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14 pages, 4189 KB  
Article
A High-Molecular-Weight Fraction of Planarian Mucus Triggers UPR-Linked Cell Death Pathway in Human Bronchioalveolar Carcinoma Cell Line NCI-H358
by Gaetana Gambino, Gemma Marcelli, Paola Iacopetti, Laura Benvenuti, Chiara Bertini, Lucia Giambastiani, Luisa Pozzo, Alessandra Salvetti and Leonardo Rossi
Int. J. Mol. Sci. 2026, 27(10), 4324; https://doi.org/10.3390/ijms27104324 - 12 May 2026
Viewed by 234
Abstract
Natural products remain a major source of anticancer agents, yet freshwater organisms are largely unexplored. Building on our previous evidence that planarian mucus exerts cytostatic and cytotoxic effects on cancer cells, we investigated the involvement of endoplasmic reticulum stress and unfolded protein response [...] Read more.
Natural products remain a major source of anticancer agents, yet freshwater organisms are largely unexplored. Building on our previous evidence that planarian mucus exerts cytostatic and cytotoxic effects on cancer cells, we investigated the involvement of endoplasmic reticulum stress and unfolded protein response (UPR) pathways. Mucus-induced cytotoxicity is ROS-dependent and associated with depletion of intracellular reduced glutathione (GSH), not through inhibition of the System Xc transporter but potentially associated with upregulation of CHAC1, a glutathione-degrading enzyme. Mucus fractionation based on molecular weight identified the high-molecular-weight crude fraction as the one containing the bioactive entity, reproducing the effects of whole mucus. Treatment with this fraction early activates the PERK–ATF4 branch of the UPR, which could be responsible for driving CHAC1 induction. Moreover, ATF4 enhances DDIT3 expression, and activates a compensatory NRF2-dependent antioxidant response. At a later stage mucus also activates the IRE1α–XBP1 axis, with no ATF6 involvement, indicating selective UPR engagement in response to oxidative and lipid stress. Overall, our data are consistent with a potential PERK–ATF4–CHAC1–GSH self-sustaining axis promoting oxidative stress that culminates in cell death, supporting the potential of planarian mucus as a source of pleiotropic bioactive compounds, although the molecular identity of the active component(s) remains still unresolved. Full article
(This article belongs to the Special Issue Breakthroughs in Anti-Cancer Agents Discovery)
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16 pages, 2887 KB  
Article
A GasPak-Based Ischemia Model for Studying ER Stress–Ischemia Interactions in Human Endothelial Cells
by Mathilde Hoareau, Grégorie Lebeau, Luce Muzi, Jérémy Fontaine, Pascale Krejbich-Trotot, Olivier Meilhac, Christine Robert-Da Silva and Wildriss Viranaicken
Methods Protoc. 2026, 9(2), 39; https://doi.org/10.3390/mps9020039 - 4 Mar 2026
Viewed by 569
Abstract
During ischemia, endothelial cell integrity is compromised, as a consequence, blood barrier homeostasis is disrupted. Therefore, the structural and functional preservation of endothelial cells is paramount when trying to improve outcomes after ischemic injury. Endoplasmic reticulum (ER) stress is increasingly recognized as a [...] Read more.
During ischemia, endothelial cell integrity is compromised, as a consequence, blood barrier homeostasis is disrupted. Therefore, the structural and functional preservation of endothelial cells is paramount when trying to improve outcomes after ischemic injury. Endoplasmic reticulum (ER) stress is increasingly recognized as a key player in ischemic injury through unfolded protein response (UPR) signalling, and its crosstalk with mitochondrial death pathways. This study provides a cost-effective and straightforward method to delve into the relationship between ER stress and ischemia in human microvascular endothelial cells-1 (HMEC-1). HMEC-1 was exposed to 8 h of oxygen–glucose deprivation (OGD) in glucose-free medium with rapidly induced hypoxia. Hypoxia, oxygen consumption, cell viability, apoptosis, and ER stress markers (BiP/GRP78, PERK, ATF6, IRE1/XBP1s, CHOP) were assessed by RT-qPCR and Western blot. Cell viability decreased by approximately 33% following OGD, while CHOP expression increased ~4-fold, indicating significant ER stress induction. The model enables quantification of metabolic stress (OCR), as well as evaluation of viability loss, membrane integrity, apoptotic commitment, and discrimination between ER stress resolution versus maladaptation. Overall, GasPak EZ Pouch Systems provide a reproducible and practical in vitro platform to study ischemic injury down to the mechanistic details of ER-mitochondria signalling. They give the opportunity to evaluate therapeutic approaches that target ER homeostasis to limit apoptosis and/or recovery of metabolic function after ischemia. This method could allow rapid screening of ER stress-modulating interventions aimed at preserving endothelial barrier function, in various ischemic contexts. Full article
(This article belongs to the Section Molecular and Cellular Biology)
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19 pages, 7768 KB  
Article
The Evolution Law of Molecular Structure of Vitrain and Durain During Low–Medium Coalification
by Yue Chen, Zan Liu, Huaichang Wang, Changjiang Ji, Liya Wang, Pengpeng Guan, Peilin Wang, Kai Ma and Liyuan Dang
Processes 2026, 14(3), 401; https://doi.org/10.3390/pr14030401 - 23 Jan 2026
Viewed by 433
Abstract
Molecular structural disparities between maceral components are intrinsic factors governing their reactivity and physicochemical behaviors during storage and transportation. To investigate the molecular structural differentiation between vitrain and durain in low- to medium-rank coals (Ro,max = 0.65–1.71%), this study selected samples [...] Read more.
