bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–08–02
88 papers selected by
Cédric Chaveroux, CNRS



  1. FEBS J. 2026 Jul 27.
      Maintenance of proteostasis is essential for cellular and organismal homeostasis, and disruption of protein quality control (QC) networks underlies numerous human diseases. The endoplasmic reticulum (ER) functions as a central organelle for the synthesis, folding, maturation, and trafficking of secretory and membrane proteins, and serves as a central hub of intracellular proteostasis. Recent studies have established that the ER membrane serves not only as a site of protein translocation but also as a dynamic platform integrating translational regulation, RNA surveillance, and multiple QC pathways. During ER-associated translation, cells continuously monitor ribosome dynamics, mRNA integrity, nascent-chain folding, and transmembrane protein insertion processes to prevent the accumulation of aberrant proteins. These surveillance systems include the PKR-like ER kinase (PERK)-mediated integrated stress response (ISR), regulated IRE1-dependent decay (RIDD), nonsense-mediated mRNA decay (NMD), RNA silencing, ribosome-associated QC (RQC), ubiquitin-fold modifier 1 conjugation (UFMylation), ER-phagy, and ER stress-induced pre-emptive QC (ERpQC). Although these pathways were originally characterized independently, increasing evidence indicates that they function cooperatively on or near the ER membrane to coordinate translational attenuation, mRNA degradation, ribosome recycling, nascent-chain elimination, and organelle remodeling. In particular, UFMylation has emerged as a central mechanism linking ER-associated RQC, translocation-associated QC (TAQC), and ER-phagy. Dysfunction of these ER-localized translational QC pathways contributes to neurodegeneration, inflammation, fibrosis, cancer, and aging-related disorders. In this review, we summarize recent advances in ER-localized translational control and discuss how integrated QC networks on the ER membrane maintain proteostasis and influence disease pathogenesis.
    Keywords:  ER stress; ER stress‐induced pre‐emptive quality control; UFMylation; endoplasmic reticulum; proteostasis; ribosome‐associated quality control; translational control
    DOI:  https://doi.org/10.1111/febs.70665
  2. Genes (Basel). 2026 Jul 13. pii: 800. [Epub ahead of print]17(7):
      This article proposes three possible explanations that relate to the process of eukaryotic translation initiation. These explanations suggest mechanisms as to how concentrations of initiation factors (by mass or by posttranslational modification) can influence start site selection, how regulation of translation by 4E-BP (an inhibitor of m7G cap-dependent translation) can be explained by "eIF4F disassembly" and how the scanning mechanism might involve initiation factor binding at the 5' end of the mRNA to provide for apparent unidirectional Brownian movement to locate the initiating AUG. These represent testable models, although the experiments would not be simple. It is hoped that the insights provided will assist researchers in defining the precise steps and mechanisms of the complex initiation process. It is noted that the better this process is understood, the easier it will be to understand how this process is regulated under a wide variety of biological situations, such as nutritional deprivation, heat shock, cell growth, or disease. Additionally, as initiation is the rate-limiting step in translation, a better understanding of this process should also suggest new avenues to treat various diseases, especially conditions of unrestricted growth.
    Keywords:  ATP; eIF4A; eIF4F disassembly; equilibrium in assembly; initiation factor; initiation of eukaryotic protein synthesis; mRNA; ribosome; scanning
    DOI:  https://doi.org/10.3390/genes17070800
  3. Am J Respir Cell Mol Biol. 2026 Jul 28. pii: aanag151. [Epub ahead of print]
      The lung is a highly dynamic organ that depends on adaptable protein translation to maintain homeostasis during mechanical, metabolic, and infectious stress. Transcriptomic studies have mapped disease‑associated changes in mRNA expression across diverse lung disorders, but standard RNA‑sequencing approaches largely overlook transfer RNAs (tRNAs), obscuring an important layer of translational control. Recent advances in tRNA‑focused sequencing and functional studies have reframed tRNAs from passive adaptors to active regulators of lung biology. In this mini‑review, we highlight three major regulatory axes of tRNA biology-aminoacyl‑tRNA charging, tRNA methylation, and tRNA‑derived fragments-and their emerging roles in lung injury, infection, and cancer. We discuss how altered tRNA charging in anti-synthetase syndrome and stress response pathways, dysregulated tRNA methylation in lung cancer, and stress‑induced tRNA fragments that signal through pattern‑recognition receptors or Argonaute complexes converge on pathways controlling inflammation, remodeling, and cell survival. Finally, we outline current technical barriers to capturing tRNA species in lung omics and propose opportunities to integrate tRNA biology in future mechanistic and translational research.
    Keywords:  Transfer RNA; aminoacyl synthetases; tRNA methylation; tRNA-derived fragments
    DOI:  https://doi.org/10.1093/ajrcmb/aanag151
  4. Microbiol Mol Biol Rev. 2026 Jul 30. e0015925
      SUMMARYThe biogenesis of ribosomes and protein synthesis are among the most energy-consuming processes in living cells and therefore rate-limiting for growth, making them key targets for controlling the growth of competitors, predators, and pathogens. Cells also restrict their own protein synthesis under nutrient limitation or other stress conditions. A universally conserved strategy involves ribosome hibernation, in which specialized factors reversibly silence ribosomes. This protects ribosomes from being degraded by RNases and proteases, and at the same time allows for their fast reactivation when conditions improve. In bacteria, multiple hibernation factors act in parallel through distinct mechanisms. Well-characterized factors, such as ribosome modulation factor (RMF) and hibernation-promoting factor (HPF) and its homologs, block the mRNA channel and occupy the A- and P-sites of the small ribosomal subunit. Other factors, such as ribosome silencing factor S (RsfS), prevent the association of the 30S ribosomal subunit with the 50S subunit. Recently characterized factors include the paralogous C-tail-anchored membrane proteins YqjD, ElaB, and YgaM, which inactivate ribosomes by blocking the peptide exit tunnel. The coordinated production of these factors is tightly linked to broader stress response pathways, ensuring that ribosomal activity is modulated in accordance with cellular needs. In this review, we describe the diverse mechanisms that bacteria such as E. coli use to silence ribosomes and highlight the flexibility and significance of ribosome hibernation as a conserved strategy for saving energy and for cellular adaptation to stress conditions.
    Keywords:  dormancy; ribosome hibernation; stress response; stringent response
    DOI:  https://doi.org/10.1128/mmbr.00159-25
  5. bioRxiv. 2026 Jul 24. pii: 2026.07.23.740346. [Epub ahead of print]
      Apicomplexan parasites, including Toxoplasma gondii and Plasmodium falciparum, are major human pathogens that cause toxoplasmosis and malaria, respectively. The existing structures of T. gondii translational machinery are from empty ribosomes that lack several key components, including ribosomal protein RACK1 (Receptor for Activated C Kinase 1). Here, we used cryo-electron microscopy (cryoEM) to determine high-resolution structures of T. gondii ribosomal complexes, including a translating 80S ribosome bound to mRNA and tRNA. These structures reveal that RACK1 occupies the conserved binding site on the 40S subunit observed in other eukaryotic ribosomes. We also determined the architecture of the ribosomal P-stalk and identified the ribosomal proteins uL10 and uL11, which were not observed in previous T. gondii ribosome structures. In addition, we determined structures of the 80S ribosome bound to mRNA, tRNA, and the translation inhibitor emetine in two distinct conformational states. These snapshots reveal two mechanisms by which emetine inhibits the translocation step of mRNA translation: either by dislodging the mRNA from the E-site of the ribosome or by acting as a molecular glue within the E-site, thereby stalling translocation. Together, these findings provide new insights into the molecular basis of protein synthesis in apicomplexan parasites and establish a structural framework for the development of future antiparasitic therapeutics.
    DOI:  https://doi.org/10.64898/2026.07.23.740346
  6. bioRxiv. 2026 Jul 21. pii: 2026.07.21.739842. [Epub ahead of print]
      Human cytomegalovirus (HCMV) is a major cause of organ disease among immunonaïve and immunocompromised individuals. HCMV infection stimulates the survival of normally short-lived circulating monocytes, allowing these blood cells to mediate the dissemination of the virus from the initial point of infection to distant organ sites. We previously showed that HCMV induces a non-canonical phosphorylation of Akt within infected monocytes that activates the stress response transcription factor Heat Shock Factor 1 (HSF1). In this study, we demonstrate that HSF1 is necessary for the survival of HCMV-infected monocytes using both pharmacological and genetic approaches. In contrast, HSF1 inhibition had minimal effect on the viability of uninfected cells, indicating the specific involvement of HSF1 on the survival of infected monocytes. Surprisingly, the aberrant activation of HSF1 by HCMV did not trigger nuclear relocalization, suggesting that HSF1's regulation of monocyte viability occurs within the cytoplasm. Indeed, we found that HCMV-activated, cytoplasmic HSF1 directly binds to mTOR, a critical component of the mTORC1 complex involved in the regulation of mRNA translation. SUnSET (Surface Sensing of Translation) assays revealed HCMV-activated HSF1 increases mRNA translation through mTORC1. Ribosomal profiling identified the increased translation of a selected subset of pro-survival transcripts, including cIAP2, which we validated to selectively stimulate the survival of HCMV-infected monocytes. Taken together, these data demonstrate that the non-canonical activation of HSF1 in infected monocytes drives mTORC1-dependent translation of antiapoptotic transcripts, ensuring the survival and dissemination of infected monocytes.
    IMPORTANCE: HCMV is a primary driver of morbidity and mortality in individuals with compromised or immature immune systems. Spread of HCMV throughout the body relies on the infection of peripheral blood monocytes, which spread the virus to end-organ tissues. However, the naturally short lifespan of monocytes must be overcome to allow for viral spread to occur. Here, we demonstrate that HCMV uniquely regulates the cellular stress response to promote the long-term survival of infected monocytes. Specifically, HCMV activates the cellular stress response transcription factor HSF1 to block the progression of apoptosis. In contrast to traditional heat shock stress where HSF1 translocates into the nucleus to mediate transcription, HCMV infection retains activated HSF1 in the cytoplasm where it binds to mTOR to promote protein synthesis of prosurvival factors necessary for the survival of infected monocytes. Overall, our study provides insight into the complex regulator mechanisms through which HCMV usurps host stress responses to promote viral dissemination.
    DOI:  https://doi.org/10.64898/2026.07.21.739842
  7. J Cell Biol. 2026 Aug 03. pii: e202409149. [Epub ahead of print]225(8):
      Cells respond to various stressors by inhibiting global translation and forming stress granules (SGs), cytoplasmic organelles enriched in certain RNA-binding proteins, and RNA. Genotoxic stress also induces SG assembly, but it is unclear how nuclear stress signals are transmitted to trigger cytoplasmic responses. We show that DNA-damaging agents that activate a nuclear poly(ADP-ribose) polymerase (PARP), PARP1, stall translation and induce SGs. We find that PARP1 activation depletes NAD+, which depletes cellular ATP, activating ATP-sensor AMPK and inhibiting mTORC1 via Raptor phosphorylation. Subsequent hypophosphorylation of 4EBP1 inhibits translation. These effects are suppressed by PAR-metabolism regulators, XRCC1, PARG, and Nudix5, and reversed by NAD+ precursor supplementation. Cells lacking SG scaffolds, G3BP1 and G3BP2, show reduced viability after genotoxic stress, which is rescued by G3BP1 overexpression. These findings link PARP1 activity to translational control and SG formation, which may protect against cell death following DNA damage. These mechanisms provide insight into PARP1- and stress granule-associated diseases, including cancer and neurodegeneration.
    DOI:  https://doi.org/10.1083/jcb.202409149
  8. Front Immunol. 2026 ;17 1864973
      Acute kidney injury (AKI) is a clinically critical condition with a high mortality rate. Its complex pathophysiological mechanisms remain incompletely understood, and there is a lack of effective targeted therapeutic strategies. In recent years, the role of epigenetic modifications in the initiation and progression of kidney disease has been increasingly clarified. N6-methyladenosine (m6A) is one of the most important and common post-transcriptional modifications among various RNAs, including eukaryotic mRNAs, lncRNAs, and miRNAs. It is dynamically and reversibly regulated by methyltransferases ('writers'), demethylases ('erasers'), and binding proteins ('readers') to modulate processes such as RNA splicing, export, stability, translation, and degradation. This modification exerts diverse biological effects and is extensively involved in both physiological and pathological pathways. Recently, a growing body of evidence has indicated that m6A modification plays a crucial regulatory role in the development and progression of AKI. Existing studies suggest that m6A modification profoundly influences the fate of renal tubular epithelial cells (TECs) by regulating the expression of genes associated with inflammatory responses and programmed cell death, thereby modulating the severity of AKI and the subsequent renal repair process. This review systematically summarizes the latest research advances regarding m6A modification in AKI, elucidates the mechanisms by which it influences the pathogenesis of AKI through various cellular processes, and explores the potential of m6A-targeted therapies for treating AKI, thereby providing insights into the regulatory networks of m6A modification in AKI and the epigenetic regulation of transcription in this condition.
    Keywords:  N6-methyladenosine; acute kidney Injury; inflamation; programmed cell death; therapeutic targets
    DOI:  https://doi.org/10.3389/fimmu.2026.1864973
  9. Viruses. 2026 Jul 07. pii: 748. [Epub ahead of print]18(7):
      Flaviviruses, encompassing notable pathogens, like Dengue, Zika, West Nile, and tick-borne encephalitis viruses, elicit complex cellular stress responses, involving pathways such as the unfolded protein response (UPR), integrated stress response (ISR), apoptosis, autophagy, and the antiviral immune response. These pathways regulate cell fate by either promoting survival to counteract virus-induced damage or triggering cell death programs under prolonged and irreparable stress. Therefore, the primary aim of flavivirus-induced cellular responses is to protect cells and hinder viral propagation. Despite cellular defenses, flaviviruses have evolved various subversion strategies, mainly involving viral proteins, which enable successful infections even when cellular responses are activated. While these cellular pathways were previously perceived as separate entities, recent studies suggest interplay and dynamic shifts among these stress response pathways, underscoring the need for further investigation in this area. In this review, we explore the key pathways activated during flavivirus infections, examine mechanisms of viral subversion, and delve into the synergy of these pathways, thereby elucidating the impact on the progression of infection. A deeper understanding of these interactions will guide future efforts to define how cellular stress responses shape flavivirus infection and leverage this knowledge toward the development of targeted antiviral strategies.
    Keywords:  apoptosis; autophagy; flaviviruses; immune response; integrated stress response; unfolded protein response
    DOI:  https://doi.org/10.3390/v18070748
  10. Int J Mol Sci. 2026 Jul 17. pii: 6365. [Epub ahead of print]27(14):
      The sequence of messenger RNA (mRNA) not only determines the protein sequence synthesized by a ribosome but also defines the efficiency of this process. Many antibiotics lethal to bacteria inhibit various stages of translation by targeting ribosomal functional centers. Some antibiotics exhibit specificity not only for particular stages of the ribosomal working cycle but also for specific patterns within mRNA sequences. This review covers a broad range of approaches-including in vivo and in vitro methods, low- and high-throughput techniques such as reporter constructs, characterization of inhibitors of protein synthesis (ChIPS), toeprinting, cryogenic electron microscopy (cryo-EM), protein labeling, and those integrated with next-generation sequencing (NGS) like ribosome profiling with following NGS (Ribo-seq), inverse toeprinting coupled with NGS (iTP-seq), high-throughput toeprinting and NGS (Toe-seq), and ribosome display-used to study the sequence specificity of translation inhibitors, a rapidly evolving field crucial to molecular biology. It presents various methodologies, discusses their applications, and provides a comparative analysis. The fundamental research value of this review lies in establishing standardized experimental selection guidelines for scientists investigating ribosome stalling mechanisms, thereby minimizing trial-and-error costs. Equally important is its applied relevance. The review highlights its translational value in aiding the screening and mechanistic analysis of sequence-specific small-molecule inhibitors. Moreover, understanding the mechanisms underlying protein biosynthesis inhibition and their dependence on particular mRNA sequences could enable the development of selective agents that precisely suppress the synthesis of certain polypeptides, such as proteins from pathogenic bacteria or cancer-associated proteins.
    Keywords:  NGS; context specificity; inhibitor; methodology; protein synthesis; ribosome stalling; translation pausing
    DOI:  https://doi.org/10.3390/ijms27146365
  11. Microbiol Mol Biol Rev. 2026 Jul 28. e0037425
      SUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modifications are well documented and play essential roles in tRNA folding, rRNA maturation, translation, and peptidyl transfer. Although mRNA modifications have been extensively characterized in eukaryotes, their functional implications for mRNA fate in prokaryotes remain uncertain, and their identities and locations are the subject of an emerging field of research. Importantly, RNA modification is a dynamic process, and variation in the presence and abundance of these modifications has significant consequences for bacterial physiology. Here, we discuss current knowledge of modified RNA nucleotides in bacteria, with a particular focus on their roles in bacterial adaptation to environmental stress.
    Keywords:  environmental stress; epitranscriptome; mRNA; rRNA; tRNA
    DOI:  https://doi.org/10.1128/mmbr.00374-25
  12. bioRxiv. 2026 Jul 22. pii: 2026.07.21.739814. [Epub ahead of print]
      Ribosomes stall when they encounter problematic codons or cellular stress that perturbs translation. Stalled ribosomes can lead to the formation of ribosome collisions, also known as disomes, that engage cellular surveillance and stress signaling pathways. How many disomes form during basal conditions and how disome levels change under stress remain poorly understood. Here, we used spike-in normalized Ribo-seq and Disome-seq to quantify transcriptome-wide disome levels. Applying this approach in yeast and human cells, we found that disomes comprise approximately 2-10% of translating ribosomes under basal conditions. A high-resolution Disome-seq experiment in human cells identified reproducible disome-forming sites that contribute to the basal level of disome formation in the cell. Exposure of yeast cells to methyl methanesulfonate and human cells to anisomycin increased disome abundance up to four-fold and changed the distribution of collisions in a stress-specific and context-dependent manner. Overall, these data provide a quantitative, transcriptome-wide framework for measuring disome levels and reveal how translational stress reshapes the landscape of ribosome collisions in cells.
