bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–10–25
seventy papers selected by
Cédric Chaveroux, CNRS
  1. mRNA Structure Regulates Translation at Every Step.
  2. Ribosome biogenesis and selective translational control as oncogenic vulnerabilities in hematologic malignancies.
  3. Structural basis for start codon selection by eIF5-mimic proteins.
  4. The Long Splice Variant of Ribosomal Protein S24 Protects Cells from Stress and Is Induced by AMPK-ULK1-Regulated Autophagy Independent of mTORC1.
  5. EIF3B is associated with m6A-related regulation of E2F7 and promotes stemness in glioblastoma multiforme.
  6. A role for eIF5A in translational control of stress-inducible proteins in multiple myeloma cell lines.
  7. RNA N6-methyladenosine modifications in plants: molecular mechanisms and biological roles.
  8. Ribo-seq rRNA reads reveal co-predicted signatures of ribosome heterogeneity and collisions.
  9. The m6A regulatory network in plant stress adaptation: from mechanisms to breeding potential.
  10. Programmable Enhancement of IRES-Mediated Translation via RNA-Guided eIF4G Recruitment.
  11. Single-cell and spatial epitranscriptomics of m6A: Technologies, regulatory mechanisms, and biological insights.
  12. Melatonin-mediated metabolic reprogramming and stress adaptation in plants.
  13. Boosted Cell-Free Gene Expression for Robust Signal Readout from a Single-Copy DNA Template in Microdroplets.
  14. UPF1-mediated mRNA decay promotes melanoma tumorigenesis through miR-101-3p-dependent destabilization of NANOS1.
  15. Full-protein release assay in a reconstituted yeast translation system using GGQ-methylated eRF1.
  16. Advances in tools and strategies for spatiotemporal regulation of gene expression in Caenorhabditis elegans.
  17. Glyoxalase 1 Regulates Methylglyoxal-Derived Nucleic Acid Adduct Burden.
  18. Context-dependent protective and pathogenic functions of YTHDF1 in MASLD and hepatocellular carcinoma: Mechanisms and design of therapeutics.
  19. The PAXT connection is a modifier of rare codon-enriched protein expression.
  20. Boldine enhances hyperthermia-induced apoptosis in AGS gastric cancer cells in association with attenuation of the HSF1-HSP stress response.
  21. Proteostasis stress alters mitochondrial levels and localization of SOD2 during cellular senescence.
  22. A transcriptional repressor co-regulatory network integrates iron homeostasis and mycobacterial stress tolerance to oxidative stress.
  23. Biomolecular Condensates in Bacteria.
  24. HSP27, cell stress, and hormesis: From mammals to humanized yeast models.
  25. Molecular functions, cellular responses and pathological implications of the RNA modification N6-methyladenosine.
  26. SnoRNA Evolution, Genomic Context and Mobility: The Role of Function and Host Gene Association.
  27. Structural features of ZAK kinase regulation at the ribosome.
  28. BRAP maintains SEC24D stability to regulate ER stress and promote cervical adenocarcinoma progression.
  29. Liquid-liquid phase separation in neurodegenerative diseases: Mechanisms, pathological transitions, and therapeutic opportunities.
  30. LncRNA-protein interactions: molecular switches for the precise regulation of innate immunity.
  31. A methylation-dependent reader couples arginine methylation to S6K2 signaling in vivo.
  32. Progress in the Mechanism of Heat Shock Proteins in Gastric Cancer: From Biomarkers to Therapeutic Targets.
  33. A comparative analysis of the tomato MAPK cascade at the transcriptional and translational levels under low-temperature conditions.
  34. Timing the effort: Chronobiological drivers of skeletal muscle adaptation and metabolic health.
  35. Deciphering the Molecular Basis of Poly(A)-Binding Protein Selectivity for Homopolymeric RNAs.
  36. The RNA binding protein RGGA acts as a sugar-responsive cofactor of the 5'-3' exoribonuclease XRN4 to function in selective mRNA degradation and post-transcriptional regulation of plant growth.
  37. Rapalink-1 reveals an mTOR- and p53-regulated transcriptional program in Neuro-2a cells.
  38. NUAK isoforms promote glucose and glutamine metabolic reprogramming driven colon cancer progression and migration through regulation of AMPK/mTOR signaling.
  39. Visualization of RNA Structures and Functional Annotations Using ArcPlot.
  40. hnRNPC promotes oral squamous cell carcinoma progression via N6-methyladenosine-dependent stabilization of BCAT1 to enhance branched-chain amino acid metabolism.
  41. RNA therapeutics in rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis: a compartment-aware translational framework.
  42. Emergence of bimodal First Passage Time distributions from Transcription Translation Coupling.
  43. ALYREF regulates glycolysis and promotes the progression of endometrial cancer through m5C modification of PKM2 mRNA.
  44. METTL14-mediated FDX1 m6A methylation inhibited the proliferation of clear cell renal cell carcinoma.
  45. Amino Acid Substitutomics: Profiling Amino Acid Substitutions at the Proteomic Scale Unveils Biological Implications and Escape Hypotheses in Cancer.
  46. HOTAIR in cancer: a context-dependent regulatory platform linking molecular mechanisms, tumor progression, and clinical translation.
  47. Receptor-Specific ER-Phagy in Neurodegenerative Diseases: Molecular Mechanisms and Emerging Therapeutic Opportunities.
  48. Binding without Docking: Small-Molecule Binding Paths on Disordered Proteins.
  49. Polystyrene nanoplastics impair mitochondrial function, quality control, and ER-mitochondria crosstalk in HeLa cells.
  50. The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs).
  51. Transient but not sustained p53 activation by targeting METTL3 prevents radiation-induced intestinal injury through dual-regulation of revival stem cells.
  52. Proteomic adaptation of the hypervirulent pandemic Vibrio parahaemolyticus ST36 lineage to salinity and temperature stress.
  53. Purification of RNA G-Quadruplex Binding Proteins.
  54. Engineered Orthogonal Translation Systems from Metagenomic Libraries Expand the Genetic Code.
  55. Capture and Purification of Endogenous Long Noncoding Ribonucleic Protein Complexes for Protein Identification Using Grad-MS.
  56. A critical mechanistic synthesis of PINK1-mediated mitophagy signaling and its therapeutic targeting in Parkinson's disease neurodegeneration.
  57. Investigation of the significance and role of androgen receptor expression in basal/squamous type urothelial carcinoma cell line J82 cells.
  58. Linking protein misfolding and heat stress: a common role for the kynurenine pathway.
  59. METTL3-METTL14 Heterodimer Assembly Enables Multivalent RNA Engagement and Is Tuned by Interface-Targeting Peptides.
  60. FTO-mediated demethylation of PRKCB mRNA activates NF-κB to trigger alveolar fibrin deposition in ARDS.
  61. A Non-Conventional Epigenetic Engineering Strategy: The ALKBH5/ITGB5 Axis Enhances Recombinant Protein Production in CHO Cells through FAK-Mediated Proliferation and Improved Redox Status.
  62. Endoplasmic reticulum stress in autoimmune skin diseases: immune activation, cutaneous cell damage, and therapeutic advances.
  63. Chaperonopathies as Disorders of Disorder: The Role of Intrinsically Disordered Regions in Proteostasis Dysfunction.
  64. Crosstalk between lactylation and m6A in cancer: emerging disease mechanisms and therapeutic targets.
  65. ExoU-Mediated Host-Cell Cytotoxicity is Associated with Phosphorylation-Dependent Regulation of DDX3Y during Pseudomonas aeruginosa Infection.
  66. From ribosomal stress to clonal adaptation: Del(5q) MDS as a paradigmatic acquired ribosomopathy.
  67. Improving Yield and Assessing Quality of Secreted Proteins Over-Expressed in Pichia Pastoris with Chaperones and Structural Mass Spectrometry.
  68. Protein disulphide isomerase protects against ALS/FTD phenotypes associated with cyclin F in zebrafish and cellular models.
  69. The unfolded protein response as a proteotoxic stress-resolution circuit: branch-selective signaling and failed resolution in environmental immunotoxicity.
  70. Aptamer-Based Targeted Protein Degradation: Mechanistic Principles, Delivery Strategies, and Translational Opportunities.
  1. Biochemistry. 2026 Oct 20. 65(20): 3144-3150
    mRNA Structure Regulates Translation at Every Step.
    Alexandra Khitun, Kevin M Weeks.
      Precise, context-sensitive control of protein synthesis is critical in eukaryotic cells, and mRNA structure has emerged as a central mechanism for achieving this control. mRNA structures influence every stage of translation. During initiation, structures within 5' untranslated regions modulate ribosome association with mRNA and the balance between translation of the main open reading frame and use of upstream or alternative start sites. During elongation, structures in the coding sequence govern ribosome pausing in ways that can either protect mRNA stability or trigger decay. During termination, structures downstream of primary stop codons promote readthrough to generate protein isoforms in a tissue-specific manner. mRNA structures are remodeled by helicase expression, post-transcriptional modifications, and translational programming to provide additional layers of regulation. We review recent advances illuminating diverse mechanisms by which RNA structure modulates translation.
    DOI:  https://doi.org/10.1021/acs.biochem.6c00561
  2. Mol Cancer. 2026 Jul 23. pii: 249. [Epub ahead of print]25(1):
    Ribosome biogenesis and selective translational control as oncogenic vulnerabilities in hematologic malignancies.
    Juan Luiz Coelho-Silva, João Agostinho Machado-Neto.
      The translation of the transcriptome into a functional proteome is not a passive readout of mRNA abundance but a primary regulatory layer that actively shapes the oncogenic landscape. In hematologic malignancies, convergent oncogenic signaling pathways, including MYC, PI3K/AKT/mTOR, and tyrosine kinase fusions, directly reprogram the translational apparatus, driving a qualitative shift toward the selective synthesis of pro-survival, proliferative, and stemness-associated proteins. This deregulated program is orchestrated through multiple interconnected axes: the accelerated biogenesis of ribosomes within the nucleolus, the assembly of the eIF4F initiation complex, the activation of stress-adaptive programs like the integrated stress response (ISR), and a sophisticated layer of epitranscriptomic, tRNA, and RNA-binding protein-mediated regulation. Hematologic cancers provide a uniquely informative framework for deconstructing these processes, illustrated by inherited ribosomopathies, such as Diamond-Blackfan anemia syndrome and Shwachman-Diamond syndrome, which resolve the paradox of how ribosomal insufficiency can evolutionarily transition into malignant transformation. Beyond pathogenesis, the translational machinery represents a rich landscape of actionable vulnerabilities. Pharmacological targeting of RNA Polymerase I, eIF4A, and the ISR has demonstrated selective antitumor activity and synergistic potential with established therapies, including BCL-2 inhibition. This review synthesizes mechanistic and clinical evidence to position the ribosome as an active regulatory node rather than a passive decoding machine. We further examine the challenges facing the field, including translational plasticity under therapeutic pressure, the lack of validated companion biomarkers, and the emerging role of translational control in modulating anti-tumor immunity. Ultimately, we argue that defining the disease-specific translational states of leukemia and lymphoma is essential for the next generation of precision oncology, moving beyond genomic landscapes toward a proteomic-centered understanding of malignancy.
    Keywords:  Hematopoiesis; Ribosome biogenesis; Translational control
    DOI:  https://doi.org/10.1186/s12943-026-02749-9
  3. Sci Adv. 2026 Oct 23. 12(43): eaeg5840
    Structural basis for start codon selection by eIF5-mimic proteins.
    Ximena Zottig, Chun-Ying Huang, Zahra Seraj, Nikolaus Grigorieff, Andrei A Korostelev.
      Start codon selection extensively regulates the cellular proteome and is implicated in cancer and other diseases. The eIF5-mimic proteins (5MPs: 5MP1/BZW2 and 5MP2/BZW2) restrict non-AUG start codon usage and thereby reprogram proteoform expression from mRNAs with alternative start sites, such as the oncogenic c-Myc. Here, using in extracto cryo-electron microscopy (cryo-EM) and biochemical assays, we report how 5MP represses translation dependent on the sequence context at start codons. Cryo-EM structures of 48S preinitiation complexes (PICs) reveal 5MP1 bound at the A site of the small ribosomal subunit. 5MPs act as initiation factors that stabilize an open PIC conformation, promoting mRNA scanning and inhibiting initiation at suboptimal start codons. We propose to designate 5MP as eIF1S (eukaryotic initiation factor 1 scanning). These findings reveal the structural basis for proteome modulation by 5MPs and may help correct dysregulated translation in disease.
    DOI:  https://doi.org/10.1126/sciadv.aeg5840
  4. Biochemistry. 2026 Sep 15. 65(18): 2916-2927
    The Long Splice Variant of Ribosomal Protein S24 Protects Cells from Stress and Is Induced by AMPK-ULK1-Regulated Autophagy Independent of mTORC1.
    Runqi Qian, Jenna Goodbrand, Shannon N Adams, Erin Trella, James Uniacke.
      All living organisms have developed complex mechanisms to detect and react to environmental changes to maintain internal balance and support survival. One strategy that cells employ to respond to stress is to refocus the translation machinery to express select stress response proteins, this includes the emerging field of specialized ribosomes. We have previously shown that a long splice variant of ribosomal protein S24 (RPS24L) is induced by several fold in hypoxic monolayers and spheroids in several human cell lines in an autophagy-dependent manner. Here, we show that an allosteric activator of AMPK is sufficient to induce RPS24L and autophagy in normoxia in an ULK1-dependent, but mTORC1-independent manner. Overexpression of RPS24L protected cells from serum starvation and hypoxia, while RPS24 short isoform overexpression during stress impaired autophagy and the ability for cells to survive relative to controls. We show that SRSF1 interacts with RPS24 mRNA and its autophagy-dependent decrease shifts splicing toward the RPS24L variant. This study provides new insights into the signaling and mechanisms that regulate a ribosomal protein splice isoform that protects cells from stress and that has been previously linked to cancer progression.
    DOI:  https://doi.org/10.1021/acs.biochem.6c00572
  5. BMC Cancer. 2026 Jul 27. pii: 1270. [Epub ahead of print]26(1):
    EIF3B is associated with m6A-related regulation of E2F7 and promotes stemness in glioblastoma multiforme.
    Jiao Meng, Xinyi Jiang, Yaling Hu, Jinyue Tian, Zhenkun Yang, Zhening Pu, Ying Yin.
       BACKGROUND: E2F transcription factors are key regulators of the cell cycle and play an important role in tumorigenesis. N6-methyladenosine (m6A), the most prevalent internal RNA modification in eukaryotic cells, is also crucial for cancer progression. However, the interplay between E2F family members and m6A modification in glioblastoma multiforme (GBM) remains poorly understood.
    METHODS: We applied weighted gene co-expression network analysis (WGCNA) to identify m6A-related gene modules co-expressed with E2F7, a gene that is significantly associated with adverse prognosis and tumor stemness. Through intersection analysis, eukaryotic translation initiation factor 3 subunit B (EIF3B) emerged as a hub gene, showing a strong positive correlation with E2F7 in GBM datasets. Functional validation was performed in GBM cells to assess the regulatory relationship between EIF3B and E2F7, including examination of mRNA and protein expression, mRNA stability, and m6A modification levels. GBM stemness was evaluated by tumor sphere formation assays and detection of stemness-associated markers.
    RESULTS: Functional validation revealed that EIF3B knockdown reduced E2F7 mRNA and protein expression, promoted E2F7 mRNA degradation, and decreased its m6A modification, suggesting an association between EIF3B and m6A-related regulation of E2F7 stability. Furthermore, EIF3B knockdown markedly suppressed GBM stemness, as demonstrated by impaired tumor sphere formation and downregulation of stemness-associated markers. Clinically, EIF3B expression increased with glioma grade and correlated with poor prognosis.
    CONCLUSIONS: Collectively, these findings suggest that the EIF3B-E2F7 axis is associated with m6A-related regulation in GBM and may warrant further investigation as a candidate for therapeutic targeting.
    Keywords:  E2F7; EIF3B; Glioblastoma multiforme; Stemness; m6A modification
    DOI:  https://doi.org/10.1186/s12885-026-16552-8
  6. Mol Oncol. 2026 Oct 21.
    A role for eIF5A in translational control of stress-inducible proteins in multiple myeloma cell lines.
    Demi Both, Ingrid A M Derks, Raphaël Vanleyssem, Marine Leclercq, Najla El Hachem, Pierre Close, Eric Eldering, Marco Vincent Haselager.
      Impaired protein folding in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR), which can induce apoptosis during prolonged ER stress. ER stress is therapeutically targeted in plasma cell malignancies, such as multiple myeloma (MM), but these treatments remain noncurative, and UPR signaling in B-cell malignancies is incompletely understood. A targeted CRISPR-Cas9 screen in RPMI-8226 cells exposed to thapsigargin identified known ER stress regulators (XBP1, IRE1, and calreticulin) and the translation factor eIF5A (eukaryotic translation initiation factor 5A), whose role in ER stress remains unclear. Competition assays showed that eIF5A depletion is detrimental under basal conditions but confers a proliferation advantage during thapsigargin treatment. Inducible EIF5A knockouts confirmed reduced sensitivity specifically to thapsigargin, loss of eIF5A had no or sensitizing effects on cell death induced by other ER stress drugs. Polysome profiling revealed that not general translation, but the translation of specific mRNA transcripts coding for UPR components and apoptotic proteins was affected by eIF5A depletion. Correspondingly, EIF5A KO cells showed reduced thapsigargin-induced UPR activation. In conclusion, these findings indicate that loss of eIF5A alters the stress response in MM cells.
    Keywords:  ER stress; UPR; apoptosis; eIF5A; multiple myeloma; translation
    DOI:  https://doi.org/10.1002/1878-0261.70328
  7. Plant Cell Rep. 2026 Oct 18. pii: 336. [Epub ahead of print]45(11):
    RNA N6-methyladenosine modifications in plants: molecular mechanisms and biological roles.
