bims-unfpre 2026-07-05 papers

bims-unfpre

Biomed News

on Unfolded protein response

Issue of 2026–07–05
thirteen papers selected by
Susan Logue, University of Manitoba

ER stress amplifies inflammation via a dual mechanism involving IκBζ-XBP1s synergism and Regnase-1 degradation.
Palmitate drives mitochondrial and ER stress through disruption of the CD73-Adenosine axis.
Single-nuclei UPR profiling by flow cytometry reveals bortezomib resistance mechanisms in multiple myeloma.
ER stress-mediated impairment of hepatic lipid export is associated with steatosis in AKI-induced remote liver injury.
ER sensing of lipid metabolism drives PRA family-dependent regulation of COPII vesicle transport.
Proteostasis and unfolded protein response dynamics in human neuron/mouse glia co-cultures reveal a cell-specific maturation response.
Decoding cellular stress states for toxicology using single-cell transcriptomics.
GRP78 in human diseases: From molecular chaperone to therapeutic target.
Die hard: when cells refuse apoptosis-the rise of paraptosis and other death pathways.
Loss of Echs1 in neural stem and progenitor cells impairs neurogenesis via ER stress activation and lipid metabolic reprogramming.
Expression of circulating GRP78 and gp96, endoplasmic reticulum stress-related proteins, in menstrual and bladder pain sensitivity.
Integrating machine learning and structure-based simulations to prioritise Z4P as a mutation-resilient IRE1α inhibitor for breast cancer.
AARS1 promotes tumor progression and immune evasion via ATF6 lactylation-mediated tryptophan metabolism in hepatocellular carcinoma.

J Immunol. 2026 Jun 07. pii: vkag151. [Epub ahead of print]215(6):

ER stress amplifies inflammation via a dual mechanism involving IκBζ-XBP1s synergism and Regnase-1 degradation.

Yuri Nakaminami, Lerdluck Ruengsinpinya, Riko Sakihara, Yoshifumi Takahata, Kenji Hata, Takao Iwawaki, Riko Nishimura, Tomohiko Murakami.

  Inflammatory diseases arise from complex interactions between immune signaling and cellular stress. Although endoplasmic reticulum (ER) stress is a key modulator of immunity, the mechanisms by which it promotes inflammatory pathology remain incompletely understood. Notably, ER stress-induced NF-κB activation alone is insufficient to account for robust IL-6 production, thus suggesting the involvement of additional regulators. Using bone marrow-derived macrophages and sepsis model mice, we identified the inducible transcription factor IκBζ as a critical mediator of this response, with ER stress synergizing with TLR signaling to markedly upregulate IκBζ. Mechanistically, ER stress triggered calcium-dependent signaling that led to IκB kinase-mediated degradation of the RNase Regnase-1, likely stabilizing Nfkbiz mRNA and promoting the accumulation of IκBζ, which was found to cooperate with the ER stress factor XBP1s to drive transcription of selected secondary-response genes, particularly Il6 and Nos2. Importantly, this synergy was required for excessive IL-6 production in septic mice, highlighting a gene-specific amplification pathway. Together, these findings identify a dual mechanism in which transcriptional synergy between IκBζ and XBP1s is coupled to posttranscriptional mRNA stabilization via Regnase-1 degradation, thereby linking proteotoxic stress to hyperinflammatory responses. Our results establish ER stress-mediated IκBζ accumulation as a key driver of inflammatory pathogenesis and a potential therapeutic target in ER stress-associated inflammatory disorders.

Keywords:  ER stress; IκBζ; Regnase-1; XBP1; inflammation

DOI:  https://doi.org/10.1093/jimmun/vkag151
Res Sq. 2026 Jun 15. pii: rs.3.rs-9902042. [Epub ahead of print]

Palmitate drives mitochondrial and ER stress through disruption of the CD73-Adenosine axis.

Shantiece Dawson, Sonia Batan, Nina Adams, Sergei Bombin, Erivan S Ramos-Junior, Ana Carolina Morandini.