    DOI:  https://doi.org/10.64898/2026.07.21.739814
  13. J Biosci Bioeng. 2026 Jul 29. pii: S1389-1723(26)00247-1. [Epub ahead of print]
      Elucidating the physiological impact of acetic acid stress and the corresponding yeast responses is essential for advancing fundamental biology and improving industrial alcoholic fermentation. Despite numerous genome-wide studies, information on the effects of acetic acid stress on yeast translational regulation remains limited. We found that a sublethal concentration of acetic acid (35 mM, 0.2% v/v) causes translational repression, accompanied by the formation of eIF2B bodies and the phosphorylation of eIF2α, both of which are involved in the regulation of translation initiation. Acetic acid also caused the sequestration of Ded1, a DEAD-box RNA helicase crucial for translation initiation, into stress granules. Removal of acetic acid restored translational activity and the proper localization of eIF2B and Ded1, indicating the reversibility of acetic acid-induced translational repression. Furthermore, when yeast cells were pretreated with 0.05% acetic acid, translational repression under subsequent 0.2% acetic acid stress was attenuated in wild-type cells but not in hrk1Δ cells. This indicates that Hrk1, a Pma1 activator, is required to sufficiently enhance tolerance to acetic acid-induced translational repression. These findings provide novel insights into the physiological effects of acetic acid stress on translational activity and translation-related factors in yeast cells.
    Keywords:  Acetic acid; Adaptation; Ded1; HRK1; Saccharomyces cerevisiae; Stress granules; Translational repression; eIF2B bodies
    DOI:  https://doi.org/10.1016/j.jbiosc.2026.07.005
  14. Biomedicines. 2026 Jun 23. pii: 1419. [Epub ahead of print]14(7):
      Across all kingdoms of life, ribosomes are indispensable molecular machines that translate genetic information into the proteome of living cells. The fundamental catalytic centers of the ribosome, constructed primarily from ribosomal RNA (rRNA), exhibit remarkable conservation between the major domains of life. The ribosome's A-site deciphers the mRNA's triplet code, while the P-site synthesizes the growing protein chain and the E-site provides exit for deacylated tRNA; a distinct tunnel facilitates nascent polypeptide export. While the conservation of ribosomal proteins is less pronounced between bacteria and eukaryotes, striking homology exists from simple eukaryotes to humans. Ribosomal proteins were traditionally viewed mainly as scaffolding agents, steering rRNA folding during ribosome biogenesis and maintaining structural stability during translation. However, since the early 2000s, advances in structural and functional ribosome analysis have ushered in a more nuanced paradigm: ribosomes are no longer considered uniform machines. Instead, an array of rRNA and ribosomal protein modifications generates a spectrum of ribosome populations capable of specialized translation. RiboScreenTM technology leverages this regulatory potential of individual ribosomal proteins, enabling deliberate modulation of target protein output and representing a promising tool for correcting dysregulated protein expression involved in rare and common diseases. This review will first introduce relevant aspects of ribosome biology and then showcase the tools of this new technology. Finally, we report examples for the delivery of small molecules to target ribosomal proteins for tailored restoration of protein production levels in rare and prevalent diseases.
    Keywords:  RiboScreenTM; customized protein production; novel drug targets; precision intervention in rare and prevalent disease; ribosomal proteins
    DOI:  https://doi.org/10.3390/biomedicines14071419
  15. Biochim Biophys Acta Mol Cell Res. 2026 Jul 28. pii: S0167-4889(26)00099-6. [Epub ahead of print] 120200
      Regulation of miRNAs in mammalian cells-including their expression, activity, transport, storage, and export-is vital for the control of gene expression and cellular function. This process is affected by external stimuli, such as stress or pathogen exposure, and regulated by interactions among miRNAs, target mRNAs, and RNA-binding proteins. Human ELAVL1 HuR, a stress-responsive nuclear protein that can shuttle to the cytoplasm, modulates miRNA activity, storage, and export in a contextual manner. As an AU-rich element (ARE)-containing RNA-binding protein, HuR plays multimodal roles in miRNA regulation. How HuR manages these diverse functions under stress, infection, or in cancer remains a key area of research. This review explores the miRNA-regulatory role of HuR across subcellular compartments, focusing on how its localization affects miRNA export or storage, and discusses potential mechanisms underlying HuR's versatile functions, including mRNA stabilization and miRNA homeostasis. This review discussed how post-translational modifications of HuR or its partners affect miRNA activity, suggesting that HuR serves as a miRNA sensor and linking HuR-related miRNA regulation to human diseases, thereby positioning HuR as a druggable target for controlling miRNA activity and target gene expression.
    Keywords:  ELAVLs; Gene expression regulation, Subcellular compartments; RNA binding proteins, Extracellular Vesicles; miRNA export
    DOI:  https://doi.org/10.1016/j.bbamcr.2026.120200
  16. bioRxiv. 2026 Jul 13. pii: 2026.07.11.737834. [Epub ahead of print]
      Bacterial gene expression depends on the coordinated regulation of RNA synthesis, processing, and decay. The conserved RNA degradosome scaffold, Ribonuclease E (RNase E), assembles into phase-separated bacterial ribonucleoprotein bodies (BR-bodies) through its C-terminal intrinsically disordered region (IDR). This IDR also scaffolds recruitment of degradosome client proteins that carry out post-transcriptional gene regulation. Whether BR-bodies regulate virulence programs to support infection, however, is largely undefined. We show that RNase E of the intracellular pathogen Brucella ovis forms RNA-dependent condensates in vivo and phase-separates with RNA in vitro, with the IDR necessary and sufficient for BR-body assembly. Deleting the IDR ( rne (ΔIDR)) did not impair growth but sensitized Brucella to host-relevant oxidative and cell-envelope stressors. Transcriptome-wide profiling that simultaneously resolved mRNA decay and processing revealed that BR-bodies primarily accelerate mRNA turnover while stabilizing a distinct subset of transcripts. Notably, BR-bodies control the processing and levels of virB type IV secretion system (T4SS) mRNA and the turnover of its key activators, linking condensate-based RNA regulation to a core virulence pathway. Consistent with virB dysregulation, the rne (ΔIDR) mutant was severely attenuated in mammalian macrophages. To test whether phase separation is sufficient for BR-body function, we replaced the B. ovis IDR with the highly divergent Caulobacter crescentus IDR. This chimera assembled BR-bodies but rescued fitness incompletely, fully restoring oxidative-stress resistance but not cell-envelope stress resistance or intracellular fitness. BR-bodies therefore link RNA metabolism to Brucella stress resistance and infection, and their full function requires both phase separation and additional native IDR-specific activities such as degradosome interactions.
    Importance: Biomolecular condensates are non-membrane bound organelles that organize biological processes across all domains of life, but their role in bacterial infection is not well characterized. We show that Brucella , an intracellular bacterial pathogen and causative agent of the disease brucellosis, relies on biomolecular condensates called BR-bodies to control RNA stability and regulate gene expression. Without BR-bodies, Brucella is sensitized to host-relevant chemical stresses, cannot properly regulate essential infection machinery, and has severely diminished fitness within mammalian host cells. These results indicate that control of RNA levels by biomolecular condensates is required for Brucella survival within animal hosts, providing evidence that phase separation is a fundamental mechanism underlying Brucella adaptation to the hostile environment encountered during infection.
    DOI:  https://doi.org/10.64898/2026.07.11.737834
  17. Antioxidants (Basel). 2026 Jun 25. pii: 793. [Epub ahead of print]15(7):
      Mitochondrial Lon peptidase 1 (LONP1) is an ATP-dependent AAA+ (ATPases associated with diverse cellular activities) protease that has emerged as a key regulator of mitochondrial proteostasis, with functions extending beyond protein quality control. In addition to degrading misfolded and oxidized proteins, LONP1 coordinates mitochondrial DNA maintenance, metabolic remodeling, and stress-responsive signaling. Recent structural and functional advances have expanded the biological significance of LONP1 beyond protein quality control, highlighting its roles in mitochondrial metabolism, genome maintenance, and stress responses. LONP1 dysregulation is increasingly implicated in cancer, metabolic disorders, neurodegeneration, and aging, where it exerts context-dependent effects on cell survival and disease progression. In cancer, LONP1 supports metabolic plasticity, redox adaptation, and therapeutic resistance, whereas in degenerative conditions, its decline contributes to mitochondrial dysfunction and tissue damage. Here, we synthesize recent insights into the structure, mechanisms, and biological functions of LONP1 and discuss their implications for human disease. We further discuss emerging therapeutic strategies and key challenges for targeting LONP1 in human disease.
    Keywords:  LONP1; cancer metabolism; mitochondrial metabolism; mitochondrial proteostasis; stress response
    DOI:  https://doi.org/10.3390/antiox15070793
  18. bioRxiv. 2026 Jul 29. pii: 2026.07.19.739412. [Epub ahead of print]
      The 26S proteasome is the hub for regulated protein turnover in eukaryotic cells. Degradation of proteins by the Ubiquitin-Proteasome System plays critical roles in every aspect of cell biology, such as the regulation of gene transcription, the quality control of translation and protein folding, and protein transport across membranes. While mRNA levels and protein abundances can be readily measured with a robust set of established tools, only a few methodologies exist to identify proteins that are degraded by the proteasome rather than the lysosome as the second major pathway for turnover. Here, we sought to address this by using genetic code expansion to introduce a photo-crosslinkable unnatural amino acid into the yeast 26S proteasome and capture cellular protein substrates as they translocate through the proteasomal ATPase motor. In vitro biochemical experiments confirmed that these modified proteasomes are functional, which allowed us to introduce them into live yeast cells for in vivo crosslinking and the identification of enriched ATP-dependent substrates by mass spectrometry. These experiments revealed a very diverse pool of proteasomal substrates that markedly changed upon cell exposure to endoplasmic reticulum stress. Together, our results represent an exciting avenue for probing the landscape of proteasomal substrates and its changes in response to various cellular conditions and stresses.
    DOI:  https://doi.org/10.64898/2026.07.19.739412
  19. Int J Mol Sci. 2026 Jul 17. pii: 6378. [Epub ahead of print]27(14):
      The ZFP36 family proteins (TTP, ZFP36L1, and ZFP36L2) are RNA-binding proteins that function as key post-transcriptional regulators of gene expression. They bind AU-rich elements (AREs) in target mRNA 3'UTRs, recruit the CCR4-NOT deadenylation complex to trigger mRNA decay, and maintain homeostasis in immunity, barrier function, and stem cell fate. Rather than acting on single targets, all family members share a conserved mRNA destabilization mechanism, with outcomes determined by member-specific expression, kinase-mediated regulation, and cell-type-dependent target availability. Dysregulation of this network stabilizes mRNAs encoding pro-inflammatory cytokines, immune checkpoints, and oncogenes, driving pathogenesis of inflammation, autoimmunity, cancer, cardiovascular and neurodegenerative diseases. Individual family members exert context-dependent and sometimes opposing effects, so their net function depends on the specific cellular and disease context. Therapeutic strategies targeting ZFP36 activity, including phosphatase agonism and epigenetic modulation, have shown promising preclinical results, but clinical translation remains early. This review summarizes the molecular regulatory networks of the ZFP36 family and their physiological and pathological roles, emphasizing the mechanistic principles that unify family-member function and the contextual factors that diversify it, to provide a foundation for future therapeutic development.
    Keywords:  ZFP36 family; inflammation; mRNA decay; post-transcriptional regulation; therapeutic targets; tumorigenesis
    DOI:  https://doi.org/10.3390/ijms27146378
  20. Pharmaceuticals (Basel). 2026 Jun 25. pii: 990. [Epub ahead of print]19(7):
      Epitranscriptomic modifications, particularly RNA methylations, have emerged as regulators of gene expression, with their dysregulation acting as a key factor in tumorigenesis and metastatic progression. This review evaluates the therapeutic landscapes of N6-methyladenosine (m6A) and N1-methyladenosine (m1A) modifications in cancer. While the m6A machinery predominantly dictates mRNA turnover and stability, the m1A network is uniquely positioned to drive translational reprogramming, allowing malignant cells to endure severe microenvironmental stress and evade cell death. Despite positional and chemical differences, these modifications exhibit profound epitranscriptomic crosstalk through shared regulatory proteins. Here, we comprehensively analyze current pharmacological strategies targeting the m6A axis, highlighting the transition from classical small-molecule inhibitors of regulatory proteins of these methylations, such as methyltransferase-like 3 (METTL3), fat mass and obesity-associated protein (FTO), and AlkB homolog 5 (ALKBH5), to the novel event-driven approach of proteolysis-targeting chimeras (PROTACs). Furthermore, we assess the emerging therapeutic potential of the m1A regulatory machinery, positioning tRNA methyltransferase 6/61A (TRMT6/61A) writers and AlkB homolog 1 to 3 (ALKBH1-3) erasers as promising therapeutic targets. Finally, we discuss clinical successes and current translational obstacles, including off-target toxicity, pharmacokinetic limitations, and epitranscriptomic escape, emphasizing that site-specific modulation and smart precision therapies will dictate the future of oncology.
    Keywords:  RNA modifications; adenosine methylations; epitranscriptomics; proteolysis-targeting chimeras (PROTACs); small molecule inhibitors; targeted cancer therapy; translational reprogramming
    DOI:  https://doi.org/10.3390/ph19070990
  21. Mol Biol Rep. 2026 Jul 28. pii: 1284. [Epub ahead of print]53(1):
      The RNA cytosine modification (RCM), particularly 5-methylcytosine (m5C) and N4-acetylcytidine (ac4C) modification, represents a rapidly advancing frontier in recent epitranscriptomic research. These reversible modifications intervene in the process of RNA generation, thus playing a critical role in the post-transcriptional regulation of RNA, including nuclear export, ribosome assembly, translation, and stability, thereby modulating various fundamental biological processes, such as cellular proliferation, differentiation, and cell death. Musculoskeletal disorders (MSDs), including osteoarthritis (OA), osteoporosis (OP), rheumatoid arthritis (RA), osteosarcoma (OS), and intervertebral disc degeneration (IVDD), are a major class of debilitating conditions that affect the locomotor system. Emerging evidence has demonstrated that dysregulation of m5C or ac4C modification contributes significantly to MSD pathogenesis through multiple mechanisms, including chondrocyte pyroptosis, lipid droplet dynamics, macrophage polarization, osteogenic and osteoclastic differentiation, synovial hyperplasia and invasion, and tumor-associated metabolic reprogramming. Moreover, these modifications are mechanistically linked to key pathological hallmarks, such as immune cell infiltration, ferroptosis, autophagy, and aberrant mechanical compression transduction. Pharmacological targeting of m⁵C- and ac⁴C-regulatory enzymes has been indicated to have therapeutic potential in animal models of MSDs. Herein, we present this review that systematically addresses the molecular basis and current knowledge on the mechanisms underlying RCMs in a variety of MSDs, along with translational strategies targeting these epitranscriptomic pathways. Finally, we present our thoughts and comments on this topic.
    Keywords:  Bone disease; Cytosine; Epitranscriptomic modification; Musculoskeletal disorder; RNA; ac4C; m5C
    DOI:  https://doi.org/10.1007/s11033-026-12466-7
  22. FEBS J. 2026 Jul 29.
      While many antagonistic antibodies are in routine clinical use, only a single agonistic antibody has received regulatory approval to date. While antibodies that activate Death Receptor 5 (DR5) were thought to have utility in the treatment of cancer by enhancing extrinsic apoptosis signaling, to date all clinical studies with these DR5 agonists have failed to deliver significant clinical benefit. A notable example of this is the DR5 agonistic antibody conatumumab. Here, we provide two potential avenues to improve the activity of DR5 agonists. First, we show that a dimeric IgA version (dIgA2) of the conatumumab antibody has a higher toxicity to cancer cells and a shorter half-life in vivo compared to the original IgG version of the antibody. Moreover, we conducted a genome-wide CRISPR screen to identify genes for which inactivation enhances the sensitivity of cancer cells to the dIgA2 DR5 antibody. We found that inhibition of mitochondrial protein translation synergizes with DR5 agonists. Consequently, antibiotics that inhibit mitochondrial protein translation also synergize with DR5 agonists. Finally, we show that these antibiotics activate the Integrated Stress Response (ISR) and upregulate DR5 through the EIF2a-ATF4 axis, which sensitizes cancer cells to DR5 activation. These data suggest a potential combination strategy for the effective use of DR5 agonistic antibodies.
