhibitors, ISRIB (an ISR inhibitor), or ATF4 knockdown abolished palmitate-induced cell death, indicating that the mTORC1-eIF2α- ATF4 pathway activation plays a mechanistic role in mediating palmitate-induced hepatocyte cell death. Our continuous investigations revealed that GPAT4-mediated metabolic flux of palmitate into the glycerolipid synthesis pathway is required for palmitate-induced mTORC1 activation and subsequent ISR induction. Specifically, we uncovered that saturated phosphatidic acid production contributes to palmitate-triggered mTORC1 activation. Our study provides the first evidence that high glucose enhances palmitate-induced activation of the mTORC1-eIF2α-ATF4 pathway, thereby exacerbating palmitate-induced hepatotoxicity. This effect is mediated by the increased availability of glycerol-3-phosphate, a substrate essential for phosphatidic acid synthesis. In conclusion, our study highlights that the activation of the mTORC1-eIF2α-ATF4 pathway, driven by saturated phosphatidic acid overproduction, plays a mechanistic role in hepatic glucolipotoxicity.

Keywords:  ISR; Palmitate; glucolipotoxicity; mTORC1; phosphatidic acid

DOI:  https://doi.org/10.1152/ajpgi.00027.2025
Nat Chem Biol. 2025 Apr 17.

Induced proximity to PML protects TDP-43 from aggregation via SUMO-ubiquitin networks.

Kristina Wagner, Jan Keiten-Schmitz, Bikash Adhikari, Upayan Patra, Koraljka Husnjak, François McNicoll, Dorothee Dormann, Michaela Müller-McNicoll, Georg Tascher, Elmar Wolf, Stefan Müller.

The established role of cytosolic and nuclear inclusions of TDP-43 in the pathogenesis of neurodegenerative disorders has multiplied efforts to understand mechanisms that control TDP-43 aggregation and has spurred searches for approaches limiting this process. Formation and clearance of TDP-43 aggregates are controlled by an intricate interplay of cellular proteostasis systems that involve post-translational modifications and frequently rely on spatial control. We demonstrate that attachment of the ubiquitin-like SUMO2 modifier compartmentalizes TDP-43 in promyelocytic leukemia protein (PML) nuclear bodies and limits the aggregation of TDP-43 in response to proteotoxic stress. Exploiting this pathway through proximity-inducing recruitment of TDP-43 to PML triggers a SUMOylation-ubiquitylation cascade protecting TDP-43 from stress-induced insolubility. The protective function of PML is mediated by ubiquitylation in conjunction with the p97 disaggregase. Altogether, we demonstrate that SUMO-ubiquitin networks protect cells from insoluble TDP-43 inclusions and propose the functionalization of PML as a potential future therapeutic avenue countering aggregation.

DOI: https://doi.org/10.1038/s41589-025-01886-4
ACS Pharmacol Transl Sci. 2025 Apr 11. 8(4): 1129-1139

Schwann Cell Protein Kinase RNA-like ER Kinase (PERK) Is Not Necessary for the Development of Diabetic Peripheral Neuropathy but Negates the Efficacy of Cemdomespib Therapy.

Sugandha Patel, Rick T Dobrowsky.

Diabetic peripheral neuropathy (DPN) is a common complication of diabetes arising in part from glycemic damage to neurons and Schwann cells (SC). While the pathogenic mechanisms of DPN are complex, mitochondrial dysfunction and endoplasmic reticulum (ER) stress contribute to the development of DPN and serve as therapeutic targets for disease modification. Cemdomespib is an orally bioavailable small molecule which alleviates clinical indices of DPN that correlate with improvements in neuronal oxidative stress and mitochondrial bioenergetics. However, the contribution of SC ER stress in the onset of DPN and the therapeutic efficacy of cemdomespib remains unknown. To address this issue, mice expressing a conditional deletion of protein kinase RNA-like ER kinase (PERK) in myelinating SCs (SC-cPERK KO) and control SC-PERKf/f mice were rendered diabetic with streptozotocin. Diabetic SC-PERKf/f and SC-cPERK KO mice developed a similar magnitude of DPN as quantified by the onset of a thermal/mechanical hypoalgesia, decreases in nerve conduction velocity (NCV) and intraepidermal fiber density (iENFD). After 8 weeks of diabetes, daily treatment with 1 mg/kg cemdomespib for an additional 8 weeks significantly improved thermal/mechanical hypoalgesia, NCV, iENFD and decreased markers of ER stress in diabetic SC-PERKf/f mice, but the drug had no effect in diabetic SC-cPERK KO mice. Nrf2 is a PERK substrate and studies using rat SCs subjected to ER stress demonstrated that cemdomespib increased Nrf2 activity. Collectively, these data suggest that activation of SC PERK by diabetes is not necessary for the onset of DPN, but serves as a target in the action of cemdomespib, potentially by increasing Nrf2 activity.

DOI: https://doi.org/10.1021/acsptsci.5c00021
Cell Chem Biol. 2025 Apr 17. pii: S2451-9456(25)00097-2. [Epub ahead of print]32(4): 620-630.e6

Genetically encoded tool for manipulation of ΔΨm identifies its role as the driver of ISR induced by ATP synthase dysfunction.