Background Metabolic disorders associated with elevated saturated fatty acids are linked to chronic inflammatory diseases, including periodontitis, yet the mechanisms connecting lipotoxic stress to gingival inflammation remain unclear. This study investigated how palmitate-induced metabolic stress affects purinergic signaling, mitochondrial function, and endoplasmic reticulum (ER) stress in murine gingival fibroblasts (mGF), and whether adenosine modulates these effects. Methods mGF were treated with BSA control, palmitate, IL-1β, or palmitate plus IL-1β, followed by bulk RNA sequencing, Seahorse metabolic analysis, biochemical assays, and transmission electron microscopy. Results Palmitate suppressed expression of key adenosine-generating ectoenzymes and purinergic signaling genes, including Cd73 (Nt5e), Cd39 (Entpd1), Adk, Ada, and adenosine receptors. Concurrently, palmitate amplified IL-1β-induced inflammatory mediators such as Cxcl1, Cxcl2, Cxcl5, Ccl2, and Il6. Gene ontology analysis demonstrated enrichment of pathways related to innate immune activation, oxidative stress, mitochondrial dysfunction, ER stress, and purine metabolism. Palmitate also induced intracellular lipid accumulation and mitochondrial dysfunction, evidenced by reduced NAD+/NADH ratio, increased mitochondrial reactive oxygen species (ROS), elevated protein oxidation, and increased proton leak despite enhanced electron transport chain protein expression. Ultrastructural analyses revealed swollen mitochondria, ER expansion, and increased ER-mitochondrial associations. Mechanistically, palmitate activated the Perk-eIF2α-Atf4 ER stress pathway, increasing phosphorylation of Perk and eIF2α and elevating Atf4 expression. Extracellular adenosine attenuated mitochondrial ROS accumulation, reversed Perk and Atf4 activation, improved mitochondrial respiration, and preserved ER and mitochondrial ultrastructure. Conclusions Palmitate disrupts the Cd73-adenosine axis while promoting mitochondrial dysfunction, oxidative stress, and Perk-mediated ER stress in gingival fibroblasts. Adenosine signaling protects against lipotoxic-induced ER stress, highlighting the Cd73-adenosine pathway as a potential therapeutic target in metabolically driven periodontal inflammation.

DOI: https://doi.org/10.21203/rs.3.rs-9902042/v1
EMBO Mol Med. 2026 Jun 29.

Single-nuclei UPR profiling by flow cytometry reveals bortezomib resistance mechanisms in multiple myeloma.

Julien P Gigan, Paulina Garcia-Gonzalez, Angelo Pilotti, Lou Galliot, Alexandre Reynaud, Yoan Ghaffar, Felipe Flores-Santibáñez, Sara Ghafoori, Eve Seillier, Rosario Lavignolle-Heguy, Daniela Barros, Caroline Bret, Sharon Fichaux, Alexis Combes, Alessandro Bani, Rejane Rua, Evelina Gatti, Béatrice Nal-Rogier, Stéphane Rocchi, Jérôme Moreaux, Philippe Pierre, Rafael J Argüello.

The unfolded protein response (UPR) is a stress-adaptation pathway and therapeutic target in cancer, yet its pro-survival versus pro-death outcome is difficult to predict because the three ER sensors, PERK, IRE1α, and ATF6, are highly interconnected. Transcriptomic analyses identified sensor-specific gene signatures associated with patient survival across malignancies, and indicated that low IRE1α activity (low XBP1 signature or higher expression of RIDD targets) correlates with improved outcome. We developed SNUPR (single nuclei analysis of the unfolded protein response), an accessible flow cytometry approach that profiles all three branches in nuclear suspensions. SNUPR reveals marked heterogeneity of UPR activation across cancer cell lines that cannot be inferred from sensor expression. This heterogeneity is derived from differences in the strength and duration of PERK-mediated translational inhibition, which gates downstream translation-dependent IRE1α and ATF6 transcriptional programs. Finally, in multiple myeloma, we show that bortezomib-tolerant cells depend on IRE1α activity for survival, linking UPR state to proteasome-inhibitor resistance and positioning SNUPR to guide branch-selective targeting.

DOI: https://doi.org/10.1038/s44321-026-00469-7
Sci Rep. 2026 Jun 29.

ER stress-mediated impairment of hepatic lipid export is associated with steatosis in AKI-induced remote liver injury.

Minghua Li, Runze Ni, Kristof Williams, Miriame Melaika, Lucas Eli Sun, Liying Fu, Vijay Subramanian, Kiran Dhanireddy, Ruisheng Liu.