Molecular structural disparities between maceral components are intrinsic factors governing their reactivity and physicochemical behaviors during storage and transportation. To investigate the molecular structural differentiation between vitrain and durain in low- to medium-rank coals (Ro,max = 0.65–1.71%), this study selected samples of long-flame coal and gas coal from the Huanglong Coalfield, coking coal from the Hedong Coalfield, and fat coal from the Weibei Coalfield. The microstructural variations in macroscopic coal components during coalification were analyzed using Fourier transform infrared spectroscopy (FTIR), 13C nuclear magnetic resonance (13C-NMR), and X-ray photoelectron spectroscopy (XPS). The results indicated that the aromatic structures of vitrain are predominantly trisubstituted, with their proportion consistently exceeding that in durain. In contrast, durain exhibits a progressive transition from trisubstituted to pentasubstituted aromatics with increasing coal rank, accompanied by higher aromaticity, condensation degree, and aromatic carbon content. The d002 size of the vitrain decreased from 3.82 to 3.47, while that of the durain decreased from 3.52 to 3.40. Both values showed a gradual decline, with the vitrain exhibiting a larger reduction than the durain. This indicates that the lateral extension of the microcrystalline structure in the durain is more developed, resulting in tighter molecular connections. 13C-NMR analysis further reveals that durain possesses higher falH/fal* and bridge carbon ratios (XBP), along with a lower faS/fa ratio, reflecting a greater degree of aromatic ring condensation. XPS analysis revealed that durain generally contains a higher oxygen-functional group content but lower C-C/C-H content compared to vitrain. Collectively, these findings confirm significant structural divergence between vitrain and durain during coalification, with durain exhibiting more developed aromaticity, structural condensation, and organizational order. Full article
(This article belongs to the Special Issue Phase Behavior Modeling in Unconventional Resources)
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25 pages, 5672 KB  
Article
Euphorbia bicolor Xylene Extract Induces Mitochondrial and Endoplasmic Reticulum Stress-Mediated Apoptotic Pathways in MDA-MB-231 and T47D Cells
by Mafia Mahabub Rumpa, Nguyen Linh Ngo and Camelia Maier
Int. J. Mol. Sci. 2026, 27(2), 962; https://doi.org/10.3390/ijms27020962 - 18 Jan 2026
Viewed by 628
Abstract
Breast cancer is a significant cause of death worldwide. Recent research has focused on identifying natural compounds for developing effective cancer treatments. Resiniferatoxin, a transient receptor potential vanilloid 1 (TRPV1) agonist, is a common diterpene in Euphorbia bicolor Engelm. & A. Gray (Euphorbiaceae), [...] Read more.
Breast cancer is a significant cause of death worldwide. Recent research has focused on identifying natural compounds for developing effective cancer treatments. Resiniferatoxin, a transient receptor potential vanilloid 1 (TRPV1) agonist, is a common diterpene in Euphorbia bicolor Engelm. & A. Gray (Euphorbiaceae), a plant native to the southern United States that has not been studied before. We investigated the antiproliferative activities and mechanisms of action of E. bicolor xylene extract in estrogen receptor-positive T47D and triple-negative MDA-MB-231 cell lines. The extract significantly reduced the viability of T47D and MDA-MB-231 cells in a dose-dependent manner. In MDA-MB-231 cells, the extract induced apoptosis via intracellular calcium overload, triggered by TRPV1 activation. This effect was diminished by the TRPV1 antagonist capsazepine and the calcium chelator BAPTA-AM. Intracellular calcium influx was confirmed through Fura-2 AM staining, revealing that E. bicolor phytochemicals activated TRPV1 in MDA-MB-231 cells. Treatment of T47D cells with E. bicolor xylene extract resulted in apoptosis associated with reactive oxygen species (ROS) generation (10-fold higher in T47D cells than in MDA-MB-231 cells) and mitochondrial calcium overload. These effects were significantly blocked when cells were pretreated with N-acetyl-l-cysteine (NAC), a ROS inhibitor. Both cell lines underwent apoptosis via multiple mitochondrial- and endoplasmic reticulum stress–mediated pathways. This was supported by the activation of caspases 3, 8, and 9; increased expression of FAS, XBP1s, and CHOP; upregulation of BAX; and downregulation of BCL-2. In addition, PI3K, AKT, and pAKT protein expressions were also reduced in both cell lines, indicating downregulation of PI3K/Akt signaling pathway. Phytochemicals in E. bicolor xylene extract could become promising ingredients for developing breast cancer therapeutics. Full article
(This article belongs to the Special Issue The Role of Natural Compounds in Cancer and Inflammation, 2nd Edition)
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18 pages, 5040 KB  
Article
B-Cell Receptor-Associated Protein 31 Deficiency Aggravates Ethanol-Induced Liver Steatosis and Liver Injury via Attenuating Fatty Acid Oxidation and Glycogen Synthesis
by Shubin Yu, Yaodong Xia, Chunyan Zhang, Xiangyue Han, Xiaoyue Feng, Liya Li, Hang Ma and Jialin Xu
Int. J. Mol. Sci. 2025, 26(24), 12173; https://doi.org/10.3390/ijms262412173 - 18 Dec 2025
Cited by 1 | Viewed by 984
Abstract
Alcoholic liver disease (ALD) is a spectrum of alcohol-induced disorders and represents a major global health challenge. B-cell receptor-associated protein 31 (BAP31) is an endoplasmic reticulum-resident chaperone involved in protein transport, apoptosis, cancer biology, and lipid metabolism. To explore its role in ALD, [...] Read more.