Mangyu Choe, Alex E Ekvik, Gretchen Stalnaker, Hijai R Shin, Denis V Titov.

  Mitochondrial membrane potential (ΔΨm) is one of the key parameters controlling cellular bioenergetics. Investigation of the role of ΔΨm in live cells is complicated by a lack of tools for its direct manipulation without off-target effects. Here, we adopted the uncoupling protein UCP1 from brown adipocytes as a genetically encoded tool for direct manipulation of ΔΨm. We validated the ability of exogenously expressed UCP1 to induce uncoupled respiration and lower ΔΨm in mammalian cells. UCP1 expression lowered ΔΨm to the same extent as chemical uncouplers but did not inhibit cell proliferation, suggesting that it manipulates ΔΨm without the off-target effects of chemical uncouplers. Using UCP1, we revealed that elevated ΔΨm is the driver of the integrated stress response induced by ATP synthase inhibition in mammalian cells.

Keywords:  ATP synthase inhibition; GEMMs; ISR; UCP1; genetically encoded tools for manipulation of metabolism; integrated stress response,; mitochondrial membrane potential; ΔΨm

DOI:  https://doi.org/10.1016/j.chembiol.2025.03.007
Nat Commun. 2025 Apr 15. 16(1): 3588

Inhibitor-based modulation of huntingtin aggregation mechanisms mitigates fibril-induced cellular stress.

Greeshma Jain, Marina Trombetta-Lima, Irina Matlahov, Hennrique Taborda Ribas, Tingting Chen, Raffaella Parlato, Giuseppe Portale, Amalia M Dolga, Patrick C A van der Wel.

Huntington's disease (HD) is a neurodegenerative disorder in which mutated fragments of the huntingtin protein (Htt) undergo misfolding and aggregation. Since aggregated proteins can cause cellular stress and cytotoxicity, there is an interest in the development of small molecule aggregation inhibitors as potential modulators of HD pathogenesis. Here, we study how a polyphenol modulates the aggregation mechanism of huntingtin exon 1 (HttEx1) even at sub-stoichiometric ratios. Sub-stoichiometric amounts of curcumin impacted the primary and/or secondary nucleation events, extending the pre-aggregation lag phase. Remarkably, the disrupted aggregation process changed both the aggregate structure and its cell metabolic properties. When administered to neuronal cells, the 'break-through' protein aggregates induced significantly reduced cellular stress compared to aggregates formed in absence of inhibitors. Structural analysis by electron microscopy, small angle X-ray scattering (SAXS), and solid-state NMR spectroscopy identified changes in the fibril structures, probing the flanking domains in the fuzzy coat and the fibril core. We propose that changes in the latter relate to the presence or absence of polyglutamine (polyQ) β-hairpin structures. Our findings highlight multifaceted consequences of small molecule inhibitors that modulate the protein misfolding landscape, with potential implications for treatment strategies in HD and other amyloid disorders.

DOI: https://doi.org/10.1038/s41467-025-58691-9
Nat Commun. 2025 Apr 15. 16(1): 3575

Mechanism of client loading from BiP to Grp94 and its disruption by select inhibitors.

Tara P Azam, Luna Han, Erin E Deans, Bin Huang, Reyal Hoxie, Larry J Friedman, Jeff Gelles, Timothy O Street.

Hsp90 chaperones are a long-standing cancer drug target with numerous ATP-competitive inhibitors in clinical trials. Client proteins are transferred from Hsp70 to Hsp90 in a stepwise process of client delivery, loading, and trapping, but little is known about how inhibitors influence these steps. By examining the ER-resident BiP/Grp94 system (Hsp70/Hsp90 paralogs), we discover that some inhibitors allow BiP to push Grp94 into the client loading conformation, whereas other inhibitors block this conformational change and destabilize a BiP/client/Grp94 ternary complex. We uncover how BiP drives Grp94 into the client loading state and identify a structural explanation for why only a select group of inhibitors disrupt client loading on Grp94. These results show a client loading mechanism with specific shared features between the Hsp70/Hsp90 systems in the ER and cytosol and open a new avenue for rational Hsp90 drug design.

DOI: https://doi.org/10.1038/s41467-025-58658-w
Int J Mol Sci. 2025 Mar 23. pii: 2905. [Epub ahead of print]26(7):

The Spectrum of Small Heat Shock Protein B8 (HSPB8)-Associated Neuromuscular Disorders.

Hebatallah R Rashed, Samir R Nath, Margherita Milone.

  The heat shock protein B8 (HSPB8) is one of the small heat shock proteins (sHSP or HSPB) and is a ubiquitous protein in various organisms, including humans. It is highly expressed in skeletal muscle, heart, and neurons. It plays a crucial role in identifying misfolding proteins and participating in chaperone-assisted selective autophagy (CASA) for the removal of misfolded and damaged, potentially cytotoxic proteins. Mutations in HSPB8 can cause distal hereditary motor neuropathy (dHMN), Charcot-Marie-Tooth (CMT) disease type 2L, or myopathy. The disease can manifest from childhood to mid-adulthood. Most missense mutations in the N-terminal and α-crystallin domains of HSPB8 lead to dHMN or CMT2L. Frameshift mutations in the C-terminal domain (CTD), resulting in elongation of the HSPB8 C-terminal, cause myopathy with myofibrillar pathology and rimmed vacuoles. Myopathy and motor neuropathy can coexist. HSPB8 frameshift mutations in the CTD result in HSPB8 mutant aggregation, which weakens the CASA ability to direct misfolded proteins to autophagic degradation. Cellular and animal models indicate that HSPB8 mutations drive pathogenesis through a toxic gain-of-function mechanism. Currently, no cure is available for HSPB8-associated neuromuscular disorders, but numerous therapeutic strategies are under investigation spanning from small molecules to RNA interference to exogenous HSPB8 delivery.