    Keywords:  CRISPR screening; apoptosis; dimeric IgA; integrated stress response; mitochondria
    DOI:  https://doi.org/10.1111/febs.70669
  23. J Cell Mol Med. 2026 Jul;30(14): e71301
      Glioblastoma (GBM) exhibits profound metabolic plasticity and resistance to conventional therapies, partly driven by mitochondrial adaptability and stress response mechanisms. ONC212, a second-generation imipridone, targets mitochondrial proteostasis, yet determinants of tumour sensitivity remain unclear. This study aimed to investigate whether ATP-sensitive potassium (KATP) channel expression modulates ONC212-induced mitochondrial dysfunction and integrated stress response (ISR) activation in GBM. Human GBM lines (U87, U251, T98G) and non-malignant SVG p12 astrocytes received ONC212 (0.5-80 μM) for 12-48 h. Viability was assessed by CCK-8. KATP subunit expression (Kir6.2, SUR1, CCDC51) was quantified by qRT-PCR and western blot. Mitochondrial ROS quantification, oxygen consumption rate (Seahorse XF), PERK/ATF4/CHOP activation (western blot, immunofluorescence) and apoptosis (caspase-3/7) were evaluated. KATP was modulated pharmacologically (glibenclamide, diazoxide) and via KCNJ11 (Kir6.2) siRNA. ONC212 induced time-dependent and tumour-selective cytotoxicity, with highest sensitivity observed in KATP-high U87 cells. Treatment significantly increased mitochondrial ROS, impaired oxidative phosphorylation and reduced ATP/ADP ratios, indicating bioenergetic collapse. Concurrently, ONC212 robustly activated the PERK/eIF2α/ATF4/CHOP axis and promoted ATF4 nuclear translocation. PERK inhibition attenuated both stress signalling and cytotoxicity, confirming ISR dependency. KATP inhibition enhanced ONC212-induced mitochondrial dysfunction, ISR activation and apoptosis, whereas KATP activation exerted protective effects. Importantly, KCNJ11 silencing markedly potentiated ONC212 sensitivity, amplifying ROS production, mitochondrial impairment and caspase-dependent apoptosis. KATP channel expression may regulate ONC212 responsiveness in GBM by modulating mitochondrial stress and ISR signalling. Targeting KATP channels may enhance imipridone efficacy and represents a promising strategy for metabolically guided GBM therapy.
    Keywords:  KATP channels; ONC212; glioblastoma; integrated stress response; mipridone; mitochondrial dysfunction
    DOI:  https://doi.org/10.1111/jcmm.71301
  24. Cell Rep. 2026 Jul 27. pii: S2211-1247(26)00804-1. [Epub ahead of print]45(8): 117726
      The integrated stress response (ISR) coordinates cellular adaptation to diverse stress conditions. In Drosophila, two bZIP transcription factors, Xrp1 and crc (ATF4 homolog), are induced during ISR. Crc protein can dimerize with two CEBP factors in vitro, but the in vivo relevance of those interactions remained unknown. Here, we report that the CEBPG homolog, Irbp18, is an essential partner of crc during ISR. Specifically, Irbp18 is broadly required for the transcriptional induction of ISR target genes in the photoreceptors of ninaEG69D, a Drosophila model of retinitis pigmentosa. Moreover, CUT&RUN analysis indicates that Irbp18 loss reduces or abolishes crc binding to target DNAs in photoreceptors and impairs crc's ability to induce target transcripts upon overexpression. Functionally, Irbp18 loss causes retinal degeneration and suppresses ISR signaling in parkin mutants, a model of Parkinson's disease. Together, these findings identify Irbp18 as a cofactor for crc, impacting pathological outcomes in Drosophila models of degeneration.
    Keywords:  ATF4; CEBP; CP: molecular biology; CP: neuroscience; ISR; Irbp18; bZIP; dimerization; integrated stress response; parkin; retinal degeneration; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2026.117726
  25. Plant Cell Rep. 2026 Jul 27. pii: 234. [Epub ahead of print]45(8):
       KEY MESSAGE: Salt stress induces ABI5 → ALKBH10B transcription; the demethylase removes m6A from RAP2.6 mRNA, accelerating its decay and attenuating salt-responsive genes, thus linking ABA signaling to reversible m6A control of Arabidopsis salt tolerance. N6-methyladenosine (m6A) is the most prevalent internal modification of RNA and plays an important role in regulating RNA metabolism that governs development and environmental adaptation of plants. Here we dissect how the Arabidopsis m6A demethylase ALKBH10B is integrated into abscisic-acid (ABA)-mediated salt-stress signaling. Under salt treatment, loss of ALKBH10B exhibited significantly delayed seed germination. Salt stress could significantly induce the expression of ALKBH10B transcription via the ABA-responsive transcription factor ABI5, which binds directly bind to the ABRE element in the ALKBH10B promoter and activate its transcription. Multi-omic integration of m6A methylomes and transcriptome identified the AP2/ERF transcription factor RAP2.6 as a direct target of ALKBH10B. ALKBH10B removed m6A modifications on RAP2.6 mRNA, accelerating its degradation and modulating the expression of salt-responsive genes. In summary, this study elucidates the salt stress response pathway ABI5-ALKBH10B-RAP2.6 that couples ABA perception to reversible m6A modification, providing mechanistic insight into the intricate regulatory network of dynamic m6A modifications in plant stress adaptation.
    Keywords:  ABI5; ALKBH10B; RAP2.6; Salt stress; m6A
    DOI:  https://doi.org/10.1007/s00299-026-03919-1
  26. Plant Cell Physiol. 2026 Jul 28. pii: pcag105. [Epub ahead of print]
      Plants dynamically adjust growth in response to short-day (SD) conditions while maintaining reactive oxygen species (ROS) homeostasis across cellular compartments. However, how light signaling is coupled to organelle-specific redox regulation remains poorly understood. Here, we identify the peroxisomal Mpv17/PMP22 family protein REGULATOR OF ROS-MEDIATED HYPOCOTYL ELONGATION 1 (RHE1) as a regulator of short-day-induced hypocotyl elongation and ROS homeostasis in Arabidopsis thaliana. RHE1 expression is associated with a light-responsive G-box element bound by HY5 and shows a strong positive relationship with N6-methyladenosine (m6A) enrichment. Environmental stresses that elevate inferred m6A levels increase RHE1 transcript abundance and stability, whereas short-day conditions reduce m6A enrichment and decrease RHE1 expression. Loss of RHE1 results in enhanced hypocotyl cell elongation and elevated ROS accumulation specifically under short-day conditions, indicating that RHE1 constrains growth through peroxisomal redox regulation. Furthermore, RHE1 transcript levels correlate with the m6A reader ECT2, and published binding datasets support direct association of ECT2 with RHE1 mRNA. Together, these findings reveal a multilayered regulatory mechanism in which HY5-associated transcription and m6A-dependent RNA stabilization converge on RHE1 to coordinate SD-dependent growth with peroxisomal ROS homeostasis. This study uncovers a previously unrecognized connection between SD signaling, epitranscriptomic regulation, and organelle-specific redox control.
    Keywords:  Hypocotyl elongation; Peroxisome; ROS regulation; Short-day signaling; m6A RNA methylation
    DOI:  https://doi.org/10.1093/pcp/pcag105
  27. Int J Med Sci. 2026 ;23(8): 2679-2714
      Protein S-palmitoylation, the reversible thioesterification of cysteine side chains, is emerging as a druggable post-translational modification that couples membrane topology to oncogenic, metabolic, immune, and epigenetic networks in cancer. ZDHHC palmitoyltransferases and depalmitoylating enzymes, including acyl-protein thioesterases and palmitoyl-protein thioesterase 1, constitute a dynamic circuitry that governs the localization, stability, and signaling competence of key regulators of tumor growth, metabolic adaptation, and immune phenotype. Here, we synthesize recent structural and chemical biology advances that clarify how human ZDHHC enzymes achieve acyl-chain recognition and substrate engagement. Structural studies show that these enzymes adopt a four-transmembrane, "tent-like" fold, in which the helices create a membrane-embedded cavity for acyl-chain accommodation. We also discuss how ankyrin-repeat domains and accessory partners shape substrate recruitment and subcellular localization, and we highlight emerging high-throughput platforms that enable quantitative profiling of isoform- and site-selective modulators. We then discuss how ZDHHC-substrate circuits rewire canonical growth-factor signaling and epithelial-mesenchymal transition programs, metabolic and ferroptotic control nodes, innate immune sensing, and chromatin-linked regulation. These convergent mechanisms position ZDHHC-mediated S-palmitoylation as a context-dependent regulator of tumor progression, therapy response, ferroptosis sensitivity, and immune phenotype. Finally, we outline a translational framework encompassing clinical-stage PPT1 inhibitors, selective ABHD17 blockade, emerging ZDHHC modulators, substrate-competitive strategies targeting checkpoint palmitoylation, and selected comparator approaches affecting Wnt and Hedgehog ligand lipidation. Current evidence positions ZDHHC-mediated S-palmitoylation as a regulatory layer with potential biomarker and therapeutic relevance; however, not all reported ZDHHC-substrate associations carry equivalent evidentiary weight. Mechanisms supported by convergent site-directed, genetic, biochemical, functional, and in vivo evidence should be distinguished from associations inferred mainly from expression profiling, overexpression systems, single-model observations, or broad pharmacological perturbation. Clinical translation remains preliminary and is constrained by isoform selectivity, substrate redundancy, incomplete pharmacodynamic read-outs, and the absence of validated biomarker-guided patient stratification.
    Keywords:  S-palmitoylation; ZDHHC palmitoyltransferases; cancer metabolism; depalmitoylases; oncogenic signaling; tumor immunity
    DOI:  https://doi.org/10.7150/ijms.130609
  28. Genes (Basel). 2026 Jun 30. pii: 777. [Epub ahead of print]17(7):
      Clinical genomics has traditionally focused on protein-coding variation, yet many pathogenic mechanisms arise through alterations in RNA processing, stability, localisation, translation, and surveillance. Prior reviews have addressed individual RNA layers, splicing, non-coding RNAs, RNA therapeutics, or RNA diagnostics in isolation. This review presents an integrated, mechanism-matched framework linking RNA-level disease mechanisms to diagnostic reasoning and therapeutic selection across all major RNA layers, offering a practical resource for clinical geneticists and translational researchers. I examine how splicing defects, pseudoexon inclusion, polyadenylation disruption, RNA editing loss, untranslated-region variants, premature termination codons, stop-loss variants, RNA-binding protein dysfunction, non-coding RNA dysregulation, altered codon usage, ribosome stalling, and surveillance pathway failure, including nonsense-mediated decay, nonstop decay, and no-go decay, each create distinct and mechanistically addressable disease states. A central argument of this review is that treatment selection must be mechanism-matched rather than gene- or variant-class-based: splice defects may require antisense oligonucleotide (ASO)-mediated correction or small-molecule splice modulation; toxic transcripts may require ASO- or siRNA-mediated silencing; haploinsufficiency may require mRNA replacement or transcript rescue; premature termination codons are candidates for readthrough only when transcript and protein context are favourable. I further argue that RNA sequencing, long-read transcriptomics, allele-specific expression analysis, and functional assays are essential for both diagnosis and therapeutic stratification. The framework described here moves clinical variant interpretation beyond descriptive classification toward mechanism-based, RNA-centric precision medicine.
    Keywords:  RNA processing; RNA surveillance; RNA therapeutics; RNA-binding proteins; non-coding RNA; nonsense-mediated decay; precision medicine; rare disease; splicing; synonymous variants; translational regulation; upstream open reading frames
    DOI:  https://doi.org/10.3390/genes17070777
  29. Wiley Interdiscip Rev RNA. 2026 Jul-Aug;17(4):17(4): e70050
      The discovery of tRNA as an adapter molecule established the foundation for understanding its essential roles in gene expression, stress responses, cellular homeostasis, and disease, including viral infections. Human tRNAs carry multiple chemical modifications that maintain their structure and ensure proper function. Since viruses depend entirely on host translation machinery, many of them can manipulate tRNA functioning at the structural level or the functional level. This review highlights how diverse viruses exploit tRNA epitranscriptomics, supported by recent advances in tRNA sequencing and profiling. Understanding the mechanisms by which viruses exploit the host tRNA landscape and the related molecules can identify novel antiviral targets, offering opportunities to interfere with viral protein synthesis and replication.
    Keywords:  epitanscriptomics; modifications; modifying enzymes; tRNA; tRNA pool; virus
    DOI:  https://doi.org/10.1002/wrna.70050
  30. J Exp Bot. 2026 Jul 28. pii: erag367. [Epub ahead of print]
      Root arbuscular mycorrhizal symbiosis (AMS) allows plants to thrive in nutrient deficient environments. This symbiosis shaped land life evolution and allowed the emergence of root nodule symbiosis (RNS). Both AMS and RNS involve the internalization of symbionts -mycorrhizal fungi and nitrogen-fixing bacteria, respectively- either in root ground tissue or in new derived cells. This internalization relies on root cellular reprogramming, which include ectopic cell cycle activation in AMS, or extensive cell cycle activation in RNS. Cell divisions and meristematic activity in the roots are accompanied by ribosome biogenesis and active mRNA translation. Whereas arbuscular infected cells show enrichment in ribosomal proteins (RPs), transcripts encoding RPs accumulate at early stages of the RNS. In addition, specific components of the translational machinery, including eukaryotic initiation and elongation factors, are detected in single-cell transcriptomes of actively dividing cortical cells that will give rise to a nodule primordium. The diversity of heterogeneous ribosomes and their regulatory associated components might contribute to the translation of specific subsets of mRNAs in different tissues, explaining the differences between the transcriptome and polysome-associated mRNAs observed in early RNS. Features of the regulated mRNAs such as upstream open reading frames may have an impact on translation initiation. In addition, evidence suggests that translation is modulated by small and long non-coding RNAs. This review discusses the relevance of translation in association with cellular reprogramming in root symbioses.
    Keywords:  Ribosome; cell division; cortex; meristem; translation
    DOI:  https://doi.org/10.1093/jxb/erag367
  31. J Vis Exp. 2026 Jul 07.
      Mitochondrial ATP-dependent proteases are essential for maintaining protein homeostasis through degradation of damaged or misfolded proteins. Among these, the ClpXP protease complex locates in mitochondrial matrix and contributes to mitochondrial quality control under physiological and stress conditions. This work demonstrates a quantitative fluorescence microscopy workflow to assess mitochondrial targeting of the fluorescent peptidyl inhibitor FAM-FAPAL-CMK and evaluate mitochondrial morphological changes associated with ClpXP inhibition in mammalian cells. HeLa cells were treated with FAM-FAPAL-CMK and analyzed using confocal microscopy combined with immunofluorescence staining of mitochondrial markers and quantitative image analysis. Colocalization analysis using Costes thresholding and Manders' overlap coefficients demonstrated mitochondrial enrichments of the inhibitor signal. As a consequence, inhibition of ClpP altered mitochondrial morphology. Immunoblot analysis showed no significant change in ClpP protein abundance upon inhibitor treatment. Taken together, this work describes a reproducible imaging-based workflow that will enable interrogation of mitochondrial ClpXP functions in intact cells in response to perturbations of homeostasis, such as oxidative stress.
    DOI:  https://doi.org/10.3791/72089
  32. bioRxiv. 2026 Jul 23. pii: 2026.07.22.740101. [Epub ahead of print]
      During early embryogenesis, gene expression relies on maternally loaded mRNAs whose translation is controlled by RNA binding proteins. Here, we identify a critical role for the cyclin B3-CDK1 complex, known for its function in mitosis, in driving early embryonic gene expression in C. elegans . The cyclin B3-CDK1 complex works by marking the RNA binding OMA proteins (OMA-1 and OMA-2) for degradation, which ensures the de-repression and translation of their target mRNAs. OMA protein degradation relies on cyclin B3's conserved phosphate-binding pocket, which promotes multi-site OMA phosphorylation and the generation of phospho-degrons. Notably, the phosphate-binding pocket of cyclin B3 does not substantially contribute to its mitotic roles, indicating that the mitotic and translational functions of the cyclin B3-CDK1 complex are separable. These findings establish that embryonic activation of the cyclin B3-CDK1 complex drives both mitotic divisions and mRNA de-repression, which ensures that cell division is coupled to the early gene expression program in development.
    DOI:  https://doi.org/10.64898/2026.07.22.740101
  33. PeerJ. 2026 ;14 e21567
       Background: Diminished ovarian reserve (DOR) is a common cause of female infertility. Prior high-throughput sequencing showed specific follicular fluid exosomal miRNA profiles in DOR patients, implicating exosomal miRNAs in DOR pathogenesis. Using miRNA PCR arrays, we found miR-483-3p was significantly upregulated in DOR follicular fluid exosomes. Bioinformatics and experiments indicated METTL3 as a potential miR-483-3p target, suggesting excess miR-483-3p exerts cytotoxicity and suppresses METTL3-mediated N6-methyladenosine (m6A) modification. This study thus investigated miR-483-3p effects on METTL3 expression, m6A levels, cell proliferation, and mitochondrial function in ovarian granulosa cells (GCs).
    Methods: The targeting interaction between miR-483-3p and METTL3 was confirmed using a dual-luciferase reporter gene assay. qRT-PCR, immunofluorescence, Western blot, and Dot blot were used to evaluate the effects of miR-483-3p mimics, cyclophosphamide (CTX), and STM2457 on METTL3 protein expression and m6A modification levels in KGN cells. Additionally, Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (EdU) assays, along with mitochondrial membrane potential (MMP) measurements, were used to examine the impact of these treatments on KGN cell proliferation and mitochondrial function.
    Results: miR-483-3p directly targeted the 3' untranslated region (3'UTR) of METTL3, and its mimics significantly suppressed METTL3 gene expression. In contrast, CTX robustly promoted METTL3 gene expression, accompanied by a substantial elevation in global m6A levels. STM2457 treatment also showed a similar trend. But miR-483-3p overexpression modestly inhibited METTL3 protein and m6A levels. Regarding cellular phenotypes, miR-483-3p overexpression, CTX, and STM2457 all exerted significant inhibitory effects on KGN cells. All three treatments consistently suppressed the cell viability of KGN cells, reduced the EdU-positive cell ratio, and decreased MMP levels.