Alcoholic liver disease (ALD) is a spectrum of alcohol-induced disorders and represents a major global health challenge. B-cell receptor-associated protein 31 (BAP31) is an endoplasmic reticulum-resident chaperone involved in protein transport, apoptosis, cancer biology, and lipid metabolism. To explore its role in ALD, we used hepatocyte-specific BAP31 knockout mice (BAP31-LKO) and wild-type (WT) littermates exposed to ethanol to assess BAP31′s biochemical and metabolic impact. Following ethanol exposure, BAP31-LKO mice exhibited elevated serum alanine transaminase (23.2%, p < 0.05) and aspartate transaminase (31.4%, p < 0.05) levels compared to WT mice. Increased malondialdehyde (8.5%, p < 0.05) and reduced superoxide dismutase (22.8%, p < 0.05) in BAP31-LKO mice indicate exacerbated liver injury. Furthermore, BAP31 deficiency increased triglyceride (35.7%, p < 0.05) and free fatty acid (16.2%, p < 0.05) accumulation following ethanol treatment, while the expression of fatty acid oxidation-related genes, including Pparα, Cd36, Fatp2, Cpt2, and Acox1, was reduced in BAP31-LKO mice. The mRNA levels of Xbp1, Xbp1s, and Chop, as well as protein levels of p-eIF2α, IRE1α, GRP78, and CHOP, were increased in BAP31-LKO mice compared to WT controls, indicating aggravated ethanol-induced ER stress. Hepatic glycogen content was also reduced in BAP31-LKO mice, along with reduced Ppp1r3c expression, demonstrating impaired glycogen synthesis. Consistently, BAP31 knockdown amplified ethanol-induced lipid accumulation, inflammation, impaired glycogen storage, ER stress, and suppression of Pparα signaling in HepG2 cells. Together, these findings demonstrate that BAP31 deficiency exacerbates ethanol-induced liver steatosis, inflammation, and liver injury by impairing fatty acid oxidation and glycogen synthesis, and by amplifying ER stress responses. Full article
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20 pages, 2290 KB  
Article
Raman-Validated Macromolecular Model of SG Coking Coal: ESP–FMO Mapping Unravels Site-Selective Oxidation in Combustion
by Xiaoxu Gao, Lu Du, Jinzhang Jia, Hao Tian and Xiaoqi Huang
Appl. Sci. 2025, 15(23), 12540; https://doi.org/10.3390/app152312540 - 26 Nov 2025
Viewed by 601
Abstract
Based on comprehensive experimental datasets—proximate/ultimate analyses, XPS, solid-state 13C NMR, and Raman spectroscopy—we constructed and optimized a compositionally faithful macromolecular model of SG coking coal. Using density-functional theory (DFT) calculations, we simulated electrostatic-potential (ESP) fields and frontier molecular orbitals (FMO) to probe [...] Read more.