Keywords:  CASA; CMT2L; CTM2; HMN; HSPB8; dHMN; myofibrillar myopathy; myopathy; rimmed vacuoles

DOI:  https://doi.org/10.3390/ijms26072905
Protein Sci. 2025 May;34(5): e70121

The role of phospholipid saturation and composition in α-synuclein aggregation and toxicity: A dual in vitro and in vivo approach.

Aidan P Holman, Tianyi Dou, Mikhail Matveyenka, Kiryl Zhaliazka, Anjni Patel, Avery Maalouf, Ragd Elsaigh, Dmitry Kurouski.

  Parkinson's disease is characterized by a progressive accumulation of α-synuclein (α-syn) aggregates in Lewy bodies, extracellular deposits found in the midbrain, hypothalamus, and thalamus. The rate of α-syn aggregation, as well as the secondary structure of α-syn oligomers and fibrils, can be uniquely altered by lipids. However, the role of saturation of fatty acids (FAs) in such lipids in the aggregation properties of α-syn remains unclear. In this study, we investigated the effect of saturation of FAs in phosphatidylcholine (PC) and cardiolipin (CL), as well as a mixture of these phospholipids on the rate of α-syn aggregation. We found that although saturation plays very little if any role in the rate of protein aggregation and morphology of α-syn aggregates, it determined the secondary structure of α-syn oligomers and fibrils. Furthermore, we found that aggregates formed in the presence of both saturated and unsaturated PC and CL, as well as mixtures of these phospholipids, exert significantly higher cell toxicity compared to the protein aggregates formed in the lipid-free environment. To extend these findings, we conducted in vivo studies using C. elegans, where we assessed the effect of lipid-modified α-syn aggregates on organismal survival and neurotoxicity. Our results suggest that the saturation of FAs in phospholipids present in the plasma and mitochondrial membranes can be a key determinant of the secondary structure and, consequently, the toxicity of α-syn oligomers and fibrils. These findings provide new insights into the role of lipids in Parkinson's disease pathogenesis and highlight potential targets for therapeutic intervention.

Keywords:  AFM‐IR; alpha‐synuclein; amyloids; lipids; oligomers

DOI:  https://doi.org/10.1002/pro.70121
Nat Prod Rep. 2025 Apr 14.

Modulators of the ubiquitin-proteasome system from natural products: chemical structures and their potential for drug discovery.

Yuki Hitora, Sachiko Tsukamoto.

Covering: up to 2024The ubiquitin-proteasome system (UPS) plays a key role in regulating intracellular protein degradation and maintaining cellular homeostasis. Within the UPS, target proteins are polyubiquitinated through sequential reactions catalyzed by ubiquitination-related enzymes. These ubiquitinated proteins are then recognized and degraded by the 26S proteasome. Deubiquitinating enzymes cleave the formed polyubiquitin chains and regulate protein degradation, thereby contributing to precise regulation of the system. Dysregulation of the UPS is associated with cancer, immune disorders, and neurodegenerative diseases, making it a potential target for drug discovery. To date, a variety of natural products that target the UPS have been discovered and used in pharmaceutical development, and these compounds have provided important insights into the molecular mechanisms of UPS regulation. This review describes natural products that inhibit protein degradation in the UPS and activate protein degradation mediated by the 20S proteasome, thus clarifying their mechanisms of action and exploring their potential applications as therapeutic agents.

DOI: https://doi.org/10.1039/d5np00004a
Sci Adv. 2025 Apr 18. 11(16): eads6830

Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.

Adam Begeman, John A Smolka, Ahmad Shami, Tejashree Pradip Waingankar, Samantha C Lewis.

Protein- and RNA-rich bodies contribute to the spatial organization of gene expression in the cell and are also sites of quality control critical to cell fitness. In most eukaryotes, mitochondria harbor their own genome, and all steps of mitochondrial gene expression co-occur within a single compartment-the matrix. Here, we report that processed mitochondrial RNAs are consolidated into micrometer-scale translation hubs distal to mitochondrial DNA transcription and RNA processing sites in human cells. We find that, during stress, mitochondrial messenger and ribosomal RNA are sequestered in mesoscale bodies containing mitoribosome components, concurrent with suppression of active translation. Stress bodies are triggered by proteotoxic stress downstream of double-stranded RNA accumulation in cells lacking unwinding activity of the highly conserved helicase SUPV3L1/SUV3. We propose that the spatial organization of nascent polypeptide synthesis into discrete domains serves to throttle the flow of genetic information to support recovery of mitochondrial quality control.

DOI: https://doi.org/10.1126/sciadv.ads6830
FEBS J. 2025 Apr 17.