  Acute kidney injury (AKI) frequently causes remote organ injury including hepatic steatosis, yet whether lipid accumulation reflects increased synthesis or impaired clearance has not been resolved. We used a murine ischemia-reperfusion AKI model. Unbiased liver proteomics was performed at 24 h after reperfusion, and dysregulated pathways were identified by Gene Set Enrichment Analysis. Results were validated by Western blotting, qPCR, and immunohistochemistry. These findings were complemented by retrospective analysis of two intensive care unit (ICU) databases (the Medical Information Mart for Intensive Care IV [MIMIC-IV] and the eICU Collaborative Research Database [eICU-CRD]). AKI significantly increased serum ALT and AST and induced hepatic lipid accumulation. Proteomic analysis revealed that key lipogenic enzymes (SCD1, FASN, ACLY, ACACA) were uniformly suppressed rather than upregulated. ApoB and MTTP, proteins essential for very-low-density lipoprotein (VLDL) assembly, were significantly downregulated, while ApoE showed a concordant downward trend (adjusted p = 0.072). Plasma triglycerides were decreased while liver triglycerides were increased, consistent with impaired hepatic lipid export. As in renal tubular cells, AKI also disrupted ER protein folding homeostasis in the liver, triggering ER stress. This was evidenced by upregulated levels of the ER chaperone GRP78, increased XBP1 splicing indicative of UPR activation, and elevated expression of the ER stress-induced pro-apoptotic transcription factor CHOP, suggesting that prolonged ER stress may also promote hepatocyte cell death. TLR4/MyD88 signaling was activated, yet inflammatory cytokines were paradoxically reduced, accompanied by Kupffer cell depletion (decreased F4/80) and monocyte infiltration (increased CD68). In 6,996 propensity-matched ICU patients (MIMIC-IV), AKI independently increased the risk of clinically significant liver injury 4-fold (adjusted OR = 4.41). Analysis of 22,727 patients across 208 hospitals (eICU-CRD) identified a lipid dissociation pattern: elevated triglycerides alongside decreased total cholesterol, HDL, and LDL, with dose-dependent scaling across KDIGO stages. These data are consistent with ER stress-associated impairment of VLDL export contributing to AKI-induced hepatic steatosis. Clinical cohort analyses across two independent ICU databases identify a dual metabolic insult: enhanced peripheral lipid delivery compounds impaired hepatic export, amplifying hepatic lipid retention. ER stress and lipid export machinery represent potential therapeutic targets for AKI-associated liver injury.

Keywords:  AKI; Clinical association; ER stress; Hepatic steatosis; Lipid dissociation; Remote organ injury; VLDL secretion

DOI:  https://doi.org/10.1038/s41598-026-59445-3
Nat Commun. 2026 Jul 03.

ER sensing of lipid metabolism drives PRA family-dependent regulation of COPII vesicle transport.

Kazuki Hanaoka, Mitsuki Nakazato, Philipp Schlarmann, Hiroki Nakamura, Mei Kato, Ryoko Ikema, Mizuki Iguchi, Katsuki Eto, Takefumi Karashima, Atsuko Ikeda, Yukari Yabuki, Javier Manzano-Lopez, Auxiliadora Aguilera-Romero, Susana Sabido-Bozo, Ana Maria Perez-Linero, Muneyoshi Kanai, Haruyuki Iefuji, Isabelle Riezman, Howard Riezman, Manuel Muñiz, Kouichi Funato.

Newly synthesized secretory proteins and lipids are transported from the endoplasmic reticulum (ER) to the Golgi prior to their ultimate destinations, which is tightly regulated during adaptation to environmental stress. However, regulatory pathways governing the formation of COPII vesicles budded from the ER remain insufficiently explored. Here, we present evidence indicating that COPII-mediated vesicle transport is transcriptionally controlled through the phosphatidic acid (PA)-dependent Opi1-Ino2/Ino4 regulatory circuit. Our analysis shows that YIP3, a target gene of Ino2/Ino4, exerts a negative regulatory impact on COPII-mediated vesicle transport. We demonstrate that Ino2/Ino4, but not Yip3 modulates Sar1 activation, the initial step in COPII vesicle formation, whereas Yip3 hinders Sec16 assembly on the ER membrane, thereby implying that Ino2/Ino4 governs COPII vesicle formation at multiple steps. Finally, we show that under ER stress conditions which are accompanied by elevated PA, vesicular transport is restricted in a PA and Yip3-dependent manner. Thus, this study provides the first evidence for an ER sensing system that transcriptionally fine-tunes vesicle formation in response to alterations in lipid composition of the ER membrane during ER stress.