    Mei Yang, Dingjie Wu, Zijian Hu, Jinxing Lin, Ye Li, Ruili Li.
      RNA N6-methyladenosine (m6A) modifications dynamically modulate RNA stability, splicing, and translation in plants, influencing developmental and stress response processes. In this review, we provide an overview of the key protein complexes involved in RNA m6A modification, including methyltransferases, demethylases, and m6A-binding proteins. We then demonstrate that m6A modulates vegetative growth, reproductive processes, responses to stresses, and hormone signaling. In agronomically important crops, RNA m6A modifications affect stress resilience, developmental timing, and quality traits, such as drought tolerance, salt resistance, male fertility, pollen viability, and fruit maturation. Furthermore, we elucidate the molecular mechanisms of RNA m6A. Finally, we explore advancements in m6A detection technologies, highlighting emerging trends and future directions. These strategies provide a conceptual framework for moving plant m6A research from descriptive epitranscriptomics toward trait-oriented crop and forest tree improvement.
    Keywords:  Biological functions; Plants; RNA modifications; Regulatory proteins; m6A methylation
    DOI:  https://doi.org/10.1007/s00299-026-04020-3
  8. Brief Bioinform. 2026 Sep 01. pii: bbag575. [Epub ahead of print]27(5):
    Ribo-seq rRNA reads reveal co-predicted signatures of ribosome heterogeneity and collisions.
    Edwin S Kyei-Baffour, William J Faller, Ferhat Alkan.
      Ribosome heterogeneity is increasingly recognized as a key factor in various biological contexts, including development, cancer, and immune responses. To enable systematic exploration of this diversity, we previously developed a bioinformatics method that utilized rRNA reads from Ribo-seq data, detecting changes in ribosomal protein composition (dripARF) and ribosome collisions (dricARF) between conditions simply and efficiently. The method works by projecting differences in rRNA read abundance onto the 3D-structure of the ribosome, following which we perform enrichment tests on predefined heterogeneity-specific rRNA position sets. In this study, we apply this tool to publicly available Ribo-seq datasets to understand the impact of experimental protocol variations and to identify shared biological signals across studies. Our analyses show that the rRNA regions assigned to our prediction sets are consistently enriched in rRNA reads, supporting the core assumptions of our approach. We further examine how various protocol factors influence rRNA read distribution and implement a single-sample rRNA position set enrichment analysis-based weight to limit false positives. Finally, we highlight consistent ribosomal changes across these studies, including prominent co-predictors such as ribosome collisions, eS25, and uS19.
    Keywords:  Ribo-seq; rRNA reads; ribosome collisions; ribosome heterogeneity
    DOI:  https://doi.org/10.1093/bib/bbag575
  9. Front Plant Sci. 2026 ;17 1940258
    The m6A regulatory network in plant stress adaptation: from mechanisms to breeding potential.
    Jun Zhang, Sainan Jiang, Jie Yang, Jingjing Zou, Wen Xing, Zeqing Li.
      N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA and is dynamically regulated by three classes of proteins: writers, erasers, and readers. Writers deposit methylation marks, erasers confer reversibility, and readers translate these signals into specific regulatory outcomes, collectively modulating mRNA stability, translation efficiency, splicing, and polyadenylation, thereby influencing plant stress adaptation. Studies across diverse plant species have revealed both conserved principles and species-specific variations in this regulatory network. Technological advances, such as methylated RNA immunoprecipitation sequencing (MeRIP-seq) and nanopore direct RNA sequencing, have enabled transcriptome-wide m6A profiling. However, functional validation of m6A modification in most crops remains limited to a few model species and controlled environments, and their practical breeding potential requires systematic evaluation. This review systematically summarizes the functions of m6A writers, erasers, and readers in crop stress responses, synthesizes the regulatory patterns at the levels of mRNA stability, translation efficiency, and splicing and discusses m6A-based breeding strategies and their current bottlenecks, providing a theoretical reference for stress-resilient crop breeding. CRISPR/dCas13-based targeted modification systems, together with methyltransferase overexpression or demethylase knockout strategies, have demonstrated breeding potential in several crops, although field-level validation remains limited. Future research needs to prioritize how the writer-eraser-reader network achieves stress-specific regulation without causing pleiotropic developmental defects, how m6A pattern differs between single and combined stresses, and how natural variation in m6A regulatory gene can be exploited for breeding. On this basis, establishing causal links between specific m6A sites and agronomic phenotypes, while integrating multi-omics approaches and precision editing technologies, will be essential to translate epitranscriptomic knowledge into crop improvement.
    Keywords:  N6-methyladenosine; crop stress-resistance breeding; mRNA stability; plant stress response; translational regulation
    DOI:  https://doi.org/10.3389/fpls.2026.1940258
  10. Biochemistry. 2026 Sep 15. 65(18): 2905-2915
    Programmable Enhancement of IRES-Mediated Translation via RNA-Guided eIF4G Recruitment.
    Binbin Ying, Feiyang Zheng, Yoshinori Kawabe, Masamichi Kamihira.
      Internal ribosome entry sites (IRESs) enable cap-independent translation but often exhibit low and variable efficiency, limiting their use in synthetic gene circuits. Here, we present a programmable strategy to enhance IRES-dependent translation by recruiting a truncated eIF4G scaffold via engineered RNA-binding protein fusions. A λN-eIF4G fusion selectively increased EMCV IRES-mediated translation without affecting cap-dependent expression, achieving up to 7.7-fold enhancement. Translation output was tunable over a broad dynamic range through effector dosage and linker design, revealing key design parameters for controlling activity. The system functioned across multiple mammalian cell lines and in tricistronic constructs, enabling coordinated regulation of polycistronic expression. Computational modeling was consistent with preferential interaction between λN and the EMCV IRES. These results establish a modular framework for the programmable control of translation, define design principles for RNA-guided translational control, and expand the synthetic biology toolkit for post-transcriptional gene regulation.
    DOI:  https://doi.org/10.1021/acs.biochem.6c00420
  11. Biochim Biophys Acta Gene Regul Mech. 2026 Oct 20. pii: S1874-9399(26)00054-4. [Epub ahead of print]1869(4): 195188
    Single-cell and spatial epitranscriptomics of m6A: Technologies, regulatory mechanisms, and biological insights.
    Oishi Mukherjee, Koustav Sarkar.
      Transcription serves as the primary mRNA blueprint for gene expression; however, transcription function is further regulated by co-transcriptional and post-transcriptional mechanisms, including N6-methyladenosine (m6A), the most widespread internal mRNA modification. The mammalian m6A landscape is primarily established by the METTL3-METTL14 writer complex, with METTL3 serving as its catalytic subunit, while accessory writer components, erasers, and readers contribute to the regulation and interpretation of m6A marks. Conventional bulk sequencing averages m6A profiles across large cell populations, masking cell- and tissue-specific heterogeneity in m6A deposition and interpretation. Studies show that the functional outcome of METTL3-mediated m6A deposition depends on the co-expression of the reader and eraser proteins in the same cell, and that these vary across cell types, developmental stages, and tissue compartments. Recent single-cell and spatial epitranscriptomic technologies are beginning to resolve this context-dependent regulation, revealing that m6A can promote mRNA decay, translation, stabilization, or altered splicing depending on cellular context. In this review, we discuss emerging technologies for single-cell and spatially resolved m6A profiling, using METTL3 as a conceptual framework for understanding how m6A deposition is linked to transcriptional state and subsequently decoded by cell-specific regulatory machinery. We further discuss their applications, technological challenges, multi-omics integration, and clinical potential in development, immunity, neuronal biology, and cancer.
    Keywords:  Bulk sequencing; Epitranscriptomics; METTL3; Single cell sequencing; Spatial transcriptomics; m(6)A RNA methylation
    DOI:  https://doi.org/10.1016/j.bbagrm.2026.195188
  12. Plant Cell Rep. 2026 Oct 17. pii: 335. [Epub ahead of print]45(11):
    Melatonin-mediated metabolic reprogramming and stress adaptation in plants.
    Barket Hussain, Hatice Colgecen, Havva Karahan, Qazi Fariduddin.
       KEY MESSAGE: Melatonin acts as a multifunctional regulator of plant stress adaptation by reprogramming primary and secondary metabolism and coordinating ROS, nitric oxide, and phytohormone signalling. Integrating metabolomics with transcriptomics and proteomics provides new insights into these mechanisms and highlights melatonin as a promising strategy for enhancing crop resilience and productivity under diverse environmental stresses. Plants, being sessile, are continuously exposed to diverse environmental challenges, which disrupt cellular homeostasis and reduce crop productivity. To survive under such conditions, plants have evolved complex defence mechanisms involving metabolic reprogramming and coordinated molecular signalling networks. Among the regulatory molecules involved in stress adaptation, melatonin (N-acetyl-5-methoxytryptamine) has emerged as a multifunctional signalling compound that plays a pivotal role in plant growth, development, and stress tolerance. Acting as a potent antioxidant and signalling regulator, melatonin modulates multiple metabolic pathways associated with energy metabolism, amino acid biosynthesis, carbohydrate metabolism, and secondary metabolite production. These metabolic adjustments enhance the accumulation of osmoprotectants, antioxidants, and defence-related metabolites, thereby improving plant resilience under stress. Recent advances in metabolomics, together with transcriptomics and proteomics, have provided deeper insights into melatonin-mediated metabolic regulation in plants. High-throughput analytical platforms such as liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) enable comprehensive profiling of stress-responsive metabolites and reveal how melatonin orchestrates metabolic network reprogramming. Emerging evidence indicates that melatonin interacts with reactive oxygen species, nitric oxide, and multiple phytohormones to regulate gene expression, protein abundance, and metabolite accumulation, thereby integrating stress perception with physiological adaptation. This review summarises current knowledge on melatonin biosynthesis, signalling pathways, cross-talk and its role in regulating primary and secondary metabolism under diverse stresses. Emphasis has been laid on metabolomics-driven insights and multi-omics integration to elucidate the molecular mechanisms underlying melatonin-mediated stress tolerance and to support strategies to improve crop resilience and productivity.
    Keywords:  Melatonin; Metabolic reprogramming; Metabolomics; Multi-omics integration; Plant stress tolerance; Stress signalling
    DOI:  https://doi.org/10.1007/s00299-026-04016-z
  13. ACS Synth Biol. 2026 Sep 18. 15(9): 3784-3794
    Boosted Cell-Free Gene Expression for Robust Signal Readout from a Single-Copy DNA Template in Microdroplets.
    Taro Furubayashi, Naohiro Terasaka, Kenya Tajima, Hiroyuki Noji.
      Cell-free gene expression in microcompartments constitutes a chassis for biotechnology and synthetic biology. Protein synthesis from low DNA concentrations, including a single copy per compartment, is essential for in vitro evolution of biomolecules and synthetic cells. However, insufficient protein yields from typically subpicomolar DNA inputs result in undetectable signals or inadequate activity of desired protein functions. Here we identify and largely mitigate yield-limiting bottlenecks of reconstituted in vitro transcription and translation (IVTT) at low DNA input. Systematic comparison of commercial reconstituted IVTT kits revealed that gene expression becomes limited by mRNA scarcity within the 20-200 pM DNA-input range. We further uncovered that the standard ribosome concentration is excessive at low-DNA input and shortens the lifetime of translation. These findings led to a simple optimization recipe that combines supplementation with a commercial highly active T7 RNA polymerase reagent and a reduction in ribosome concentration, which synergistically amplified gene expression by ∼10-fold across diverse fluorescent proteins and enzymes. This low-DNA-optimized formulation in picoliter droplets achieved ∼94 nM protein expression from a single copy of a PCR-derived linear DNA template (∼0.12 pM). The user-friendly boosted IVTT protocol paves the way for straightforward functional screening and in vitro reconstitution of cellular functions in DNA-scarce environments.
    Keywords:  PURE system; cell-free gene expression; droplet screening; in vitro evolution; in vitro transcription and translation (IVTT); synthetic cell
    DOI:  https://doi.org/10.1021/acssynbio.6c00471
  14. Int J Biol Sci. 2026 ;22(15): 8492-8510
    UPF1-mediated mRNA decay promotes melanoma tumorigenesis through miR-101-3p-dependent destabilization of NANOS1.
    Suman Lee, Jae-Won Yoon, Dayeon Woo, Hyunho Cha, Seungwon Jung, Je-Min Choi, Jungwook Hwang.
      Numerous studies have reported Up-frameshift protein 1 (UPF1) as a crucial posttranscriptional regulator in nonsense-mediated mRNA decay (NMD), attributing its role to tumorigenesis across various cancers. However, its recently unveiled function in UPF1-mediated mRNA decay (UMD), intricately coordinated with miRNA, remains unexplored in the context of tumorigenesis. Here, we demonstrate that UPF1 contributes to melanoma tumorigenesis by regulating NANOS1 expression in a miR-101-3p-dependent manner. Depletion of UPF1 across three melanoma cell lines significantly impaired cell growth, migration, and invasion by cell cycle arrest and disrupted tumor formation in vivo. Through comprehensive RNA-seq and biochemical analyses, we elucidate that attenuation of UPF1 leads to an increase in NANOS1 expression, consequently suppressing melanoma tumorigenesis. Mechanistically, UPF1 orchestrates the destabilization of NANOS1 via UPF1-mediated mRNA decay (UMD) facilitated by miR-101-3p. Intriguingly, UPF1 depletion and NANOS1 upregulation were associated with reduced ERK and ELK1 phosphorylation, suggesting that attenuation of MAPK/ERK/ELK1 signaling may contribute, at least in part, to the observed melanoma-suppressive phenotypes. Importantly, the biological relevance of UPF1 and NANOS1 in melanoma cell lines was further supported in drug-resistant melanoma cells and in xenograft mouse models. Collectively, these findings expand our understanding of UMD in melanoma and identify the UPF1/NANOS1 regulatory relationship as a potential therapeutic vulnerability in both parental and drug-resistant melanoma cells.
    Keywords:  ELK1; NANOS1; UPF1; drug resistance; melanoma; miR-101-3p
    DOI:  https://doi.org/10.7150/ijbs.134804
  15. Front Mol Biosci. 2026 ;13 1933983
    Full-protein release assay in a reconstituted yeast translation system using GGQ-methylated eRF1.
    Shuai Huang, Yichen Xu, Wenting Chen, Ziang Miao, Chang Liu, Riku Nagai, Muhoon Lee, Hitomi Seike, Shinji Nagata, Nono Takeuchi-Tomita.
      Translation termination in eukaryotes requires the concerted action of release factors eRF1 and eRF3, together with accessory factors including eIF5A and Rli1, to achieve efficient peptide release from the ribosome. Here, we establish a yPURE system-based Termi-nLuc assay, in which pre-termination complexes (PreTCs), carrying full-length nanoluciferase (nLuc) peptidyl-tRNA, are formed by simply omitting release factors from the reconstituted yeast translation system, enabling rapid and sensitive analysis without the need for sucrose density gradient purification. To enable direct biochemical analysis of GGQ methylation-a physiologically important modification of eRF1 whose effects on peptide release activity had not previously been examined in vitro-we also established an Escherichia coli co-expression system of eRF1 and its GGQ-methylating enzyme, yielding fully GGQ-methylated eRF1. Using this platform, we characterized the individual and combined contributions of eRF1, eRF3, eIF5A, and Rli1 to peptide release, and demonstrated that the full complement of these factors is sufficient for efficient release. Under the current assay conditions, neither GGQ methylation of eRF1 nor the identity of the penultimate amino acid of the protein detectably affected peptide release activity, consistent with the possibility that eRF1•eRF3 recruitment to the ribosome, rather than the chemical hydrolysis step, is rate-limiting under these conditions. The yPURE-based Termi-nLuc assay is readily amenable to manipulation of the composition of translation factors, tRNAs, and mRNA sequences, making it a versatile and high-throughput-compatible platform for future studies of context-dependent regulation of translation termination, with potential applications in the screening of small molecules that modulate termination efficiency or promote readthrough of premature stop codons for the treatment of genetic diseases.
    Keywords:  GGQ methylation; eRF1; peptide release; reconstituted yeast translation system; translation termination
    DOI:  https://doi.org/10.3389/fmolb.2026.1933983
  16. Yi Chuan. 2026 Oct;48(10): 973-985
    Advances in tools and strategies for spatiotemporal regulation of gene expression in Caenorhabditis elegans.
    Yi-Meng Wang, Xiao Zang.
      Spatiotemporal manipulation of gene expression is essential for dissecting gene function, elucidating developmental processes, and uncovering complex physiological mechanisms. As a model organism, Caenorhabditis elegans has played an important role in basic biology research and provides an ideal experimental system for achieving such precise control. With the development of single-copy transgenesis, CRISPR/Cas9-mediated genome editing, and conditional recombination and inducible systems, the genetic toolkits for spatiotemporal regulation of gene expression, and even at the single-cell-resolution, have been greatly expanded in C. elegans. In this review, we systematically summarize the major strategies for spatiotemporal regulation of gene expression in C. elegans, with a focus on tissue-specific RNA interference, conditional protein degradation systems, inducible transcriptional regulation systems, and recently developed approaches such as Ribo-on/Ribo-off. These methods are compared in terms of regulatory levels, technical advantages, limitations, and suitable applications. Together, these tools cover multiple layers of regulation, ranging from transcriptional and post-transcriptional control to protein-level manipulation, and provide powerful approaches for developmental biology, aging, inter-tissue signaling, and disease models, while also establishing a methodological foundation for dissecting cell-autonomous and non-cell-autonomous regulatory mechanisms in complex biological processes.