Left-handed conformations of glycyl residues may confer protection against protein aggregation.

Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu.

  The lack of Cβ atom allows glycyl to adopt left-handed Ramachandran conformations, typically disallowed for l-amino acids. The underlying significance remains under-appreciated. Through conformational analysis of glycyls at 1104 disease and 343 benign variant sites, we show that the left-handed glycyls are over-represented (odds ratio > 1.3) at disease variant sites and are evolutionarily conserved. Mutations involving l-disallowed glycyls destabilize native folding by altering free energies (P = 2.4 × 10-4). The l-disallowed glycyls are enriched at the aggregation gatekeepers, more profoundly so in thermophiles (P = 2.0 × 10-6), implying heightened selection to impede aggregation. Mutations of l-disallowed glycyls also reduce the protein solubility (P = 0.001). Due to mostly positive Φ dihedral-angle, Cα atom of l-disallowed glycyl flips to conform a crescent that likely disrupts β-strand alignment, discouraging the intermolecular aggregation of β-strands. Deep learning confirms the predictive value of l-disallowed glycyls in identifying pathogenic variants (accuracy = 0.81 vs. 0.69, area under the curve = 0.88 vs. 0.79). The findings underscore the evolutionary selection of l-disallowed conformations of glycyls to maintain proteostasis by modulating protein stability and aggregation, and suggest applications for disease-associated genetic prioritization and soluble protein design.

Keywords:  Ramachandran plot; glycyl residues; left‐handed conformation; protein aggregation

DOI:  https://doi.org/10.1111/febs.70092
ACS Chem Biol. 2025 Apr 15.

Identification of a Selective Pharmacologic IRE1/XBP1s Activator with Enhanced Tissue Exposure.

Jie Sun, Kyunga Lee, Sergei Kutseikin, Adrian Guerrero, Bibiana Rius, Aparajita Madhavan, Chavin Buasakdi, Ka-Neng Cheong, Priyadarshini Chatterjee, Dorian A Rosen, Leonard Yoon, Maziar S Ardejani, Alejandra Mendoza, Jessica D Rosarda, Enrique Saez, Jeffery W Kelly, R Luke Wiseman.

Activation of the IRE1/XBP1s signaling arm of the unfolded protein response (UPR) has emerged as a promising strategy to mitigate etiologically diverse diseases. Despite this promise, few compounds are available to selectively activate IRE1/XBP1s signaling to probe the biologic and therapeutic implications of this pathway in human disease. Recently, we identified the compound IXA4 as a highly selective activator of protective IRE1/XBP1s signaling. While IXA4 has proven useful for increasing IRE1/XBP1s signaling in cultured cells and mouse liver, the utility of this compound is restricted by its limited activity in other tissues. To broaden our ability to pharmacologically interrogate the impact of IRE1/XBP1s signaling in vivo, we sought to identify IRE1/XBP1s activators with greater tissue activity than IXA4. We reanalyzed 'hits' from the high throughput screen used to identify IXA4, selecting compounds from structural classes not previously pursued. We then performed global RNAseq to confirm that these compounds showed transcriptome-wide selectivity for IRE1/XBP1s activation. Functional profiling revealed compound IXA62 as a selective IRE1/XBP1s activator that reduced Aβ secretion from CHO7PA2 cells and enhanced glucose-stimulated insulin secretion from rat insulinoma cells, mimicking the effects of IXA4 in these assays. IXA62 robustly and selectively activated IRE1/XBP1s signaling in the liver of mice dosed compound intraperitoneally or orally. In treated mice, IXA62 showed broader tissue activity, relative to IXA4, inducing expression of IRE1/XBP1s target genes in additional tissues such as kidney and lung. Collectively, our results designate IXA62 as a selective IRE1/XBP1s signaling activating compound with enhanced tissue activity, which increases our ability to pharmacologically probe the biologic significance and potential therapeutic utility of enhancing adaptive IRE1/XBP1s signaling in vivo.

DOI: https://doi.org/10.1021/acschembio.4c00867
Trends Biochem Sci. 2025 Apr 11. pii: S0968-0004(25)00056-8. [Epub ahead of print]

Emerging mechanisms of human mitochondrial translation regulation.

Michele Brischigliaro, Ahram Ahn, Seungwoo Hong, Flavia Fontanesi, Antoni Barrientos.

  Mitochondrial translation regulation enables precise control over the synthesis of hydrophobic proteins encoded by the organellar genome, orchestrating their membrane insertion, accumulation, and assembly into oxidative phosphorylation (OXPHOS) complexes. Recent research highlights regulation across all translation stages (initiation, elongation, termination, and recycling) through a complex interplay of mRNA structures, specialized translation factors, and unique regulatory mechanisms that adjust protein levels for stoichiometric assembly. Key discoveries include mRNA-programmed ribosomal pausing, frameshifting, and termination-dependent re-initiation, which fine-tune protein synthesis and promote translation of overlapping open reading frames (ORFs) in bicistronic transcripts. In this review, we examine these advances, which are significantly enhancing our understanding of mitochondrial gene expression.

Keywords:  RNA folding; mitochondrial translation; programmed ribosomal frameshifting; ribosome stalling; termination-reinitiation

DOI:  https://doi.org/10.1016/j.tibs.2025.03.007
Biol Chem. 2025 Apr 14.