DOI: https://doi.org/10.1038/s41467-026-75057-x
Proc Natl Acad Sci U S A. 2026 Jul 07. 123(27): e2521663123

Proteostasis and unfolded protein response dynamics in human neuron/mouse glia co-cultures reveal a cell-specific maturation response.

Lea A Barny, Sarah K Garcia, Aiden J Houcek, Burak Uzay, Minsoo Kim, Ege T Kavalali, Lars Plate.

  Proteostasis, or protein homeostasis, is a tightly regulated network of cellular pathways essential for maintaining proper protein folding, trafficking, and degradation. Neurons are particularly vulnerable to proteostasis collapse due to their postmitotic and long-lived nature and thus represent a unique cell type to understand the dynamics of proteostasis throughout development and maturation. Here, we utilized a dual-species co-culture model of human excitatory neurons and mouse glia to recapitulate and investigate cell type-specific, maturation-related changes in the proteostasis network using data-independent acquisition LC-MS/MS proteomics. We quantified branch-specific unfolded protein response (UPR) activation by monitoring curated effector proteins downstream of the ATF6, IRE1/XBP1s, and PERK pathways, enabling a comprehensive, unbiased evaluation of UPR dynamics during in vitro neuronal maturation between 30 d and 60 d. Species-specific analysis revealed that mature neurons largely preserved proteostasis, although they showed some signs of collapse, primarily in endoplasmic reticulum (ER)-to-Golgi transport mechanisms. However, these changes were accompanied by upregulation of proteostasis-related machinery and activation of the ATF6 branch, as well as maintenance of the XBP1s and PERK branches of the UPR over time. In contrast, glia exhibited broad downregulation of proteostasis factors and UPR components, independent of neuronal presence. Furthermore, we quantified stimulus-specific modulation of select UPR branches in matured neurons exposed to pharmacologic ER stressors. These findings highlight distinct, cell-type-specific stress adaptations during in vitro maturation and provide a valuable proteomic resource for dissecting proteostasis and UPR regulation in human neurons.

Keywords:  activating transcription factor 6; data-independent acquisition (DIA) mass spectrometry; inositol requiring enzyme 1; neuronal maturation; protein kinase R-like ER kinase

DOI:  https://doi.org/10.1073/pnas.2521663123
NAM J. 2025 ;1 100046

Decoding cellular stress states for toxicology using single-cell transcriptomics.

Imran Shah, David Gallegos, Brian Robinette, Bryant A Chambers, Dennis J Eastburn, Douglas A Bell, Michelle R Campbell, Suzanne N Martos, Salvatore Camiolo, Kevin S White, Nicole Martin, Gioele Montis, Joel McComb, Bruce Seligmann, Brian N Chorley.

  We applied the TempO-LINC® platform to generate single-cell transcriptomic (SCTr) profiles of ∼40,000 HepaRG cells exposed to etoposide, brefeldin A, cycloheximide, rotenone, tBHQ, troglitazone, and tunicamycin at three concentrations for 24 hours. SCTr enabled a detailed analysis of adaptive stress response pathways (SRPs), including the unfolded protein response (UPR), oxidative stress response (OSR), heat shock response (HSR), and DNA damage response (DDR). Troglitazone upregulated lipid metabolism genes (PLIN2, ACOX1) along with HSR and UPR activation, with co-expression of DNAJA1, HSP90AA1, and DDIT3 in subsets of cells. Brefeldin A and tunicamycin strongly induced UPR markers (HSPA5, SYVN1, LMF2, PDIA4) in subsets of cells, with some also expressing apoptotic (DDIT3, CASP8) and autophagic (SQSTM1) genes, indicating diverse stress responses. Rotenone activated GDF15, TRIB3, and DDIT3 in a fraction of cells, accompanied by PLIN2 and mild UPR induction, reflecting heterogeneous mitochondrial stress responses. We scored individual cells using literature-derived SRP gene signatures to characterize overall stress phenotypes and clustered them using a generalized Jaccard metric. The clustering revealed five phenotypic groups spanning cell states associated with homeostasis, adaptive responses, terminal outcomes, autophagy, and apoptosis. By systematically analyzing the distributions of cells in different states across treatments, we visualized dynamic shifts in cellular subpopulations responding to chemicals, revealing early stress responses and potential transitions to cell death. Our findings suggest the utility of SCTr in decoding stress states that could provide possible insights into transitions between cellular adaptive and terminal transitions involved in toxicity.