Based on comprehensive experimental datasets—proximate/ultimate analyses, XPS, solid-state 13C NMR, and Raman spectroscopy—we constructed and optimized a compositionally faithful macromolecular model of SG coking coal. Using density-functional theory (DFT) calculations, we simulated electrostatic-potential (ESP) fields and frontier molecular orbitals (FMO) to probe elementary oxidation steps relevant to combustion, and focused on how heteroatom speciation and carbon ordering govern site-selective reactivity. Employing multi-peak deconvolution and parameter synthesis, we obtained an aromatic fraction fa = 76.56%, a bridgehead-to-periphery ratio XBP = 0.215, and Raman indices ID1/IG ≈ 1.45 (area) with FWHM(G) ≈ 86.7 cm−1; the model composition C190H144N2O21S and its predicted 13C NMR envelope validated the structural assignment against experiment. ESP–FMO synergy revealed electron-rich hotspots at phenolic/ether/carboxyl and thiophenic domains and electron-poor belts at H-terminated edges/aliphatic bridges, rationalizing carbon-end oxidation of CO, weak electrostatic steering by O2/CO2, and a benzylic H-abstraction → edge addition → O-insertion/charge-transfer sequence toward CO2/H2O, with thiophenic sulfur comparatively robust. We quantified surface functionalities (C–O 65.46%, O–C=O 24.51%, C=O 10.03%; pyrrolic/pyridinic N dominant; thiophenic-S with minor oxidized S) and determined a naphthalene-dominant, stacked-polyaromatic architecture with sparse alkyl side chains after Materials Studio optimization. The findings are significant for mechanistic understanding and control of coking-coal oxidation, providing actionable hotspots and a reproducible workflow (multi-probe constraints → model building/optimization → DFT reactivity mapping → spectral back-validation) for blend design and targeted oxidation-inhibition strategies. Full article
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28 pages, 7715 KB  
Article
Functional pH-Responsive Nanoparticles for Immune Reprogramming in MSS Colorectal Cancer via ER Stress-Induced Proteostasis Disruption, PD-L1-Targeting miRNA, and TLR7 Activation
by Yu-Li Lo, Hua-Ching Lin, Ching-Yao Li, Bryant Huang, Ching-Ping Yang, Hui-Yen Chuang and Tsui-Fen Chou
Pharmaceutics 2025, 17(11), 1503; https://doi.org/10.3390/pharmaceutics17111503 - 20 Nov 2025
Cited by 1 | Viewed by 1588
Abstract
Background: Colorectal cancer (CRC), particularly the microsatellite-stable (MSS) subtype, remains largely unresponsive to immune checkpoint inhibitors (ICIs) due to immune escape, tumor-associated macrophage (TAM) enrichment, and cytokine-driven suppression that sustain a TAM-dominant tumor microenvironment (TME). To overcome these barriers, a pH-responsive solid lipid [...] Read more.
Background: Colorectal cancer (CRC), particularly the microsatellite-stable (MSS) subtype, remains largely unresponsive to immune checkpoint inhibitors (ICIs) due to immune escape, tumor-associated macrophage (TAM) enrichment, and cytokine-driven suppression that sustain a TAM-dominant tumor microenvironment (TME). To overcome these barriers, a pH-responsive solid lipid nanoparticle (SLN) system was engineered to co-deliver CB-5083 (a VCP/p97 inhibitor), miR-142 (a PD-L1-targeting microRNA), and imiquimod (R, a TLR7 agonist) for spatially confined induction of endoplasmic reticulum stress (ERS) and immune reprogramming in MSS CRC. Methods: The SLNs were coated with PEG–PGA for pH-triggered de-shielding and functionalized with PD-L1- and EGFR-binding peptides plus an ER-homing peptide, enabling tumor-selective and subcellular targeting. Results: The nanoplatform displayed acid-triggered PEG–PGA detachment, selective CRC/TAM uptake, and ER localization. CB-mediated VCP inhibition activated IRE1α/XBP1s/LC3II, PERK/eIF2α/ATF4/CHOP, and JNK/Beclin signaling, driving apoptosis and autophagy, while miR-142 suppressed PD-L1 expression and epithelial–mesenchymal transition markers. R facilitated dendritic cell maturation and M1 polarization. Combined CB + miR + R/SLN-CSW suppressed IL-17, G-CSF, and CXCL1, increased infiltration of CD4+ and CD8+ T cells, reduced Tregs and M2-TAMs, and inhibited tumor growth in CT-26 bearing mice. The treatment induced immunogenic cell death, reprogramming the TME into a T cell-permissive state and conferring resistance to tumor rechallenge. Biodistribution analysis confirmed tumor-preferential accumulation with minimal off-target exposure, and biosafety profiling demonstrated low systemic toxicity. Conclusions: This TME-responsive nanoplatform therefore integrates ERS induction, checkpoint modulation, and cytokine suppression to overcome immune exclusion in MSS CRC, representing a clinically translatable strategy for chemo-immunotherapy in immune-refractory tumors. Full article
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19 pages, 3069 KB  
Article
Cyclophilin Inhibitor Rencofilstat Combined with Proteasome Inhibitor Ixazomib Increases Proteotoxic Cell Death in Advanced Prostate Cancer Cells with Minimal Effects on Non-Cancer Cells
by Carlos Perez-Stable, Alicia de las Pozas, Medhi Wangpaichitr, Robert T. Foster and Daren R. Ure
Biomedicines 2025, 13(10), 2442; https://doi.org/10.3390/biomedicines13102442 - 7 Oct 2025
Viewed by 1514
Abstract
Background/Objective: Proteotoxic stress induced by inhibitors of the ubiquitin–proteasome system has been successful in multiple myeloma but not in solid cancers such as prostate cancer. Our objective is to find a combination with proteasome inhibitors that increases apoptotic cell death in all types [...] Read more.