The proteostasis burden of aneuploidy.

Prince Saforo Amponsah, Zuzana Storchová.

  Aneuploidy refers to chromosome number abnormality that is not an exact multiple of the haploid chromosome set. Aneuploidy has largely negative consequences in cells and organisms, manifested as so-called aneuploidy-associated stresses. A major consequence of aneuploidy is proteotoxic stress due to abnormal protein expression from imbalanced chromosome numbers. Recent advances have improved our understanding of the nature of the proteostasis imbalance caused by aneuploidy and highlighted their relevance with respect to organellar homeostasis, dosage compensation, or mechanisms employed by cells to mitigate the detrimental stress. In this review, we highlight the recent findings and outline questions to be addressed in future research.

Keywords:  SQSTM1/p62; aging; aneuploidy; cancer; mitochondria; proteostasis

DOI:  https://doi.org/10.1515/hsz-2024-0163
Nat Commun. 2025 Apr 17. 16(1): 3401

Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.

Koki Nakamura, Saeko Aoyama-Ishiwatari, Takahiro Nagao, Mohammadreza Paaran, Christopher J Obara, Yui Sakurai-Saito, Jake Johnston, Yudan Du, Shogo Suga, Masafumi Tsuboi, Makoto Nakakido, Kouhei Tsumoto, Yusuke Kishi, Yukiko Gotoh, Chulhwan Kwak, Hyun-Woo Rhee, Jeong Kon Seo, Hidetaka Kosako, Clint Potter, Bridget Carragher, Jennifer Lippincott-Schwartz, Franck Polleux, Yusuke Hirabayashi.

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identify the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-electron tomography, and correlative light-electron microscopy. Single molecule tracking reveals highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and captures at MERCS. Overexpression of FKBP8 is sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrate their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

DOI: https://doi.org/10.1038/s41467-025-58538-3
Bone Res. 2025 Apr 14. 13(1): 47

SPI1 activates mitochondrial unfolded response signaling to inhibit chondrocyte senescence and relieves osteoarthritis.

Xiangyu Zu, Shenghong Chen, Zhengyuan Li, Lin Hao, Wenhan Fu, Hui Zhang, Zongsheng Yin, Yin Wang, Jun Wang.

Chondrocyte senescence is a critical pathological hallmark of osteoarthritis (OA). Aberrant mechanical stress is considered a pivotal determinant in chondrocyte aging; however, the precise underlying mechanism remains elusive. Our findings demonstrate that SPI1 plays a significant role in counteracting chondrocyte senescence and inhibiting OA progression. SPI1 binds to the PERK promoter, thereby promoting its transcriptional activity. Importantly, PERK, rather than GCN2, facilitates eIF2α phosphorylation, activating the mitochondrial unfolded protein response (UPRmt) and impeding chondrocyte senescence. Deficiency of SPI1 in mechanical overload-induced mice leads to diminished UPRmt activation and accelerated OA progression. Intra-articular injection of adenovirus vectors overexpressing SPI1 and PERK effectively mitigates cartilage degeneration. In summary, our study elucidates the crucial regulatory role of SPI1 in the pathogenesis of chondrocyte senescence by activating UPRmt signaling through PERK, which may present a novel therapeutic target for treating OA. SPI1 alleviates the progression of OA by inhibiting mechanical stress-induced chondrocyte senescence through mitochondrial UPR signaling.

DOI: https://doi.org/10.1038/s41413-025-00421-4
Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2421953122

Active control of mitochondrial network morphology by metabolism-driven redox state.

Gaurav Singh, Vineeth Vengayil, Aayushee Khanna, Swagata Adhikary, Sunil Laxman.

  Mitochondria are dynamic organelles that constantly change morphology. What controls mitochondrial morphology however remains unresolved. Using actively respiring yeast cells growing in distinct carbon sources, we find that mitochondrial morphology and activity are unrelated. Cells can exhibit fragmented or networked mitochondrial morphology in different nutrient environments independent of mitochondrial activity. Instead, mitochondrial morphology is controlled by the intracellular redox state, which itself depends on the nature of electron entry into the electron transport chain (ETC)-through complex I/II or directly to coenzyme Q/cytochrome c. In metabolic conditions where direct electron entry is high, reactive oxygen species (ROS) increase, resulting in an oxidized cytosolic environment and rapid mitochondrial fragmentation. Decreasing direct electron entry into the ETC by genetic or chemical means, or reducing the cytosolic environment rapidly restores networked morphologies. Using controlled disruptions of electron flow to alter ROS and redox state, we demonstrate minute-scale, reversible control between networked and fragmented forms in an activity-independent manner. Mechanistically, the fission machinery through Dnm1 responds in minute-scale to redox state changes, preceding the change in mitochondrial form. Thus, the metabolic state of the cell and its consequent cellular redox state actively control mitochondrial form.

Keywords:  electron transport chain; mitochondrial network; reactive oxygen species; redox state

DOI:  https://doi.org/10.1073/pnas.2421953122
Int J Mol Sci. 2025 Mar 27. pii: 3092. [Epub ahead of print]26(7):

Endoplasmic Reticulum Stress in Acute Myeloid Leukemia: Pathogenesis, Prognostic Implications, and Therapeutic Strategies.

