bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–07–19
72 papers selected by
Cédric Chaveroux, CNRS



  1. Plants (Basel). 2026 Jul 01. pii: 2043. [Epub ahead of print]15(13):
      Ribosomes are essential macromolecular complexes responsible for protein synthesis and have traditionally been regarded as uniform and passive components of translational machinery. However, accumulating evidence has revealed that ribosomes exhibit substantial heterogeneity in both composition and function. In this review, we summarize the major sources of ribosome heterogeneity in plants, including ribosomal protein (RP) paralog diversity, sequence variation in rDNA/rRNA, dynamic chemical modifications of rRNAs and RPs, alterations in RP stoichiometry, and the involvement of ribosome-associated factors. These mechanisms collectively generate structurally and functionally distinct ribosome populations. Emerging evidence suggests that these heterogeneous ribosomes can actively regulate gene expression by preferentially translating specific subsets of mRNAs in response to developmental cues and environmental conditions. We further discuss the potential biological implications of ribosome heterogeneity in plant growth, development, and stress adaptation, and highlight current challenges in the field. Advances in high-resolution structural and single-ribosome profiling technologies are expected to provide new insights into the regulatory roles of heterogeneous ribosomes. This review provides a comprehensive framework for understanding the causes and functional significance of ribosome heterogeneity in plants, offering new perspectives on translational regulation and plant adaptive biology.
    Keywords:  heterogeneity; mRNA translation; ribosomal DNA/RNA (rDNA/rRNA); ribosomal protein (RP); ribosome
    DOI:  https://doi.org/10.3390/plants15132043
  2. Trends Mol Med. 2026 Jul 17. pii: S1471-4914(26)00166-8. [Epub ahead of print]
      The nucleolus is a master regulator of ribosome biogenesis and cellular homeostasis, as well as an increasingly key determinant of neuromuscular diseases. Across these conditions, diverse genetic and molecular lesions converge on alterations in nucleolar organization and function. These changes impact ribosomal RNA synthesis and reshape translational output, linking nuclear events to cytoplasmic protein homeostasis in disease-relevant contexts. In this review, we propose a comprehensive framework in which the nucleolus integrates RNA dysfunction, genome organization, and translational control across neuromuscular disorders. This perspective provides a conceptual basis for interpreting disease heterogeneity and highlights nucleolar pathways as potential, underexploited targets for therapeutic intervention.
    Keywords:  RNA metabolism; neuromuscular diseases; noncoding RNA; nucleolus; ribosome biogenesis; translational control
    DOI:  https://doi.org/10.1016/j.molmed.2026.06.013
  3. Discov Oncol. 2026 Jul 16.
      N6-methyladenosine (m6A) is a major epitranscriptomic modification of RNA that plays a crucial role in regulating RNA metabolism and function, thereby participating in diverse biological processes such as cellular homeostasis and stress responses. The dynamic regulation of m6A is orchestrated by three classes of proteins: methyltransferases that install the modification, demethylases that remove it, and m6A-binding proteins that recognize modified transcripts and mediate downstream effects. Accumulating evidence has shown that dysregulation of m6A is critically involved in the initiation and progression of various malignancies. Hepatocellular carcinoma (HCC), a primary liver malignancy with high mortality and poor prognosis, has also been closely linked to m6A-mediated RNA regulation. In this review, we summarize the molecular mechanisms by which m6A regulates both coding and noncoding RNAs in HCC, highlight the functional roles of key m6A regulators in hepatocarcinogenesis, and discuss the therapeutic potential of targeting the m6A machinery in HCC.
    Keywords:  Hepatocellular carcinoma; N6-methyladenosine; Noncoding RNA; m6A modification; mRNA
    DOI:  https://doi.org/10.1007/s12672-026-05612-x
  4. Int J Mol Sci. 2026 Jul 06. pii: 6052. [Epub ahead of print]27(13):
      Stress granules (SGs) are stress-induced ribonucleoprotein condensates assembled around untranslated mRNAs and RNA-binding proteins. G3BP1 is a central regulator of SG formation, yet the molecular events that initiate G3BP1-mediated condensation remain poorly understood. Current models propose that condensation is initiated by RNA-RNA interactions, G3BP1 self-association, or RNA-dependent assembly of G3BP1 into higher-order networks. To define the earliest steps of condensate formation, we employed high-speed atomic force microscopy (HS-AFM) to monitor G3BP1-RNA assembly at the nanometer scale. HS-AFM revealed that G3BP1 first associates with RNA to form discrete nascent assemblies that progressively recruit additional RNA and G3BP1 molecules. These assemblies subsequently grow into higher-order RNA-protein condensates through stepwise assembly. Together, these observations identify RNA-bound G3BP1 assemblies as the initiating structures of condensate formation and provide a framework for understanding the early stages of stress granule assembly.