    Conclusion: This study provides preliminary evidence suggesting a specific regulatory interaction between miR-483-3p and METTL3. We demonstrate that aberrantly high expression of miR-483-3p significantly suppresses METTL3 mRNA levels but only moderately reduces METTL3 protein and m6A levels, suggesting the involvement of complex post-transcriptional regulatory mechanisms. Furthermore, overaccumulation of miR-483-3p markedly inhibits the proliferation of ovarian GCs and impairs their mitochondrial function. Further investigation into the role of the candidate miR-483-3p-METTL3-m6A axis in DOR will be conducted using in vivo models alongside an expanded cohort of clinical samples.
    Keywords:  Cell proliferation; Diminished ovarian reserve; Methyltransferase like 3 (METTL3); MiR-483-3p; Mitochondrial membrane potential; N6-methyladenosine (m6A)
    DOI:  https://doi.org/10.7717/peerj.21567
  34. Viruses. 2026 Jun 30. pii: 719. [Epub ahead of print]18(7):
      Virus infection requires coordinated activation of pathogen-sensing, innate immune, and cellular stress response pathways to mount an effective antiviral defense. Recognition of nucleic acid pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs) initiates signaling cascades that drive the production of type I interferons (IFNs) and proinflammatory cytokines. These responses are often accompanied by the activation of integrated stress response pathways that help optimize host defense. Cytosolic double-stranded dsDNA, generated during viral infection or released from damaged mitochondria, is sensed by cyclic GMP-AMP synthase (cGAS), which generates 2'3'-cGAMP to activate stimulator of interferon genes (STING). Activated STING translocates from the endoplasmic reticulum to the Golgi, where it drives TBK1-dependent IFN and cytokine production. Previous reports show that cGAS activity is enhanced by Ras-GAP SH3 domain binding protein 1 (G3BP1), a key nucleator of stress granules (SGs), independent of its role in SG assembly. Here, we identify a non-canonical role of G3BP1 as a regulator of DNA sensing responses at multiple levels, including STING intracellular trafficking, in addition to potentiating cGAS activity. Loss of G3BP1 impaired STING-dependent IFN and cytokine responses to HSV-1 infection and viral DNA. G3BP1-deficient cells showed reduced cGAMP-induced STING translocation to the Golgi, induction of type I IFN and proinflammatory cytokines, and activation of the ER stress kinase PERK and stress granule formation. Together, these findings demonstrate G3BP1-STING as a node linking DNA sensing, innate immunity, and stress signaling with broad implications for antiviral defense and diseases characterized by aberrant DNA sensing and stress responses, including neurodegeneration, fibrosis, and autoimmunity.
    Keywords:  2′3′cGAMP; G3BP1; HSV-1; PERK; STING; cGAS; innate immunity; stress granules
    DOI:  https://doi.org/10.3390/v18070719
  35. Genes Dev. 2026 Jul 31.
      Biomolecular condensates, such as germ granules, organize RNAi pathways critical for fertility and genome regulation. However, the protein composition and functional contributions of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that contribute to fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors associated with defects in WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has coevolved with PRG-1 across clade V nematodes, with a conserved structured N terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily coadapted PIWI interactor critical for siRNA biogenesis.
    Keywords:  PIWI; RNA inheritance; RNAi; fertility; germ granule; piRNA pathway
    DOI:  https://doi.org/10.1101/gad.353482.125
  36. Int J Mol Sci. 2026 Jul 22. pii: 6532. [Epub ahead of print]27(14):
      Methylation of proteins is a critical post-translational modification that regulates diverse cellular processes, including signal transduction, protein stability, and enzymatic activity. The methyltransferase enzymes that catalyse the addition of such methyl groups onto target molecules fall into a wide variety of categories and as such are classified into numerous families. Among them, the methyltransferase-like (METTL) family represents a unique cluster of enzymes with structural similarity to arginine methyltransferases. This family comprises 27 members, many of which methylate lysine residues on proteins, while others target various forms of RNA. Although discovered just over a decade ago, the protein-methylating METTLs remain incompletely characterised. Notably, most identified protein substrates are non-histone proteins, underscoring the distinctive functional roles of these enzymes. This review focuses exclusively on the protein-methylating METTL family members, summarising current knowledge of their structural features, enzymatic targets, sub-cellular localisation, and expression patterns. Their emerging relevance to disease, particularly cancer, is also highlighted, alongside areas where mechanistic understanding remains limited. By consolidating recent advances, this review aims to provide a comprehensive overview of protein-methylating METTLs in humans and to identify the critical knowledge gaps that will guide future research into their biological roles and therapeutic potential.
    Keywords:  colorectal cancer; glioblastoma; methyltransferase-like (METTL) enzymes; protein methyltransferases
    DOI:  https://doi.org/10.3390/ijms27146532
  37. Cold Spring Harb Perspect Biol. 2026 Jul 29. pii: a041869. [Epub ahead of print]
      Protein synthesis is tightly regulated in cells; however, in cancer, ribosomes deviate from canonical translation, generating altered protein products. These deviations arise from cell-intrinsic alterations, as well as extrinsic pressures within the tumor microenvironment, collectively reshaping the translational landscape and reducing translation fidelity. Translational recoding in cancer expands proteome diversity and promotes tumor fitness by enhancing stress adaptation, metabolic, and phenotypic plasticity. At the same time, recoding events generate peptides that are often presented as tumor-specific antigens, thereby eliciting immune responses against cancer. Accordingly, therapeutic strategies that modulate translational fidelity and induce recoding are emerging to enhance tumor immunogenicity and improve immunotherapy responses. Here, we examine the drivers and consequences of translational recoding in cancer, its dual role in promoting tumor adaptation while shaping immune surveillance, and its potential as a targetable vulnerability in cancer therapy.
    DOI:  https://doi.org/10.1101/cshperspect.a041869
  38. Adv Med Sci. 2026 Jul 28. pii: S1896-1126(26)00031-3. [Epub ahead of print]
      Epitranscriptomic regulation has emerged as a critical mechanism in cancer biology, particularly in the development of chemoresistance. RNA modifications including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and A-to-I editing dynamically control mRNA stability, splicing, translation, and degradation. RNA-modifying proteins called 'writers,' 'erasers,' and 'readers' regulate post-transcriptional networks to enable tumor adaptation and chemoresistance. In platinum-resistant tumors, epitranscriptomic changes modulate DNA damage response, apoptosis, drug efflux, and detoxification pathways. Preclinical studies demonstrate that pharmacological inhibition of key regulators, such as METTL3 inhibitors (STC-15, STM2457, UZH2) or FTO inhibitors, can sensitize tumors to platinum drugs and stimulate anti-tumor immunity. However, clinical translation remains limited by off-target effects, toxicity, and highly context-specific responses. Epitranscriptomic profiling may help identify novel biomarkers and guiding precision strategies to overcome chemoresistance.
    Keywords:  Antineoplastic Agents; Biomarkers; Drug Resistance; Neoplasms; RNA Methylation
    DOI:  https://doi.org/10.1016/j.advms.2026.07.002
  39. ACS Chem Neurosci. 2026 Jul 26.
      Emerging evidence suggests that dysregulated cellular stress responses, particularly the formation and persistence of stress granules (SGs), may significantly contribute to Alzheimer's disease (AD) pathogenesis. SGs are dynamic, membrane-less ribonucleoprotein assemblies that sequester stalled translation preinitiation complexes during cellular stress. Under physiological conditions, SGs are transient and disassemble upon stress resolution, often facilitated by heat shock proteins (HSPs). However, under chronic stress, persistent or aberrant SGs can form, which may seed pathological protein aggregation and exacerbate proteostatic imbalance, neuroinflammation, and neurodegeneration. Despite the growing body of evidence linking HDAC6 to SG dynamics and AD pathology, the precise mechanistic relationship remains unresolved. This review highlights the current understanding of HDAC6-mediated SG regulation in AD, identifies critical knowledge gaps, and discusses the therapeutic potential of selective HDAC6 inhibition in modulating SG pathology and neuroinflammation.
    Keywords:  Alzheimer’s disease (AD); DNA damage; epigenetic; inflammation; ubiquitin-protease system (UPS)
    DOI:  https://doi.org/10.1021/acschemneuro.6c00264
  40. Neurobiol Dis. 2026 Jul 27. pii: S0969-9961(26)00294-9. [Epub ahead of print]228 107549
      Neuronal loss in neurodegenerative disease is driven in part by maladaptive stress signaling and impaired adaptation to proteotoxic challenges. ENL and AF9 are YEATS-domain acyl-lysine reader proteins best characterized in leukemia, but their functions in neurons remains unclear. Here, we defined the role of the ENL/AF9 YEATS domain using complementary chemical and genetic perturbations. We applied the selective YEATS inhibitor SR-0813 in differentiated human neurons and modulated ENL/AF9 activity in Drosophila using either SR-0813 or ENL/AF9 knockdown. In flies, SR-0813 phenocopied ENL/AF9 knockdown by extending lifespan and enhancing stress tolerance. To test disease-context specificity, we performed a Drosophila genetic modifier screen across neurodegeneration models. ENL/AF9 reduction was beneficial in UBQLN2P497H and SOD1G94A but showed reduced efficacy or became detrimental in chronic aggregation or mitochondrial stress models such as (GGGGCC)49 and polyQ disease. In human neurons, SR-0813 improved survival across multiple stress conditions, with the strongest protection during endoplasmic reticulum stress. Mechanistically, ENL/AF9 YEATS inhibition dampened PERK-dependent integrated stress response signaling and reduced apoptotic commitment without broadly enhancing proteostasis capacity. Together, these findings identified ENL/AF9 as modulators of neuronal stress-response dynamics and established ENL/AF9 YEATS-domain inhibition as a context-dependent strategy to enhance neuronal resilience with relevance to ALS and related proteotoxic disorders.
    Keywords:  Amyotrophic lateral sclerosis; Chemical probe; Chromatin reader; ENL/AF9; Integrated stress response
    DOI:  https://doi.org/10.1016/j.nbd.2026.107549
  41. Exp Ther Med. 2026 Sep;32(3): 250
      Pulmonary fibrosis (PF) is a progressive and often irreversible interstitial lung disease characterized by aberrant wound healing, excessive extracellular matrix deposition and distortion of lung architecture. N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNA, dynamically regulates RNA metabolism through m6A writers, erasers and readers. Evidence indicates that m6A dysregulation contributes to PF by modulating fibroblast activation, epithelial injury and senescence, epithelial-mesenchymal plasticity, macrophage-associated inflammation, oxidative stress responses and extracellular matrix remodeling. In the present review, the expression characteristics and functional alterations of m6A machinery in fibrotic lung tissue, the role of m6A-mediated epitranscriptomic remodeling in pulmonary cell fate determination and the potential translational value of m6A regulators as biomarkers and therapeutic targets are summarized. In addition, particular focus is placed on cell-type-specific and context-dependent mechanisms, including the distinct roles of METTL3, METTL14, FTO, ALKBH5 and YTHDF proteins in different fibrotic settings. The present review highlights that m6A modification is not a uniform pro-fibrotic or anti-fibrotic switch, but rather a dynamic regulatory network that links RNA metabolism to PF progression and therapeutic opportunities.
    Keywords:  RNA methylation; epitranscriptomic; fibroblast activation; m6A modification; pulmonary fibrosis
    DOI:  https://doi.org/10.3892/etm.2026.13246
  42. Cells. 2026 Jul 10. pii: 1247. [Epub ahead of print]15(14):
      The ubiquitin-proteasome system (UPS) has traditionally been described as a tightly regulated degradative network driven mainly by the specificity of its ubiquitin-conjugating enzymatic components. The 26S proteasome is the catalytic arm of the system that acts downstream to the conjugation machinery. For a long time, it has been considered to be a constitutive multi-subunit proteolytic complex that recognizes in a non-discriminatory manner ubiquitin-marked target substrates with less than a handful of exceptions. However, emerging evidence reveals that the 26S proteasome function is also dynamically regulated by multiple factors, such as subunit composition and synthesis, post-translational modifications, and spatial localization, all of which are tightly regulated by the metabolic and stress states of the cell. Importantly, dysregulation of these newly emerging regulatory mechanisms has pathogenic sequelae. These mechanisms fine-tune proteasome activity and expand its role as an active regulator of protein homeostasis rather than being a passive degradation machinery. Given the rapid expansion of these findings and their impact on our understanding of proteasome biology, an integrated overview of these regulatory mechanisms is timely.
    Keywords:  26S proteasome; biomolecular condensates; cellular stress; cytosol; liquid–liquid phase separation (LLPS); nucleus; ubiquitin
    DOI:  https://doi.org/10.3390/cells15141247
  43. Insects. 2026 Jul 07. pii: 703. [Epub ahead of print]17(7):
      RNA N6-methyladenosine (m6A) modification is a pivotal post-transcriptional regulator of diverse biological processes. Despite the growing interest in insect epitranscriptomics, a systematic evaluation of research trends and hotspots remains lacking. Here, we conducted a bibliometric analysis to map the global landscape of METTL3 and m6A research in entomology over the past decade. Our results reveal a steady increase in publications, signaling a phase of rapid expansion in this field. Notably, the number of studies on METTL3 is significantly lower than that of general m6A research, suggesting that current efforts prioritize phenotypic over the mechanistic roles of core regulatory components. Keyword co-occurrence analysis identifies Bombyx mori, Locusta migratoria, and Drosophila melanogaster as the primary model systems. Research hotspots predominantly center on METTL3-mediated regulation of development, behavioral plasticity, immunity, and host-pathogen interactions. These findings highlight insect METTL3 as a burgeoning research frontier. Future studies should emphasize cross-species comparisons and the systematic dissection of regulatory networks to provide novel theoretical frameworks and molecular targets for sustainable pest management and resource insect utilization.
    Keywords:  METTL3; bibliometrics; insect developmental regulation; m6A; methylation modification
    DOI:  https://doi.org/10.3390/insects17070703
  44. RNA. 2026 Jul 31. pii: rna.081234.126. [Epub ahead of print]
      The H/ACA ribonucleoprotein complex component dyskerin is essential for the biogenesis of H/ACA RNAs, including the human telomerase RNA (hTR). The N-terminal extension and α2' helix of dyskerin are hotspots for disease-associated mutations linked to X-linked dyskeratosis congenita (X-DC), a premature aging disorder. Some of these mutations disrupt dyskerin-hTR interactions, leading to hTR destabilization and reduced telomerase activity. Cryo-EM structures of human telomerase have shown that the N-terminal extension and α2' helix participate in dyskerin dimerization. However, biochemical evidence for dyskerin dimerization is still lacking, and it remains unclear whether mutations in these regions impair hTR binding by disrupting dimerization. Here, we provide the first biochemical evidence that dyskerin undergoes dimerization. We further demonstrate that dimerization is RNA independent and not abolished by disease mutations in the N-terminal extension or α2' helix. Instead, these mutations impair hTR binding. Our findings offer new mechanistic insight into how mutations in the dyskerin N-terminal extension and α2' helix contribute to the pathogenesis of X-DC.
    Keywords:  dimerization; dyskeratosis congenita; dyskerin; protein-RNA interactions; telomerase
    DOI:  https://doi.org/10.1261/rna.081234.126
  45. Curr Biol. 2026 Jul 29. pii: S0960-9822(26)00873-0. [Epub ahead of print]
      Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations within the ancient molecular machines that execute the central dogma. Octopuses exhibit complex nervous systems and sophisticated behaviors that rival vertebrates but via an entirely divergent evolutionary history. Here, we serendipitously discovered that octopus ribosomes contain a structural break in the core ribosomal RNA that is unique among all animals. This break site enhances translation fidelity to reduce miscoding and subsequent protein aggregation, even when engineered into evolutionarily distant bacterial ribosomes. Furthermore, high-fidelity translation by octopus ribosomes supports proteomic stability during extensive RNA editing observed in cephalopods, suggesting synergy between distinct non-canonical modes of gene regulation. This adaptation emerged in recently derived octopuses with expanded nervous systems, thereby revealing a mechanism that could broadly support the evolution of novel organismal traits.
    Keywords:  28S rRNA; RNA editing; cephalopod; octopus; protein aggregation; proteostasis; rRNA break; ribosome; ribosome evolution; translation fidelity
    DOI:  https://doi.org/10.1016/j.cub.2026.07.008
  46. bioRxiv. 2026 Jul 17. pii: 2026.07.16.739020. [Epub ahead of print]
      The regulation of protein stability is essential for cellular homeostasis and is determined by a combination of intrinsic sequence motifs and extrinsic recognition enzymes. Despite growing knowledge of the protein degradation machinery, the ability to predict a protein's stability from its amino acid sequence remains challenging. Here we develop a machine learning model to predict protein stability from N-terminal amino acid sequences. Using our model and experimental validation, we identify known and novel sequence motifs governing protein stability. We additionally use this model to predict the stability of alternative translational isoforms with distinct N-termini produced from the same mRNA. Despite differing by a limited number of amino acids, we identify N-terminal isoforms with drastically different stabilities relative to their annotated counterparts, highlighting the potential of N-terminal extensions and truncations to regulate protein function. Together, this model provides a valuable tool for evaluating additional protein datasets and protein design strategies.