    Keywords:  CRISPR/Cas9; Caenorhabditis elegans ; conditional protein degradation; inducible expression systems; spatiotemporal regulation; tissue-specific RNA interference
    DOI:  https://doi.org/10.16288/j.yczz.26-140
  17. Chem Res Toxicol. 2026 Sep 21. 39(9): 1772-1779
    Glyoxalase 1 Regulates Methylglyoxal-Derived Nucleic Acid Adduct Burden.
    Alana Battad, Francisco Nunez, Seigmund W T Lai, Elise Desjarlais, Sarah C Shuck.
      Increased metabolic stress associated with diabetes and cancer increases the level of reactive dicarbonyl molecules that covalently modify nucleic acids. Methylglyoxal (MG), one of the most abundant endogenous dicarbonyl electrophiles, reacts with guanine bases in DNA and RNA to form covalent adducts that compromise genomic and RNA integrity. The primary MG-derived adduct in DNA is N2-carboxyethyl deoxyguanosine (CEdG), and in RNA, it is N2-carboxyethyl guanosine (CEG). CEdG is mutagenic, while CEG decreases mRNA stability and impairs translation. To prevent adduct formation, cells utilize the glyoxalase pathway, which is the primary pathway for detoxifying MG. Glyoxalase 1 (GLO1) is the first enzyme in this pathway. While GLO1 is frequently dysregulated in metabolic disease and cancer, its role in regulating MG-induced nucleic acid adduct burden and the downstream functional consequences remains incompletely defined. Here, we demonstrate that the genetic ablation of GLO1 significantly increases the accumulation of MG-derived DNA and RNA adducts. We found that an elevated CEdG adduct burden is associated with increased DNA strand breaks, whereas increased CEG modifications are associated with reduced translational efficiency. These findings establish GLO1 as a critical regulator of the endogenous nucleic acid modification burden and mechanistically link metabolic stress-derived chemical lesions to genome instability and translational dysfunction.
    DOI:  https://doi.org/10.1021/acs.chemrestox.6c00169
  18. Biochem Pharmacol. 2026 Oct 17. pii: S0006-2952(26)00893-2. [Epub ahead of print] 118550
    Context-dependent protective and pathogenic functions of YTHDF1 in MASLD and hepatocellular carcinoma: Mechanisms and design of therapeutics.
    Shangyu Ao, Yibing Wang.
      Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease and can progressively develop into inflammatory metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis. During this progression, activation of hepatic stellate cells (HSCs) leads to excessive accumulation of extracellular matrix. There is a growing trend to develop into hepatocellular carcinoma (HCC). The limited availability of effective therapeutics highlights the need to better understand the underlying pathogenic mechanisms. N6-methyladenosine (m6A) is a key post-transcriptional RNA modification that regulates gene expression and governs a broad range of physiological and pathological processes. YTH domain family 1 (YTHDF1) is a reader protein that recognizes m6A modifications on mRNAs and enhances their stability or translation by interacting with key components of the translation machinery. YTHDF1 exhibits context-dependent functions in MASLD and liver fibrosis, while it promotes HCC pathogenesis. Hepatocytic YTHDF1 alleviates MASLD by improving mitochondrial function, serving as a protective factor during its early stages. YTHDF1 in HSCs is important for initiating liver fibrosis, yet it also plays a crucial role in regulating HSC ferroptosis to counteract established fibrosis. Our structure-based analyses of YTHDF1 inhibitors reveal novel concepts, including inhibition of YTHDF1-induced condensates and direct degradation of YTHDF1 proteins by fullerene derivatives and metal-organic frameworks. YTHDF1 inhibitors serve as selective chemical probes for interrogating YTHDF1's cell type-specific functions in MASLD. They are also promising candidates for in vivo evaluation to treat MASLD and HCC and to prevent liver fibrosis at early stages.
    Keywords:  Hepatocellular carcinoma; Liver fibrosis; MASLD; Therapeutics; YTHDF1; m6A modification
    DOI:  https://doi.org/10.1016/j.bcp.2026.118550
  19. Nat Commun. 2026 09 17. pii: 10928. [Epub ahead of print]17(1):
    The PAXT connection is a modifier of rare codon-enriched protein expression.
    Taylor Niehoff, Jackson Peterson, Siqi Li, Sijin Chen, Christopher V Nicchitta, Alain Laederach, Christopher M Counter.
      Synonymous codons occur at unequal rates in the coding genome, with those represented least often termed 'rare.' Rare codon-enriched genes typically exhibit poor expression due to reduced transcription, mRNA stability, export, and translation. However, there are an increasing number of examples whereby rare codon-enriched genes are paradoxically highly expressed, suggestive of mechanisms to overcome the poor expression imposed by rare codons. To identify codon-dependent modifiers, we screen a targeted sgRNA library for genes that, when inactivated, increase the expression of rare versus common codon-enriched fluorescent reporters. This identifies the PAXT connection, a nuclear complex that targets transcripts to the exosome for degradation. Targeted loss of a PAXT component leads to a small but preferential increase in mRNA levels and stability and a more pronounced increase in protein expression of rare compared to common codon-enriched reporters. Transcriptomics coupled to proteomics further reveals that this leads to a preferential increase in the expression of endogenous proteins encoded by poorly expressed and long mRNAs specifically enriched in rare codons. Thus, we identify the PAXT connection as a genetic suppressor of poorly expressed genes enriched in rare codons.
    DOI:  https://doi.org/10.1038/s41467-026-77792-7
  20. Mol Biol Rep. 2026 Oct 23. pii: 1799. [Epub ahead of print]53(1):
    Boldine enhances hyperthermia-induced apoptosis in AGS gastric cancer cells in association with attenuation of the HSF1-HSP stress response.
    Chae Ryeong Ahn, Seung Ho Baek.
       BACKGROUND: Gastric cancer presents therapeutic challenges owing to treatment resistance and stress adaptation. This study investigated whether boldine enhances mild hyperthermia-induced cytotoxicity in AGS gastric cancer cells and evaluated its association with attenuation of the heat shock response involving heat shock proteins (HSPs) and heat shock factor 1 (HSF1).
    METHODS AND RESULTS: AGS cells were pretreated with boldine (1 h) and exposed to 37-43 °C (30 min). Combined treatment reduced viability, wound closure, and colony formation more than single treatments. The apoptotic fraction increased from 8.08% in untreated controls to 28.79% with boldine alone and 3.55% with hyperthermia alone, reaching 46.33% after cotreatment. Cotreatment altered cell cycle distribution (S and G2/M fractions), increased reactive oxygen species (ROS) accumulation, and enhanced MAPK phosphorylation. N-acetylcysteine (NAC) pretreatment reduced ROS levels and apoptotic cell fraction while partially restoring HSP27 expression. Boldine suppressed HSP expression-most notably HSP27-and attenuated HSF1 phosphorylation under hyperthermia. In NCI-N87 cells, confirmatory experiments showed higher apoptosis after cotreatment, whereas hyperthermia did not further reduce viability or alter HSP levels.
    CONCLUSIONS: Boldine enhances hyperthermia-induced apoptosis in AGS gastric cancer cells in association with attenuation of the HSF1-HSP stress response and ROS accumulation, supporting boldine as a potential thermosensitizing adjunct in gastric cancer therapy.
    Keywords:  Apoptosis; Boldine; Gastric cancer; Heat shock response; Hyperthermia
    DOI:  https://doi.org/10.1007/s11033-026-12971-9
  21. Cell Struct Funct. 2026 Oct 20.
    Proteostasis stress alters mitochondrial levels and localization of SOD2 during cellular senescence.
    Yasuhiro Takenaka, Masataka Hirasaki, Yoshihiko Kakinuma.
      Proteostasis decline is a hallmark of aging and contributes to stress-induced premature senescence (SIPS) through proteotoxic stress and mitochondrial dysfunction. Although mitochondria-derived reactive oxygen species (ROS) are critically involved in SIPS, the behavior of nuclear-encoded mitochondrial antioxidant proteins under proteostasis impairment remains poorly understood. Here, we investigated the dynamics of superoxide dismutase 2 (SOD2) during SIPS induced by the proteasome inhibitor MG132 or the lysosomal inhibitor bafilomycin A1 (BAFA1) in human fibroblasts. Both MG132 and BAFA1 induced cellular senescence and caused an early reduction of SOD2 protein levels in the mitochondrial fraction without a corresponding decrease in SOD2 mRNA or total cellular SOD2 protein levels. Immunofluorescence analysis revealed that SOD2 was partially dissociated from mitochondria under these conditions, indicating impaired mitochondrial localization rather than decreased protein abundance. Quantitative colocalization analysis confirmed a significant reduction in SOD2-mitochondria overlap, which was partially restored by short-term co-treatment with antimycin A (AA), a mitochondrial electron transport chain inhibitor that attenuates excessive ROS production. Furthermore, mislocalized SOD2 was frequently associated with aggregate-like structures, and biochemical analyses demonstrated an increase in high-molecular-weight SOD2-containing complexes under proteostasis stress. These findings suggest that proteostasis disruption is associated with early changes in the intracellular distribution and aggregate-associated accumulation of SOD2, leading to a transient reduction of mitochondrial SOD2 and potentially contributing to mitochondrial oxidative imbalance and the progression of cellular senescence.Key words: cellular senescence, MnSOD, SOD2, mitochondria, oxidative stress, proteostasis, MG132, proteasome.
    Keywords:  MG132; MnSOD; SOD2; cellular senescence; mitochondria; oxidative stress; proteasome; proteostasis
    DOI:  https://doi.org/10.1247/csf.26039
  22. J Bacteriol. 2026 Oct 20. e0048426
    A transcriptional repressor co-regulatory network integrates iron homeostasis and mycobacterial stress tolerance to oxidative stress.
    Khushboo Mehta, Kajal, Harsh Goar, Bhanwar Bamniya, Dibyendu Sarkar.
      A hallmark of Mycobacterium tuberculosis survival and proliferation within the host is attributable to the effective stress response of the pathogen against hostile environmental conditions. Although controlled iron (Fe) uptake and maintenance of Fe homeostasis are closely associated with intracellular survival of mycobacteria, the underlying mechanism that accounts for the interdependence of mycobacterial Fe regulation and oxidative stress response remains unknown. In this study, we discovered that Fe accumulation connects intra-bacterial redox environment via the phoP locus. Gene expression analyses coupled with genetic, biochemical, and transcriptomic studies uncover a distinct mechanism that utilizes Lsr2 and the virulence regulator PhoP to modulate transcriptional control of the major Fe storage protein-encoding gene bfrB. Remarkably, regulated expression of bfrB determines bacterial tolerance to oxidative stress and its intracellular survival. Although both regulators could independently influence bfrB expression, the most fundamental insights are derived from the inhibition of Lsr2 binding at the bfrB regulatory region of the phoP-KO mutant strain owing to Lsr2-PhoP protein-protein interactions. Building on these results, we proposed a model suggesting how Lsr2-PhoP interaction, or lack thereof, contributes to stress-specific regulation of bfrB expression. Collectively, these results uncover a key mechanism integrating Fe accumulation to oxidative stress response, an essential pathogenic determinant of M. tuberculosis.IMPORTANCEWhile the availability of Fe remains essential for Mycobacterium tuberculosis infection and replication of the pathogen in human macrophages, Fe may be harmful as it catalyzes the generation of toxic reactive oxygen species from products of aerobic respiration to induce oxidative stress. Although interdependence of mycobacterial Fe regulation and oxidative stress response has been reported, the mechanism connecting Fe acquisition and oxidative stress response is yet to be fully understood. Results reported in this study identify and elaborate on a new mechanism of regulation of expression of the major mycobacterial Fe storage protein, which determines bacterial tolerance to oxidative stress and impacts intracellular survival of the pathogen. We demonstrate that the virulence-associated phoP locus controls Fe accumulation and contributes to the intra-bacterial redox environment. The results uncover a distinctly different transcriptional control mechanism of the major Fe storage protein requiring a co-repressor-dependent regulatory circuit, including nucleoid-associated protein Lsr2 and the virulence regulator PhoP. Together, these results unveil a unique mechanism of stress-specific gene expression, which integrates Fe homeostasis to oxidative stress response, an essential pathogenic determinant of M. tuberculosis.
    Keywords:  Fe accumulation; Lsr2-PhoP interaction; bacterioferritin; intracellular survival; oxidative stress; pathogenic determinant
    DOI:  https://doi.org/10.1128/jb.00484-26
  23. Annu Rev Microbiol. 2026 Oct;80(1): 593-618
    Biomolecular Condensates in Bacteria.
    David Moses, Anamika Avni, Keren Lasker.
      Bacteria use membraneless compartments, or biomolecular condensates, to organize cellular processes in space and time. These condensates assemble and function within a highly constrained physical landscape shaped by a crowded cytoplasm, structured nucleoid, membrane surfaces, and distinct polar zones. In this review, we examine condensates involved in genome maintenance, RNA metabolism, cell division, signaling, and metabolic regulation, focusing on how cellular microenvironments and physiological state shape when and where these condensates form, which molecules they recruit, and the material states they adopt. In turn, condensates can concentrate molecules for biochemical reactions, sequester them for storage or protection, release or redistribute them as conditions change, and position them at specific cellular sites. Disentangling the contribution of the condensed state from that of the underlying molecular interactions will be essential for determining how condensates regulate bacterial physiology.
    Keywords:  RNA metabolism; cell division; genome organization; phase transitions; stress adaptation; subcellular organization
    DOI:  https://doi.org/10.1146/annurev-micro-042424-021950
  24. Biochem Pharmacol. 2026 Oct 23. pii: S0006-2952(26)00905-6. [Epub ahead of print] 118562
    HSP27, cell stress, and hormesis: From mammals to humanized yeast models.
    Vittoria de Lima Camandona, Gabriela Maria Redondo da Silva, Esther Dantas Batista, Eduardo Vieira Vilaronga, Jose Ribamar Ferreira-Junior.
      Hormesis is a biphasic dose-response phenomenon characterized by beneficial or stimulatory effects at low exposure levels to a stressor, followed by inhibitory or toxic effects at higher doses. This effect is related to the level of oxidative stress in the cell. Human HSPB1 (HSP27) is a small heat shock protein involved in the oxidative stress response, whose overexpression correlates with increased longevity in mammalian models. HSP27 protects neurons from damage caused by protein aggregation observed in neurodegenerative diseases; however, this same survival capability also favors tumor cells, hindering chemotherapeutic treatment. This review describes HSP27 and demonstrates that the humanized yeast model can aid in understanding the function of this protein, which protects neurons and enhances tumor survival. HSP27 exhibits a dose-dependent hormetic effect when expressed at varying levels in yeast. This expression-dependent response enhances longevity, proteasome activity, and resistance to thermal and oxidative stresses. The humanized yeast model may help elucidate the relationship between the quaternary structure of the protein and its hormetic effect. In addition, the humanization of partial or complete pathways involved in both neurodegenerative diseases and apoptosis may provide a way to identify small molecules that enhance neuronal protection and potentially inhibit HSP27's pro-survival function in cancer treatment.
    Keywords:  Aging; Cancer; HSP27; Hormesis; Neurodegenerative diseases; Saccharomyces cerevisiae
    DOI:  https://doi.org/10.1016/j.bcp.2026.118562
  25. Nat Rev Mol Cell Biol. 2026 Oct 22.
    Molecular functions, cellular responses and pathological implications of the RNA modification N6-methyladenosine.
    Zihong Kang, Feng Zhang, Guo-Li Ming, Hongjun Song, Jun Liu.
      The RNA modification N6-methyladenosine (m6A) precisely regulates eukaryotic gene expression. The deposition of m6A is governed by chromatin environment, transcription and RNA processing. m6A modifications influence chromatin function and RNA splicing, stability, localization and translation, and enable cellular adaptation to environmental changes. Dysregulation of m6A has been implicated in pathological processes, including neurodegenerative diseases and cancer. In this Review, we dissect the m6A machinery by describing how writers and erasers coordinate m6A deposition and reader proteins translate these modifications into diverse functional outcomes. We illustrate how this dynamic regulatory network orchestrates cellular stress responses, metabolic homeostasis and antitumour immunity, and outline the pathological consequences of m6A dysregulation in brain disorders and cancer. Finally, we highlight translational prospects of m6A biology, including the development of specific small-molecule inhibitors and precise editing technologies, and address the remaining challenges for clinical interventions targeting m6A.
    DOI:  https://doi.org/10.1038/s41580-026-01039-y
  26. Genome Biol Evol. 2026 Oct 24. pii: evag269. [Epub ahead of print]
    SnoRNA Evolution, Genomic Context and Mobility: The Role of Function and Host Gene Association.
    Samuel Coderre, Alphonse Birane Thiaw, Michelle S Scott.
      Small nucleolar RNAs (snoRNAs) are best known for guiding chemical modifications of ribosomal and spliceosomal RNAs. Most vertebrate snoRNAs are encoded within introns of host genes and therefore depend on the production and processing of host precursor RNAs for their biogenesis. Despite this close genomic association, how host-gene context is associated with snoRNA abundance and evolution remains poorly understood. Here, we combined human snoRNA annotations from snoDB, Ensembl gene annotations, snoRNA-sensitive abundance data across multiple tissues, and vertebrate orthology analyses to systematically characterize snoRNA-host-gene relationships. Host genes were grouped into functional classes to compare snoRNA genomic organization, abundance, and conservation across host contexts. We confirmed that snoRNAs are enriched in ribosome-related and lncRNA host genes. SnoRNAs embedded in ribosome-related host genes, particularly ribosomal protein genes, showed the highest abundance and were predominantly broadly detected across tissues, whereas snoRNAs in other host classes were generally less abundant and more tissue-restricted. Across vertebrates, snoRNA sequences were often widely conserved, but the exact host-gene association was less stable, showing that sequence conservation can persist despite changes in genomic embedding. Ribosome-related host classes nevertheless emerged as comparatively stable environments. Together, these results show that snoRNA-host-gene relationships vary across host contexts and evolutionary histories and are consistent with a conceptual continuum from functionally concordant associations to more independent passenger relationships.