    Keywords:  G3BP1; HS-AFM; stress granule
    DOI:  https://doi.org/10.3390/ijms27136052
  5. RSC Chem Biol. 2026 Jul 03.
      Chemical damage to ribosomal RNA (rRNA) during oxidative or inflammatory stress can impact protein synthesis. Human cells were exposed to an H2O2 titration to induce oxidative stress, or tumor necrosis factor-α (TNF-α) over a time course to induce inflammation, followed by direct nanopore RNA sequencing of cytosolic and mitochondrial rRNAs to reveal damage sites. Guanosine (G) oxidation and deamination of adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) were identified by changes in the base-called data. Both stressors induced G oxidation in cytosolic rRNA, whereas mitochondrial rRNA was less oxidatively modified. Nitrosative stress during inflammation caused deamination lesions in rRNAs in both compartments. Inspection of highly modified sites found that GC-rich tentacles in the 28S rRNA expansion sequences were hotspots for G oxidation and C deamination in the cytosolic ribosome. Outside of tentacles, lesions generally occurred on surface nucleotides. The minimalist mitochondrial ribosome structure, compared to the cytosolic ribosome, alters reaction patterns such that nucleotides on the surface or in functionally relevant regions are damaged. These patterns suggest that tentacles on cytosolic rRNA direct reactive oxygen and nitrogen species away from the catalytic core to maintain activity during stress, while the mitochondrial ribosome is damaged in regions that can deactivate protein synthesis. These results provide molecular insight into metabolic dysfunction and suggest a new function for the GC-rich tentacles evolved in mammalian cells.
    DOI:  https://doi.org/10.1039/d6cb00068a
  6. Front Cell Dev Biol. 2026 ;14 1890102
      Epithelial-mesenchymal transition (EMT) is a flexible cell-state program that supports tumor invasion, metastasis, immune escape, and therapy resistance. It is not a simple switch from an epithelial to a mesenchymal phenotype. Instead, cancer cells often move through intermediate or partial EMT states, which allow them to retain cell-cell adhesion while gaining motility and stress tolerance. Recent studies show that RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), A-to-I RNA editing, pseudouridine (Ψ), N4-acetylcytidine (ac4C), and N7-methylguanosine (m7G), add an important post-transcriptional layer to EMT regulation. These modifications control RNA stability, translation, splicing, export, and innate immune sensing. They therefore connect environmental cues, such as hypoxia, TGF-β signaling, inflammatory cytokines, and therapeutic stress, to EMT-related gene expression programs. This review summarizes how major RNA modification systems regulate EMT in cancer. Rather than listing individual findings, we compare common regulatory patterns across tumor types. m6A has the strongest evidence base and acts through writer-reader-eraser modules that regulate EMT transcription factors and signaling pathways such as TGF-β/SMAD, Wnt/β-catenin, PI3K/AKT, EGFR/STAT3, and Notch. m5C and ac4C mainly promote EMT by stabilizing transcripts and enhancing translation, whereas m7G influences EMT through translational reprogramming and codon-biased protein synthesis. A-to-I editing has more complex effects because it can either support immune evasion and plasticity or generate tumor-suppressive RNA isoforms. Ψ-related mechanisms remain less developed, but early evidence suggests roles in RNA stability, stress adaptation, and invasive behavior. We also discuss how EMT and RNA modifications interact with the tumor microenvironment, especially immune suppression and checkpoint resistance. Finally, we evaluate therapeutic opportunities and key challenges. Current studies are limited by reliance on bulk assays, incomplete site-specific validation, weak causal evidence, and insufficient clinical standardization. Future work should integrate single-cell and spatial epitranscriptomics, functional RNA editing tools, and clinical cohorts to define which RNA modification events are true drivers of EMT and which are only associated markers.
    Keywords:  EMT; HIF-1α; RNA modification; cancer invasion; cell migration; epitranscriptomics; hypoxia; immune evasion
    DOI:  https://doi.org/10.3389/fcell.2026.1890102
  7. Int J Mol Sci. 2026 Jun 29. pii: 5858. [Epub ahead of print]27(13):
      More than 160 types of post-transcriptional RNA modifications have been identified, revealing considerable diversity in their types, abundances, distributions, and functional roles across different RNAs, cells, and tissues in humans. Recent advances in high-throughput sequencing technologies have enabled the systematic detection of dynamic RNA modifications, including N6-methyladenosine (m6A) and inosine (I). In this review, we focus on RNA modifications in eukaryotic mRNA and provide an overview of current high-throughput methodologies for detecting the most abundant adenosine-related modifications, including m6A and adenosine-to-inosine (A-to-I) RNA editing. Finally, we discuss the major challenges that remain in the field and highlight key directions for future research.