Keywords:  Adaptive stress response; HepaRG; cell states; cell strate transition graph; computational toxicology; single-cell transcriptomics (SCTr)

DOI:  https://doi.org/10.1016/j.namjnl.2025.100046
Theranostics. 2026 ;16(13): 7196-7243

GRP78 in human diseases: From molecular chaperone to therapeutic target.

Yang Li, Dan Mu, Jiajie Feng, Zhijia Li, Lan Zhang, Lei Wang.

  Glucose-regulated Protein 78 (GRP78, also known as BiP/HSPA5) is a central member of the Hsp70 family. As a key molecular chaperone in the endoplasmic reticulum (ER), it plays an important role in cell survival and biological function by maintaining protein folding homeostasis and regulating endoplasmic reticulum stress (ERS) and the unfolded protein response (UPR). Its function is precisely regulated by various post-translational modifications (PTMs), including phosphorylation and acetylation. In addition, GRP78 can translocate to subcellular locations such as the cell membrane and nucleus, where it performs non-classical functions under stress conditions. Under pathological states, the aberrant expression and function of GRP78 are extensively involved in the onset and progression of diverse human diseases, including cancer, neurodegenerative diseases, infectious diseases, cardiovascular diseases, inflammatory diseases and metabolic diseases, and often exhibit a dual role dependent on tissue specificity and disease stage. To date, a variety of intervention strategies have been developed, such as small-molecule modulators, antibodies and genetic intervention approaches. These strategies have demonstrated promising potential in preclinical studies, yet are confronted with challenges including insufficient specificity and delayed clinical translation. This paper systematically elucidates the structure, PTMs, biological functions and disease regulatory mechanisms of GRP78, summarizes the existing intervention strategies, and discusses the unresolved issues and future research directions in this field. Future research should focus on developing highly specific regulatory tools and integrating precision medicine strategies to advance the clinical translation and application of GRP78 as a therapeutic target.

Keywords:  GRP78; human diseases; molecular chaperone; post-translational modifications; structure and function; targeted therapy

DOI:  https://doi.org/10.7150/thno.136060
Cell Death Discov. 2026 Jun 29.

Die hard: when cells refuse apoptosis-the rise of paraptosis and other death pathways.

Cecilia Anceschi, Elena Frediani, Jessica Ruzzolini, Francesca Margheri, Anastasia Chillà, Noemi Formica, Elena Andreucci, Fabio Cianchi, Anna Laurenzana, Serena Martinelli.

Resistance to apoptosis remains a major barrier in cancer therapy, driving interest in alternative regulated cell death (RCD) programs. Paraptosis, a caspase-independent RCD marked by cytoplasmic vacuolization, ER dilation, and mitochondrial swelling, emerges as a promising vulnerability in apoptosis-refractory tumors. Its therapeutic potential has been limited by incomplete understanding of its dynamic regulation within heterogeneous tumor ecosystems. In this review, we introduce paraptotic plasticity, describing cancer cells' ability to reversibly switch between paraptosis-sensitive and -resistant states in response to metabolic stress, therapeutic pressure, and tumor microenvironmental cues. This plasticity reveals a previously unrecognized mechanism of therapeutic resistance and uncovers exploitable vulnerabilities for precision targeting. We outline key molecular determinants, including ER stress, mitochondrial dysfunction, ion homeostasis, and proteotoxic stress, and highlight the emerging influence of microbiota-derived metabolites in shaping paraptotic outcomes. Finally, we discuss nanotechnology-enabled strategies that leverage these vulnerabilities, offering a translational roadmap to overcome resistance in hard-to-treat cancers.

DOI: https://doi.org/10.1038/s41420-026-03193-w
Nat Commun. 2026 Jul 01.

Loss of Echs1 in neural stem and progenitor cells impairs neurogenesis via ER stress activation and lipid metabolic reprogramming.