Wojciech Wiese, Grzegorz Galita, Natalia Siwecka, Wioletta Rozpędek-Kamińska, Artur Slupianek, Ireneusz Majsterek.

  Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy that poses a significant therapeutic challenge due to its high recurrence rate and demanding treatment regimens. Increasing evidence suggests that endoplasmic reticulum (ER) stress and downstream activation of the unfolded protein response (UPR) pathway play a key role in the pathogenesis of AML. ER stress is triggered by the accumulation of misfolded or unfolded proteins within the ER. This causes activation of the UPR to restore cellular homeostasis. However, the UPR can shift from promoting survival to inducing apoptosis under prolonged or excessive stress conditions. AML cells can manipulate the UPR pathway to evade apoptosis, promoting tumor progression and resistance against various therapeutic strategies. This review provides the current knowledge on ER stress in AML and its prognostic and therapeutic implications.

Keywords:  ATF6; IRE1α; PERK; acute myeloid leukemia; endoplasmic reticulum stress; hematopoietic stem cells; unfolded protein response

DOI:  https://doi.org/10.3390/ijms26073092
J Neuroinflammation. 2025 Apr 18. 22(1): 111

Phosphatidate phosphatase Lipin1 alters mitochondria-associated endoplasmic reticulum membranes (MAMs) homeostasis: effects which contribute to the development of diabetic encephalopathy.

Shan Huang, Mengyu Hua, Wei Liu, Ziyun Zhuang, Xiaolin Han, Xiaochen Zhang, Zhonghao Liang, Xiaojing Liu, Nengjun Lou, Shuyan Yu, Shihong Chen, Xianghua Zhuang.

  Diabetic encephalopathy (DE) is a common, chronic central nervous system complication of diabetes mellitus, and represents a condition without a clear pathogenesis or effective therapy. Findings from recent studies have indicated that a dyshomeostasis of mitochondria-associated endoplasmic reticulum membranes (MAMs) may be involved in the development of neurodegenerative diseases such as DE. MAMs represent a dynamic contact site between mitochondrial and endoplasmic reticulum (ER) membranes, where phospholipid components are exchanged with each other. Previous work within our laboratory has revealed that Lipin1, a critical enzyme related to phospholipid synthesis, is involved in the pathogenesis of DE. Here, we show that Lipin1 is downregulated within the hippocampus of a DE mouse model, an effect which was accompanied with a decrease in MAMs. Knockdown of Lipin1 in the hippocampus of normal mice resulted in a reduction of MAMs, ER stress, abnormal mitochondrial function, as well as impaired synaptic plasticity and cognitive function. These same phenomena were observed in the DE model, while an upregulation of Lipin1 within the hippocampus of DE mice improved these symptoms. Low levels of Lipin1 in DE mice were also associated with neuroinflammation, while an overexpression of Lipin1 significantly ameliorated the neuroinflammation observed in DE mice. In conclusion, Lipin1 ameliorates pathological changes associated with DE in a mouse model via prevention of dyshomeostasis in MAMs. Such findings suggest that Lipin1 may be serve as a new potential target for the treatment of DE.

Keywords:  Cognitive dysfunction; Diabetic encephalopathy; Lipin1; MAMs; Mitochondria

DOI:  https://doi.org/10.1186/s12974-025-03441-3
Mol Cell. 2025 Apr 17. pii: S1097-2765(25)00196-0. [Epub ahead of print]85(8): 1487-1508

Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis.

Brandon Chen, Costas A Lyssiotis, Yatrik M Shah.

  Mitochondria serve as central hubs in cellular metabolism by sensing, integrating, and responding to metabolic demands. This integrative function is achieved through inter-organellar communication, involving the exchange of metabolites, lipids, and signaling molecules. The functional diversity of metabolite exchange and pathway interactions is enabled by compartmentalization within organelle membranes. Membrane contact sites (MCSs) are critical for facilitating mitochondria-organelle communication, creating specialized microdomains that enhance the efficiency of metabolite and lipid exchange. MCS dynamics, regulated by tethering proteins, adapt to changing cellular conditions. Dysregulation of mitochondrial-organelle interactions at MCSs is increasingly recognized as a contributing factor in the pathogenesis of multiple diseases. Emerging technologies, such as advanced microscopy, biosensors, chemical-biology tools, and functional genomics, are revolutionizing our understanding of inter-organellar communication. These approaches provide novel insights into the role of these interactions in both normal cellular physiology and disease states. This review will highlight the roles of metabolite transporters, lipid-transfer proteins, and mitochondria-organelle interfaces in the coordination of metabolism and transport.

Keywords:  endoplasmic reticulum; inter-organellar communication; mitochondria; organellar metabolism; organelle membrane contact sites

DOI:  https://doi.org/10.1016/j.molcel.2025.03.003
Cell Rep Methods. 2025 Apr 08. pii: S2667-2375(25)00063-3. [Epub ahead of print] 101027

Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.

Liam P Kelley, Song-Hua Hu, Sarah A Boswell, Peter K Sorger, Alison E Ringel, Marcia C Haigis.