    Keywords:  gene mobility; host gene; noncoding RNA; small nucleolar RNA (snoRNA); vertebrate evolution
    DOI:  https://doi.org/10.1093/gbe/evag269
  27. FEBS J. 2026 Oct 21.
    Structural features of ZAK kinase regulation at the ribosome.
    Shuangshuang Niu, Vienna L Huso, Roland Beckmann, Rachel Green.
      ZAKα is a MAP3K that interacts with ribosomes and autophosphorylates upon widespread ribosome collisions mediating the ribotoxic stress response pathway. While activation of ZAKα determines downstream cell fate outcomes such as cell cycle arrest and apoptosis, the exact nature of ribosome binding and the mechanism of activation have not been fully understood. Our recent cryo-EM structures contribute to bridging this gap by visualizing ZAKα bound to ribosomes in various states (hibernating, translating, and colliding) providing a clear molecular blueprint for ZAKα kinase regulation at the ribosome.
    Keywords:  RACK1; ZAK; cryo‐EM; expansion segments; phosphorylation; ribosome collision; signaling
    DOI:  https://doi.org/10.1111/febs.70766
  28. J Transl Med. 2026 Aug 13. pii: 1331. [Epub ahead of print]24(1):
    BRAP maintains SEC24D stability to regulate ER stress and promote cervical adenocarcinoma progression.
    Hui Wang, Yingying Li, Jiaoyun Zheng, Jie Wang, Junyi Duan, Yuhuan Wang, Horst Christian Weber, Quanli Yang, Xiangping Qu, Mubiao Liu.
       BACKGROUND: Cervical adenocarcinoma (ADC) exhibits a poorer prognosis than cervical squamous cell carcinoma and lacks effective targeted therapies. Bombesin receptor- activated protein (BRAP, encoded by C6orf89) has been implicated in cell proliferation and stress responses in multiple biological contexts; however, its role in ADC progression and endoplasmic reticulum (ER) homeostasis remains unknown.
    METHODS: BRAP expression was evaluated in human cervical adenocarcinoma (ADC) tissues by immunohistochemistry and western blotting, and its clinicopathological significance was analyzed. BRAP function was investigated by siRNA-mediated knockdown in HeLa and SiHa cells using proliferation, apoptosis, migration, invasion, and epithelial-mesenchymal transition (EMT) assays, and further validated in xenograft models. Ultrastructural alterations were examined by transmission electron microscopy. BRAP-interacting proteins were identified by yeast two-hybrid screening and validated by co-immunoprecipitation. ER stress, ER exit site (ERES) homeostasis, and autophagic flux were evaluated, and rescue experiments were performed by re-expression of BRAP or SEC24D.
    RESULTS: BRAP was markedly upregulated in cervical adenocarcinoma tissues and was associated with poor tumor differentiation. BRAP depletion selectively inhibited proliferation, migration, invasion, and EMT while promoting apoptosis in ADC-derived HeLa cells, but not in squamous cell carcinoma-derived SiHa cells. Mechanistically, BRAP deficiency disrupted ER homeostasis and selectively activated the PERK-ATF4-DDIT3/CHOP branch of the unfolded protein response (UPR), whereas pharmacological inhibition with GSK2606414 largely reversed these phenotypic alterations. We identified the COPII cargo adaptor SEC24D as a novel BRAP-interacting protein. BRAP maintained SEC24D protein stability by preventing excessive autophagy-lysosome-mediated degradation, thereby preserving ERES number and function, as reflected by SEC16A-positive ERES and peripheral LMAN1-positive structures, and maintaining ER-Golgi trafficking homeostasis. Restoration of SEC24D rescued ERES defects, attenuated PERK-dependent UPR activation, and reversed the impaired proliferation, migration, invasion, apoptosis, and EMT induced by BRAP depletion.
    CONCLUSION: BRAP promotes cervical adenocarcinoma progression by maintaining SEC24D stability and preserving ERES organization and function, thereby sustaining COPII-dependent ER export and ER homeostasis. Disruption of the BRAP-SEC24D axis impairs ERES integrity, activates PERK-dependent ER stress, and suppresses malignant phenotypes. These findings identify BRAP as a previously unrecognized regulator of ER homeostasis and establish the BRAP-SEC24D signaling axis as a potential therapeutic target for cervical adenocarcinoma.
    Keywords:  BRAP; Cervical adenocarcinoma; EMT; ER stress; URP
    DOI:  https://doi.org/10.1186/s12967-026-08780-0
  29. Sci Prog. 2026 Oct-Dec;109(4):109(4): 368504261499190
    Liquid-liquid phase separation in neurodegenerative diseases: Mechanisms, pathological transitions, and therapeutic opportunities.
    Jinxi Huang, Shengxi Zhang, Dan Zhang, Tianhang Yang, Can Li, Mengjia He, Jialin Wang, Tao Song, Xianyao Wang, Yanxin Lu, Qinghong Kong, Jun Tan, Jidong Zhang.
      Liquid-liquid phase separation (LLPS) provides a biophysical framework for understanding biomolecular organization, yet its pathological relevance in neurodegeneration remains incompletely resolved. In this narrative review, we critically synthesize current evidence on LLPS in Huntington's disease, Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis, focusing on mutant huntingtin, α-synuclein, amyloid-β, tau, TDP-43, and FUS. We first outline the molecular principles-including intrinsic disorder, multivalent interactions, and environmental sensitivity-that govern their phase behavior. We then examine how dynamic condensates may, under specific cellular contexts, transition toward less reversible oligomeric, gel-like, or solid assemblies, integrating evidence from in vitro, cellular, and in vivo studies. Importantly, current evidence does not support LLPS as a universal or obligatory precursor of pathological aggregation; rather, its biological consequences appear to depend on condensate composition, material properties, subcellular localization, and proteostasis capacity, while direct demonstration of disease-relevant condensates in vivo remains limited. We further discuss whether aberrant LLPS represents a cause, consequence, or context-dependent component of neurodegeneration and highlight emerging strategies that modulate condensate formation, maturation, or clearance while preserving physiological functions. Overall, this review defines both the mechanistic potential and current limitations of the LLPS framework and identifies key questions that must be addressed before pathological phase-state modulation can become a clinically actionable therapeutic strategy.
    Keywords:  Biomolecular condensates; Intrinsically disordered proteins; Liquid-liquid phase separation; Neurodegenerative diseases; Protein aggregation
    DOI:  https://doi.org/10.1177/00368504261499190
  30. Front Immunol. 2026 ;17 1994058
    LncRNA-protein interactions: molecular switches for the precise regulation of innate immunity.
    Chenhao Yang, Yanxia Feng, Chengfang Li, Ting He, Linglong Xu, Zilin Qiao, Jiamin Wang, Zhenbin Liu.
      Long non-coding RNAs (lncRNAs) have emerged as important regulators of innate immunity, acting across multiple molecular layers to shape antiviral and inflammatory responses. Among their diverse functions, protein-centered regulation provides a particularly versatile means of controlling immune signaling by altering the functional state, interactions, localization, or turnover of proteins without necessarily changing their transcription. In this review, we synthesize current evidence for lncRNA-mediated protein regulation in innate immunity and propose a protein-centered framework that connects molecular regulatory mechanisms with their functional and immunological consequences. At the mechanistic level, lncRNA-protein interactions can modulate post-translational modifications, alter protein conformations, and facilitate or disrupt protein-protein interactions. These regulatory modes, in turn, affect four major properties of immune proteins: protein stability, subcellular localization, molecular activity, and protein-protein interaction-dependent signal transmission, ultimately reshaping innate immune responses. Across these mechanisms, several recurrent principles emerge, including preferential regulation of functionally important signaling nodes, integration of multiple regulatory mechanisms, and strong dependence on cellular and immunological context. Emerging evidence further suggests that some lncRNAs may act on defined protein states or regulatory interfaces without altering total protein abundance, although the generality of such functional selectivity remains to be established. Together, these findings support a hierarchical model in which lncRNAs translate specific molecular interactions into changes in protein function and, ultimately, innate immune states. This framework provides a basis for understanding how lncRNA-protein interactions contribute to the fine-tuning of innate immunity and for evaluating their potential as targets for selective immune modulation.
    Keywords:  antiviral immunity; innate immunity; lncRNA-protein interaction; long non-coding RNA; protein regulation
    DOI:  https://doi.org/10.3389/fimmu.2026.1994058
  31. Sci Adv. 2026 Oct 23. 12(43): eaei1547
    A methylation-dependent reader couples arginine methylation to S6K2 signaling in vivo.
    Yalong Wang, Bin Liu, Rongjie Fu, Wei He, Daniel J McGrail, Han Xu, Mark T Bedford.
      Arginine methylation regulates diverse cellular processes, yet how methyl-arginine reader proteins couple this modification to kinase signaling in vivo remains poorly defined. Here, we identify staphylococcal nuclease and Tudor domain containing 1 (SND1) as a pancreas-enriched effector that links symmetric dimethylarginine (SDMA) recognition to S6 kinase 2 (S6K2) activation. Disruption of SDMA-mediated binding by a point mutation in the SND1 Tudor domain markedly diminishes ribosomal protein S6 (S6) phosphorylation in the pancreas. Mechanistically, SND1 engages SDMA-modified arginines within the carboxyl-terminal glycine-arginine-rich (GAR) motif of S6K2 and promotes S6K2-dependent S6 phosphorylation. Mice harboring lysine substitutions at these GAR arginines (S6k2 RK) phenocopy Snd1 Tudor-mutant (Snd1 knock-in) animals, exhibiting impaired pancreatic S6 phosphorylation. Transcriptomic analyses reveal extensive overlap in dysregulated pathways between Snd1 and S6k2 mutant pancreata, supporting a shared signaling cascade. Together, these findings establish a methylation-dependent reader-kinase axis that links protein arginine methyltransferase 5-catalyzed arginine methylation to tissue-specific control of ribosome signaling and cellular stress adaptation.
    DOI:  https://doi.org/10.1126/sciadv.aei1547
  32. Immun Inflamm Dis. 2026 Oct;14(10): e70542
    Progress in the Mechanism of Heat Shock Proteins in Gastric Cancer: From Biomarkers to Therapeutic Targets.
    Wang Yanan, Zhang Jinpeng, Zhou Peng, Wang Yuan, Wang Qingyi, Liang Guoying.
       BACKGROUND: Gastric cancer remains a major challenge in public health, with low early diagnosis rates and poor prognosis for advanced patients. Heat shock proteins (HSPs) are highly conserved molecular chaperones that maintain proteostasis and promote cell survival under stress. Aberrantly elevated HSPs in gastric cancer are closely linked to tumor initiation, invasion, metastasis, and poor prognosis. This review aims to comprehensively synthesize the latest advances concerning HSPs in gastric cancer across three core dimensions: their utility as diagnostic/prognostic biomarkers, their regulatory mechanisms in key signaling pathways and the tumor microenvironment (TME), and their viability as therapeutic targets.
    MATERIALS AND METHODS: This review is structured as a narrative synthesis of the literature. A structured search was performed across PubMed, EMBASE, Web of Science Core Collection, and Cochrane Library, from their inception to March 2026. The search strategy combined keywords and MeSH terms related to three domains: (1) HSPs; (2) gastric cancer; and (3) therapeutics/inhibitors. Two authors independently screened titles and abstracts, and disagreements were resolved through discussion or consultation with a third author. Observational human studies, experimental studies (in vitro and in vivo), and preclinical animal models relevant to the three thematic pillars were included. Reference lists of included papers and relevant review articles were also manually searched. Given the broad scope and qualitative, integrative nature of this review, no formal quantitative meta-analysis or standardized risk-of-bias assessment was performed. Instead, findings were synthesized thematically, emphasizing critical appraisal of conflicting data, identification of knowledge gaps, and discussion of translational barriers.
    RESULTS: HSPs exhibit heterogeneous expression in gastric cancer tissues, which is associated with tumor differentiation, lymph node metastasis, and progression. HSP70 expression correlates with poor differentiation, high invasiveness, intestinal-type gastric cancer, and lymphovascular invasion, and is involved in proliferation, migration, anti-apoptosis, and chemoresistance; inhibition of HSP70 enhances therapeutic sensitivity. HSP90ab1 interacts with LRP5, inhibits its ubiquitin-mediated degradation, activates AKT and Wnt/β-catenin signaling, and promotes epithelial-mesenchymal transition and invasive metastasis. Plasma HSP90α is elevated in gastric cancer patients and correlates with CEA, CA125, CA153, CA199, and immune cells, as well as with metastatic stage. HSP27 is elevated in gastric cancer tissues, promotes tumor growth by inhibiting PANoptosis, and is associated with progression and poor prognosis. HSPs also participate in TME remodeling by regulating cancer-associated fibroblasts, immune cells, vascular endothelial cells, and the extracellular matrix. They can both activate anti-tumor immunity and promote immunosuppression and immune evasion, and are involved in multidrug resistance. Mechanistically, HSPs interact with pathways such as PI3K/Akt, MAPK, and TGF-β, showing context-dependent and biphasic regulatory roles. HSP inhibitors, especially HSP90 inhibitors such as ganetespib, have shown preclinical and clinical activity in gastric cancer, but single-agent efficacy is limited by toxicity, poor tumor penetration, and HSF1-driven compensatory upregulation of HSP70, HSP40, and HSP27. Combination with chemotherapy, immunotherapy, photothermal/photodynamic therapy, and nanocarrier-based delivery has shown potential to improve efficacy. Dual targeting of HSP70/HSF1 and individualized combination regimens are proposed future directions.
    DISCUSSION: HSPs are key molecules in the initiation and progression of gastric cancer. Their abnormal expression reflects tumor biological characteristics and provides new avenues for clinical diagnosis and treatment. The mechanisms of HSPs in gastric cancer are complex, involving stress responses, protein folding/repair, signaling pathway regulation, and immune evasion, which determine their critical roles in the TME. As biomarkers, HSPs have shown sensitivity and specificity in early diagnosis and prognosis, but clinical translation still faces challenges such as inhibitor selection, protection of normal cells, and drug resistance. Future research requires multidisciplinary collaboration to resolve existing controversies, clarify molecular mechanisms, and develop efficient and safe targeted drugs, so as to improve the diagnosis and treatment outcomes of gastric cancer and enhance patient survival and quality of life.
    Keywords:  biomarkers; heat shock proteins; stomach neoplasms; therapeutic targets; tumor
    DOI:  https://doi.org/10.1002/iid3.70542
  33. Funct Plant Biol. 2026 Oct 23. pii: FP26167. [Epub ahead of print]53(10):
    A comparative analysis of the tomato MAPK cascade at the transcriptional and translational levels under low-temperature conditions.
    Alexandra V Suhorukova, Ivan O Klychkov, Irina V Goldenkova-Pavlova, Michail S Piotrovskii, Alexander A Tyurin.
      Mitogen-activated protein kinases (MPKs) are involved in the cold response of plants; however, in tomatoes, their regulation has been studied only at the mRNA level. In this study, a comparative analysis of the transcriptional and translational regulation of the MAPK cascade in tomato (Solanum lycopersicum) under cold stress and hardening was conducted using polysomic profiling with parallel sequencing of total and polysomic RNA fractions. For representatives of all four groups (A-D), as well as the upstream kinases SlMAPKKK, we calculated mRNA differential expression and translational efficiency. Most cascade components were regulated predominantly at the translational level and mRNA levels remained stable. Groups C and D were profiled for the first time under cold conditions, and candidate translational cold regulators were identified.
    Keywords:  RNA-seq; abiotic stress; cold stress; mitogen-activated protein kinases (MPK); polysome profiling; tomato (Solanum lycopersicum); translational efficiency; translational regulation
    DOI:  https://doi.org/10.1071/FP26167
  34. Chronobiol Int. 2026 Oct 19. 1-20
    Timing the effort: Chronobiological drivers of skeletal muscle adaptation and metabolic health.
    Emrah Aykora, Gülfem Erbil, Damla Aykora.
      Exercise acts as a non-photic zeitgeber, resetting skeletal muscle circadian clocks that regulate metabolism, mitochondrial function, and insulin sensitivity. This review synthesizes current evidence on how exercise timing modulates skeletal muscle clock function and metabolic adaptation, with emphasis on divergent molecular pathways, sex-specific regulation, chrono-nutrition, and emerging evidence on immune-circadian interactions, myokine-mediated muscle-organ communication, and cellular stress responses. Exercise performed at different circadian phases activates distinct signaling networks despite identical mechanical workloads. Early active phase exercise, typically performed following an overnight fast, preferentially activates the AMPK-SIRT1-HIF1α axis, promoting lipid oxidation, metabolic stress sensing, and circadian phase advancement through PER/CRY modulation. Conversely, late phase exercise favors p38 MAPK-ATF2/CREB-PGC-1α signaling, enhancing mitochondrial biogenesis, oxidative phosphorylation, and Akt-AS160-GLUT4-mediated glucose disposal. Emerging evidence further suggests that circadian regulation of macrophage polarization, cGAS-STING signaling, contraction-induced myokine secretion, and proteostasis may contribute to time-dependent systemic adaptations, although direct human evidence remains limited. In addition, pronounced sexual dimorphism indicates that estrogen-mediated regulation of BMAL1/CLOCK signaling influences mitochondrial function and substrate selection. In conclusion, exercise timing represents an important regulator of metabolic health. Integrating circadian biology, nutritional timing, chronotype, sex, metabolic phenotype, and immune-metabolic context may facilitate the development of precision chrono-exercise strategies for metabolic and cardiometabolic disorders.