Chun-Hui Duan, Pei-Pei Liu, Xin Sun, Wen-Hui Ma, Jia-Ying Pang, Zi-Han Zhang, Xiao Li, Lin-Fei Jiao, Hong-Zhen Du, Zhao-Qian Teng, Hou-Zao Chen, Chang-Mei Liu.

Mitochondrial short-chain enoyl-CoA hydratase 1 deficiency (ECHS1D) is a rare and severe encephalopathy linked to neurodevelopmental disorders, yet the connection between metabolic dysfunction and impaired neurogenesis remains unclear. In this study, we demonstrate that the loss of Echs1 in neural stem/progenitor cells (NSPCs) leads to fatty acid accumulation, which hinders proliferation and differentiation while promoting apoptosis. Mechanistically, Echs1 deficiency increases crotonyl-CoA levels, resulting in global histone crotonylation (Kcr) with an enrichment of H3K9cr. Neurodevelopmental gene promoters, such as the endoplasmic reticulum (ER) stress regulator Atf4, acquire H3K9cr. Atf4 then upregulates fatty acid synthase (Fasn), creating a feed-forward loop that exacerbates lipid accumulation. Inhibiting Fasn can rescue these defects. Alleviating ER stress through tauroursodeoxycholic acid (TUDCA) or Atf4 inhibition restores neurogenesis in vitro and enhances survival in vivo. This study uncovers an Echs1-H3K9cr-Atf4-Fasn axis that links metabolism to neurogenesis through epigenetic reprogramming and suggests TUDCA as a potential treatment for ECHS1D.

DOI: https://doi.org/10.1038/s41467-026-75063-z
Sci Rep. 2026 Jun 30.

Expression of circulating GRP78 and gp96, endoplasmic reticulum stress-related proteins, in menstrual and bladder pain sensitivity.

Chandrashekara N Kyathanahalli, Sarah E Darnell, Frank F Tu, Kevin M Hellman.

  Dysmenorrhea is often linked to uterine inflammation, but the additional factors and pathways that contribute to its pathophysiology remain poorly understood. Given growing evidence linking endoplasmic reticulum (ER) stress to inflammation and pain sensitization, we examined circulating ER stress-associated heat shock proteins (HSPs) GRP78 and gp96 in individuals with dysmenorrhea (n = 82), a dysmenorrhea subtype with bladder pain sensitivity (DYSB, n = 26) previously shown to increase risk for chronic pain, and controls (n = 19). After correcting for Menstrual phase, naproxen exposure, and oral contraceptive use, GRP78 was higher in DYSB than in DYS (ratio 1.33; p = .028), while gp96 was lower in both DYS (ratio 0.62; p = .019) and DYSB (ratio 0.59; p = .031) compared to controls. gp96 was also lower during the menstrual phase with naproxen compared to the non-menstrual phase (ratio 0.73; p = .014), whereas GRP78 was not significantly affected by menstrual phase, naproxen, or oral contraceptive use, and neither protein was associated with anxiety, depression, or sleep disturbance scores. These cross-sectional findings suggest that dysmenorrhea, particularly the bladder-sensitive subtype (DYSB), is associated with divergent circulating levels of two ER stress-related proteins. The inverse pattern of higher GRP78 and lower gp96 levels points to selective, rather than global, ER chaperone dysregulation as a candidate mechanism. However, future mechanistic and longitudinal investigations will be required to establish whether GRP78 and gp96 carry predictive or pathophysiological relevance.

Keywords:  Biomarkers; Bladder pain; Dysmenorrhea; Heat shock proteins; Systemic circulation

DOI:  https://doi.org/10.1038/s41598-026-58824-0
Sci Rep. 2026 Jul 02.

Integrating machine learning and structure-based simulations to prioritise Z4P as a mutation-resilient IRE1α inhibitor for breast cancer.

Nithisha L Bastin, P K Praveen Kumar, Baranitharan Ethiraj, Ravikumar Rajarathinam, J Shrihari, Rajkumar Sivanraju.