  Mitochondrial stress arises from a variety of sources, including mutations to mitochondrial DNA, the generation of reactive oxygen species, and an insufficient supply of oxygen or fuel. Mitochondrial stress induces a range of dedicated responses that repair damage and restore mitochondrial health. However, a systematic characterization of transcriptional and metabolic signatures induced by distinct types of mitochondrial stress is lacking. Here, we defined how primary human fibroblasts respond to a panel of mitochondrial inhibitors to trigger adaptive stress responses. Using metabolomic and transcriptomic analyses, we established integrated signatures of mitochondrial stress. We developed a tool, stress quantification using integrated datasets (SQUID), to deconvolute mitochondrial stress signatures from existing datasets. Using SQUID, we profiled mitochondrial stress in The Cancer Genome Atlas (TCGA) PanCancer Atlas, identifying a signature of pyruvate import deficiency in IDH1-mutant glioma. Thus, this study defines a tool to identify specific mitochondrial stress signatures, which may be applied to a range of systems.

Keywords:  CP: Metabolism; CP: Systems biology; cancer metabolism; integrated multi-omics; integrated stress response; metabolomics; mitochondria; mitochondrial stress response; mitochondrial unfolded protein response; stress signatures

DOI:  https://doi.org/10.1016/j.crmeth.2025.101027
Biochim Biophys Acta Mol Basis Dis. 2025 Apr 10. pii: S0925-4439(25)00184-X. [Epub ahead of print] 167839

Mitochondrial classic metabolism and its often-underappreciated facets.

João P Moura, Paulo J Oliveira, Ana M Urbano.

  For many decades, mitochondria were essentially regarded as the main providers of the adenosine triphosphate (ATP) required to maintain the viability and function of eukaryotic cells, thus the widely popular metaphor "powerhouses of the cell". Besides ATP generation - via intermediary metabolism - these organelles have also traditionally been known, albeit to a lesser degree, for their notable role in biosynthesis, both as generators of biosynthetic intermediates and/or as the sites of biosynthesis. From the 1990s onwards, the concept of mitochondria as passive organelles providing the rest of the cell, from which they were otherwise isolated, with ATP and biomolecules on an on-demand basis has been challenged by a series of paradigm-shifting discoveries. Namely, it was shown that mitochondria act as signaling effectors to upregulate ATP generation in response to growth-promoting stimuli and that they are actively engaged, through signaling and epigenetics, in the regulation of a plethora of cellular processes, ultimately deciding cell function and fate. With the focus of mitochondrial research increasingly placed in these "non-classical" functions, the centrality of mitochondrial intermediary metabolism to biosynthesis and other mitochondrial functions tends to be overlooked. In this article, we revisit mitochondrial intermediary metabolism and illustrate how its intermediates, by-products and molecular machinery underpin other mitochondrial functions. A certain emphasis is given to frequently overlooked functions, namely the biosynthesis of iron‑sulfur (FeS) clusters, the only known function shared by all mitochondria and mitochondrion-related organelles. The generation of reactive oxygen species (ROS) and their putative role in signaling is also discussed in detail.

Keywords:  Educational article; Intermediary metabolism; Iron‑sulfur clusters; Metabolic energy; Mitochondrion-related organelles; ROS signaling

DOI:  https://doi.org/10.1016/j.bbadis.2025.167839
J Mol Biol. 2025 Apr 10. pii: S0022-2836(25)00203-7. [Epub ahead of print] 169137

Initiation of Translation in Bacteria and Chloroplasts.

Michael W Webster.

  Relative rates of protein synthesis in bacteria generally depend on the number of copies of a messenger RNA (mRNA) and the efficiency of their loading with ribosomes. Translation initiation involves the multi-stage assembly of the ribosome on the mRNA to begin protein synthesis. In bacteria, the small ribosomal subunit (30S) and mRNA form a complex that can be supported by RNA-protein and RNA-RNA interactions and is extensively modulated by mRNA folding. The initiator transfer RNA (tRNA) and large ribosomal subunit (50S) are recruited with aid of three initiation factors (IFs). Equivalent translation initiation processes occur in chloroplasts due to their endosymbiotic origin from photosynthetic bacteria. This review first summarizes the molecular basis of translation initiation in bacteria, highlighting recent insight into the initial, intermediate and late stages of the pathway obtained by structural analyses. The molecular basis of chloroplast translation initiation is then reviewed, integrating our mechanistic understanding of bacterial gene expression supported by detailed in vitro experiments with data on chloroplast gene expression derived primarily from genetic studies.

Keywords:  Shine-Dalgarno; Translation; bacteria; chloroplast; ribosome

DOI:  https://doi.org/10.1016/j.jmb.2025.169137
Curr Obes Rep. 2025 Apr 14. 14(1): 36

Understanding the Link Between Sterol Regulatory Element Binding Protein (SREBPs) and Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD).

Pervej Alom Barbhuiya, Ren Yoshitomi, Manash Pratim Pathak.