    DOI:  https://doi.org/10.64898/2026.07.16.739020
  47. Cell Genom. 2026 Jul 30. pii: S2666-979X(26)00194-1. [Epub ahead of print] 101332
      PUS7 is a major mRNA pseudouridine synthase that influences gene expression and is dysregulated in neurodevelopmental disorders and cancer. PUS7 recognizes a prevalent and degenerate UNUAR sequence, but the mechanisms underlying PUS7's specificity remain unknown. We developed Nano-Mod-Amp, a targeted Nanopore high-throughput pseudouridine detection method, to interrogate PUS7 regulatory features. We established that USUAG, accessibility of the target uridine, and RNA structure are drivers of mRNA modification by PUS7. Perturbing structure through mutations or antisense oligos modulates pseudouridine levels. In cells, pseudouridines are responsive to PUS7 levels, demonstrating the regulatory potential of varying PUS7 levels across cell states. Conversely, PUS7 activity varies across cell types independently of expression levels, suggesting a potential regulatory role for RNA-binding proteins, RNA structure, or other cellular factors. We uncovered principles guiding PUS7 activity, enabling site-specific modulation of pseudouridines. These epitranscriptomic mechanisms provide molecular insight into the regulation and dysregulation of PUS7.
    Keywords:  PUS7; RNA modification; RNA structure; antisense oligo; cell type regulation; epitranscriptome; nanopore sequencing; pseudouridine
    DOI:  https://doi.org/10.1016/j.xgen.2026.101332
  48. Nucleic Acids Res. 2026 Jul 17. pii: gkag735. [Epub ahead of print]54(14):
      Efficient purification of specific RNAs from lysates remains a major challenge. Existing methods, such as MS2 tagging or oligonucleotide hybridization, require protein immobilization or sequence-specific hybridization, limiting scalability and compatibility with diverse RNAs. Current approaches often have low recovery, exhibit slow kinetics, and generate background contamination, limiting their use in RNA-protein interaction studies. To overcome these limitations, we developed FS2, an RNA sequence that binds Sephadex beads with high affinity, thus acting as an affinity tag for protein-free, rapid, and simple RNA purification. FS2 consists of two copies of the dextran-binding D8 aptamer embedded within the highly stable F30 three-way junction RNA scaffold, which promotes aptamer folding and enhances avidity. Systematic optimization revealed that FS2 exhibits rapid binding kinetics, efficient purification, and efficient elution under mild conditions (50°C, 10 mM EDTA), representing substantial improvements over existing RNA purification systems. We validated the utility of FS2 by purifying an FS2-tagged MYC mRNA fragment from HEK293T cells and demonstrating that N6-methyladenosine (m6A)-containing mRNAs can be pulled down along with the m6A-binding protein YTHDF2. Overall, FS2 provides a highly simple and efficient RNA-based affinity tag for recovering RNA from complex mixtures and lysates for diverse applications.
    DOI:  https://doi.org/10.1093/nar/gkag735
  49. Redox Biol. 2026 Jul 25. pii: S2213-2317(26)00323-X. [Epub ahead of print]96 104324
      Maintenance of endoplasmic reticulum (ER) proteostasis is essential for cellular homeostasis and survival during stress. Beyond canonical quality control pathways, ER-to-cytosol signaling (ERCYS) enables the reflux of ER-resident proteins into the cytosol, where they can acquire noncanonical functions that promote cell survival. However, the mechanisms governing ERCYS and its relationship to ER stress remain poorly understood. Here, we show that ER protein reflux is restricted to a defined stress window and is governed by the ER redox environment. Mild ER stress maximizes protein reflux, whereas severe or reductive stress markedly suppresses this process. Mechanistically, we identify the ER-resident cochaperones DNAJB12 and DNAJB14 as redox-sensitive regulators of ERCYS. Under mild stress, intramolecular disulfide bonds stabilize DNAJB12 and DNAJB14, thereby supporting efficient protein reflux. In contrast, severe or reductive stress increases intracellular glutathione, reducing these disulfide bonds and promoting degradation of DNAJB12 and DNAJB14, resulting in the loss of chaperone-mediated reflux. We further show that protein reflux requires cysteine-dependent interactions between refluxed substrates and the cytosolic cochaperone SGTA, revealing a previously unrecognized redox-sensitive step in the ERCYS pathway. When ERCYS is impaired during severe ER stress, cells instead engage an alternative apoptosis-associated pathway mediated by BAX/BAK-dependent ER membrane permeabilization. This transition is driven by enhanced recruitment of BAX and BAK to the ER by the BH3-only protein BIK, amplifying apoptotic signaling. Together, these findings establish redox regulation as a molecular switch that determines whether cells mount an adaptive ER protein reflux response or commit to BAX/BAK-dependent ER membrane permeabilization and apoptosis.
    DOI:  https://doi.org/10.1016/j.redox.2026.104324
  50. Talanta. 2026 Jul 26. pii: S0039-9140(26)01026-X. [Epub ahead of print]312(Pt A): 130370
      m6A (N6-methyladenosine), a prevalent RNA modification in eukaryotic mRNA involved in multiple biological processes, enables early cancer screening via its detection. m6A methylation detection is considered challenging, with most existing methods being limited by complex chemical transformations that incur high cost and procedural complexity. To overcome these challenges, a novel droplet-based digital CRISPR-Cas13a (Dd-Cas13a) approach was developed for the detection of m6A modifications in RNA. The method employs an m6A-specific antibody enrichment strategy to selectively enrich RNA molecules harboring m6A modifications, while RNA molecules lacking m6A remain unselected. Integration of the targeted recognition capability of the CRISPR/Cas13a system with droplet technology enables amplification-free detection of m6A-modified RNA at fM concentrations, with a significant improvement in sensitivity. The Dd-Cas13a detection platform enables visualization and quantitative analysis of methylation site proportions in cellular RNA, providing a novel approach for rapid and sensitive detection of RNA methylation, with significant potential for applications in early disease diagnosis and therapeutic efficacy assessment.
    Keywords:  CRISPR/Cas13a; Droplet digital; Free amplification; N6-methyladenosine; m6A-specific antibody
    DOI:  https://doi.org/10.1016/j.talanta.2026.130370
  51. Trop Anim Health Prod. 2026 Jul 28. pii: 459. [Epub ahead of print]58(7):
      Climate-induced heat stress poses a major challenge to small ruminant productivity in arid and semi-arid regions, affecting growth, metabolism, and immune function. This study examined tissue-specific molecular responses to chronic heat stress in lambs by evaluating the expression of key genes associated with inflammation, oxidative stress, proteostasis, and muscle function in the liver and skeletal muscle. Twenty-four lambs were reared at two climatically contrasting field sites (thermoneutral vs. high-THI) for 42 days. In the liver, exposure to the heat-stressed environment was associated with decreased SOD1 expression alongside increased FOXO3 and pro-inflammatory IL-6, while TNF-α and PPARγ were significantly lower. In muscle, a different profile emerged: heat shock proteins (HSP70, HSP90) and the apoptotic marker CASP3 were strongly upregulated, MYOD was suppressed, and ACTB3 remained stable. These results suggest candidate tissue-specific transcriptional signatures associated with impaired muscle regeneration and enhanced proteotoxic stress, although the field-based design confounds thermal load with other site-specific factors and does not permit causal attribution. Composite gene expression ratios-such as SOD1/IL-6 and FOXO3/TNF-α-were elevated under heat stress and negatively correlated with rectal temperature, indicating a potential role as candidate molecular indices associated with thermal response. Principal component analysis further distinguished control and heat-stressed animals based on transcriptional profiles. These findings highlight the coordinated yet divergent molecular strategies employed by liver and muscle tissues under prolonged thermal stress. The study provides preliminary, hypothesis-generating insight into gene-level responses associated with contrasting thermal environments and identifies candidate molecular targets warranting further validation in controlled designs before application to selection or intervention strategies.
    Keywords:  Gene expression; Heat stress; Lamb; Liver; Oxidative stress; Skeletal muscle
    DOI:  https://doi.org/10.1007/s11250-026-05253-w
  52. Nat Rev Mol Cell Biol. 2026 Jul 30.
      The classical view of gene regulation complexes as stable, modular machines needs amending based on emerging insights into their dynamic nature. Whereas recent advances in structural biology have provided high-resolution snapshots of these complex machines, single-molecule and live-cell imaging techniques reveal a more fluid picture: biological function emerges not from static architectures but from transient, dynamic assemblies that continually exchange their components and whose activity is tuned through kinetic control. In this Perspective, we propose dynamic, reversible assembly as a framework for understanding the mechanisms of RNA processing and gene regulation. Drawing on specific case studies from ribosome biogenesis, spliceosomes, small RNAs and transcription factors, we explore how ribonucleoprotein complexes and transcriptional ensembles form and dissolve in time, how protein intrinsically disordered regions collectively enable transcription factors to achieve specificity, and the kinetic principles underlying the fidelity, adaptability and robustness of cellular processes and their related pathologies. In doing so, we show how molecular interactions are governed by rates rather than by equilibrium affinities, providing a foundation for time-integrated structure-function studies.
    DOI:  https://doi.org/10.1038/s41580-026-00991-z
  53. Angew Chem Int Ed Engl. 2026 Jul 27. e8731921
      mRNA is a new medical modality as vaccine and raises hopes to become a protein replacement agent. Despite notable advances in manufacturing, stabilization and modification, its short half-life remains a major limitation. Circular RNA bears potential to solve this issue, as degradation of mRNA proceeds primarily from the 5' and 3' ends. However, circular RNAs normally lack a 5' cap and are less efficiently translated. We present a strategy to circularize mRNA covalently via click chemistry by modifying the 5' cap and the 3' poly(A) tail with bioorthogonal functional groups. The resulting Cyclic Click Cap-containing mRNA (CyCliCap-mRNA) is translationally muted by a photocleavable protecting group. Upon irradiation by light, the photocleavable protecting group is removed and the respective linear Cap0-mRNA released. We show that CyCliCap-mRNA can be activated for efficient translation at late timepoints (24-48 h post transfection) in HeLa cells, which is not possible with the respective linear mRNA. The light-mediated opening releases linear mRNA with a native Cap0 and thus overcomes the problem of inefficient translation of circular RNAs.
    Keywords:  5′ cap; circular RNA; mRNA; optochemical biology; translation
    DOI:  https://doi.org/10.1002/anie.8731921
  54. Signal Transduct Target Ther. 2026 Jul 29. pii: 295. [Epub ahead of print]11(1):
      Mitochondria are essential for cellular homeostasis, integrating various signals to control key cellular functions such as metabolism, apoptosis, inflammation, cell proliferation and redox balance. Given their multifaceted functions, it is not surprising that mitochondrial dysfunction has been implicated as a key contributor to the pathogenesis of numerous human diseases. Consequently, preserving mitochondrial integrity and functionality is vital for overall organismal health. Mitochondrial health is safeguarded by a sophisticated and tightly regulated network of quality control systems. These include mitochondrial proteostasis, which ensures proper protein folding and degradation; mitochondrial biogenesis, which governs the synthesis of new mitochondria; mitochondrial dynamics, encompassing fusion and fission processes; and mitophagy, the selective autophagic removal of damaged mitochondria. Additionally, these core systems are intricately connected to other crucial mitochondrial processes, such as the maintenance of mitochondrial DNA integrity, the regulation of cristae architecture, and the control of mitochondrial permeability transition, all of which are indispensable for optimal mitochondrial performance. Preclinical and clinical studies consistently demonstrate a strong link between impairments in these quality control mechanisms and both aging and the development of a wide spectrum of diseases. These include cancer, metabolic disorders, cardiovascular conditions, neurodegenerative diseases and autoimmune pathologies. In this review, we explore the different facets of mitochondrial quality control and discuss their implications in disease progression and aging. Furthermore, we highlight recent advances in interventions and therapies aimed at modulating mitochondrial quality control, providing an overview of their potential to mitigate disease burden and promote healthy aging.
    DOI:  https://doi.org/10.1038/s41392-026-02813-2
  55. Mol Biol Rep. 2026 Jul 29. pii: 1293. [Epub ahead of print]53(1):
      Colorectal cancer (CRC) remains a major cause of cancer-related mortality, particularly in advanced or metastatic disease. The Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway mediates cytokine-driven signaling, and its persistent activation contributes to tumor growth, invasion, immune escape, and therapeutic resistance. Suppressor of cytokine signaling 3 (SOCS3) is a key negative regulator of cytokine and growth factor signaling, especially the IL-6/JAK/STAT3 axis. This review summarizes the structure and physiological functions of SOCS3 and discusses its dysregulation in CRC initiation, progression, metastasis, prognosis, and treatment response. Current evidence indicates that SOCS3 is frequently downregulated in CRC through promoter methylation and post-transcriptional regulation by oncogenic microRNAs, leading to sustained STAT3 activation, increased proliferation, reduced apoptosis, and enhanced invasiveness. SOCS3 also interacts with MEK/ERK and PI3K/AKT signaling and influences the tumor microenvironment by regulating T-cell balance, PD-L1 expression, and macrophage activity. Clinically, reduced SOCS3 expression has been associated with lymph node metastasis, advanced TNM stage, and poorer prognosis, whereas higher SOCS3 levels may correlate with improved outcomes and chemosensitivity. Emerging therapeutic strategies include epigenetic modulation, JAK/STAT pathway inhibition, regulation of IL-6 signaling in adoptive T-cell therapy, AhR/IL-22 modulation, and FXR activation. Further translational studies are needed to validate SOCS3 as a biomarker and therapeutic target in CRC.
    Keywords:  Colorectal cancer; JAK-STAT pathway; SOCS; SOCS3
    DOI:  https://doi.org/10.1007/s11033-026-12500-8
  56. Biochim Biophys Acta Rev Cancer. 2026 Jul 25. pii: S0304-419X(26)00141-1. [Epub ahead of print] 189669
      Lysosomes are vital organelles that maintain cellular homeostasis and orchestrate dynamic adaptations during physiological and pathological stress. Lysosomal damage, caused by various extrinsic and intrinsic factors, impairs its integrity and simultaneously disrupts the normal functioning of other organelles, including the endoplasmic reticulum and mitochondria. Lysosomal homeostasis through the lysosomal stress response (LSR) network aids cells in adapting to organelle damage, nutrient fluctuations, oxidative stress, and metabolic irregularities. This coordinated network is primarily governed by proteins, including mTOR, TFEB/TFE3, AMPK, Rag GTPases, Ragulator, and TRPML1, which integrates mechanisms involving rapid lysosomal membrane repair, selective elimination of extensively damaged lysosomes, de novo lysosomal biogenesis, and lysosomal reformation pathways. Dysregulation of the LSR network leads to different types of diseases, including cancer. This review summarizes the current understanding of lysosomal damage mitigation, particularly in cancer, where remodeling of the LSR network not only enables cancer cells to maintain metabolic plasticity by resisting therapeutic stress and promoting malignancy but also identifies the LSR network as a critical determinant in tumorigenesis. We further provide a detailed discussion of emerging evidence on the disruption of lysosomal homeostasis, highlighting strong links between lysosome-targeting drugs and cancer therapeutics. Altogether, we establish the LSR network as a central regulator of cellular homeostasis, thereby emerging as a promising therapeutic target in cancer and other lysosome-associated disorders.
    Keywords:  Cancer; Lysosomal damage; Lysosomal homeostasis; Lysosomal stress response (LSR) network
    DOI:  https://doi.org/10.1016/j.bbcan.2026.189669
  57. Biology (Basel). 2026 Jul 15. pii: 1155. [Epub ahead of print]15(14):
      Understanding gene expression requires integrating multiple regulatory layers, because transcript abundance does not necessarily correspond to translational activity or protein abundance. Ribosome profiling and proteomics help distinguish increased translation from ribosome stacking or translational buffering, but no de facto standard framework exists for unsupervised integration of transcriptome, translatome, and proteome profiles. Here, we propose a four-dimensional tensor decomposition-based unsupervised feature extraction approach for tri-omics integration. We applied higher-order singular value decomposition to transcriptome, Ribo-seq, and proteome profiles measured under branched-chain amino acid starvation. The resulting singular value vectors captured relationships among the three omics layers, including a component consistent with ribosome stacking, where transcriptome and translatome signals increased while proteome signals decreased, and another consistent with translational buffering, where proteome variation was suppressed despite transcriptome and translatome changes. Gene selection identified 1781 genes associated with ribosome stacking and 227 genes associated with translational buffering. Enrichment analyses linked the former to translation, post-translational protein modification, RNA polymerase II transcription, cell cycle regulation, endoplasmic reticulum protein processing, ubiquitin-mediated proteolysis, and stress-related pathways, and the latter to ribosome, translation elongation and termination, spliceosome, immune- and stress-related pathways, and ribosomopathy-associated diseases. Robustness analyses indicated that the results were not substantially affected by the duplicated proteome replicate or missing-value handling. Under the tested settings, comparison with MOFA+ and mixOmics suggested that our approach more directly extracted components interpretable as ribosome stacking and translational buffering. These results demonstrate that tensor decomposition-based unsupervised feature extraction is useful for identifying functionally relevant gene clusters from tri-omics data.
    Keywords:  BCAA starvation; tensor decomposition; tri-omics
    DOI:  https://doi.org/10.3390/biology15141155
  58. Sci Adv. 2026 Jul 31. 12(31): eaef0140
      Metabolic adaptation to nutrient deprivation requires coordinated control of mitochondrial anaplerosis and cataplerosis; however, how metabolite flux across the mitochondrial membrane is regulated during fasting remains less defined. Here, we report SLC25A34 as a fasting-inducible mitochondrial carrier that is highly expressed in oxidative skeletal muscle. Using bacterial reconstitution, proteo-liposomes, and tracer studies, we showed that SLC25A34 mediates the import of phosphoenolpyruvate (PEP) into the mitochondrial matrix. Loss of SLC25A34 impaired glutamine-supported anaplerosis under nutrient-deprived conditions, while glucose and pyruvate utilization remained largely intact. Muscle-specific deletion of Slc25a34 resulted in reduced fasting-induced amino acid catabolism and the accumulation of amino acids, leading to activation of mTORC1 signaling even under fasted conditions. Consequently, SLC25A34-deficient soleus muscle exhibited hypertrophy and myopathic features, accompanied by mTORC1-dependent increase in protein synthesis. Together, these results highlight a unique biological role for the inducible mitochondrial carrier SLC25A34, which couples PEP import to amino acid catabolism and proteostasis to preserve skeletal muscle integrity in response to metabolic stress.