  Breast cancer is one of the most prevalent and lethal malignancies affecting women globally. The increasing resistance to current therapeutic strategies highlights the need for novel molecular targets. Inositol-requiring enzyme 1 alpha (IRE1α), a key sensor in the unfolded protein response (UPR), has emerged as a promising therapeutic target due to its role in tumour progression and survival. This study employed an integrative in silico approach combining machine learning, molecular docking, and molecular dynamics simulations to identify potent, non-toxic IRE1α inhibitors for breast cancer treatment. An initial library of 115 compounds retrieved from ChEMBL and MedChemExpress was used for machine learning-based toxicity modelling. Literature curation identified 44 reported IRE1α inhibitors, which were reduced to 38 unique compounds following duplicate removal. Drug-likeness and ADMET screening using SwissADME and ProTox retained 22 compounds for further evaluation. Molecular docking was performed using AutoDock, followed by Dynamics simulations in GROMACS to assess stability. Machine Learning (ML) models were developed for both toxicity regression and binary toxicity classification analyses. Toxicity prediction models were developed using twenty physicochemical and pharmacokinetic descriptors. In the regression analysis, Random Forest demonstrated the strongest cross-validation performance (R² = 0.5998 ± 0.3439), while the stacking ensemble achieved the highest test-set performance (R² = 0.9765), although differences among ensemble methods were not statistically significant. In the complementary classification analysis, the Support Vector Machine (SVM) achieved the highest discriminative performance with an ROC-AUC value of 0.98. Docking studies revealed that Z4P exhibited the strongest binding affinity (- 7.93 kcal/mol) to the wild-type IRE1, compared with the control drug MKC8866 (- 6.7 kcal/mol). Additionally, Z4P exhibited a higher binding energy of - 9.5 kcal/mol, whereas MKC8866 had a binding energy of - 6.94 kcal/mol. MD simulations over 200 ns confirmed the stability of the IRE1-Z4P complex, with favourable RMSD, RMSF, Rg, and SASA profiles relative to the control. These findings highlight Z4P as a promising mutation-resilient IRE1 inhibitor and validate the effectiveness of the integrated computational pipeline for identifying potential anti-cancer therapeutics.

Keywords:  Breast Cancer; IRE1α; MKC8866; Machine Learning; Molecular Docking; Z4P

DOI:  https://doi.org/10.1038/s41598-026-60596-6
Cell Metab. 2026 Jun 30. pii: S1550-4131(26)00229-9. [Epub ahead of print]

AARS1 promotes tumor progression and immune evasion via ATF6 lactylation-mediated tryptophan metabolism in hepatocellular carcinoma.

Yiming Wang, Fan Li, Jiongyuan Li, Tianning Huang, Tian Huang, Nan Zhang, Yiran Li, Ziyu Xun, Zhe Zhu, Qiaorui Tan, Xuanyu Zhao, Liangwei Zou, Mingjian Piao, Chengjie Li, Boyu Sun, Jingwen Ma, Pengyao Chen, Jian Gu, Shipeng Dai, Hao Wang, Ming Ni, Haitao Zhao, Ling Lu.

  Glycolysis and protein lactylation both drive hepatocellular carcinoma (HCC) progression, yet their mechanistic interplay remains unclear. Through integrated single-cell and spatial transcriptomic analyses stratified by glycolytic activity, we identified alanyl-tRNA synthetase 1 (AARS1), a recently characterized protein lactyltransferase, as a key metabolic-immune regulator in HCC. Clinically, AARS1 is upregulated in tumors, correlates with elevated glycolytic flux measured by 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT), poor prognosis, and immunotherapy resistance. In murine models, hepatocyte-specific knockout of AARS1 suppressed tumor growth and reduced the abundance of regulatory T cells (Tregs). Mechanistically, AARS1 catalyzes the lactylation of activating transcription factor 6 (ATF6) at lysine 424, preventing its degradation and leading to transcriptional activation of TDO2. This process promotes L-kynurenine production and supports Treg differentiation and function. Furthermore, L-kynurenine-AHR signaling drives eNAMPT secretion from Tregs, which augments tumor cell glycolysis and lactate production, thereby reinforcing a feedback loop that sustains AARS1-catalyzed ATF6 lactylation. Pharmacological inhibition of AARS1 with β-alanine sensitized tumors to PD-1/PD-L1 blockade.

Keywords:  AARS1; ER stress; HCC; Treg; immune evasion; lactylation; tryptophan metabolism

DOI:  https://doi.org/10.1016/j.cmet.2026.06.003