    Keywords:  Circadian rhythm; chronobiology phenomena; clock genes; exercise; muscle; skeletal
    DOI:  https://doi.org/10.1080/07420528.2026.2750361
  35. J Phys Chem B. 2026 Oct 22. 130(42): 11088-11102
    Deciphering the Molecular Basis of Poly(A)-Binding Protein Selectivity for Homopolymeric RNAs.
    Arun Chakrabortty, Sanjoy Bandyopadhyay.
      Protein-RNA interactions are essential for numerous biological processes, including RNA transport, translation, splicing, and gene silencing. Poly(A)-binding proteins (PABPs), a class of RNA-binding proteins, specifically recognize and bind to poly(A) tails, thereby playing a crucial role in mRNA regulation. In this study, we performed molecular dynamics (MD) simulations of PABP complexed with four homopolymeric RNAs, namely, poly(A), poly(G), poly(C), and poly(U), to elucidate the molecular basis underlying PABP's preferential binding toward different RNA analogs. Our simulations of preformed complexes reveal that different RNAs induce distinct conformational responses in PABP, leading to variations in interfacial flexibility and domain coordination. In particular, we demonstrate that complex formation promotes long-range anticorrelated motions among key protein regions, with the most significant effect observed in the poly(A)-bound complex. Importantly, we find poly(G), poly(C), and poly(U) RNAs populate disordered ensembles over the protein surface, forming fuzzy binding interfaces mediated by transient interactions and multiple binding modes, unlike the stable extended binding mode of poly(A) RNA, which is stabilized by favorable base stacking and persistent hydrogen bonding. Such structural and dynamic features are consistent with the enhanced stability of the PABP complex formed with poly(A) RNA, reflecting favorable shape-specific and base-specific interactions. Binding free energy analyses further reveal that the preferential association of PABP with poly(A) involves more favorable hydrophobic contributions and a reduced entropic penalty as compared to association with poly(G), poly(C), and poly(U).
    DOI:  https://doi.org/10.1021/acs.jpcb.6c02480
  36. Plant Commun. 2026 Oct 20. pii: S2590-3462(26)00464-5. [Epub ahead of print] 102156
    The RNA binding protein RGGA acts as a sugar-responsive cofactor of the 5'-3' exoribonuclease XRN4 to function in selective mRNA degradation and post-transcriptional regulation of plant growth.
    Ru Yu, Xin Lei Gao, Cheng Yang Ren, Hong Zhang, Xiao Qian Sun, Chang Xiang Zhu, Chang Ai Wu, Li Wei Geng, Jin Wen Du, Hao Ran Ma, Yun Zhi Song, Shu Mei Zhou, Hong Mei Liu.
      Sugar signaling governs carbon allocation between source and sink organs in plants, and excess sugar is known to repress transcripts of photosynthesis and sugar-metabolism genes. How this regulation operates post-transcriptionally remains unclear. Here we study RGGA, a RGG-repeat RNA-binding protein, and its interaction with the 5'-3' exoribonuclease XRN4 to understand how selective mRNA degradation contributes to sugar-responsive growth. In loss-of-function and domain-deletion analyses, RGGA promotes selective degradation of a defined mRNA subset, including genes involved in sucrose transport/metabolism, chlorophyll biosynthesis, and root development. In rgga mutants, these transcripts exhibit markedly extended half-lives. Disruption of the RGGA-XRN4 interaction, either by RGGA loss or deletion of the XRN4-binding domain, prevents XRN4 from recognizing these targets, leading to robust upregulation of the corresponding mRNAs. Phenotypically, rgga mutants show enhanced growth under exogenous sucrose, with a detectable growth boost after only a 5-day sucrose supply during the seedling stage. This growth pattern aligns with upregulated sugar-transport/metabolism and developmental programs driven by stabilized transcripts. These results suggest that RGGA functions as a sugar responsive cofactor that guides XRN4-mediated selective mRNA degradation, shaping post-transcriptional gene expression and plant growth in response to sugar availability. Prolonged stability of specific mRNAs promotes sugar-dependent growth, revealing a mechanism by which plants modulate carbon allocation via mRNA turnover. Targeting RGGA could help enhance crop growth under variable sugar conditions without broad transcriptional changes.
    Keywords:  Growth regulation; RGGA; Sucrose metabolism; XRN4; mRNA degradation
    DOI:  https://doi.org/10.1016/j.xplc.2026.102156
  37. Biol Open. 2026 Oct 15. pii: bio062902. [Epub ahead of print]15(10):
    Rapalink-1 reveals an mTOR- and p53-regulated transcriptional program in Neuro-2a cells.
    Joel Karikari Nyarkoh, Matthew Wolan, Eric Barrett, Aidan M Sokolov, Rachel A Lyman, Trudy F C Mackay, David M Feliciano.
      The mammalian target of rapamycin (mTOR) is the catalytic subunit of two exclusive complexes referred to as mTORC1 and mTORC2. The mTORCs phosphorylate different substrates and control different cellular processes. Inhibitors of mTORC1 include rapamycin analogs (rapalogs) that are useful in many clinical settings. However, they have failed in cancer trials potentially due to resistance mechanisms and incomplete inhibition of mTORC1 phosphorylation of select substrates. The rapamycin sensitivity of mTORC1 substrates is likely encoded by the substrate's primary amino acid sequence determinants and the ability of substrates to fit into the catalytic region of the kinase super-complex. Thus, some mTORC1 substrates are unaffected by rapalogs. Second-generation ATP-binding pocket inhibitors are mTOR catalytic inhibitors that bind in an ATP-competitive manner. Torin1 is an exemplary second-generation mTOR inhibitor with superior inhibition of mTORC1 substrates, including 4EBP. However, these inhibitors fail to demonstrate selectivity between mTORC1 and mTORC2. Third-generation bisteric mTORC1 inhibitors are exemplified by Rapalink-1, which links a rapamycin moiety to the ATP-competitive inhibitor MLN-0128. Here, we report that Rapalink-1 inhibits three mTORC1 substrates, including 4EBP and Ulk1, which are rapamycin insensitive. To provide additional mechanistic insight into the Rapalink-1 mechanism of action, RNA sequencing of Neuro-2a cells treated with Rapalink-1 was performed. Rapalink-1 caused transcriptomic changes indicative of reductions in the mTOR pathway and brain development. Many transcripts contained a p53 binding site, and consistent with this finding, we also observed reduced levels of p53. These results confirm and expand upon the Rapalink-1 mechanism of action.
    Keywords:  Cancer; Rapalink-1; mTOR; mTORC1
    DOI:  https://doi.org/10.1242/bio.062902
  38. J Mol Med (Berl). 2026 Oct 20. pii: 122. [Epub ahead of print]104(1):
    NUAK isoforms promote glucose and glutamine metabolic reprogramming driven colon cancer progression and migration through regulation of AMPK/mTOR signaling.
    Acily Skadon Worral Wilfred Raj, Jaithanya Yesupogu Moorthy Babu, Rajalakshmi Sabanayagam, Sridhar Muthusami, Ravi Manoharan.
      Colorectal cancer (CRC) cells undergo significant alterations in glucose and glutamine metabolism to support rapid growth and migration. However, the molecular mechanisms underlying these metabolic changes remain incompletely understood. Although NUAK1 and NUAK2, members of the NUAK kinase family have been implicated in CRC tumorigenesis, their specific roles in metabolic reprogramming that drives CRC progression and metastasis have not been elucidated. In this study, we demonstrate that NUAK1 and NUAK2 are overexpressed in human CRC tissues and that their expression is associated with increased tumor metastasis and poorer patient survival. NUAK1/2 promotes CRC cell proliferation and migration, whereas their depletion markedly reduces cell growth and migratory capacity. Furthermore, knockout of NUAK1/2 disrupts key metabolic pathways, including aerobic glycolysis, pentose phosphate pathway (PPP), and glutamine metabolism. Mechanistically, NUAK1/2 facilitates mTOR-driven metabolic reprogramming and promotes CRC growth and migration by suppressing AMPK activity. Depletion of NUAK1/2 impairs metabolic function, cellular growth, and migration potential in CRC cells, effects that are further enhanced by pharmacological activation of AMPK with AICAR and inhibition of mTOR using Rapamycin. In conclusion, these findings identify NUAK1/2 as critical regulators of CRC progression and migration through AMPK/mTOR-mediated metabolic reprogramming, highlighting their potential as therapeutic targets in colorectal cancer.
    Keywords:  AMPK/mTOR signalling; Colorectal cancer; Glucose and glutamine metabolic reprogramming; NUAK1/2
    DOI:  https://doi.org/10.1007/s00109-026-02730-5
  39. Methods Mol Biol. 2027 ;3091 207-231
    Visualization of RNA Structures and Functional Annotations Using ArcPlot.
    Khoa M Dao, Anthony M Mustoe.
      RNA molecules intrinsically fold into complex base-paired structures that critically shape RNA function and mechanisms. Recent innovations in chemical probing now make it straightforward to interrogate RNA structures in cells. New technologies, such as single-molecule chemical probing, further make it possible to directly measure secondary and tertiary base pairing interactions. However, visualizing and interpreting these structural data remains nontrivial. To address this challenge, we developed ArcPlot, a Python program for visualizing DMS and SHAPE reactivity data, PAIR and RING single-molecule probing data, and secondary structure arc diagrams. ArcPlot also facilitates the retrieval and juxtaposition of functional annotations of RNA elements from experiments such as enhanced crosslinking and immunoprecipitation (eCLIP). For advanced users, ArcPlot has an application programming interface (API) that can be used to generate highly customized data visualizations. We provide stepwise instructions and specific examples of different ArcPlot usage applications. The flexibility and ease of use of ArcPlot make visualization and interpretation of complex RNA structural datasets routine, broadly facilitating hypothesis generation and mechanistic understanding of RNA function.
    Keywords:  DMS; Data visualization; RNA structural ensembles; RNA structure; RNA–protein interactions; SHAPE ; chemical probing
    DOI:  https://doi.org/10.1007/978-1-0716-5627-3_13
  40. Oncol Lett. 2026 Nov;32(5): 535
    hnRNPC promotes oral squamous cell carcinoma progression via N6-methyladenosine-dependent stabilization of BCAT1 to enhance branched-chain amino acid metabolism.
    Zhixin Zhang, Xin Gao, Ting Han, Fei Chai, Menghui Gao, Yulin An.
      Oral squamous cell carcinoma (OSCC) remains a major cause of cancer-associated mortality worldwide, with current treatments limited by chemoresistance and long-term toxicities. N6-methyladenosine (m6A) modification regulates mRNA fate to drive cancer progression. However, how m6A modification regulates OSCC progression remains to be elucidated. The present study integrated bioinformatics analysis of The Cancer Genome Atlas and Genotype-Tissue Expression datasets and experimental validation to explore the role of heterogeneous nuclear ribonucleoprotein C (hnRNPC), an m6A-associated RNA-binding protein, in OSCC. Bioinformatics analysis of 515 patients with head and neck squamous cell carcinoma (HNSCC) suggested that hnRNPC may have prognostic relevance in HNSCC. High hnRNPC expression associated with advanced pathological stages, poor overall survival and served as a potential risk factor for HNSCC. Functional experiments demonstrated that hnRNPC knockdown in OSCC cell lines inhibited cell proliferation, colony formation, tumor sphere formation and in vivo tumor growth, while downregulating stemness-associated genes (Oct4, Sox2 and Nanog). Mechanistically, hnRNPC promoted branched-chain amino acid (BCAA) metabolism in OSCC. High hnRNPC expression was associated with activated BCAA metabolic pathways and hnRNPC knockdown reduced BCAA uptake, glutamate levels, oxygen consumption rate and glutathione levels. Furthermore, hnRNPC stabilized BCCAA transaminase 1 (BCAT1) mRNA in an m6A-dependent manner. BCAT1 inhibition via ERG240 enhanced the tumor-suppressive effects of hnRNPC knockdown. Exogenous supplementation of α-ketoglutarate rescued energy deficiency and functional defects in hnRNPC-knockdown OSCC cells. Collectively, the present study findings revealed a novel mechanism driving OSCC progression. In this mechanism, hnRNPC regulates BCAA metabolism by stabilizing BCAT1 mRNA in an m6A-dependent manner. The present study supports the prognostic relevance of hnRNPC and may offer a promising therapeutic direction in improving OSCC treatment outcomes by disrupting tumor-specific metabolic and epigenetic adaptations.
    Keywords:  N6-methyladenosine modification; branched-chain amino acid transaminase 1; heterogeneous nuclear ribonucleoprotein C; oral squamous cell carcinoma
    DOI:  https://doi.org/10.3892/ol.2026.15890
  41. Front Immunol. 2026 ;17 1950465
    RNA therapeutics in rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis: a compartment-aware translational framework.
    Yusif Afandizada, Hikmet Memmedov, Mushfig Orujov, Shahla Eyvazova, Shirkhan Amikishiyev.
      Rheumatoid arthritis (RA), systemic lupus erythematosus/lupus nephritis (SLE/LN), and systemic sclerosis (SSc) remain major causes of chronic inflammation, disability, organ damage, and treatment burden despite therapeutic advances. RNA therapeutics offer programmable transcript suppression, network-level microRNA modulation, transient restoration of protective proteins, and targeting-ligand functions. Existing reviews largely catalogue modalities or individual delivery systems; this review instead asks whether a candidate forms an interpretable translational program across target biology, disease compartment, intended cell, productive intracellular access, direct target engagement, pathway pharmacodynamics, repeat-dose safety, and manufacturing feasibility. RA is primarily a synovial immune-stromal delivery problem in which RNA programs must also demonstrate an advantage over effective biologic or targeted synthetic therapies. SLE/LN offers interferon, B-cell, co-stimulatory, microRNA, messenger RNA (mRNA), and complement opportunities, but therapeutic nucleic acids and carriers must not intensify nucleic-acid sensing, interferon activity, or complement-associated injury. SSc combines strong antifibrotic RNA biology with an accessible skin proof-of-mechanism window, whereas lung, vascular, and internal-organ programs remain more delivery-limited. We separate human pathway validation, RNA-platform evidence outside the target disease, disease-specific RNA evidence, and patient efficacy. Recent human complement-factor-B pharmacodynamic data strengthen the platform-level evidence but do not establish efficacy in RA or LN. The most informative early trials will therefore be biomarker-enriched and mechanism-rich, with prespecified criteria that distinguish target failure from delivery, dose, endotype, or safety failure.
    Keywords:  RNA therapeutics; antisense oligonucleotides; drug delivery; lupus nephritis; rheumatoid arthritis; small interfering RNA; systemic lupus erythematosus; systemic sclerosis
    DOI:  https://doi.org/10.3389/fimmu.2026.1950465
  42. Biosystems. 2026 Oct 21. pii: S0303-2647(26)00295-9. [Epub ahead of print]270 105985
    Emergence of bimodal First Passage Time distributions from Transcription Translation Coupling.
    Arnab Saha, Anandamohan Ghosh.
      Transcription and translation are fundamentally stochastic processes that drive significant variability in mRNA and protein levels within living cells. In certain cellular environments, these processes occur simultaneously, motivating the Transcription-Translation Coupled (TTC) model. We present a simple model of stochastic gene regulation incorporating TTC that yields bimodality in protein synthesis dynamics. By casting the estimation of protein synthesis times as a first-passage time (FPT) problem, we demonstrate that TTC generates robust bimodal FPT statistics with possible implications for bacterial survival strategies.
    Keywords:  Coupled transcription-translation; First passage time; Gene expression
    DOI:  https://doi.org/10.1016/j.biosystems.2026.105985
  43. Front Cell Dev Biol. 2026 ;14 1831562
    ALYREF regulates glycolysis and promotes the progression of endometrial cancer through m5C modification of PKM2 mRNA.
    Yun Feng, Xueyin Li.
      Endometrial cancer (EC) is one of the most common gynecologic malignancies, and effective treatment options for advanced or recurrent cases remain limited. Here, we investigated the biological function and molecular mechanism of the RNA-binding protein ALYREF in EC. Bioinformatics analysis of public datasets revealed that ALYREF is significantly upregulated in EC tissues, and high ALYREF expression is associated with poor overall survival in the Kaplan-Meier Plotter cohort. Clinical validation using paired EC tissues confirmed ALYREF upregulation at protein level, and high ALYREF expression was associated with aggressive clinicopathological features. Functional assays revealed that ALYREF promotes EC cell proliferation, migration, and invasion in vitro and enhances tumor growth and metastasis in vivo. Mechanistically, ALYREF increases the stability of PKM2 mRNA, which we demonstrate to be m5C-modified in EC, leading to elevated PKM2 protein expression, enhanced glycolytic metabolism and tumor progression. Rescue experiments confirmed that PKM2 is an important downstream effector of ALYREF-mediated oncogenic activity. Collectively, this study identifies the ALYREF-PKM2 axis as an important regulator linking RNA methylation and glucose metabolism in EC, suggesting that this axis may be a potential therapeutic target for EC.
    Keywords:  ALYREF; PKM2; endometrial cancer; glycolysis; m5C modification; proliferation
    DOI:  https://doi.org/10.3389/fcell.2026.1831562
  44. Med Oncol. 2026 Oct 20. pii: 341. [Epub ahead of print]43(11):
    METTL14-mediated FDX1 m6A methylation inhibited the proliferation of clear cell renal cell carcinoma.
    Zhijie Bai, Chun Wang, Junlin Shen, Yanjie Yang, Qian Liu, Zhiqun Shang.