    Keywords:  Illumina; RNA editing; RNA modifications; direct RNA sequencing; epitranscriptomics; long-read sequencing; m6A
    DOI:  https://doi.org/10.3390/ijms27135858
  8. bioRxiv. 2026 Jul 06. pii: 2026.07.03.736420. [Epub ahead of print]
      Dietary methionine restriction has been shown to improve metabolic health and treat multiple diseases. Methionine metabolism regulates transmethylation reactions, including N6-methyladenosine (m6A) RNA methylation, by modulating the availability of S-adenosyl methionine (SAM). Both m6A RNA methylation and methionine metabolism are involved in the regulation of the circadian clock. However, it remains unclear whether dietary methionine influences circadian rhythms through the regulation of m6A RNA modification. In this study, we investigated the effects of short-term methionine deprivation on the diurnal oscillations of m6A RNA methylation in the mouse liver. We found that a methionine-deficient (MD) diet reprogrammed the cyclic expression patterns of m6A writers, erasers, and readers. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that the MD diet induced de novo diurnal m6A oscillations in genes associated with RNA processing, protein translation, protein ubiquitination, and mTORC1 signaling pathways. RNA-seq and quantitative proteomics analyses demonstrated that MD-induced changes in m6A RNA levels were linked to alterations in mRNA and protein abundance. We observed that dynamic m6A RNA methylation of the transcripts encoding two key enzymes, MAT2A and CBS, helps maintain methionine homeostasis in response to methionine starvation. These findings identify m6A RNA methylation as a key mechanism linking methionine metabolism to circadian regulation.
    DOI:  https://doi.org/10.64898/2026.07.03.736420
  9. Elife. 2026 Jul 13. pii: RP111336. [Epub ahead of print]15
      Stress granules are large cytoplasmic bodies formed in response to environmental insults by eukaryotic cells. Stress granule formation is key for post-stress recovery, and many diseases and infections are characterized by dysregulation of these membraneless organelles. How specific and non-specific macromolecular interactions drive the formation of stress granules and other large assemblies is an area of active research. Stress granules are comprised of dense, ~200 nm cores, and these are known to contain numerous RNAs and proteins. Now, we have discovered that more than half of the nucleic acid content of stress granule cores is circular, double-stranded DNA. We demonstrate cytologically that these extrachromosomal circular DNAs (eccDNAs) colocalize cytoplasmically with canonical stress granule marker proteins in HEK293T cells, and through CRISPR targeting in budding yeast, that they are required for stress granule formation upon stress. This discovery thus reveals a key function for eccDNA in the eukaryotic stress response.
    Keywords:  RNA–DNA heteroduplex; budding yeast; cell biology; circular dsDNA; eccDNA; human; stress granules; yeast
    DOI:  https://doi.org/10.7554/eLife.111336
  10. bioRxiv. 2026 Jul 08. pii: 2026.07.07.737135. [Epub ahead of print]
      Bacteria use post-transcriptional regulatory mechanisms to rapidly adjust gene expression during environmental change. In the gut-associated genus Bacteroides, these mechanisms remain poorly defined as these organisms lack canonical RNA chaperones like Hfq and CsrA that coordinate post-transcriptional stress responses in many well-studied model bacteria. Most Bacteroides possess conserved RNA recognition motif-1 (RRM-1) domain-containing RNA-binding proteins (more common in eukaryotes than bacteria) that have been proposed to act as global RNA chaperones. Here, we show that these RNA binding proteins (RBPs) are central to cold stress adaptation. Simultaneous deletion of all rbp genes produces a cold-sensitive growth defect across multiple Bacteroides species, while single deletions do not, revealing conserved functional redundancy. RBP transcripts and proteins accumulate rapidly after temperature downshift, and loss of RBPs extensively reprograms the transcriptome. Cold sensitivity of Bacteroides rbp mutants is not caused by defects in ribosome assembly or rRNA maturation. Instead, we find that in Bacteroides thetaiotaomicron, RBPs act together with BT1884, the sole canonical cold shock protein possessed by this organism. The combined loss of RBPs and BT1884 produces a synthetic severe cold sensitivity phenotype, defining two functionally redundant cold stress systems belonging to unrelated protein families. Strains lacking RBPs show reduced survival under simultaneous cold and oxygen stress, the conditions Bacteroides cells are expected to encounter during host-to-host transmission. Together, these findings establish RRM-1 RBPs as non-canonical cold shock proteins that enable cold adaptation and environmental survival in Bacteroides and suggest how these organisms withstand the stresses of transmission between hosts.