    DOI:  https://doi.org/10.1126/sciadv.aef0140
  59. Mol Biol Rep. 2026 Jul 30. pii: 1308. [Epub ahead of print]53(1):
      Pulmonary arterial hypertension (PAH) is a complex vascular disease characterized by endothelial dysfunction, pulmonary arterial smooth muscle cell (PASMC) hyperproliferation, metabolic reprogramming, and immune-inflammatory remodeling. These pathological features are not fully explained by isolated signaling abnormalities and increasingly point to post-translational modification (PTM) crosstalk as an important layer of protein regulation. In this review, we examine the interplay among phosphorylation, ubiquitination, and SUMOylation, with a focus on how these PTMs influence protein stability, subcellular localization, and degradation in the PAH microenvironment. To distinguish disease-supported mechanisms from broader biological extrapolation, we apply a tiered evidence framework that separates crosstalk axes validated in human PAH or relevant experimental pulmonary hypertension models from those inferred from hypoxia- or cancer-related systems. Across these studies, several recurring patterns emerge, including phosphodegron-dependent substrate recognition, PTM-dependent enzyme recruitment, and context-specific coupling between SUMOylation and ubiquitin-mediated turnover. These mechanisms help explain how PTM dysregulation may weaken vasculoprotective signaling, including BMPR2-related pathways, while sustaining proliferative, inflammatory, and hypoxia-responsive signaling programs. We also discuss a conceptual systems-level model in which chronic stress reshapes the effective PTM enzyme pool through changes in enzyme abundance, substrate allocation, and subcellular compartmentalization. Finally, we consider the translational implications of targeting PTM crosstalk, including opportunities for selective intervention and current barriers related to network redundancy, off-target toxicity, and drug delivery.
    Keywords:  Metabolic reprogramming; Post-translational modification crosstalk; Protein fate; Pulmonary arterial hypertension; Vascular remodeling
    DOI:  https://doi.org/10.1007/s11033-026-12478-3
  60. Front Physiol. 2026 ;17 1846390
       Introduction: The nerve-derived growth factor neuregulin (NRG) plays a role in the regulation of skeletal muscle mass through Akt and mTOR signaling transduction pathways that regulate both protein synthesis and degradation. We previously reported that NRG increases muscle protein synthesis (~20%) in a PI3 kinase (PI3K)/Akt-dependent manner. However, the effects of NRG on protein degradation are still poorly understood and are needed to elucidate the role of NRG in the maintenance of skeletal muscle protein balance.
    Methods: Neonatal diaphragm muscle ex vivo preparations were pharmacologically treated with NRG and pharmacological inhibitors of PI3K (LY294002, 50 μM), MEK (PD98059, 50 μM) or mTOR (rapamycin, 100 nM). Tyrosine release from muscle was used as a surrogate measure of protein degradation.
    Results: We report that basal protein degradation in the neonatal rat diaphragm muscle is significantly reduced by NRG treatment (19%). Basal protein degradation was increased following treatment with inhibitors of PI3K, MEK or mTOR, with inhibition of each pathway sufficient to increase basal protein degradation greater than 30%. Importantly, NRG treatment in the presence of each of these inhibitors blunts the increase in protein degradation induced by inhibition of PI3K, MEK or mTOR. NRG effects were significantly blunted by rapamycin (p < 0.05 compared to NRG alone), but not by LY294002 or PD98059.
    Discussion: We suggest that both the PI3K/Akt and MAP kinase pathways are important for NRG effects on protein degradation, but that mTOR may be a critical modulator of these effects and thus of protein balance in skeletal muscle.
    Keywords:  epidermal growth factor; heregulin; muscle atrophy; protein balance; skeletal muscle; trophic factor
    DOI:  https://doi.org/10.3389/fphys.2026.1846390
  61. Front Oncol. 2026 ;16 1836263
       Introduction: Adenoid cystic carcinoma is a rare salivary gland malignancy of the head and neck region characterized by perineural invasion, distant metastasis, and a lack of effective targeted therapies. The molecular mechanisms underlying its progression remain poorly understood.
    Methods: In this study, we identified the cystic fibrosis transmembrane conductance regulator (CFTR) as a consistently downregulated gene in adenoid cystic carcinoma through differential expression analysis of multiple independent transcriptomic cohorts. Functional experiments were performed in SACC-83 and SACC-LM cell lines, including ectopic expression and knockdown of CFTR, RNA sequencing, quantitative polymerase chain reaction, and Western blot analyses. Pharmacological inhibition of Hsp70 using VER155008 and activation of the heat shock response by HSF1A were also assessed for effects on cell viability, migration, invasion, and apoptosis. Subcutaneous xenograft experiments in nude mice were conducted to evaluate tumor growth following stable CFTR knockdown in SACC-LM cells.
    Results: Preliminary Kaplan-Meier survival analysis demonstrated that low CFTR expression was significantly associated with inferior overall survival, although this finding requires validation in a larger independent cohort. Protein interaction network modeling revealed that CFTR occupies a hub position within a conserved interaction network linking ion channel regulation, protein quality control, and kinase signaling. Functional experiments showed that ectopic expression of CFTR suppressed cell proliferation, migration, and invasion, whereas CFTR knockdown enhanced these malignant phenotypes, supporting a tumor-suppressive role for CFTR in these model systems. RNA sequencing of CFTR-overexpressing cells revealed coordinated downregulation of heat shock protein family members, including HSPA1A, HSPA1B, and HSPA6, with enrichment of pathways related to protein refolding. Quantitative polymerase chain reaction and Western blot analyses confirmed that CFTR expression is inversely associated with Hsp70 family members and MAPK1 (ERK2) at both mRNA and protein levels. Pharmacological inhibition of Hsp70 using VER155008 suppressed cell viability, migration, and invasion in a dose-dependent manner and induced apoptosis, phenocopying the effects of CFTR restoration. Subcutaneous xenograft experiments in nude mice further demonstrated that stable CFTR knockdown in SACC-LM cells markedly accelerated tumor growth. Conversely, activation of the heat shock response by HSF1A promoted proliferation, migration, and invasion, recapitulating the consequences of CFTR loss. Notably, Hsp70 inhibition was accompanied by compensatory upregulation of MAPK1 transcripts, suggesting that CFTR is inversely associated with Hsp70 and MAPK1 through parallel rather than linear mechanisms.
    Discussion: These findings indicate that CFTR silencing in adenoid cystic carcinoma is accompanied by elevated Hsp70 chaperone expression, and that pharmacological targeting of Hsp70 phenocopies, rather than necessarily mediates, the tumor-suppressive effects of CFTR restoration in the SACC-83 and SACC-LM lineage. Targeting Hsp70 therefore provides a preclinical rationale, rather than direct translational evidence, for further investigation in this otherwise treatment-refractory malignancy.
    Keywords:  CFTR; HSP (heat shock protein); Hsp70; adenoid cystic carcinoma; tumor suppressor
    DOI:  https://doi.org/10.3389/fonc.2026.1836263
  62. Plant J. 2026 Aug;127(3): e71077
      The mechanisms linking Golgi function to stress adaptation and senescence remain poorly understood. Here, we identify the conserved oligomeric Golgi (COG) subunit COG7 as a non-redundant determinant of Golgi integrity and stress adaptation in Arabidopsis thaliana. Functional disruption of COG7 reduces Golgi size, enhances Rapid Stress Response Element (RSRE)-dependent stress signaling, and accelerates dark-induced senescence. Complementation analyses reveal functional specialization within the COG complex, as only COG3, COG5, and COG6 partially restore stress signaling and senescence phenotypes. At the molecular level, cog7 exhibits altered glycosylation, increased ubiquitination, and elevated autophagy. However, disruption of glycosylation pathways or dark-induced candidate glycosyltransferases does not affect RSRE activation, proteostasis-associated responses, or senescence progression, indicating that glycosylation changes are downstream consequences rather than drivers of the stress phenotype. Similarly, CAMTA3-dependent RSRE activation is genetically separable from senescence and proteostasis pathways. Together, these findings show that Golgi dysfunction generates multiple parallel outputs rather than a single linear stress pathway and establish COG7 as a central regulator linking Golgi integrity to stress signaling, proteostasis, and senescence during dark-induced stress.
    Keywords:  COG complex; Golgi apparatus; autophagy; proteostasis; senescence; stress signaling
    DOI:  https://doi.org/10.1111/tpj.71077
  63. Cells. 2026 Jul 15. pii: 1272. [Epub ahead of print]15(14):
      Lipid droplets (LDs) were long thought to be passive organelles merely for neutral lipid storage. Mounting evidence redefines LDs as dynamic metabolic signaling hubs orchestrating cellular stress adaptation, with multifaceted roles in organelle crosstalk, metabolic reprogramming, redox balance and immune signaling. LD function is tightly intertwined with liquid-liquid phase separation (LLPS) and epigenetic remodeling, bridging cellular metabolism to gene expression and cell fate control. LD biogenesis relies on ER lipid structures, phase-separated protein assemblies and lipid regulatory proteins. Via contacts with multiple organelles, LDs regulate lipid catabolism, ferroptosis, inflammation and chromatin accessibility, while their metabolites directly reshape epigenetic modifications and transcription. LLPS-driven biomolecular condensates further coordinate LD-linked metabolic and stress signaling. Dysregulated LD remodeling mediates metabolic flexibility, immune escape and drug resistance in obesity, metabolic dysfunction-associated steatotic liver disease (MASLD), neurodegeneration, viral infection and cancer. This review summarizes progress in LD biogenesis and metabolism, dissects mechanistic crosstalk between LDs, LLPS and epigenetic control, and outlines LD-driven pathogenic reprogramming across human disorders. We also discuss therapeutic approaches targeting LD and LLPS pathways. Despite promising translational prospects, unresolved mechanistic and clinical hurdles persist. Further research on LD biology will reshape our framework linking metabolism, chromatin regulation and stress adaptation.
    Keywords:  cancer metabolism; cellular adaptation; epigenetics; ferroptosis; lipid droplets; metabolic reprogramming; phase separation
    DOI:  https://doi.org/10.3390/cells15141272
  64. J Virol. 2026 Jul 31. e0170025
      Coronavirus nonstructural protein 15 (Nsp15) is a conserved uridine-preferring endoribonuclease (EndoU). Studies using mouse hepatitis virus (MHV), SARS-CoV-2, and other coronaviruses have shown that Nsp15 associates with replication-transcription complexes (RTCs) and contributes to viral immune evasion. Structural studies of alpha- and beta-coronavirus Nsp15 proteins reveal a hexameric enzyme that engages viral RNA substrates and cleaves at unpaired uridines through an RNase A-like, largely metal-independent mechanism stimulated by divalent cations. The Nsp15 hexamer functions as a dynamic, cooperative platform capable of accommodating extended double-stranded and structured RNA substrates. Genetic studies in several coronaviruses indicate that EndoU activity is dispensable for viral RNA synthesis in cell culture, but critical for suppressing host antiviral responses. Loss of EndoU activity promotes accumulation of immunostimulatory RNA species and activation of dsRNA-sensing pathways, including MDA5-dependent interferon signaling, PKR-mediated translational arrest, and the OAS/RNase L system. Mechanistically, Nsp15 is proposed to suppress these responses by selectively processing uridine-rich and structurally accessible regions in viral RNA, including poly(U)-containing negative-strand RNAs, and elements within untranslated regions and transcription regulatory sequences. Beyond catalysis, Nsp15 may contribute to RTC organization and regulate viral RNA recombination or defective viral genome formation, although these roles remain less well-defined and may vary among coronavirus species. Together, these findings support a model in which Nsp15 functions as a regulator of viral RNA composition and immunogenicity rather than solely as a degradative nuclease. This review summarizes recent advances in Nsp15 structure, RNA processing, immune evasion, and antiviral targeting, and highlights key unresolved questions.
    Keywords:  Nsp15; RNA processing; coronavirus; endoribonuclease; immune evasion; viral fitness
    DOI:  https://doi.org/10.1128/jvi.01700-25
  65. Genes (Basel). 2026 Jul 05. pii: 781. [Epub ahead of print]17(7):
      Cancer is one of the leading causes of mortality and morbidity worldwide. Various studies have highlighted the involvement of microRNAs (miRNAs) in tumor initiation and progression. MiRNAs are endogenous, non-coding, single-stranded RNA molecules that interact with the 3'-untranslated region (3'-UTR) of target mRNAs to inhibit mRNA translation or promote mRNA degradation. Various studies have reported that MIR133A is expressed at reduced levels in many tumor tissues and inhibits tumor progression. In this review, we comprehensively summarize the interactions of MIR133A and its target genes in the most commonly diagnosed cancers, namely, breast, lung, colorectal, gastric, and prostate. These results demonstrated that MIR133A is one of the optimal biomarkers for the diagnosis, prognosis, and prediction of various tumors, providing insights into the clinical management and practice of malignant tumors.
    Keywords:  MIR133A; apoptosis; biomarker; cell migration
    DOI:  https://doi.org/10.3390/genes17070781
  66. Plant Mol Biol. 2026 Jul 30. pii: 81. [Epub ahead of print]116(4):
      Plants rarely experience environmental stresses as isolated events. Instead, they are exposed to recurring, overlapping, or sequential challenges that require not only immediate local responses but also coordinated systemic adaptation and memory. Although plant stress memory has traditionally been discussed in terms of transcriptional, epigenetic, and metabolic reprogramming, accumulating evidence suggests that long-distance communication is equally important in determining how prior stress exposure shapes future responses. In this context, mobile RNAs and extracellular vesicles (EVs) are emerging as key mediators of local-to-systemic information transfer. Mobile RNAs, including small RNAs, mRNAs, long non-coding RNAs, and related RNA species, can move across cells, tissues, organs, and even species boundaries to regulate stress adaptation, whereas plant EVs carry complex molecular cargoes that participate in intercellular signalling, defense, and stress-responsive communication. Recent studies further indicate that EV secretion is stress-inducible and that plant EVs can amplify immune signalling during systemic acquired resistance (SAR), highlighting their potential contribution to plant-wide memory-like states. This review proposes that cross-stress memory should be reconsidered as a systemic signaling phenomenon, in which local stress encounters generate transmissible molecular information that reshapes distal tissue responsiveness and influences later reactions to the same or different stresses. We synthesize current knowledge on plant stress memory, RNA mobility, EV biogenesis and cargo, and systemic signalling networks, with emphasis on how these components may converge to establish, propagate, and recall stress information across the plant body. By linking mobile RNAs and EV-mediated communication with recurrent and cross-stress acclimation, this review provides a new conceptual framework for plant stress tolerance and identifies experimental priorities and translational opportunities for crop resilience under dynamic environments.
    Keywords:  Cross-stress memory; Extracellular vesicles; Local-to-systemic communication; Mobile RNAs; Plant stress priming; Systemic signaling
    DOI:  https://doi.org/10.1007/s11103-026-01746-2
  67. bioRxiv. 2026 Jul 17. pii: 2026.07.16.738943. [Epub ahead of print]
      Cellular processes are compartmentalized within immiscible heterotypic condensates, yet the functional consequences of losing their physical segregation remain unclear. Here, we show that genetic inactivation of the RNA chaperone SMN forces the aberrant intermixing of the two most prominent nuclear condensates: nucleolus and Cajal Body (CB). Upon SMN depletion, CB components invade the nucleolus and undergo reduced mobility and solubility consistent with a liquid-to-gel-like hardening transition. The CB-scaffold coilin aberrantly enriches at the nucleolar FC/DFC boundary and occupies rDNA chromatin, thereby locally suppressing rRNA production. Concurrently, this sequestration globally impairs coilin targeting to snRNA/snoRNA loci and limits telomerase access to telomeres, reducing telomeric synthesis. Crucially, genetic coilin depletion alone alleviates this mistargeting and rescues these functional impairments across condensates. Our findings reveal an inter-condensate rheostat model in which the loss of CB-nucleolar immiscibility is directly sensed, communicated, and executed by CB remnants, thereby proportionally coupling the functional outputs of otherwise distinct RNPs essential for splicing, translation, and genomic integrity.
    DOI:  https://doi.org/10.64898/2026.07.16.738943
  68. Autophagy. 2026 Jul 31. 1-18
      Aging is associated with the deterioration of various biological processes including disrupted proteostasis and impaired macroautophagy/autophagy. Biomolecules can undergo liquid-liquid phase separation (LLPS) to form biomolecular condensates that exert specific biological functions. Trr1 (thioredoxin reductase 1) is a pivotal enzyme in the thioredoxin antioxidant system. Deletion of TRR1 results in impaired autophagy; however, the underlying mechanism is largely unexplored. In this study, we explored whether LLPS of Trr1 affected autophagy. Trr1 formed dynamic LLPS condensates during replicative aging in yeast. Phase separation of Trr1 occurred in response to endoplasmic reticulum (ER) stress generated by cellular aging, rather than to oxidative stress. Furthermore, Trr1 condensates participated at the phagophore assembly site during endoplasmic reticulophagy and promoted autophagosome development by affecting lipidation of the Atg8 protein. Additionally, maintaining the liquid-like dynamic nature of Trr1 condensates was essential for cellular fitness. Our findings revealed an unconventional role of Trr1 through LLPS in aging. The function of phase-separated condensates of Trr1 in mitigating aging-associated ER stress offers insights into the mechanisms underlying healthy cellular aging. These findings highlight a potential target for developing interventions to combat aging and associated diseases.Abbreviations: Atg: autophagy related; DTT: dithiothreitol; ER: endoplasmic reticulum; ERAD: endoplasmic reticulum-associated degradation; ERphagy: endoplasmic reticulophagy; FRAP: fluorescence recovery after photobleaching; GFP: green fluorescent protein; LLPS: liquid-liquid phase separation; PAS: phagophore assembly site; PLDs: prion-like domains; RFP: red fluorescent protein; RLS: replicative lifespan; Trr1: thioredoxin reductase 1; Trx: thioredoxin; UPR: unfolded protein response; IDRs: intrinsically disordered regions.