Background/Objective: Proteotoxic stress induced by inhibitors of the ubiquitin–proteasome system has been successful in multiple myeloma but not in solid cancers such as prostate cancer. Our objective is to find a combination with proteasome inhibitors that increases apoptotic cell death in all types of prostate cancer without harming non-cancer cells. Methods: The effectiveness of rencofilstat, a pan-cyclophilin inhibitor, combined with the ixazomib proteasome inhibitor, was investigated in multiple prostate cancer and non-cancer cells. Inducible knockdown of stress response XBP1s and cyclophilins A/B and inducible expression of XBP1s and cyclophilin B were developed in prostate cancer to determine functional roles. Results: Rencofilstat + ixazomib increased apoptotic cell death in prostate cancer but not in non-cancer cells. We investigated the effects on XBP1s and PERK, important unfolded protein response factors required for cells to survive proteotoxic stress. The results revealed that XBP1s had a pro-survival role early, but maintenance at later times of rencofilstat + ixazomib treatment resulted in cell death. In addition, decreased PERK and phospho-eIF2α likely maintained protein synthesis to further enhance proteotoxic stress. In contrast, rencofilstat + ixazomib did not alter XBP1s or PERK in non-cancer cells. Additional genetic experiments showed that the RCF targets cyclophilins A, B, and D had protective effects. Rencofilstat increased extracellular secretion of cyclophilin B, but rencofilstat + ixazomib reduced glycosylation and, likely, the biological function of CD147 (CypB receptor) and decreased downstream ERK signaling. Conclusions: Rencofilstat + ixazomib may be a new strategy for increasing proteotoxic stress and apoptotic cell death in advanced prostate cancer cells with less toxic side effects. Full article
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22 pages, 7591 KB  
Article
Exercise-Induced Changes in Enterohepatic Communication Are Linked to Liver Steatosis Resolution
by Yong Zou, Jie Xia, Sen Zhang, Yingjie Guo, Weina Liu and Zhengtang Qi
Nutrients 2025, 17(18), 2962; https://doi.org/10.3390/nu17182962 - 15 Sep 2025
Cited by 1 | Viewed by 1588
Abstract
Background/Objectives: This study aimed to investigate the effects of long-term aerobic exercise on high-fat diet (HFD)-induced hepatic steatosis and its underlying enterohepatic communication mechanisms. Methods: C57BL/6J mice were divided into four groups: normal-diet with sedentary (ND-SED), normal-diet with exercise (ND-EXE), HFD [...] Read more.
Background/Objectives: This study aimed to investigate the effects of long-term aerobic exercise on high-fat diet (HFD)-induced hepatic steatosis and its underlying enterohepatic communication mechanisms. Methods: C57BL/6J mice were divided into four groups: normal-diet with sedentary (ND-SED), normal-diet with exercise (ND-EXE), HFD with sedentary (HFD-SED), and HFD with exercise (HFD-EXE). After 16 weeks of HFD feeding, ND-EXE and HFD-EXE groups underwent an 8-week aerobic exercise intervention. Hepatic lipid accumulation was assessed via histology and triglyceride (TG) quantification. Liver function and glucose tolerance were evaluated. Gut microbiota composition (16S rRNA sequencing), hepatic bile acid profiles (LC-MS metabolomics), and gene expression were analyzed. Results: HFD induced hepatic steatosis, glucose intolerance, and liver injury in mice, all of which were ameliorated by exercise. Compared to HFD-SED mice, which exhibited impaired gut microbiota diversity, exercise restored key genera such as Faecalibaculum, and Turicibacter. Functional analysis revealed that exercise modulated microbiota shifts in lipid metabolism and secondary bile acid biosynthesis. HFD-EXE mice displayed altered hepatic bile acid composition, characterized by increased tauroursodeoxycholic acid (TUDCA) and reduced taurohyodeoxycholic acid (THDCA). Notably, TUDCA levels correlated with Turicibacter abundance, while deoxycholic acid (DCA) was associated with Faecalibaculum, independent of precursor availability. Exercise also suppressed hepatic endoplasmic reticulum (ER) stress and downregulated lipogenic genes via the inositol-requiring enzyme 1 alpha (IRE1α)- spliced X-box binding protein 1 (Xbp1s) pathway, while concurrently activating farnesoid X receptor (FXR) signaling to enhance fatty acid oxidation through the FXR-short heterodimer partner (SHP) related to hepatic secondary bile acid abundance change. Conclusions: The beneficial effect of long-term aerobic exercise on high-fat diet-induced hepatic steatosis in mice is potentially mediated through structural changes in the gut microbiota, which influence the abundance of hepatic secondary bile acids (TUDCA, DCA) and subsequently regulate the expression of genes involved in lipid metabolism. Full article
(This article belongs to the Special Issue Effects of Exercise and Diet on Health)
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22 pages, 5853 KB  
Article
Generating a Cell Model to Study ER Stress in iPSC-Derived Medium Spiny Neurons from a Patient with Huntington’s Disease
by Vladlena S. Makeeva, Anton Yu. Sivkov, Suren M. Zakian and Anastasia A. Malakhova
Int. J. Mol. Sci. 2025, 26(18), 8930; https://doi.org/10.3390/ijms26188930 - 13 Sep 2025
Viewed by 1673
Abstract
iPSCs and their derivatives are used to investigate the molecular genetic mechanisms of human diseases, to identify therapeutic targets, and to screen for small molecules. Combining technologies for generating patient-specific iPSC lines and genome editing allows us to create cell models with unique [...] Read more.