    IMPORTANCE: Bacteroides species are among the most abundant and stable members of the human gut microbiome, and they are also among the most readily transmitted between people. Reaching a new host requires surviving conditions outside the gut, including cold and oxygen exposure, yet how these bacteria withstand such stress is not well understood. Most bacteria manage stress using a well-defined set of RNA-binding proteins, but Bacteroides lack these canonical factors. We show that Bacteroides instead rely on a different family of RNA-binding proteins, more typical of eukaryotes than bacteria, to survive cold stress, and that these proteins promote survival under the conditions encountered during transmission. This work identifies a molecular system that allows an abundant and ecologically successful gut bacterium to endure the environmental challenges of moving between hosts.
    DOI:  https://doi.org/10.64898/2026.07.07.737135
  11. Int J Mol Sci. 2026 Jul 02. pii: 5954. [Epub ahead of print]27(13):
      The spatial organization of the eukaryotic nucleus plays a pivotal role in regulating pre-mRNA splicing; however, the underlying principles governing this organization remain incompletely understood. Recent advances in imaging and sequencing technologies have revealed that splicing regulation is orchestrated across multiple hierarchical levels, from nanoscale protein-RNA interactions to large-scale nuclear architecture. Intrinsically disordered regions (IDRs) in RNA-binding proteins (RBPs) mediate multivalent interactions that drive liquid-liquid phase separation, leading to the formation of dynamic biomolecular condensates, such as nuclear speckles, paraspeckles, and nuclear stress bodies (nSBs). These structures act as functional hubs that modulate RNA processing efficiency and respond to cellular stress. In addition, emerging evidence highlights nucleus-wide RBP meshworks that spatially organize co-transcriptional splicing through dynamic RNA-dependent interactions. The interplay between these condensates and meshworks forms a spatially organized network that fine-tunes the efficiency and fidelity of pre-mRNA splicing. Collectively, this review presents a unified model in which phase separation and higher-order nuclear architecture coordinately regulate transcriptomic output in space and time.
    Keywords:  RNA-binding protein; intrinsically disordered region; meshwork; phase separation; speckle; splicing
    DOI:  https://doi.org/10.3390/ijms27135954
  12. Angew Chem Int Ed Engl. 2026 Jul 17. e8835235
      A series of disulfide-based, self-immolative acyl conjugates have been designed and tested for reversibly protecting the ribose 2'-hydroxy position of RNA. These modifications were found to be responsive to endogenous glutathione levels for efficient RNA recovery both in solution and cultured cells. Through this modification strategy, we achieve shielding of the biomolecule from both nuclease enzymes and translational machinery, allowing for a tunable release of RNA with improved cellular stability and minimal innate immune activation. The self-immolative RNA deprotection includes a cyclization step which exhibits differing kinetic profiles based on ring size and electronic properties. Moreover, we demonstrate sustained target protein production for both green-fluorescent protein and nanoluciferase in cell models. Both acylated mRNA models resulted in significant increases in protein expression compared to the unmodified mRNA control, with increases in protein expression of up to 600% and sustained higher protein expression of modified mRNA samples observed over 120 h in comparison to unmodified RNA. These exciting results highlight the versatility of our approach in the design of next-generation RNA-based prodrugs.
    Keywords:  RNA; acyl‐modification; decaging; glutathione‐responsive; mRNA
    DOI:  https://doi.org/10.1002/anie.8835235
  13. J Mol Biol. 2026 Jul 13. pii: S0022-2836(26)00316-5. [Epub ahead of print] 169943
      Nonsense-mediated decay (NMD) is a vital RNA surveillance mechanism in eukaryotic cells that ensures mRNA quality and regulates gene expression. NMD targets mRNAs with premature translation-termination codons to prevent the production of potentially harmful truncated proteins. But NMD is also involved in modulating the expression of physiological mRNAs to maintain cellular homeostasis. This NMD function is particularly relevant to calibrate the cellular transcriptome in response to environmental signals and stress. Its conservation across eukaryotes highlights its essential role. When active, NMD promotes mRNA degradation involving exoribonucleases like XRN1 (5' to 3') and the exosome (3' to 5'). DIS3L2, an exosome-independent exonuclease that primarily targets substrates marked by the non-templated addition of uridine residues to the 3' end of RNA molecules by terminal uridylyl transferases, can also degrade some NMD substrates, especially those that underwent 3' end uridylation. This review explores DIS3L2's interaction with the NMD pathway (DIS3L2/NMD pathway) and the human disorders associated with a dysfunctional DIS3L2/NMD pathway. A better understanding of the interplay between NMD and DIS3L2 will certainly allow the development of novel treatments for disorders associated with an affected DIS3L2/NMD pathway.