    Keywords:  Aging; ERphagy; endoplasmic reticulum stress; liquid-liquid phase separation; thioredoxin reductase 1
    DOI:  https://doi.org/10.1080/15548627.2026.2702873
  69. Oncogene. 2026 Jul 29.
      HERC4 is a well-known HERC family ubiquitin ligase in several types of cancer but its role in lung cancer remains elusive. In the present study, we found that HERC4 is highly dysregulated in lung adenocarcinoma (LUAD) and promotes LUAD cell growth. Mechanically, HERC4 interacts with translation-related proteins and specifically stabilizes RPS15, a component of 40S ribosomal subunit, by promoting its deubiquitination in a manner independent of E3 ligase activity. HERC4 collaborates with USP16, a deubiquitinase that also interacts with translation-related proteins, to stabilize RPS15 by preventing its K48-linked ubiquitination. Further studies revealed that the interaction between HERC4 and USP16 is important to regulate RPS15 and to promote LUAD cell proliferation. Knockdown of HERC4 or USP16 prevents the recruitment of translation-related proteins to ribosomes, increases their nuclear retention and reduces global translational efficacy. Overexpression of RPS15 partially rescues reduced protein translation efficiency and cell survival triggered by HERC4/USP16 knockdown. Moreover, knockdown of HERC4 or USP16 upregulates p53 and downregulates p38 via RPS15 dysregulation. In conclusion, the present study reveals a novel ubiquitination modulation on ribosomal stability and protein translation. HERC4 synergizes with USP16 to deubiquitinate and stabilize RPS15, thereby potentiating global protein translation and promoting LUAD growth. The HERC4/USP16-RPS15 axis may represent a potential therapeutic target for LUAD treatment.
    DOI:  https://doi.org/10.1038/s41388-026-03902-w
  70. Front Plant Sci. 2026 ;17 1879625
      RNA editing in plant organelles is an important post-transcriptional process that helps maintain organelle gene function and may contribute to plant responses to environmental stress. However, drought-responsive RNA editing events and their regulatory factors remain poorly understood in soybean. Pentatricopeptide repeat (PPR) proteins, especially DYW-type PPR proteins, are key components of plant organellar RNA editing complexes and often determine the recognition of specific editing sites. In this study, we analyzed plastid and mitochondrial RNA editing in the soybean cultivar Dongfudou 3 under natural dehydration stress and investigated DYW-type PPR genes as potential regulators. A total of 60 plastid and 684 mitochondrial RNA editing sites were identified, most of which were located in coding regions and caused nonsynonymous C-to-U changes. Under drought stress, 19 plastid and 71 mitochondrial coding-region sites showed marked changes in editing efficiency, suggesting dynamic regulation of organellar RNA editing by water deficit. Genome-wide analysis identified 822 high-confidence soybean PPR genes, and DYW-type members were further screened using drought-responsive transcriptome data and predicted editing targets. Gm_DFD3_00451 was selected as a candidate regulator because it showed drought-responsive expression, was associated with the plastid ndhD-878 editing site and was confirmed to localize in plastids. The RNA EMSA result supports the interaction between Gm_DFD3_00451 and the ndhD-878 upstream RNA probe. In CRISPR-edited soybean hairy roots, disruption of Gm_DFD3_00451 reduced ndhD-878 editing efficiency and altered drought-related physiological traits. These results suggest that Gm_DFD3_00451 participates in plastid RNA editing during drought stress in soybean.
    Keywords:  PPR gene family; RNA editing; drought stress; organelle; soybean
    DOI:  https://doi.org/10.3389/fpls.2026.1879625
  71. Vet Med Sci. 2026 Sep;12(5): e71135
       OBJECTIVES: This study investigated the effects of selenium supplementation in the form of selenium nanoparticles (SeNPs) and sodium selenite (SSe) on the transcriptional regulation of heat shock proteins (HSP60, HSP70, and HSP90) in periparturient cloned and non-cloned Saanen goats and their offspring.
    METHODS: A total of 24 pregnant goats (12 cloned via somatic cell nuclear transfer and 12 non-cloned) were divided into three groups: SeNPs, SSe and control. Supplementation was administered orally from 21 days before expected parturition. Serum selenium levels and HSP gene expression were measured at multiple time points relative to parturition.
    RESULTS: Both SeNPs and SSe significantly increased serum selenium levels, with SeNPs demonstrating superior bioavailability. Supplemented groups exhibited significantly lower transcriptional levels of HSP60, HSP70 and HSP90 during the periparturient period, with SeNPs showing a more potent suppressive effect. A significant negative correlation was observed between serum selenium and HSP transcription. No differences were found between cloned and non-cloned animals in selenium levels or HSP expression.
    CONCLUSIONS: These findings suggest that selenium supplementation, particularly as SeNPs, enhances antioxidant capacity and reduces cellular stress, as reflected by the downregulation of HSP genes. This study highlights the potential of nano-selenium to improve stress resilience during the critical transition period in goats and their offspring, irrespective of cloning status.
    Keywords:  Selenium nanoparticle; cloned goat; heat shock protein; selenium
    DOI:  https://doi.org/10.1002/vms3.71135
  72. bioRxiv. 2026 Jul 17. pii: 2026.07.16.738376. [Epub ahead of print]
      High molecular weight fibrous proteins such as silk, elastin, and collagens, are fundamental for providing shape to macroscopic biological structures, yet their recombinant production remains challenging because of their extreme size and sequence repetitiveness. Here, we report a circular RNA-based ribosome translation platform that enables iterative ribosome synthesis of fibrous proteins through continuously "looped" translation. To promote efficient circularization of repetitive fibrous protein transcripts, we combined a synonymous codon locker sequence strategy with RNA circularization chaperones. Guided by a ribosome traffic model, we further optimized the translation bottlenecks within the circular RNA, substantially improving translation yields. The established looped translation platform is applicable to at least six classes of fibrous proteins and generated products with molecular weight exceeding titin at 3.8 MDa. The synthesized polypeptides were characterized through electron microscopy, bulk material fabrication, and mechanical analysis, demonstrating properties associated with ultra-high molecular weight polypeptides. Finally, we coupled looped translation to secretion through a programmed ribosomal frameshift, enabling export of fibrous protein across cellular membranes in both Escherichia coli and Bacillus subtilis . We envision that the genetic tools presented here could find a range of applications in bioplastics and engineered living materials.
    DOI:  https://doi.org/10.64898/2026.07.16.738376
  73. PLoS Comput Biol. 2026 Jul 31. 22(7): e1014588
      Proline is a chemically unique amino acid that influences protein structure and slows peptide-bond formation during translation. While its enrichment in intrinsically disordered regions is well known, the functional importance of its organization along protein sequences remains unclear. Here, we performed a proteome-wide analysis of inter-domain linkers in human proteins to investigate how proline organization relates to domain architecture and folding demands. We find that clustered and consecutive prolines are enriched in linkers following topologically complex domains that require the formation of long-range contacts. This suggests that proline clusters may act as intrinsic sequence-encoded pauses during translation, helping coordinate co-translational folding. We further show that linkers with enriched proline clusters frequently flank aggregation-prone domains and that proteins containing such linkers tend to have longer cellular half-lives. Together, our results demonstrate that the organization of proline residues, beyond their overall abundance, is an important determinant of protein folding, aggregation, and stability, revealing a general mechanism by which amino acid sequences regulate protein behavior.
    DOI:  https://doi.org/10.1371/journal.pcbi.1014588
  74. Exp Clin Transplant. 2026 Jul;24(Suppl 2): 218-224
       OBJECTIVES: Hypoxia is a key regulator of renal epithelial cell function and contributes to the pathogenesis of kidney diseases. Although two-dimensional cell cultures are commonly used to study hypoxic responses, three -dimensional spheroid cultures better represent the in vivo microenvironment, including cell -cell and cell -matrix interactions. In this study, we compared hypoxia -induced gene expression in two - and three -dimensional cultures of HK2 cells.
    MATERIALS AND METHODS: We induced hypoxia at 12 hours in two -dimensional cultures and at 24 hours in three -dimensional spheroids, with confirmation of hypoxia by hypoxia -inducible factor 1α protein expression and vascular endothelial growth factor mRNA upregulation. With quantitative real -time polymerase chain reaction analysis, we noted that long noncoding RNA H19 was significantly upregulated in both culture models, accompanied by modulation of NLRP3, Wnt1, β -catenin, interleukin 1 β, interleukin 6, tumor necrosis factor α, interleukin 10, microRNA -30a -5p, and microRNA -196a.
    RESULTS: Tumor necrosis factor α and microRNA -30a-5p expression were decreased, with strong interleukin 10 upregulation, in two -dimensional cultures. In three -dimensional cultures, expression levels of both microRNA -30a -5p and microRNA -196a were further upregulated, with less pronounced reduction of tumor necrosis factor α and limited increase of interleukin 10 expression.
    CONCLUSIONS: Our findings suggested that microRNA -30a -5p and microRNA -196a may play a role in modulating hypoxia -induced cytokine responses, contributing to a more balanced cellular adaptation in three -dimensional cultures. Three-dimensional HK2 spheroids may provide a physiologically relevant model for studying hypoxic stress and may reveal the potential involvement of long noncoding RNA H19 and specific microRNAs in regulation of inflammatory and signaling pathways. Of note, this study represents one of the first investigations of hypoxia -induced gene expression in three -dimensional HK2 cultures, offering a novel contribution to understanding renal epithelial responses under low oxygen conditions.
    DOI:  https://doi.org/10.6002/ect.MESOT2025.O89
  75. Hum Cell. 2026 Jul 25. pii: 115. [Epub ahead of print]39(8):
      Colorectal cancer (CRC) remains a leading cause of cancer mortality globally, underscoring the need to identify key molecular drivers. Cell division cycle 20 (CDC20), a regulator of cell cycle progression, is frequently dysregulated in malignancies. Its specific role and mechanisms in CRC pathogenesis are poorly understood, warranting investigation to uncover novel therapeutic targets. In this study, CDC20 mRNA expression was quantified by quantitative real-time polymerase chain reaction (qRT-PCR), while its protein levels were assessed using Western blotting. Cell proliferation was evaluated via the 5-Ethynyl-2'-deoxyuridine (EdU) assay. Cell apoptosis was analyzed by flow cytometry. Migration and invasion capabilities were examined using wound-healing and Transwell invasion assays, respectively. Angiogenesis was assessed using a tube formation assay. To investigate the in vivo effects of CDC20 knockdown, a xenograft mouse model was employed to monitor tumor growth. Flow cytometry was performed to quantify CD206( +) macrophages. Mechanistic studies included chromatin immunoprecipitation (ChIP), dual-luciferase reporter, RNA immunoprecipitation (RIP), and methylated RNA immunoprecipitation (MeRIP) assays to explore GATA binding protein 6 (GATA6) and methyltransferase-like 3 (METTL3) interactions with CDC20. The results showed that CDC20 expression at the mRNA and protein levels was significantly upregulated in CRC tissues in comparison with normal colorectal tissues. Moreover, its protein expression was higher in CRC cells than in human normal colonic epithelial cells. Its knockdown suppressed CRC cell proliferation, migration, invasion, and tube formation, while promoting apoptosis. In addition, CDC20 depletion inhibited tumor growth and immune escape. Transcription factor GATA6 directly activated transcription of the CDC20 gene. Crucially, restoring CDC20 expression counteracted the tumor-suppressive effects of GATA6 knockdown on malignant behaviors and immune escape. METTL3 stabilized CDC20 transcripts via insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)-mediated mRNA stability. Further, overexpressing CDC20 similarly reversed the inhibitory effects of METTL3 knockdown on CRC cell malignancy and immune escape. Thus, CDC20, upregulated transcriptionally by GATA6 and post-transcriptionally by METTL3, drove CRC progression, angiogenesis, and immune evasion. Targeting CDC20 or its regulators holds significant clinical promise for developing therapies in CRC patients.
    Keywords:  Cell division cycle 20; Colorectal cancer; GATA binding protein 6; Methyltransferase-like 3
    DOI:  https://doi.org/10.1007/s13577-026-01423-y
  76. Amyotroph Lateral Scler Frontotemporal Degener. 2026 Jul 27. 1-15
      Neurodegenerative diseases such as amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease are usually framed as consequences of aging-related pathogenic processes, including impaired proteostasis with protein aggregation, mitochondrial dysfunction, oxidative stress, and neuroinflammation. Yet, most individuals, even into advanced age, do not develop clinically significant neurodegenerative disease. This discrepancy suggests that the nervous system possesses robust and redundant protective mechanisms that maintain neural integrity despite cumulative molecular and cellular stress. In this perspective, we propose that neurodegenerative diseases arise not simply from the presence of pathogenic processes, but when integrated resilience systems fail to maintain homeostasis or when reserve mechanisms no longer compensate for accumulated pathology. We have synthesized a threshold-based model of disease emergence based on evidence across proteostasis, mitochondrial function, neuroimmune regulation, glial biology, network-level compensation, and barrier integrity, while integrating genetic, environmental, developmental, and stochastic modifiers. We distinguish biological resilience, which actively limits or repairs pathology, from reserve, which permits function despite pathology. We further propose that clinical disease emerges only when age-related cumulative stress exceeds the combined capacity of resilience and reserve. Reframing neurodegeneration as a failure of preservation systems offers new directions for prevention and therapeutic development.
    Keywords:  Aging; neurodegeneration; resilience; senescence
    DOI:  https://doi.org/10.1080/21678421.2026.2705693
  77. bioRxiv. 2026 Jul 22. pii: 2026.07.15.738801. [Epub ahead of print]
      Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimer's disease and promotes neuronal dysfunction through incompletely understood mechanisms. Here, we integrated transcriptomic, translatomic, and proteomic profiling of isogenic APOE3 and APOE4 human iPSC-derived neurons and found that APOE4 fundamentally impairs neuronal proteome renewal. Although transcriptional changes were modest, APOE4 disrupted ribosome occupancy, altered translational dynamics, and uncoupled protein abundance from transcript levels. Proteome-wide turnover measurements revealed a global extension of protein half-lives and widespread accumulation of long-lived proteins. Functional proteomic analyses demonstrated concurrent lysosomal and proteasomal impairments associated with reduced proteasome activity and increased association of APOE with neuronal proteasomes. Longitudinal proteomics further showed that protein accumulation emerges during neuronal maturation and precedes a senescence-like cellular stress state. Together, these findings identify impaired proteome renewal as a central mechanism underlying neuronal vulnerability to APOE4 and establish defective proteostasis as an early pathogenic event in Alzheimer's disease.
    DOI:  https://doi.org/10.64898/2026.07.15.738801
  78. J Biol Chem. 2026 Jul 28. pii: S0021-9258(26)02248-9. [Epub ahead of print] 113376
      Mutations in RNA-binding proteins are increasingly identified in cancers through tumor sequencing and are correlated with disease progression, therapy response, and overall patient outcomes, underscoring the need to study them. Here, we focus on the RNA-binding protein Poly-C binding protein 1 (PCBP1), which binds target RNAs through K-homology (KH) domains to regulate RNA fate. PCBP1 is a tumor suppressor gene and hotspot missense mutations at leucine residues 100 and 102 are observed in colorectal cancer (CRC). PCBP1 mutations have been recurrently reported in CRC genome-wide mutation studies and are associated with poor clinical outcomes; however, their effects on PCBP1 expression and function remain largely unexplored. We show that cancer-associated mutations substituting leucine 100 and 102 with glutamine, proline, or arginine destabilize PCBP1. The L100/L102 residues occur at the interface of the RNA-binding KH1 and KH2 domains, and our molecular dynamics simulations show that mutations at these residues disrupt the secondary structure of PCBP1. Additionally, these mutants display increased cytoplasmic localization. Importantly, mutant PCBP1 physically interacts with wild type PCBP1 and suppresses its expression through a dominant-negative mechanism. Together, our data demonstrate that CRC-associated PCBP1 mutations destabilize the protein and act as dominant-negative variants, revealing a novel mechanism of tumor suppressor inactivation in colorectal cancer.