iPSCs and their derivatives are used to investigate the molecular genetic mechanisms of human diseases, to identify therapeutic targets, and to screen for small molecules. Combining technologies for generating patient-specific iPSC lines and genome editing allows us to create cell models with unique characteristics. We obtained and characterized three iPSC lines by reprogramming peripheral blood mononuclear cells of a patient with Huntington’s disease (HD) using episomal vectors encoding Yamanaka factors. iPSC lines expressed pluripotency marker genes, had normal karyotypes and were capable of differentiating into all three germ layers. The obtained iPSC lines are useful for modeling disease progression in vitro and studying pathological mechanisms of HD, such as ER stress. A transgene of genetically encoded biosensor XBP1-TagRFP was introduced into the iPSCs to visualize ER stress state of cells. The study demonstrated that iPSC-derived medium spiny neurons develop ER stress, though the IRE1-mediated pathway does not seem to be involved in the process. Full article
(This article belongs to the Section Molecular Neurobiology)
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30 pages, 4541 KB  
Article
Role of Endoplasmic Reticulum Stress-Associated Genes in Septic Neonatal Foals
by Dipak Kumar Sahoo, David Wong, Biswaranjan Paital, Rebecca E. Ruby and Ashish Patel
Antioxidants 2025, 14(8), 1024; https://doi.org/10.3390/antiox14081024 - 21 Aug 2025
Cited by 4 | Viewed by 2604
Abstract
The progression of inflammation during sepsis represents a multifaceted biological cascade that requires effective therapeutic interventions to improve survival. In septic neonatal foals, oxidative stress (OS) arises due to a compromised antioxidant defense system. Oxidative stress may disrupt the functionality of redox-sensitive organelles, [...] Read more.
The progression of inflammation during sepsis represents a multifaceted biological cascade that requires effective therapeutic interventions to improve survival. In septic neonatal foals, oxidative stress (OS) arises due to a compromised antioxidant defense system. Oxidative stress may disrupt the functionality of redox-sensitive organelles, such as the endoplasmic reticulum (ER). Endoplasmic reticulum stress disorder affects multiple cellular signaling pathways, including redox balance, inflammation, and apoptosis, and contributes to the pathogenesis of sepsis. The study aimed to elucidate whether OS conditions in sepsis influenced gene expression associated with ER stress. Blood samples were collected from 7 healthy and 21 hospitalized neonatal foals and processed for RNA extraction. RNA sequencing was employed to identify ER stress-responsive genes. Novel findings reported here indicate activation of the ER stress pathway in foals with sepsis. Several genes associated with ER stress, such as clusterin (CLU), BCL2-like 1 (BCL2L1), ubiquitin specific peptidase 14 (USP14), bifunctional apoptosis regulator (BFAR), and optic atrophy 1 (OPA1), were upregulated and positively correlated with sepsis scores and negatively correlated with the combined activities of antioxidant enzymes. In contrast, X-box binding protein 1 (XBP1), homocysteine inducible ER protein with ubiquitin-like domain 1 (HERPUD1), leucine-rich repeat kinase 2 (LRRK2), and selenoprotein S (SELENOS) were negatively correlated with sepsis scores and were downregulated in sepsis and positively correlated with the combined activities of antioxidant enzymes. Furthermore, a positive correlation was observed between cAMP responsive element binding protein 3 like 2 (CREB3L2) and BCL2L1, as well as between the expressions of USP14 and YOD1 deubiquitinase (YOD1) in sepsis. Similarly, the expression levels of XBP1 and Herpud1 demonstrated a positive correlation with each other in sepsis. Additionally, the downregulation of genes with protective function against OS, such as XBP1, HERPUD1, and SELENOS, in septic foals also highlights their significance in mitigating OS in sepsis treatment. The study reported here highlights the potential of ER stress as a promising therapeutic target and prognostic marker in septic foals. Full article
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17 pages, 12102 KB  
Article
Multiomics Integration of Parkinson’s Disease Datasets Reveals Unexpected Roles of IRE1 in Its Pathology
by Bianka Alexandra Pasat, Matthieu Moncan, Eleftherios Pilalis, Afshin Samali, Aristotelis Chatziioannou and Adrienne M. Gorman
Int. J. Mol. Sci. 2025, 26(14), 6711; https://doi.org/10.3390/ijms26146711 - 12 Jul 2025
Viewed by 1796
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease. It primarily affects the motor system but is also associated with a range of cognitive impairments that can manifest early in disease progression, indicating its multifaceted nature. In this paper, we performed a [...] Read more.