   PURPOSE OF THE REVIEW: This review aims to summarize the current scientific understanding on the complex interplay between sterol regulatory element-binding proteins (SREBPs) and metabolic dysfunction associated steatotic liver disease (MASLD) by critically examining a few significant molecular pathways. Additionally, the review explores the potential of both natural and synthetic SREBP inhibitors as promising therapeutic candidates for MASLD.
RECENT FINDINGS: SREBPs are central regulators of lipid homeostasis, with SREBP-1c primarily controlling fatty acid synthesis and SREBP-2 regulating cholesterol metabolism. Dysregulation of SREBP activity, often triggered by excessive caloric intake, insulin resistance, or endoplasmic reticulum (ER) stress, contributes to the development of metabolic syndrome and MASLD. SREBP-1c overexpression leads to increased de novo lipogenesis (DNL), hepatic lipid accumulation, and insulin resistance, while SREBP-2 modulates cholesterol metabolism via miRNA-33 and ABCA1 regulation leading to the pathogenesis of MASLD. The PI3K-Akt-mTORC1 pathway plays a critical role in SREBP activation, linking nutrient availability to lipid synthesis. Synthetic SREBP inhibitors, such as fatostatin and 25-hydroxycholesterol, and natural compounds, including kaempferol and resveratrol, show promise in modulating SREBP activity in vivo.
CONCLUSION: While targeting SREBP pathways presents a promising avenue for mitigating MASLD, further scientific investigation is imperative to identify and validate potential molecular targets. Although current studies on synthetic and natural SREBP inhibitors demonstrate encouraging results, rigorous pre-clinical and clinical research is warranted to translate these findings into effective MASLD treatments.

Keywords:  MASLD; NAFLD; Obesity; SREBP; SREBP inhibitors

DOI:  https://doi.org/10.1007/s13679-025-00626-y
J Steroid Biochem Mol Biol. 2025 Apr 11. pii: S0960-0760(25)00086-X. [Epub ahead of print]251 106758

Comprehensive survey of disease-causing missense mutations of the cholesterol synthesis enzyme NSDHL: Low temperature and a chemical chaperone rescue low protein expression of select mutants.

Nicole M Fenton, Laura J Sharpe, Dylan M Fitzsimmons, Isabelle M Capell-Hattam, Andrew J Brown.

  Cholesterol is essential to human life. Perturbations to any of the 22 cholesterol synthesis enzymes can lead to devastating developmental diseases. Each enzyme is exquisitely regulated both transcriptionally and post-translationally, playing a critical role in providing cholesterol to cells. We examined 13 missense mutations and one deletion mutation in the cholesterol synthesis enzyme NSDHL (NAD(P) Dependent Steroid Dehydrogenase-Like), known to cause the X-linked developmental disorders CHILD (congenital hemidysplasia with ichthyosiform erythroderma and limb defects) syndrome and CK syndrome. Little is known about the effect of these missense mutations on the stability and function of NSDHL. Here we show that protein expression levels were low for all mutants, but some could be rescued by a lower temperature (30°C vs. 37°C) and/or the chemical chaperone glycerol. Additionally, heat shock proteins 70 and 90 are needed for optimal NSDHL protein expression suggesting that disease mutations in NSDHL may interfere with this interaction, perhaps during translation resulting in lower protein synthesis. Our findings that these disease-causing mutations reduce NSDHL protein expression, but some respond to lower temperature and/or the chemical chaperone glycerol, can help inform future treatments for CHILD and CK syndrome.

Keywords:  CHILD syndrome; CK syndrome; Chemical chaperones; Cholesterol; Mutations; NSDHL; Protein

DOI:  https://doi.org/10.1016/j.jsbmb.2025.106758
Int J Mol Sci. 2025 Mar 21. pii: 2843. [Epub ahead of print]26(7):

Dynamic Lipidome Reorganization in Response to Heat Shock Stress.

Luis E Solano, Uri Keshet, Andrew Reinschmidt, Yonny Chavez, William Drew Hulsy, Oliver Fiehn, Nikolas Nikolaidis.

  The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2700 upregulated and 2300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.

Keywords:  cellular stress adaptation; heat shock response; lipidomics

DOI:  https://doi.org/10.3390/ijms26072843
Nat Commun. 2025 Apr 13. 16(1): 3514

Engineered depalmitoylases enable selective manipulation of protein localization and function.

Srinidhi Jayaraman, Audrey Kochiss, Thy-Lan Alcalay, Pedro J Del Rivero Morfin, Manu Ben-Johny.

S-Palmitoylation is a reversible post-translational modification that tunes the localization, stability, and function of an impressive array of proteins including ion channels, G-proteins, and synaptic proteins. Indeed, altered protein palmitoylation is linked to various human diseases including cancers, neurodevelopmental and neurodegenerative diseases. As such, strategies to selectively manipulate protein palmitoylation with enhanced temporal and subcellular precision are sought after to both delineate physiological functions and as potential therapeutics. Here, we develop chemogenetically and optogenetically inducible engineered depalmitoylases to manipulate the palmitoylation status of target proteins. We demonstrate that this strategy is programmable allowing selective depalmitoylation in specific organelles, triggered by cell-signaling events, and of individual protein complexes. Application of this methodology revealed bidirectional tuning of neuronal excitability by distinct depalmitoylases. Overall, this strategy represents a versatile and powerful method for manipulating protein palmitoylation in live cells, providing insights into their regulation in distinct physiological contexts.

DOI: https://doi.org/10.1038/s41467-025-58908-x