    Keywords:  PCBP1; RNA-binding protein; colorectal cancer; dominant negative; tumor suppressor
    DOI:  https://doi.org/10.1016/j.jbc.2026.113376
  79. Curr Issues Mol Biol. 2026 Jul 14. pii: 718. [Epub ahead of print]48(7):
      Salinity stress has a debilitating effect on crop productivity and triggers complex molecular changes in plants, and understanding these responses is important for improving stress tolerance. This study investigated transcriptomic changes in the salt-tolerant barley line CC89/Giza123 by analyzing gene expression in roots and leaves following exposure to 200 mM NaCl for 12 and 24 h. The number of differentially expressed genes (DEGs) showed a much stronger response in roots than in leaves. At 12 h, roots showed 1836 DEGs, and this number increased to 2696 at 24 h, whereas leaves showed 256 DEGS at 12 h, and 787 at 24 h. The presence of strong and early activation in roots appears to indicate that roots play a key role in the adaptive response to salinity stress initiation. GO and KEGG analyses of differentially expressed genes revealed tissue- and time-specific responses. Roots showed rapid activation of ribosome and secondary-metabolite pathways at 12 h, followed by shifts toward carbon fixation and energy-related pathways at 24 h. Leaves responded early by adjusting photosynthesis-antenna proteins and later expanded their response to defense-related and amino-acid biosynthesis pathways. Important salt-responsive genes were identified in both tissues, including protein kinases, protein phosphatases 2C (PP2Cs), phospholipases, aquaporins, detoxification enzymes, molecular chaperones, and Late Embryogenesis Abundant (LEA) proteins. These results highlight clear tissue-specific and time-dependent differences in how plants respond to salt stress, providing insights into the metabolic and regulatory mechanisms involved in salt tolerance. Overall, these results provide evidence that the response of barley to salinity is achieved by using coordinated and dynamic molecular changes in different tissues. The transcriptomic dataset is a useful source of candidate genes for further functional studies and is a significant resource for breeding and biotechnological approaches to the production of salt-tolerant cereal crops.
    Keywords:  and putative salt-responsive genes; barley breeding line CC89/Giza123; differentially expressed gene (DEG); salinity; transcriptome
    DOI:  https://doi.org/10.3390/cimb48070718
  80. Physiol Plant. 2026 Jul-Aug;178(4):178(4): e71039
      Plants, being sessile organisms, depend on finely tuned biochemical mechanisms to cope with environmental challenges. Among these, the phenylpropanoid pathway plays a central role in the production of a diverse array of secondary metabolites. These PAL-derived secondary metabolites accumulate in distinct spatiotemporal patterns across plant organs and adjust dynamically in response to environmental cues. Such spatiotemporal dynamics, regulated by distinct mechanisms, allow plants to maintain physiological function while improving tolerance to abiotic stresses. Recent advances in spatial and temporal omics technologies, such as imaging mass spectrometry (IMS) and spatial transcriptomics (ST), have revolutionized our ability to visualize the localization of secondary metabolites in plant tissues, providing insights into stress resilience. The spatial multi-omics reveals secondary metabolite accumulation and informs on the genes driving their production at each stage of the stress response. High-resolution, advanced computational, and emerging spatial multi-omics frameworks, coupled with machine-learning algorithms for spatial data interpretation, are rapidly enhancing our ability to visualize and model dynamic stress responses. However, significant challenges, including the structural complexity of plant tissues (e.g., rigid cell walls), metabolite diversity, and long life spans, complicate the exploration of secondary metabolite accumulation. Generally, the spatiotemporal accumulation of PAL-derived secondary metabolites under abiotic stress represents a sophisticated adaptive system that optimizes defence, signaling, and growth coordination in plants, aided by regulatory mechanisms such as transcriptional regulation, hormonal signaling, and secondary metabolite transport. This fundamental understanding offers practical insights into plant improvement, enabling targeted engineering and manipulation of phenylpropanoid metabolism to enhance stress tolerance.
    Keywords:  abiotic stress; phenylpropanoid pathway; secondary metabolites; spatiotemporal accumulation
    DOI:  https://doi.org/10.1111/ppl.71039
  81. Drug Discov Today. 2026 Jul 27. pii: S1359-6446(26)00153-4. [Epub ahead of print] 104748
      Alzheimer's disease (AD) involves amyloid-β aggregation, tau hyperphosphorylation and mitochondrial dysfunction with defective mitophagy. Emerging evidence implicates RNA N6-methyladenosine (m6A) modification and transglutaminase 2 (TG2) as critical regulators of mitochondrial quality control in AD. Downregulation of METTL3/METTL14 and upregulation of fat mass and obesity-associated protein reduce m6A methylation, impair PTEN-induced putative kinase 1/Parkinson protein 2-mediated mitophagy and promote reactive oxygen species accumulation and synaptic loss. Conversely, TG2 overexpression exacerbates mitochondrial stress by crosslinking Aβ and tau, disturbing dynamin-related protein 1- and mitochondrial fission 1 protein-mediated dynamics and suppressing mitophagy. Crosstalk between TG2-induced oxidative stress and m6A dysregulation amplifies neuronal damage. Pharmacological modulation, using TG2 inhibitors (e.g. Z-DON) and m6A enhancers (e.g. METTL3 overexpression), restores mitophagic flux and mitigates pathology in preclinical models, suggesting dual m6A-TG2 targeting as a promising disease-modifying approach in AD.
    Keywords:  Alzheimer’sdisease; m(6)A mRNA modification; mitophagy; neuroprotective effects; transglutaminase2
    DOI:  https://doi.org/10.1016/j.drudis.2026.104748
  82. Immunol Rev. 2026 Aug;341(1): e70150
      Autoimmune responses are often attributed to failed tolerance to self-proteins, yet protein expression alone cannot explain why certain antigens dominate disease, why autoreactivity emerges under stress, or why specific HLA alleles shape risk. This review presents a framework in which autoimmunity arises from posttranslational remodeling of antigen identity. Rather than limiting PTMs to side chain chemistry, we consider how covalent modifications, altered processing, aberrant translation, peptide recombination, and supramolecular assembly expand the repertoire of molecular forms available for immune recognition. Classical PTMs such as citrullination, deamidation, oxidation, glycosylation, phosphorylation, sulfation, and ubiquitin-like remnants can modify proteolysis, HLA binding, and antibody recognition. Noncanonical pathways, including signal peptide processing, ERAP-dependent trimming, defective ribosomal products, cryptic ORFs, proteasome-catalyzed splicing, and hybrid insulin peptides, further demonstrate that the presented antigenome extends beyond annotated proteins. We also propose that aggregation functions as a supramolecular antigenic modification by altering uptake, persistence, protease accessibility, and local reaction chemistry. Examples from rheumatoid arthritis, celiac disease, type 1 diabetes, multiple sclerosis, systemic lupus erythematosus, inflammatory bowel disease, and autoimmune thyroid disease illustrate how these mechanisms converge. Finally, we discuss mass spectrometry and immunopeptidomics strategies for identifying, validating, and functionally interpreting remodeled antigens in autoimmune disease.
    DOI:  https://doi.org/10.1111/imr.70150
  83. bioRxiv. 2026 Jul 14. pii: 2026.07.13.738277. [Epub ahead of print]
      Insulin can misfold and assemble into amyloid fibrils, a process linked not only to complications of insulin therapy but also to proteotoxic stress in pancreatic β-cells. Despite growing interest in the pathological consequences of insulin aggregation, prevention efforts are limited by an incomplete understanding of the endogenous mechanisms that counteract it. Here, we identify Fas apoptosis inhibitory molecule (FAIM) as an endogenous suppressor of insulin amyloid formation. FAIM reduces β-sheet formation and redirects insulin toward disordered, growth-incompetent assemblies. Further, FAIM attenuates the cytotoxicity of insulin aggregates in vitro . We hypothesize that this effect arises from masking aggregation-prone regions of insulin and show through structural modeling that FAIM interacts with both insulin chains. These findings extend the anti-aggregation function of FAIM to insulin and suggest a mechanism for endogenous suppression of insulin amyloid formation. More broadly, our results provide insight into the regulation of insulin assembly and highlight FAIM as a candidate modulator of proteostasis in metabolic disease.
    Statement for a broader audience: Insulin can clump together into harmful aggregates, contributing to complications of insulin therapy and potentially damaging the insulin-producing cells of the pancreas. This study identifies the naturally occurring protein FAIM as a protective factor that inhibits the formation of these harmful aggregates and reduces their toxicity. These findings improve our understanding of how cells protect insulin from harmful aggregation and may open new avenues for developing therapies to combat diabetes-related protein aggregation.
    DOI:  https://doi.org/10.64898/2026.07.13.738277
  84. J Cell Sci. 2026 Jul 27. pii: jcs.264641. [Epub ahead of print]
      NIFK is a nucleolar protein involved in ribosome biogenesis which interacts with Ki-67 and is recruited to the perichromosomal layer during mitosis. NIFK expression is elevated in multiple cancers and its expression correlates with poor prognosis. Although NIFK is highly phosphorylated, the regulation and functional significance of NIFK phosphorylation is not fully understood. Here, we identify Ser247 as a stress- and mitosis-responsive phosphorylation site on NIFK. Stress induces Ser247 phosphorylation through p38 and MSK1. Independently of stress, Ser247 is phosphorylated during mitosis by Aurora B. In vitro assays confirm that MSK1 and Aurora B directly phosphorylate Ser247. During mitosis, Ser247 phosphorylation acts as a priming event enabling extensive multisite phosphorylation of NIFK. Mutation of Ser247 (S247A) abolishes this phosphorylation cascade but does not impair recruitment of NIFK to mitotic chromosomes. Nonetheless, cells with a NIFK S247A mutation display a delay in mitotic entry. Whether S247A phosphorylation affects the ribosome biogenesis function of NIFK is not clear. These findings reveal Ser247 as a hub integrating stress and mitotic cues and establish it as a priming site for mitotic hyperphosphorylation of NIFK.
    Keywords:  Ki-67; Mitosis; NIFK; Ribotoxic stress
    DOI:  https://doi.org/10.1242/jcs.264641
  85. Int J Biol Sci. 2026 ;22(12): 6670-6688
      Synaptotagmin-binding cytoplasmic RNA-interacting protein (SYNCRIP) is an RNA-binding protein (RBP) implicated in the pathogenesis of various cancers through involvement in regulating multiple cellular processes. Notably, this study identified that SYNCRIP expression is significantly elevated in glioblastoma (GBM) and is associated with poor prognosis and tumor progression. Mechanistically, SYNCRIP upregulates SIRT1 expression at both the transcriptional and post-transcriptional levels by stabilizing SIRT1 mRNA. Meanwhile, loss of SYNCRIP leads to reduced SIRT1 expression, accumulation of reactive oxygen species (ROS), and induction of ferroptosis. Notably, restoration of SIRT1 rescues cells from ferroptotic cell death, supporting the critical role of SIRT1 in SYNCRIP-mediated ferroptosis resistance. SYNCRIP also enhances hexokinase 2 (HK2) expression through transcriptional activation and internal ribosome entry site (IRES)-mediated translation, thereby promoting glycolytic activity in GBM. Furthermore, depletion of SYNCRIP results in mitochondrial dysfunction and impairs GBM cell migration and invasion by downregulating epithelial-mesenchymal transition (EMT)-associated factors. Collectively, these findings suggest that SYNCRIP is a key regulator of GBM progression by maintaining metabolic homeostasis and ferroptosis resistance, highlighting SYNCRIP as a potential therapeutic target in GBM.
    Keywords:  HK2; IRES; SIRT1; SYNCRIP; ferroptosis; transcription
    DOI:  https://doi.org/10.7150/ijbs.127096
  86. FASEB J. 2026 Aug 15. 40(15): e72130
      Retinitis pigmentosa (RP) is a hereditary retinal degeneration disorder often caused by mutations in the rhodopsin gene, leading to photoreceptor death and vision loss. While structural misfolding of rhodopsin is a known contributor to disease pathology, the mechanisms of its cellular and in particular metabolic consequences are poorly understood. To study the direct effects of rhodopsin misfolding and structural rescue on cellular metabolism, we used the P23A mutant and its N2C/D282C stabilized counterpart as a structural tool to assess how differences in folding stability relate to measurable changes at the metabolite level. The engineered cysteine pair allows the formation of a disulfide bond restoring structural integrity and reinforcing the stable seven-transmembrane bundle. We used untargeted Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics analysis conducted in inducible rhodopsin-expressing cell lines, providing a broad and general profiling of metabolic pathway alterations in response to the expression of RP mutants and their structurally rescued counterparts. Principal component analysis, hierarchical clustering, and K-means clustering revealed distinct metabolic signatures associated with each rhodopsin-expressing cell line, demonstrating a highly significant effect of genotype on global metabolite composition (F = 71.679; R2 = 0.93724; p = 0.001). Pairwise comparisons and background-subtracted analyses identified consistent alterations in arginine and proline metabolism, glutathione metabolism, and the TCA cycle, nucleotide, amino acid metabolism, redox regulation, and mitochondrial function in cells expressing misfolded P23A. Pathway enrichment highlighted key metabolites in the respective pathways as candidate biomarkers for the rhodopsin P23A mutation. As this study employs a non-retinal cell system, the observed metabolic changes reflect conserved responses to rhodopsin misfolding and proteostatic stress in the ER rather than a direct model of rod cell degeneration. Our findings support the hypothesis that there is a biochemical link, most likely the UPR, between rhodopsin folding/misfolding status and metabolic homeostasis and suggest that targeted metabolic modulation may offer a complementary therapeutic avenue for treating RP.
    DOI:  https://doi.org/10.1096/fj.202505024R
  87. Front Biosci (Landmark Ed). 2026 Jul 20. 31(7): 52436
       BACKGROUND: Colorectal cancer (CRC) is a leading cause of cancer-related morbidity and mortality worldwide; thus, understanding its molecular mechanisms is critical for developing novel therapeutic targets. Long non-coding RNAs (lncRNAs) play crucial isoform-specific roles in cancer. While oncogenic lncRNA LINC00673 is known to be involved in multiple malignancies and possesses five distinct transcript variants, the functional role of LINC00673-V4-a highly expressed transcript variant in CRC-remains largely unexplored. This study investigated how LINC00673-V4 drives CRC proliferation by modulating the Hippo-Yes-associated protein (Hippo-YAP) signaling pathway.
    METHODS: Survival analysis was performed using the GSE39582 dataset to assess the prognostic value of LINC00673 in patients with CRC. The expression of LINC00673 transcript variants in CRC cell lines was detected by quantitative PCR. Cell Counting Kit-8 and 5-ethynyl-2'-deoxyuridine (EdU) incorporation assays were used to assess cell proliferation upon LINC00673-V4 knockdown or overexpression. Western blotting and immunofluorescence staining were utilized to analyze the expression of Hippo-YAP target genes. To confirm the interaction between LINC00673-V4 and fused in sarcoma (FUS), RNA immunoprecipitation (RIP) was performed, while co-IP was used to investigate potential protein-protein interactions.
    RESULTS: High LINC00673 expression was observed in CRC cell lines and was associated with a poor prognosis in patients with CRC. Among the five LINC00673 transcript variants, LINC00673-V3 and LINC00673-V4 were the predominantly expressed isoforms; however, only LINC00673-V4 significantly promoted CRC cell proliferation. LINC00673-V4 inhibited YAP phosphorylation at Ser127, promoted YAP nuclear translocation, and upregulated the expression of Hippo-YAP target genes (connective tissue growth factor, cysteine-rich angiogenic inducer 61, survivin). RIP assays confirmed an association between LINC00673-V4 and FUS, while co-immunoprecipitation (co-IP) assays revealed that FUS interacted with both YAP and large tumor suppressor 1 (LATS1), suggesting FUS may facilitate LATS1-mediated YAP phosphorylation. FUS was found to promote LATS1-mediated YAP Ser127 phosphorylation, induce YAP cytoplasmic retention, and down-regulate Hippo-YAP target gene expression. Rescue experiments showed that LINC00673-V4 reversed the FUS-induced suppression of Hippo-YAP target gene expression.
    CONCLUSIONS: Our study identified LINC00673-V4 as an isoform-specific oncogenic lncRNA in CRC. By associating with FUS, LINC00673-V4 sequesters FUS away from the LATS1/YAP complex; thereby inhibiting FUS-mediated YAP phosphorylation and enhancing Hippo-YAP target gene expression. These findings expand the landscape of lncRNA isoform-specific regulation in cancer, highlighting LINC00673-V4 as a potential prognostic biomarker and therapeutic target for CRC.
    Keywords:  Hippo signaling pathway; LINC00673-V4; RNA-binding protein FUS; colorectal cancer
    DOI:  https://doi.org/10.31083/FBL52436
  88. Genes (Basel). 2026 Jul 13. pii: 797. [Epub ahead of print]17(7):
      Background: As a major regulator, methyltransferase-like 3 (METTL3) catalyzes N6-methyladenosine (m6A) modification in mRNA. The m6A modifications mediated by METTL3 influence RNA splicing, nucleocytoplasmic distribution, stability, and other functions, thereby playing a vital and indispensable role in genetic regulatory network. Although several studies have shown its critical role in mRNA fate, the global pattern of mRNA methylation alteration driven by METTL3 remain unclear. Methods: Here, a HEK293T cell line with METTL3 depletion was constructed, and RNA sequencing (RNA-seq) and methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) were implemented. Additionally, quantitative Reverse Transcription PCR (qRT-PCR) technology was used to confirm some of the differentially expressed genes. Result: The mRNA methylation alteration landscape was clarified and the regions altered by m6A modification due to METTL3 deletion that was annotated and characterized, with 5763 hypomethylated/269 hypermethylated genes after METTL3 silence. Several methylation-related innate anti-infection immune genes, including MYD88, RIG-1, CYLD and IRF9, were exposed through comprehensive analysis to MeRIP-seq and RNA-seq data, and these genes were principally enriched in pathogen infection and innate immune response pathways such as Shigellosis, Yersinia infection, and the HIV-1 viral life cycle. Conclusion: Our study discovered that the METTL3 association with differentially expressed genes, suggested that METTL3 and the genes it regulates might serve as targets for defense against infection.
    Keywords:  METTL3; anti-infection immune genes; mRNA methylation
    DOI:  https://doi.org/10.3390/genes17070797