Parkinson’s disease (PD) is the second most common neurodegenerative disease. It primarily affects the motor system but is also associated with a range of cognitive impairments that can manifest early in disease progression, indicating its multifaceted nature. In this paper, we performed a meta-analysis of transcriptomics and proteomics data using MultiOmicsIntegrator to gain insights into the post-transcriptional modifications and deregulated pathways associated with this disease. Our results reveal differential isoform usage between control and PD patient brain samples that result in enriched alternative splicing events, including an extended UTR length, domain loss, and the upregulation of non-coding isoforms. We found that Inositol-Requiring Enzyme 1 (IRE1) is active in PD samples and examined the role of its downstream signaling through X-box binding mRNA 1 (XBP1) and regulated IRE1-dependent decay (RIDD). We identified several RIDD candidates and showed that the enriched alternative splicing events observed are associated with RIDD. Moreover, in vitro mRNA cleavage assays demonstrated that OSBPL3, C16orf74, and SLC6A1 mRNAs are targets of IRE1 RNAse activity. Finally, a pathway enrichment analysis of both XBP1s and RIDD targets in the PD samples uncovered associations with processes such as immune response, oxidative stress, signal transduction, and cell–cell communication that have previously been linked to PD. These findings highlight a potential regulatory role of IRE in PD. Full article
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18 pages, 3134 KB  
Article
A Novel Chemotherapy Combination to Enhance Proteotoxic Cell Death in Hepatocellular Carcinoma Experimental Models Without Killing Non-Cancer Cells
by Carlos Perez-Stable, Alicia de las Pozas, Teresita Reiner, Jose Gomez, Manojavan Nagarajan, Robert T. Foster, Daren R. Ure and Medhi Wangpaichitr
Int. J. Mol. Sci. 2025, 26(14), 6699; https://doi.org/10.3390/ijms26146699 - 12 Jul 2025
Cited by 1 | Viewed by 1774
Abstract
Inhibitors of the ubiquitin–proteasome system increase proteotoxic stress and have achieved clinical success for multiple myeloma but not for solid cancers such as hepatocellular carcinoma. Our objective is to identify a combination with proteasome inhibitors that enhances proteotoxic stress and apoptotic cell death [...] Read more.
Inhibitors of the ubiquitin–proteasome system increase proteotoxic stress and have achieved clinical success for multiple myeloma but not for solid cancers such as hepatocellular carcinoma. Our objective is to identify a combination with proteasome inhibitors that enhances proteotoxic stress and apoptotic cell death in hepatocellular carcinoma but with less toxicity to non-cancer cells. We found that rencofilstat, a pan-cyclophilin inhibitor, combined with ixazomib, a proteasome inhibitor, increased apoptotic cell death in hepatocellular carcinoma but not in umbilical vein or dermal fibroblast non-cancer cells. We then analyzed the effects of rencofilstat + ixazomib on XBP1s and PERK, critical factors in the unfolded protein response used by cells to survive proteotoxic stress. Rencofilstat + ixazomib maintained higher expression of XBP1s and genetic models suggested that XBP1s was a pro-survival protein early and pro-death protein at later times. Simultaneously, decreased PERK expression prevented the block in protein synthesis via phospho-eIF2α and likely further amplified proteotoxic stress. Rencofilstat + ixazomib did not have effects on XBP1s or PERK in non-cancer cells. Further genetic experiments revealed the pro-survival roles for cyclophilin A and B in mediating rencofilstat + ixazomib-induced cell death. In the Hep3B xenograft model, rencofilstat + ixazomib significantly inhibited tumor volumes/weights without general toxicity. We conclude that rencofilstat + ixazomib amplified proteotoxic stress in hepatocellular carcinoma past a threshold pro-survival pathways could not tolerate, whereas non-cancer cells were less affected. Full article
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19 pages, 5609 KB  
Article
Effects of Chronic Low-Salinity Stress on Growth, Survival, Antioxidant Capacity, and Gene Expression in Mizuhopecten yessoensis
by Haoran Xiao, Xin Jin, Zitong Wang, Qi Ye, Weiyan Li, Lingshu Han and Jun Ding
Biology 2025, 14(7), 759; https://doi.org/10.3390/biology14070759 - 25 Jun 2025
Cited by 3 | Viewed by 1429
Abstract
Extreme weather events such as heavy rainfall significantly reduce surface salinity in coastal waters, presenting considerable challenges to the aquaculture of Japanese scallops (Mizuhopecten yessoensis) in shallow cage systems. This study investigated the effects of chronic low-salinity stress on the growth [...] Read more.