      FDX1 exerts a significant influence in the process of cuproptosis by facilitating the lipoacylation of proteins and reducing copper ions to monovalent copper ions. The methyltransferase METTL14 is an enzyme that modulates the m6A methylation of RNA, which can impact the stability, translation efficiency, and degradation rate of RNA. Nevertheless, the regulatory association between METTL14 and FDX1 in kidney cancer requires further investigation. The differential expression of METTL14 and FDX1 between normal tissues and renal cancer tissues was analyzed via the GEO public database. The association between these factors and patient survival was analyzed by utilizing the TCGA public database. A correlation analysis between METTL14 and FDX1 was performed based on the TCGA database. The findings were validated through RT - qPCR, Western blot, and immunohistochemistry assays. By using SRAMP tools and m6A correlation experiments, the study elucidated the reason for the decreased expression of FDX1 in renal cancer cells. In vivo and in vitro experiments were conducted to verify the regulatory effect of METTL14 on FDX1. In clear cell renal cell carcinoma (ccRCC), METTL14 and FDX1 exhibit downregulation and are correlated with a poor prognosis among ccRCC patients. METTL14 augments the expression of FDX1 by enhancing the stability of the FDX1 messenger RNA. METTL14 upregulates FDX1 expression and consequently enhances cuproptosis in ccRCC cells. Methyltransferase METTL14 preserves the stability of FDX1 messenger RNA via m6A modification of FDX1 messenger RNA and acts as a crucial mediator of cuproptosis. Nevertheless, in clear cell renal cell carcinoma (ccRCC), the level of cuproptosis declines as a result of the diminished expression of these two factors, and the proliferation capabilities of ccRCC cells are augmented.
    Keywords:  Cuproptosis; FDX1; METTL14; Renal cancer; ccRCC; m6A modification
    DOI:  https://doi.org/10.1007/s12032-026-03438-9
  45. J Proteome Res. 2026 Oct 02. 25(10): 5452-5468
    Amino Acid Substitutomics: Profiling Amino Acid Substitutions at the Proteomic Scale Unveils Biological Implications and Escape Hypotheses in Cancer.
    Peize Zhao, Shengzhi Lai, Shuaijian Dai, Chen Zhou, Ning Li, Weichuan Yu.
      Amino acid (AA) substitutions are pivotal modulators of cellular signaling and homeostasis. Current studies of AA substitutions rely mainly on genomic and transcriptomic evidence, while proteome-level characterization remains underexplored, even though such substitutions can arise beyond DNA and RNA mutations. Here we address this gap with PIPI-C, an open-search mass spectrometry tool, and establish an integrated AA substitutomics pipeline to profile AA substitutions across five cancer cohorts and dissect the regulatory roles of substitution-bearing proteins. By cross-referencing 13,399 identified AA substitutions with matched whole-exome sequencing data, we observed no overlap with patient somatic mutations. Specifically, 61% of these substitutions required two or more base alterations and could not be derived from single-nucleotide variants, rendering them exclusively detectable at the proteomic level. The remaining 39% of substitutions were compatible with single-base variations. PIPI-C captured these candidate substitutions at the proteome scale, consistent with a translational-stage origin as reported for alternate RNA decoding in mammals. We further identified notable substitutions, including F43S and E91D in hemoglobin subunit beta, P584T in filamin A, and A175N in fructose-bisphosphate aldolase B, and our pipeline provides a framework for generating hypotheses about AA substitutions in cancer escape.
    Keywords:  amino acid substitutomics; amino acid substitutome; cancer escape; cancer proteome
    DOI:  https://doi.org/10.1021/acs.jproteome.6c00455
  46. Mol Biol Rep. 2026 Oct 21. pii: 1775. [Epub ahead of print]53(1):
    HOTAIR in cancer: a context-dependent regulatory platform linking molecular mechanisms, tumor progression, and clinical translation.
    Qingmiao Shi, Chengran Gao, Chen Xue.
      Long non-coding RNA HOX transcript antisense intergenic RNA (HOTAIR) has emerged as a representative cancer-associated lncRNA with diverse regulatory functions in tumor biology. Initially characterized as an epigenetic scaffold that recruits polycomb repressive complex 2 (PRC2) and lysine-specific demethylase 1 (LSD1), HOTAIR is now recognized as a multifunctional regulatory platform involved in chromatin remodeling, RNA-mediated regulation, metabolic adaptation, cellular plasticity, and therapeutic resistance. Increasing evidence indicates that the biological effects of HOTAIR are highly context dependent and are influenced by tumor lineage, molecular partners, RNA modifications, and cellular environments, challenging the concept of HOTAIR as a universally oncogenic factor. In this review, we summarize recent advances in understanding the molecular architecture and regulatory mechanisms of HOTAIR, including its interactions with chromatin-modifying complexes, RNA-binding proteins, and post-transcriptional regulatory networks. We further discuss the involvement of HOTAIR in cancer progression, emphasizing its roles in tumor adaptation, metastasis, epithelial-mesenchymal transition, metabolic regulation, and resistance to anticancer therapies. We also summarize current approaches for HOTAIR detection and discuss their potential clinical relevance and limitations. Although HOTAIR represents a promising candidate for biomarker development and therapeutic intervention, several challenges remain before clinical translation, including tumor heterogeneity, insufficient clinical validation, delivery limitations of HOTAIR-targeting agents, potential off-target effects, and the need for precise patient selection. Future studies integrating molecular profiling, functional characterization, and clinical evaluation will be essential to determine the translational value of HOTAIR-based strategies. A deeper understanding of HOTAIR as a context-dependent regulatory hub may facilitate the development of more precise approaches for cancer diagnosis and therapy.
    Keywords:  Biomarker; Cancer; Clinical translation; Epigenetic regulation; HOTAIR; Long non-coding RNA; Therapeutic targeting
    DOI:  https://doi.org/10.1007/s11033-026-12973-7
  47. Ageing Res Rev. 2026 Oct 22. pii: S1568-1637(26)00418-6. [Epub ahead of print] 103426
    Receptor-Specific ER-Phagy in Neurodegenerative Diseases: Molecular Mechanisms and Emerging Therapeutic Opportunities.
    Suramya Malhotra, Rajat Sandhir.
      Neurodegenerative diseases (NDs) constitute a major global health burden driven by rising life expectancy and the lack of disease-modifying therapies. Central to these progressive pathologies is the accumulation and aggregation of conformationally altered proteins, categorizing them as 'proteinopathies'. These aberrant aggregates disrupt cellular homeostasis and trigger chronic stress responses that drive progressive neuronal dysfunction and loss. The endoplasmic reticulum (ER) is a dynamic organelle defined by remarkable structural diversity and functional plasticity, that preserves cellular homeostasis by orchestrating protein folding and quality control, lipid biosynthesis, calcium sequestration and metabolic detoxification. However, sustained ER stress and functional dysregulation are increasingly implicated in neurodegenerative cascades. In this context, ER-selective autophagy (ER-phagy) has emerged as an indispensable quality-control pathway. Mediated by dedicated ER-phagy receptors that target distinct subdomains for lysosomal clearance, this pathway preserves organellar integrity and mitigates proteotoxic burden in post-mitotic neurons. Nonetheless, the full mechanistic landscape of ER-phagy remains poorly defined, with receptor-specific functions, regulatory signalling networks and CNS expression profiles only beginning to be resolved. This review synthesizes current insights into ER-phagy in neurodegeneration, dissects receptor-specific mechanisms, and highlights emerging pharmacological interventions. Ultimately, the therapeutic potential of modulating receptor-specific ER-phagy as an untapped strategy to resolve ER stress, re-establish neuronal proteostasis and to combat neurodegenerative conditions is highlighted.
    Keywords:  Autophagy; ER-phagy; Endoplasmic Reticulum; Misfolded protein; Neurodegenerative diseases; Proteinopathy
    DOI:  https://doi.org/10.1016/j.arr.2026.103426
  48. J Am Chem Soc. 2026 Oct 14. 148(40): 42969-42980
    Binding without Docking: Small-Molecule Binding Paths on Disordered Proteins.
    Adelie Louet, Gerhard Hummer, Michele Vendruscolo.
      Disordered proteins are challenging targets for drug design because they lack well-defined binding pockets. Small molecules can bind them, but when the bound state remains conformationally heterogeneous, these interactions are not readily characterized in terms of conventional binding pockets. Here, we use the concept of binding paths to describe how small molecules interact with disordered proteins. A binding path is a stochastic sequence of transient residue clusters that a ligand engages as it diffuses across a disordered protein, with each cluster forming and breaking up on time scales comparable to the overall residence time. We formalize this approach using a Markov state model (MSM), in which each state corresponds to a set of residues simultaneously contacting the ligand and the transition probabilities capture how the ligand moves between these sets. We apply this framework to the interactions of 10074-G5 with Aβ42 and of fasudil with α-synuclein, two disordered proteins associated with Alzheimer's disease and Parkinson's disease, respectively. The MSM enables both a dynamic mapping of transient binding sites and a calculation of dissociation constants consistent with experimental measurements. By generalizing the concept of static binding pockets to dynamic binding paths, this approach provides a quantitative framework for characterizing small-molecule binding by disordered proteins and for identifying druggable regions on these challenging targets.
    DOI:  https://doi.org/10.1021/jacs.6c05891
  49. Front Toxicol. 2026 ;8 1907794
    Polystyrene nanoplastics impair mitochondrial function, quality control, and ER-mitochondria crosstalk in HeLa cells.
    Giuseppe Petito, Maria Teresa Gentile, Arianna Cuomo, Angelo Fusco, Sara Falvo, Maria Della Valle, Gianluca D'Abrosca, Carla Isernia, Roberto Fattorusso, Maria Emanuela Errico, Antonia Lanni, Gaetano Malgieri, Rosalba Senese.
       Introduction: Polystyrene nanoplastics (PS-NPs) represent persistent environmental contaminants derived from the degradation of plastic debris and are increasingly detected in biological systems, raising concerns regarding their potential effects on human health. Emerging evidence suggests that, following cellular internalization, PS-NPs can induce intracellular stress responses and interfere with mitochondrial homeostasis, highlighting mitochondria as key targets of nanoplastic-induced cellular dysfunction. This study aimed to investigate the effects of PS-NPs on mitochondrial function in HeLa cells. Particular attention was devoted to Mitochondrial Quality Control (MQC) pathways, including the mitochondrial Unfolded Protein Response (UPRmt), a stress-adaptive mechanism that remains poorly characterized in response to nanoplastic exposure in human cellular model. In addition, the study examined the functional crosstalk between the Endoplasmic Reticulum and mitochondria.
    Methods: HeLa cells were exposed to PS-NPs, and mitochondrial bioenergetics, oxidative stress, mitochondrial membrane potential, cellular ATP levels, extracellular lactate levels, and calcium homeostasis were assessed using functional assays. MQC-related pathways, including UPRmt, mitochondrial biogenesis, dynamics, autophagy/mitophagy, and ER stress responses, were evaluated through biochemical, molecular, and imaging approaches.
    Results: Our results demonstrate that PS-NP exposure induces mitochondrial dysfunction, characterized by impaired mitochondrial coupling, mitochondrial membrane depolarization, increased H2O2 levels in cell lysates, and altered cellular redox homeostasis. Moreover, PS-NPs disrupt MQC processes, leading to an imbalance in the mechanisms that maintain mitochondrial homeostasis, including modulation of UPRmt-associated proteins and dysregulation of ER-mitochondria communication via Mitochondria-Associated Membranes (MAMs).
    Conclusion: Collectively, these data advance our understanding of PS-NP toxicity by identifying alterations in MQC systems and ER-mitochondria crosstalk as key events in nanoplastic-induced cellular stress. These findings provide novel mechanistic insights into nanoplastic toxicity and highlight the potential impact of environmental PS-NP exposure on cellular homeostasis and human health.
    Keywords:  HeLa cells; mitochondria associated membranes (MAMs); mitochondrial dysfunction; mitochondrial unfolded protein response (UPRmt); nanoplastics (NPs); oxidative stress
    DOI:  https://doi.org/10.3389/ftox.2026.1907794
  50. Adv Exp Med Biol. 2026 ;1359 475-485
    The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs).
    Rama R Yakubu.
      Proteins function through coordinated interactions and dynamic post-translational modifications (PTMs) that regulate cellular processes. This chapter provides a comprehensive overview of experimental and computational methods for detecting protein-protein interactions (PPIs) and characterizing PTMs, with emphasis on mass spectrometry-based approaches. We discuss classical techniques, including yeast two-hybrid screening, co-immunoprecipitation, and biophysical methods, alongside emerging proximity labeling and imaging strategies. The chapter examines major PTM classes-phosphorylation, ubiquitination, palmitoylation, glycosylation, methylation, acetylation, and SUMOylation-highlighting enrichment strategies, detection workflows, and biological significance. Together, these methodologies enable systems-level mapping of interactomes and post-translational regulatory networks, which are essential for understanding cellular function and disease mechanisms.
    DOI:  https://doi.org/10.1007/978-3-032-29437-1_28
  51. Free Radic Biol Med. 2026 Oct 17. pii: S0891-5849(26)01226-8. [Epub ahead of print]257 713-725
    Transient but not sustained p53 activation by targeting METTL3 prevents radiation-induced intestinal injury through dual-regulation of revival stem cells.
    Ruiqiu Zhu, Mingyue Li, Chengzhi Liu, Defu Kong, Jialu Qian, Ming Li, Ye Tian, Liwei Xie, Shang Cai.
      Radiation-induced intestinal injury (RIII) remains a severe complication of radiotherapy. Although p53 activation is known to be protective, no clinically available p53 activators exist. Different p53 activation dynamics (transient or sustained) are linked with radio-sensitivity, yet their therapeutic relevance to RIII has not been explored. The emerging role of N6-methyladenosine (m6A) in radiation injury is recognized, but the mechanistic link between m6A and p53 signaling in RIII remains elusive. Here, we investigated how m6A regulates p53 signaling, as well as the functional consequences and mechanisms of transient or sustained p53 activation via pharmacologically targeting m6A in RIII. After radiation, m6A writer METTL3 increases m6A on MDM2 mRNA, which is recognized by m6A reader IGF2BP3, upregulating MDM2 and suppressing intestinal p53. Then, METTL3 inhibitor S-Adenosylhomocysteine (SAH) was used to induce transient or sustained p53 activation. Functionally, a single dose of SAH suppressed MDM2 and induced transient p53 activation, thereby protecting against RIII, whereas multiple dosing induced sustained p53 activation but failed to confer a protective benefit. Mechanistically, transient p53 activation prevented RIII by stimulating YAP signaling and revival stem cells (revSCs) regeneration, a newly defined stress-induced intestinal stem cell population, whereas sustained p53 activation failed to. Importantly, SAH did not protect colorectal cancer cells from radiation. Together, these findings reveal that radiation inhibits intestinal p53 expression through the METTL3/m6A/IGF2BP3/MDM2 axis, and that transient p53 activation via METTL3 inhibition offers a promising protective strategy for RIII through YAP-mediated revSCs regeneration.
    Keywords:  MDM2; METTL3; Radiation-induced intestinal injury; Revival stem cells; m6A modification; p53; p53 activation dynamics
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.10.035
  52. Front Microbiol. 2026 ;17 1947974
    Proteomic adaptation of the hypervirulent pandemic Vibrio parahaemolyticus ST36 lineage to salinity and temperature stress.
    Eloisa González-Vidal, Sara Eslava-Alcón, Estefanía Jurado-Tarifa, Inmaculada Guerrero-Lozano, MaCarmen Durán-Ruiz, Manuel A Rodriguez-Iglesias.
      Vibrio parahaemolyticus is a halophilic Gram-negative bacterium widely distributed in marine and estuarine ecosystems, and a leading cause of seafood-borne gastroenteritis worldwide. Among its genetic lineages, sequence type 36 (ST36) has emerged as a pandemic clone with remarkable environmental persistence and global dissemination. Its pathogenicity is closely associated with environmental conditions, particularly salinity and temperature, which modulate the expression of virulence factors, stress-response proteins, and metabolic pathways. In this study, we investigated the differential protein expression profiles of Vibrio parahaemolyticus under controlled salinity (1 and 3%) and temperature (20 °C, 31 °C, and 37 °C) using a label free-quantitative (LFQ) proteomic approach. Our results demonstrate that the Vibrio parahaemolyticus proteome is dynamically and non-linearly modulated by specific combinations of salt and heat rather than a simple additive effect of these factors. Temperature-salinity interactions drove most expression changes (2,144 proteins), with temperature acting as the primary driver (1,302 proteins). Proteome changes peaked mostly at 31 °C for salinity variations and at 3% salinity for temperature shifts, each affecting ~80% of proteins, though specific responses ultimately depended on the nature of individual proteins. Functionally, protein changes were representative of a shift from relatively balanced cellular metabolism at mild stress conditions toward respiratory remodeling, central-carbon reorganization, ATP production, and redox defense under elevated salinity and temperature. Additionally, virulence-, toxin-, motility-, chemotaxis-, and defense-associated proteins were distributed across several trend clusters. Overall, the proteomic patterns detected in Vibrio parahaemolyticus in response to temperature and salinity fluctuations reveal a coordinated regulation of virulence, stress-response, and metabolic proteins that underpins its ecological fitness. Beyond these biological insights, the proteomic workflow employed provides a robust methodological framework for studying bacterial stress adaptation. Ultimately, these findings deepen our understanding of the pathogen dynamics under climate change and for improving seafood safety and risk management. Future research is warranted to experimentally validate the molecular pathways identified and confirm their functional roles in adaptation.
    Keywords:  Vibrio parahaemolyticus; environmental adaptation; foodborne diseases; marine pathogens; proteomic profile; salinity stress; thermal stress; virulence factors
    DOI:  https://doi.org/10.3389/fmicb.2026.1947974
  53. Methods Mol Biol. 2027 ;3091 145-154
    Purification of RNA G-Quadruplex Binding Proteins.
    Johanna Luige, Ulf Andersson Vang Ørom.