Extreme weather events such as heavy rainfall significantly reduce surface salinity in coastal waters, presenting considerable challenges to the aquaculture of Japanese scallops (Mizuhopecten yessoensis) in shallow cage systems. This study investigated the effects of chronic low-salinity stress on the growth performance, antioxidant capacity, and gene expression profile of M. yessoensis using a 60-day salinity gradient experiment. S33 represents the control treatment with normal seawater salinity (33‰), while S30, S28, and S26 represent experimental groups with progressively lower salinities of 30‰, 28‰, and 26‰, respectively. A decline in salinity was accompanied by an increase in oxygen consumption. The S26 group exhibited a higher ammonia excretion rate (2.73 μg/g·h) than other groups, indicating intensified nitrogen metabolism. Growth was inhibited under low-salinity conditions. The S33 group exhibited greater weight gain (16.7%) and shell growth (8.4%) compared to the S26 group (11.6% and 6%), which also showed a substantially higher mortality rate (46%) compared to the control (13%). At 28‰, antioxidant enzyme activities (T-AOC, SOD, CAT, POD) were elevated, indicating a moderate level of stress. However, at the lowest salinity (26‰), these indicators decreased, reflecting the exhaustion of the antioxidant systems and indicating that the mollusks’ adaptive capacity had been exceeded, leading to a state of stress fatigue. NAD-MDH activity was elevated in the S26 group, reflecting enhanced aerobic metabolism under stress. Transcriptome analysis revealed 564 differentially expressed genes (DEGs) between the S33 and S26 groups. Functional enrichment analysis indicated that these DEGs were mainly associated with immune and stress response pathways, including NF-κB, TNF, apoptosis, and Toll/Imd signaling. These genes are involved in key metabolic processes, such as alanine, aspartate, and glutamate metabolism. Genes such as GADD45, ATF4, TRAF3, and XBP1 were upregulated, contributing to stress repair and antioxidant responses. Conversely, the expressions of CASP3, IKBKA, BIRC2/3, and LBP were downregulated, potentially mitigating apoptosis and inflammatory responses. These findings suggest that M. yessoensis adapts to chronic low-salinity stress through the activation of antioxidant systems, modulation of immune responses, and suppression of excessive apoptosis. This study provides new insights into the molecular mechanisms underlying salinity adaptation in bivalves and offers valuable references for scallop aquaculture and selective breeding programs. Full article
(This article belongs to the Special Issue Metabolic and Stress Responses in Aquatic Animals)
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Article
Deficits of Alzheimer’s Disease Neuropsychological Architecture Correlate with Specific Exosomal mRNA Expression: Evidence of a Continuum?
by Ernesto Barceló, María I. Mosquera-Heredia, Oscar M. Vidal, Daniel A. Bolívar, Ricardo Allegri, Luis C. Morales, Carlos Silvera-Redondo, Mauricio Arcos-Burgos, Pilar Garavito-Galofre and Jorge I. Vélez
Int. J. Mol. Sci. 2025, 26(10), 4897; https://doi.org/10.3390/ijms26104897 - 20 May 2025
Viewed by 1831
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by cognitive decline and complex molecular changes. Extracellular vesicles (EVs), particularly exosomes, play a key role in intercellular communication and disease progression, transporting proteins, lipids, and nucleic acids. While altered exosomal mRNA profiles have emerged [...] Read more.
Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by cognitive decline and complex molecular changes. Extracellular vesicles (EVs), particularly exosomes, play a key role in intercellular communication and disease progression, transporting proteins, lipids, and nucleic acids. While altered exosomal mRNA profiles have emerged as potential biomarkers for AD, the relationship between mRNA expression and AD neuropsychological deficits remains unclear. Here, we investigated the correlation between exosomx10-derived mRNA signatures and neuropsychological performance in a cohort from Barranquilla, Colombia. Expression profiles of 16,585 mRNAs in 15 AD patients and 15 healthy controls were analysed using Generalized Linear Models (GLMs) and the Predictive Power Score (PPS). We identified significant correlations between specific mRNA signatures and key neuropsychological variables, including the Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), Functional Assessment Screening Tool (FAST), Boston Naming Test, and Rey–Osterrieth Figure test. These mRNAs were in key AD-associated genes (i.e., GABRB3 and CADM1), while other genes are novel (i.e., SHROOM3, SLC7A2, GJB4, and XBP1). PPS analyses further revealed predictive relationships between mRNA expression and neuropsychological variables, accounting for non-linear patterns and asymmetric associations. If replicated in more extensive and heterogeneous studies, these findings provide critical insights into the molecular basis governing the natural history of AD, potential personalized and non-invasive diagnosis, prognosis, follow-up, and potential targets for future therapies. Full article
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