      G-quadruplex (G4) nucleic acids have been shown to regulate a wide range of cellular processes, including replication, telomere maintenance, epigenetic landscape, and various aspects of transcription and translation. In this method, we describe an experimental purification procedure for identifying RNA G-quadruplex-binding proteins from nuclear extracts. Using biotinylated oligonucleotides allows immobilization to streptavidin-coated magnetic beads and convenient washing during the pulldown. Importantly, the experimental protocol presented here can distinguish protein interactions with structured and unstructured RNA within the same oligonucleotide by controlling ionic conditions throughout the folding, RNA pulldown, and washing steps. The binding of individual candidate proteins can be determined by western blotting, while mass spectrometry can readily identify the whole RNA G-quadruplex-interacting proteome.
    Keywords:  G-quadruplex; RNA affinity pulldown; RNA structure; RNA-binding proteins; RNA–protein interactions
    DOI:  https://doi.org/10.1007/978-1-0716-5627-3_9
  54. ACS Synth Biol. 2026 Oct 16. 15(10): 4157-4171
    Engineered Orthogonal Translation Systems from Metagenomic Libraries Expand the Genetic Code.
    Kosuke Seki, Michael T A Nguyen, Petar I Penev, Jillian F Banfield, Farren J Isaacs, Michael C Jewett.
      Genetic code expansion with noncanonical amino acids (ncAAs) opens new opportunities for the design and engineering of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation into proteins is limited both by a small collection of orthogonal aminoacyl-tRNA synthetases (aaRSs) and tRNAs and by low-throughput methods to discover them. Here, we report the discovery, characterization, and engineering of a UGA suppressing orthogonal translation system mined from metagenomic data. We develop an integrated computational and experimental pipeline based on cell-free gene expression to screen the orthogonality of >200 tRNAs, test >1,250 combinations of aaRS/tRNA pairs, and identify the AP1 TrpRS/tRNATrpUCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS/tRNATrpUCA is highly active in cell-free and cellular contexts. We then use Ochre, a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion.
    Keywords:  bioprospecting; cell-free gene expression; genetic code expansion; noncanonical amino acids; orthogonal translation systems; protein engineering, genomically recoded organisms
    DOI:  https://doi.org/10.1021/acssynbio.6c00373
  55. Methods Mol Biol. 2027 ;3091 173-189
    Capture and Purification of Endogenous Long Noncoding Ribonucleic Protein Complexes for Protein Identification Using Grad-MS.
    Isabela T Pereira, Lucia Ferrero, Federico Ariel, John L Rinn.
      The composition of long noncoding ribonucleic protein (lncRNPs) complexes has a major impact on lncRNA function, revealing a multitude of modalities for RNA-protein interactions. However, long noncoding RNAs (lncRNAs) also interact with an array of proteins during their processing that are not related to their function. For example, different proteins involved in splicing, maturation, and nuclear export are likely to interact with a newly transcribed lncRNA. Thus, a major limitation is the purification of fully complexed lncRNPs after the transient, intermediate RNA-protein interactions. Here we outline a newly developed protocol called Sucrose Gradient coupled to Mass Spectrometry (Grad-MS): a lncRNA-centric approach to enrich lncRNPs of specified sedimentation value-indicative of fully complexed lncRNP-and identify their associated proteins. RNA-integrated complexes are cross-linked in vivo and fractionated in a sucrose gradient. Then, target lncRNAs are purified from the specific sedimentation fraction using biotinylated tiling antisense oligos, followed by protein detection using mass-spectrometry. We further outline the steps using Grad-MS to isolate discrete lncRNPs in the cytoplasm (e.g., Norad) and nucleus (e.g., Firre). Overall, Grad-MS allows the enrichment and purification of lncRNPs to facilitate protein identification.
    Keywords:  Mass spectrometry; RNA pulldown; RNA–protein complexes; Sucrose gradient; lncRNA
    DOI:  https://doi.org/10.1007/978-1-0716-5627-3_11
  56. Exp Neurol. 2026 Oct 18. pii: S0014-4886(26)00446-2. [Epub ahead of print]408 116078
    A critical mechanistic synthesis of PINK1-mediated mitophagy signaling and its therapeutic targeting in Parkinson's disease neurodegeneration.
    Abida Khan, Talha Jawaid, Zia Ur Rehman, Mohammed Kanan Alshammari, Md Afroz Bakht, Faiyaz Shakeel, Mohammed Zawiah, Mohd Imran.
      Parkinson's disease (PD) is a progressive neurodegenerative disorder that is associated with loss of dopaminergic neurons, mitochondrial dysfunction and disruption of cellular homeostasis. PTEN-induced kinase 1 (PINK1) plays a crucial role in mitochondrial quality control by regulating mitophagy, mitochondrial dynamics, and calcium signaling to maintain neuronal bioenergetic homeostasis. This review critically evaluates the molecular pathways underlying PINK1-mediated mitochondrial integrity and the mechanisms by which loss-of-function mutations contribute to the pathogenesis of PD. Familial early-onset PD is strongly associated with pathogenic PINK1 mutations identified through genetic studies. Therapeutic approaches targeting the PINK1 pathway are examined, including adeno-associated virus (AAV)-based gene delivery, direct small-molecule PINK1 activation (MTK458), and indirect modulation of mitophagy and mitochondrial homeostasis by compounds such as curcumin, resveratrol, cannabidiol, gastrodin, and quercetin. Moreover, the complementary restoration of mitochondrial homeostasis through the modulation of downstream targets, such as transcription factor EB (TFEB) activation and BCL2-interacting protein 3-like (BNIP3L/NIX)-mediated mitophagy, is discussed as an indirect therapeutic strategy. Another important finding is that PD is a biologically and clinically heterogeneous disease that requires biomarker-directed and genotype-stratified therapeutic development. Finally, major translational issues are critically evaluated, including challenges related to blood-brain barrier penetration, target specificity, and long-term safety of mitochondrial modulators.
    Keywords:  Mitochondrial dysfunction; Mitophagy; Oxidative stress; PINK1/Parkin; Parkinson's disease
    DOI:  https://doi.org/10.1016/j.expneurol.2026.116078
  57. BMC Cancer. 2026 Jul 28. pii: 1283. [Epub ahead of print]26(1):
    Investigation of the significance and role of androgen receptor expression in basal/squamous type urothelial carcinoma cell line J82 cells.
    Ryotaro Sakai, Hiroki Shimada, Shuko Hata, Atsushi Yokoyama, Yasuhiro Nakamura.
       BACKGROUND: Urothelial carcinoma (UC) is a prevalent malignancy that shows higher incidence in males but reportedly poorer outcomes in females. Among molecular subtypes, the basal/squamous (Ba/Sq) subtype is associated with poor prognosis and therapeutic resistance. Androgen receptor (AR) signaling has been implicated in UC pathogenesis, but its precise role in the Ba/Sq subtype remains unclear.
    METHODS: J82 cells stably expressing AR (J82-FLAG-AR) were established by retroviral transduction. Gene and protein expression were assessed by quantitative reverse transcription PCR (RT-qPCR) and Western blotting following dihydrotestosterone (DHT) treatment. To test AR-dependency, J82-FLAG-AR cells were co-treated with DHT and the AR antagonist enzalutamide (10 µM) for 24 h. To test p21 dependency of DHT-induced growth suppression, J82-FLAG-AR cells were transfected with siControl or siP21 (50 nM) followed by DHT treatment, with proliferation assessed by WST-8 assay. Co-immunoprecipitation was used to examine AR-enhancer of zeste homolog 2 (EZH2) interaction.
    RESULTS: AR expression in J82 cells was associated with reduced CLDN1 and CLDN4 (epithelial markers), increased GATA3 (luminal marker), and increased CDKN1A (p21) expression at both mRNA and protein levels following DHT stimulation. DHT treatment suppressed proliferation of J82-FLAG-AR cells. Co-immunoprecipitation demonstrated AR-EZH2 interaction. Combined DHT and EZH2 inhibitor (GSK126) treatment further increased p21 mRNA but did not produce additional antiproliferative effect. Pharmacological AR antagonism with enzalutamide attenuated DHT-induced p21 mRNA induction in a DHT-dose-dependent manner, consistent with competitive AR antagonism. siP21-mediated p21 knockdown abolished the DHT-induced suppression of proliferation observed in siControl-transfected cells (siRNA × DHT interaction, P = 0.047).
    CONCLUSIONS: In the Ba/Sq UC cell line J82, AR-dependent p21 induction contributes to DHT-induced suppression of proliferation, together with altered epithelial and luminal marker transcription. These observations support a p21-mediated, AR-dependent growth-restraining role for AR signaling in this subtype.
    Keywords:  Androgen receptor ; Basal/squamous subtype ; EZH2; Urothelial carcinoma; p21
    DOI:  https://doi.org/10.1186/s12885-026-16533-x
  58. Metab Brain Dis. 2026 Oct 21. pii: 243. [Epub ahead of print]41(1):
    Linking protein misfolding and heat stress: a common role for the kynurenine pathway.
    Dorothy Wasike, Petra Majerova, Timotej Jankech, Andrej Kovac.
      The kynurenine pathway (KP) of tryptophan metabolism is emerging as a key regulator of immune response, neuroinflammation, and neurodegeneration. Tryptophan-derived metabolites influence multiple processes, including excitotoxicity, oxidative stress, mitochondrial dysfunction, and protein aggregation, which are underlying mechanisms in major neurological disorders. Dysregulation of the KP leads to an imbalance between neuroactive metabolites such as kynurenic acid quinolinic acid and 3-hydroxykynurenine, contributing to neuronal dysfunction and disease progression. This imbalance is associated with chronic proteinopathies such as Alzheimer's disease and Parkinson's disease, where persistent neuroinflammation and excitotoxicity sustain the activation of KP and subsequent neurodegeneration. Importantly, KP activation is not only limited to chronic conditions but may also occur in acute neurological insults such as heatstroke, where impaired thermoregulation contributes to systemic inflammatory responses, oxidative stress, and disruption of the blood-brain barrier. Consequently, this facilitates the influx of peripheral kynurenine into the brain and its conversion into neuroactive metabolites, linking peripheral immune activation and neuronal injury. These findings highlight KP as a mechanistic bridge between acute and chronic neuropathological processes. In addition, the KP involvement in NAD⁺ production links immune activation and cellular energy metabolism, subsequently increasing neuronal vulnerability, particularly under stress. Emerging evidence further supports the potential of KP metabolites as diagnostic biomarkers for disease progression and severity, as well as possible therapeutic targets. Targeting key enzymes within the KP may offer novel strategies to reduce neurotoxicity and restore metabolic balance, which subsequently improves clinical outcomes.
    Keywords:  Heat stress; Heatstroke; Kynurenine pathway; Neurodegenerative diseases; Neuroinflammation; Protein misfolding; Proteinopathies; Tryptophan metabolism
    DOI:  https://doi.org/10.1007/s11011-026-02011-7
  59. J Am Chem Soc. 2026 Oct 21. 148(41): 44138-44155
    METTL3-METTL14 Heterodimer Assembly Enables Multivalent RNA Engagement and Is Tuned by Interface-Targeting Peptides.
    Francesco Fiorentino, Boyi Xiao, Bianca Cesaro, Sara Venezia, Jujun Zhou, Emanuele Fabbrizi, Fabrizio Casano, Gebremedhin Solomon Hailu, Xiaodong Cheng, Robin A Corey, Alessandro Fatica, Antonello Mai, Stefano Tomassi, Dante Rotili.
      RNA N6-methyladenosine (m6A) deposition by the METTL3-METTL14 complex regulates RNA metabolism and thereby influences cell differentiation and stress responses. Dysregulated m6A deposition has been implicated in multiple cancers, where METTL3-METTL14 supports oncogenic programs. Yet the molecular basis of RNA recognition by this complex remains unclear, in part due to the lack of an RNA-bound structure of the full assembly. Here, we combined native mass spectrometry (MS), molecular modeling, biochemical assays, and cell-based studies to define how METTL3-METTL14 engages RNA and how this process can be perturbed through interface targeting. Native MS of the intact heterodimer revealed simultaneous binding of multiple RNA molecules, with RNA-dependent stoichiometries and higher-occupancy states consistent with cooperative interactions. Molecular dynamics simulations identified a structured RNA-bound assembly in which the METTL14 C-terminal RGG-rich region stabilizes two RNA molecules, supporting a pre-engaged substrate configuration. We further developed a focused library of METTL14-derived peptides that bind METTL3 and interfere with protein-protein interactions, identifying the minimal METTL14 epitope for interface engagement. The most potent peptide, R8-14, binds with submicromolar affinity, disrupts both METTL3-METTL14 association and higher-order RNA-bound states, and reduces m6A levels, c-Myc expression, and cancer cell viability. Together, these findings demonstrate that RNA recognition by METTL3-METTL14 is governed by multivalent, higher-order interactions that enhance binding avidity. Notably, this assembly can be perturbed allosterically through protein-protein interface targeting rather than active-site inhibition, highlighting multivalent RNA recognition as a mechanistically and pharmacologically actionable feature of the RNA m6A writer complex.
    DOI:  https://doi.org/10.1021/jacs.6c09634
  60. Front Immunol. 2026 ;17 1960313
    FTO-mediated demethylation of PRKCB mRNA activates NF-κB to trigger alveolar fibrin deposition in ARDS.
    Xianjun Chen, Ying Liu, Song Mu, Tingting Chen, Jia Yuan, Chuan Xiao, Qi Dong, Qing Li, Ying Wang, Qimin Chen, Shuwen Li, Wei Li, Feng Shen.
       Background: Acute Respiratory Distress Syndrome (ARDS) is characterized by alveolar fibrin deposition, driven by dysregulated hypercoagulation and impaired fibrinolysis. Although alveolar epithelial type II (AEC II) cells contribute to this imbalance by overexpressing Tissue Factor (TF) and Plasminogen Activator Inhibitor-1 (PAI-1), the upstream regulatory mechanisms, particularly at the epitranscriptomic level, remain unclear. The potential role of the N6-methyladenosine (m6A) RNA demethylase FTO in ARDS pathogenesis is unexplored.
    Methods: In this study, we employed lipopolysaccharide (LPS)-induced rat ARDS models and LPS-stimulated AEC II cells as primary experimental systems to investigate the underlying mechanisms. Multi-omics profiling, combining methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq), was performed. Gain and loss-of-function studies were conducted using lentiviral vectors both in vitro and in vivo. Mechanistic investigations involved MeRIP-qPCR, mRNA stability assays, co-immunoprecipitation (Co-IP), Western blot, immunofluorescence, and pharmacological modulation of the NF-κB pathway.
    Results: Lungs from ARDS rats showed decreased global levels and increased FTO expression. Knockdown of FTO alleviated lung injury, reduced pulmonary edema, and suppressed the expression of TF and PAI-1, concomitant with inhibition of NF-κB signaling. Integrated multi-omics analysis identified Protein Kinase C Beta (PRKCB), a serine/threonine kinase known to regulate inflammatory signaling, as a key target of FTO. Mechanistically, FTO-mediated demethylation of PRKCB mRNA reduced its recognition by reader proteins that typically promote mRNA decay, thereby prolonging its half-life and enhancing protein translation. Elevated PRKCB promoted IKKβ phosphorylation and subsequent NF-κB activation. Rescue experiments confirmed that FTO regulates alveolar hypercoagulation and fibrinolytic inhibition in ARDS via PRKCB-dependent activation of the NF-κB pathway.
    Conclusion: Our study identifies the FTO-PRKCB-NF-κB axis as a novel epitranscriptomic pathway driving alveolar fibrin deposition in ARDS. These findings reveal FTO as a potential therapeutic target for mitigating alveolar hypercoagulation and fibrinolysis inhibition in ARDS.
    Keywords:  FTO alpha-ketoglutarate dependent dioxygenase (FTO); N6-methylAdenosine (m6A); NF-κB signaling; acute respiratory distress syndrome (ARDS); alveolar fibrin deposition; protein kinase C beta (PRKCB)
    DOI:  https://doi.org/10.3389/fimmu.2026.1960313
  61. ACS Synth Biol. 2026 Oct 16. 15(10): 4291-4306
    A Non-Conventional Epigenetic Engineering Strategy: The ALKBH5/ITGB5 Axis Enhances Recombinant Protein Production in CHO Cells through FAK-Mediated Proliferation and Improved Redox Status.
    Zhao-Ming Cui, Jiang-Tao Lu, Yan-Ping Gao, Yang Guo, Yin-Qi Gao, Yuan-Ye Xu, Zhi-Qing Ye, Siti Nurfatimah Mohd Shahpudin, Ying-Ying Feng, Le-Le Qiu, Chun-Peng Zhao, Ju-Fang Wang, Zi-Chun Hua, Ida Shazrina Ismail, Tian-Yun Wang, Yan-Long Jia.
      Chinese hamster ovary (CHO) cells are the predominant host for producing complex recombinant therapeutic proteins. N6-methyladenosine (m6A) regulates recombinant protein production in CHO cells by influencing RNA stability and translation; however, the role of the m6A demethylase ALKBH5 remains poorly characterized in this context. Here, ALKBH5 overexpression increased the titers of three recombinant products by up to 2.87-fold, enhanced CHO cell proliferation, and reduced oxidative stress. Co-immunoprecipitation supported an association between ALKBH5 and ITGB5, and structure-guided mutagenesis identified Tyr205 of ITGB5 as functionally important for this association and ITGB5 protein stability. ALKBH5 overexpression did not measurably alter ITGB5 mRNA stability or m6A enrichment, supporting a mechanism that does not involve detectable m6A changes on the ITGB5 transcript, while not excluding m6A-dependent effects on other targets. FAK inhibition attenuated but did not abolish the production advantage, indicating that FAK signaling contributes to, but may not fully account for, the ALKBH5-ITGB5-associated phenotype. Metabolic and redox measurements further linked ALKBH5 overexpression to increased antioxidant capacity and ATP abundance, together with altered nutrient consumption and by-product formation. These findings identify ALKBH5 as a candidate host-cell engineering target for improving recombinant protein production and support further validation under industry-relevant fed-batch conditions.
    Keywords:  ALKBH5; CHO cells; FAK/PI3K/AKT signaling; ITGB5; N6-methyladenosine (m6A); recombinant protein production
    DOI:  https://doi.org/10.1021/acssynbio.6c00520
  62. Front Immunol. 2026 ;17 1980040
    Endoplasmic reticulum stress in autoimmune skin diseases: immune activation, cutaneous cell damage, and therapeutic advances.
    Jiaxi Qiao, Jia Chen, Jinbo Chen, Liuqing Chen.
      Endoplasmic reticulum stress (ERS) arises when the protein-folding load, or perturbations in calcium and redox homeostasis, outpace the adaptive capacity of the endoplasmic reticulum (ER). The unfolded protein response (UPR) initially reduces secretory load and restores proteostasis. Persistent stress can redirect the same pathways toward inflammatory signaling, altered antigen processing, and potentially immunogenic cell death. We term this context-dependent transition ERS-immune tolerance breaking, and propose it as a unifying framework for understanding how unresolved ERS may contribute to loss of cutaneous immune homeostasis. It is especially relevant in skin, where keratinocytes and melanocytes encounter ultraviolet radiation and oxidative injury while infiltrating immune cells face large biosynthetic demands. Evidence from vitiligo, pemphigus vulgaris, psoriasis, lupus erythematosus, and systemic sclerosis links dysregulated IRE1α, PERK, and ATF6 signaling to target-cell damage and immune amplification. In this review, we evaluate this evidence with particular attention to disease-specific mechanisms and the strength of causal inference supporting a pathogenic role for ERS. The case for a pathogenic role is strongest when ERS has been manipulated in defined cell types or experimental models; associations based only on UPR markers in lesions remain harder to interpret. Therapeutic studies also caution against treating the UPR as a uniformly harmful pathway. Intervention will probably need to preserve adaptive proteostasis while limiting the pathogenic output that predominates in a particular cell population and disease phase.
    Keywords:  ERS–immune tolerance breaking; autoimmune skin diseases; cutaneous immunology; endoplasmic reticulum stress; unfolded protein response
    DOI:  https://doi.org/10.3389/fimmu.2026.1980040
  63. J Phys Chem B. 2026 Oct 22. 130(42): 11132-11165
    Chaperonopathies as Disorders of Disorder: The Role of Intrinsically Disordered Regions in Proteostasis Dysfunction.
    Adna Berilo, Naida Odobašić, Merjem Husić, Altijana Hromić-Jahjefendić, Muhamed Adilović, Vladimir N Uversky.
      Molecular chaperones are central regulators of the proteostasis network, ensuring proteome integrity through protein folding, the prevention of aggregation, and targeted degradation. These mechanisms are essential for limiting proteotoxic stress and preventing the accumulation of pathogenic proteins. Consequently, chaperone dysfunction is linked to various diseases including genetic chaperonopathies caused by pathogenic mutations. The most commonly affected chaperones include small heat shock proteins (sHSPs; HSPB1, HSPB3, HSPB5, HSPB8), Hsp60 (HSPD1), Hsp70 (HSPA9/mortalin), and the CCT/TRiC complex. sHSPs are ATP-independent chaperones critical under stress conditions and are characterized by intrinsically disordered regions (IDRs), particularly in flexible terminal regions. Although structurally important, IDRs are frequently targets of disease-associated mutations. In this study, intrinsic disorder in chaperones linked to genetic chaperonopathies was analyzed using bioinformatics tools, followed by a focused evaluation of highly disordered proteins and their disease associations. The results highlight intrinsic disorder as a conserved and functionally essential feature. HSPB1 and HSPB8 show high disorder levels, consistent with roles in neural proteostasis and neuropathies. HSPB3 and HSPB5 exhibit moderate disorder but harbor mutations linked to muscle and cardiac diseases. In contrast, HSPB6 dysfunction is mainly driven by post-translational modifications, rather than mutations. Overall, genetic chaperonopathies can be viewed as intrinsic-disorder-related diseases.
    DOI:  https://doi.org/10.1021/acs.jpcb.6c05122
  64. Prog Biophys Mol Biol. 2026 Oct 23. pii: S0079-6107(26)00079-9. [Epub ahead of print] 101962
    Crosstalk between lactylation and m6A in cancer: emerging disease mechanisms and therapeutic targets.
    Chen-Ye Yuan, Jin-Yao Zhao, Xue Li.
      Protein post-translational modifications (PTMs) and RNA modifications represent cutting-edge frontiers in cancer research. As a novel PTM, lactylation has been extensively implicated in tumor progression. Meanwhile, N6-methyladenosine (m6A), the most prevalent RNA modification, dictates cancer cell fate by governing RNA. Both modifications play pivotal roles in cancer initiation and progression, metabolic reprogramming, immune microenvironment remodeling, and therapeutic resistance. Accumulating evidence has revealed extensive and intricate functional crosstalk between lactylation and m6A, serving as a central bridge linking tumor metabolic reprogramming and epigenetic transcriptional regulation, and offering a novel perspective for elucidating cancer pathogenesis. This review provides an in-depth dissection of the crosstalk mechanisms between lactylation and m6A, highlighting their implications for targeted cancer therapy. Combination therapeutic strategies based on these mechanisms exhibit promising clinical translational potential.
    Keywords:  cancer; lactylation; m(6)A; targeted therapy
    DOI:  https://doi.org/10.1016/j.pbiomolbio.2026.101962
  65. ACS Infect Dis. 2026 Oct 09. 12(10): 3335-3350
    ExoU-Mediated Host-Cell Cytotoxicity is Associated with Phosphorylation-Dependent Regulation of DDX3Y during Pseudomonas aeruginosa Infection.
    Cheng Nong, Derong Dai, Yibo Zhu, Yunjiao Li, Jiajin Chenghuang, Mingming Gao, Jianping Ying, Yuxiao Gui, Rui Bao.
      The Pseudomonas aeruginosa type III secretion system effector ExoU is a potent phospholipase A2 that causes rapid host-cell injury, but how it engages intracellular host networks during infection remains incompletely understood. Here, using an endogenously Flag-tagged infection model in male-derived A549 cells, we identified MYH6 and DDX3Y as ExoU-associated host factors. Knockdown of either protein reduced PA14-induced cytotoxicity, indicating that both contribute to the cellular response to ExoU-positive P. aeruginosa. An in vitro pull-down assay using purified proteins further supported a direct but relatively weak association between ExoU-S142A and DDX3Y. Quantitative phosphoproteomic analysis revealed extensive host phosphorylation changes associated with ExoU catalytic activity and identified multiple phosphorylation sites on DDX3Y. Phosphorylation at S506 was detected following PA14 infection but not following exoU-S142A infection. Phospho-deficient DDX3Y mutants at S101, S141, and S506 showed increased association with ExoU, whereas the combined S101A/S141A/S506A mutant further enhanced this association and reduced infection-induced cytotoxicity. Conversely, the phosphomimetic S506E mutant showed reduced association with ExoU and restored cytotoxicity relative to S506A. RNA sequencing and DDX3Y RIP analyses further showed that ExoU catalytic activity was associated with a broader inflammatory transcriptional response and with changes in the DDX3Y-bound transcriptome, including altered association with IL6ST and NFKBIZ transcripts. Together, these findings identify MYH6 and DDX3Y as distinct ExoU-associated host factors and support a model in which ExoU catalytic activity is linked to multisite regulation of DDX3Y, altered ExoU-DDX3Y association, and changes in DDX3Y-associated RNAs. These results extend the current understanding of ExoU-mediated cytotoxicity beyond direct membrane damage.
    Keywords:  DDX3Y RNA helicase; ExoU effector; Pseudomonas aeruginosa; host−pathogen interactome; phosphorylation-dependent regulation
    DOI:  https://doi.org/10.1021/acsinfecdis.6c00279
  66. Semin Hematol. 2026 Sep 30. pii: S0037-1963(26)00096-X. [Epub ahead of print]
    From ribosomal stress to clonal adaptation: Del(5q) MDS as a paradigmatic acquired ribosomopathy.
    Juliette E Pearce, Stephani Schmitz, Rebekka K Schneider.
      Ribosomopathies reveal how defects in ribosome biogenesis generate lineage-specific hematopoietic phenotypes and create selection pressure that shapes clonal evolution. Using the germline ribosomopathies Diamond-Blackfan anemia and Shwachman-Diamond syndrome to inform a conceptual framework, we examine del(5q) myelodysplastic neoplasm as a paradigmatic acquired ribosomopathy. We propose that disease trajectory is governed not only by the initiating ribosomal defect, but by adaptive responses to persistent ribosomal stress, including compensatory rescue mutations, p53 checkpoint bypass, and internalization of ribosomal stress. This framework links lineage-specific failure, inflammatory niche remodeling, and p53-driven progression to therapeutic vulnerabilities, offering a rationale for risk stratification and targeted treatment in ribosome-stressed myeloid neoplasms.
    Keywords:  Acute myeloid leukemia; Clonal hematopoiesis; Del(5q) Myelodysplastic neoplasms; Erythroid Differentiation; Ribosomal stress; Ribosomopathy
    DOI:  https://doi.org/10.1053/j.seminhematol.2026.09.006
  67. ACS Synth Biol. 2026 Sep 18. 15(9): 3807-3820
    Improving Yield and Assessing Quality of Secreted Proteins Over-Expressed in Pichia Pastoris with Chaperones and Structural Mass Spectrometry.
    Xinzhe Ren, E-Ming Rau, Lauren Coutu, Travis Tran, Thomas J Begley, Peter C Dedon, Shane R Byrne, Stephen D Fried.
      Pichia pastoris is a widely used host for recombinant protein production because it combines the advantages of microbial cultivation with eukaryotic protein folding and secretion. However, secretion efficiency is often limited by the folding capacity of the endoplasmic reticulum (ER), where recombinant proteins must be translocated, folded, and processed prior to export. When ER folding capacity is exceeded, proteins may be retained, degraded, or secreted in non-native conformations, reducing both yield and product quality. Chaperone engineering and codon optimization represent two promising strategies to address these limitations. Here, we generated stable Pichia strains expressing four model secreted proteins (human serum albumin, interleukin-2, thaumatin-I, and thaumatin-II) using either conventional codon optimization or Epi-MAX codon engineering, which adapts transgene codon usage to stress-responsive translational programs. We also engineered strains containing an additional chromosomal copy of either the ER Hsp70 chaperone Kar2 or protein disulfide isomerase (Pdi1). To assess protein quality, we applied limited proteolysis mass spectrometry (LiP-MS), a structural proteomics approach that can detect subtle conformational differences to secreted proteins. Increased Pdi1 levels improved secretion of all four proteins tested, whereas Kar2 overexpression generally reduced yield. For thaumatin-II, Pdi1 enhanced secretion but promoted release of a non-native conformation, which we could correct through codon engineering. Together, these results demonstrate that maximizing recombinant protein production requires optimization of both yield and structural quality and establish complementary strategies for improving secreted protein expression in Pichia.
    Keywords:  Pichia pastoris; chaperones; codon usage; protein production; strain engineering; structural mass spectrometry
    DOI:  https://doi.org/10.1021/acssynbio.6c00497
  68. Redox Rep. 2026 Dec 31. 31(1): 2732775
    Protein disulphide isomerase protects against ALS/FTD phenotypes associated with cyclin F in zebrafish and cellular models.
    Sina Shadfar, Sonam Parakh, Emma Perri, Cyril Jones Jagaraj, Sara Assar Kashani, Keelin Beyers, Audrey M G Ragagnin, Angela S Laird, Julie D Atkin.
       BACKGROUND: Mutations in CCNF, encoding cyclin F, cause a small proportion of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases. Mutant cyclin F mislocalises from the nucleus to the cytoplasm, impairs the ubiquitin proteasome system, disrupts endoplasmic reticulum (ER) to Golgi transport, and triggers ER stress and apoptosis. Protein disulphide isomerase (PDI), a redox-active ER chaperone of the thioredoxin superfamily, protects against ALS phenotypes induced by mutant SOD1, TDP-43, and FUS, but its activity against mutant cyclin F has not been examined.
    OBJECTIVES: To test whether PDI overexpression prevents the cellular and behavioural phenotypes induced by the ALS/FTD-associated cyclin FS621G mutation.
    METHODS: Neuro-2a cells were co-transfected with mCherry-tagged wild-type or mutant cyclin FS621G and V5-tagged PDI or empty vector. Subcellular localisation, XBP-1 and CHOP activation, proteasome reporter (GFPu) accumulation, nuclear morphology, and cleaved caspase-3 immunoreactivity were assessed by confocal microscopy. Transient transgenic zebrafish larvae generated by mRNA co-injection of cyclin F and PDI were assessed by photomotor response at 48 h post-fertilisation.
    RESULTS: Mutant cyclin FS621G induced cytoplasmic mislocalisation, ER stress (assessed by XBP-1 and CHOP activation), proteasome dysfunction (indicated by GFPu accumulation), and apoptosis (assessed by nuclear condensation and caspase-3 activation), all of which were significantly attenuated by PDI co-expression. Zebrafish larvae expressing cyclin FS621G swam significantly shorter distances than uninjected or wildtype controls, and co-expression of PDI restored motor function to near-wildtype levels.
    CONCLUSION: PDI protects against ALS/FTD-associated mutant cyclin F in both cellular and in vivo zebrafish models, identifying PDI as a redox-based therapeutic target for CCNF-linked ALS/FTD.
    Keywords:  CCNF; ER stress; FTD; MND; ageing; cyclin F; neurodegeneration; proteostasis; zebrafish
    DOI:  https://doi.org/10.1080/13510002.2026.2732775
  69. Chem Biol Interact. 2026 Oct 19. pii: S0009-2797(26)00500-4. [Epub ahead of print]440 112392
    The unfolded protein response as a proteotoxic stress-resolution circuit: branch-selective signaling and failed resolution in environmental immunotoxicity.
    Ardie Barry Sailis.
      Environmental immunotoxicity is commonly framed through oxidative stress, cytotoxicity, inflammation, receptor-mediated signaling and cell- or tissue-specific mechanisms. This review proposes that proteotoxic stress resolution represents an additional layer linking environmental exposure to immune dysfunction. Specifically, the unfolded protein response (UPR) is considered as a branch-selective proteotoxic stress-resolution circuit that can shape immune outcomes when endoplasmic reticulum (ER) homeostasis is perturbed. The framework is offered as a hypothesis-generating conceptual structure rather than an established mechanistic paradigm, and the causal step linking failed resolution to immune dysfunction remains largely extrapolated from non-toxicological ER-stress models. Evidence from ER proteostasis biology, immune-cell function and toxicology indicates that environmental toxicants can disrupt protein folding, ER calcium balance, redox homeostasis, lipid composition, degradation pathways and secretory load, thereby engaging distinct combinations of IRE1α, PERK and ATF6 signaling. These branches generate immune-relevant outputs: IRE1α links ER stress to RNA processing and inflammatory signaling, PERK controls translational suppression and fate selection, and ATF6 supports restoration of folding capacity and secretory competence. Across macrophages, dendritic cells, T cells, plasma cells and barrier epithelial cells, immune outcomes depend on branch bias, signaling duration, cell-type context and resolution through ER-associated degradation, autophagy, ER-phagy, translational recovery and restoration of calcium and redox balance. This framework predicts that repeated low-dose exposures, mixed toxicant inputs and incomplete post-exposure recovery can shift immune or barrier cells into inflammatory, suppressive or barrier-disruptive states without overt cytotoxicity. It also supports time-resolved, branch-specific and cell-specific profiling for immunotoxic risk assessment.
    Keywords:  ER stress; Environmental immunotoxicity; Proteostasis; Stress resolution; Toxicant exposure; Unfolded protein response
    DOI:  https://doi.org/10.1016/j.cbi.2026.112392
  70. Med Res Rev. 2026 Oct 18.
    Aptamer-Based Targeted Protein Degradation: Mechanistic Principles, Delivery Strategies, and Translational Opportunities.
    Ambrin Malik, Suyeon Son, Jaesung Lee, Ki Soo Park.
      Targeted elimination of pathogenic proteins remains a fundamental challenge in therapeutic intervention, particularly for proteins considered "undruggable" by conventional inhibition-based approaches. Aptamer-based targeted protein degradation (TPD) has emerged as a versatile strategy that leverages the high specificity, structural programmability, and chemical tunability of nucleic acid aptamers to redirect disease-relevant proteins toward endogenous degradation pathways. Intracellular platforms, exemplified by aptamer-conjugated proteolysis-targeting chimeras (PROTACs), induce ubiquitination and proteasomal degradation of cytosolic and nuclear targets. In parallel, extracellular and membrane-targeting modalities, including aptamer-conjugated lysosome-targeting chimeras (LYTACs) and related lysosomal degradation systems, enable clearance of secreted and membrane-bound proteins that are inaccessible to proteasome-based strategies. Collectively, these approaches broaden the potentially degradable proteome and offer opportunities to improve target selectivity and therapeutic safety. However, most aptamer-based TPD systems remain at the proof-of-concept or early preclinical stage, with limited standardization of degradation potency, kinetics, selectivity, and in vivo efficacy. Additional challenges include the discovery of functionally active aptamers, preservation of affinity and activity after chemical modification or conjugation, efficient delivery, chemical stability, controlled biodistribution, and mitigation of innate immune activation. This review provides a mechanistic and comparative framework for intracellular and extracellular aptamer-based TPD strategies, with emphasis on quantitative performance, delivery considerations, technical bottlenecks, and their translational potential for precision protein-targeted therapeutics.
    Keywords:  LYTAC; PROTAC; aptamer; lysosomal degradation; targeted protein degradation
    DOI:  https://doi.org/10.1002/med.70110
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