    Keywords:  DIS3L2; NMD factors; human disease; nonsense-mediated decay (NMD)
    DOI:  https://doi.org/10.1016/j.jmb.2026.169943
  14. bioRxiv. 2026 Jul 07. pii: 2026.07.02.736190. [Epub ahead of print]
      Type I diabetes (T1D) is an autoimmune disorder in which the insulin producing cells of the pancreas are attacked and destroyed by autoreactive T cells. The innate immune mechanisms that contribute to T1D remain incompletely defined. Genome-wide association studies in humans have identified alleles of the IFIH1 gene, which encodes the intracellular RNA sensor MDA5, that are strongly associated with development of T1D. We previously found that MDA5 signaling drives disease and mortality in a mouse model of Aicardi-Goutieres Syndrome (AGS) caused by mutations in the ADAR1 RNA editing enzyme. Genetic dissection of disease in this ADAR1 mutant mouse model revealed that the double stranded RNA-activated kinase PKR and the RNA sensor ZBP1 are also essential for disease. To test the role of intracellular RNA detection in T1D in the nonobese diabetic (NOD) mouse model, we used CRISPR targeting to generate NOD mice targeted for Ifih1, Eif2ak2 (PKR) and Zbp1 . We found that haploinsufficiency for Ifih1 resulted in modest but significant protection from T1D only in male NOD mice, but neither PKR nor ZBP1 contributed to T1D onset or incidence. Moreover, treatment of NOD mice with a pharmacological inhibitor of the integrated stress response (ISR) had no effect on T1D incidence in female NOD mice, but accelerated and exacerbated disease in male NOD mice. Together, our findings demonstrate that MDA5 and the ISR contribute to sex-specific disease incidence in NOD mice.
    DOI:  https://doi.org/10.64898/2026.07.02.736190
  15. Aging Cell. 2026 Jul;25(7): e70641
      Aging involves a gradual loss of cellular balance, leading to reduced function and increased disease risk. While impaired proteostasis is a key hallmark of aging, more evidence shows the importance of RNA homeostasis (ribostasis), particularly the regulation of circular RNAs (circRNAs). CircRNAs are stable RNA molecules that build up over time and are linked to age-related cellular dysfunctions. In this regard, Kim et al. 2026 provide new insights into the impact of circRNA turnover on aging and lifespan. Their findings indicate that the accumulation of circRNAs is partly due to a decline in ribonuclease K (RNASEK), an enzyme that breaks down circRNAs. Using models such as worms, mice, and human cells, they show that RNASEK is crucial for healthy aging and longevity, suggesting its role is conserved across species. The research also shows that circRNAs gather in stress granules (SGs), which are ribonucleoprotein complexes formed during cell stress. RNASEK collaborates with heat shock protein 90 to prevent harmful RNA-rich aggregates, maintaining cellular dynamics in balance. These findings suggest a link between ribostasis and proteostasis, identifying circRNA clearance as a potential factor in longevity. The study also points to RNASEK as a promising target for treating age-related diseases. However, key questions remain, such as how RNASEK specifically degrades circRNAs, whether specific circRNAs or overall circRNA levels drive aging traits, and whether circRNA buildup is a cause or result of cell aging. Further research is needed to evaluate the conservation, safety, and therapeutic potential of this proteostasis-ribostasis axis in human biology.
    Keywords:  CircRNAs; RNASEK; aging; longevity; proteostasis; ribostasis; stress granules
    DOI:  https://doi.org/10.1111/acel.70641
  16. G3 (Bethesda). 2026 Jul 13. pii: jkag188. [Epub ahead of print]
      Transfer RNAs (tRNAs) are known for delivering amino acids to the growing polypeptide chain during translation. They can also influence gene expression, especially in times of nutrient starvation, through differential tRNA expression and modification. tRNAs have a highly consistent cloverleaf structure, but relatively few known regulatory elements govern this conserved structure despite the 20 different standard isotypes. This study examines gene enrichment patterns near tRNA genes across 1149 fungal genomes. Genes enriched in proteasome regulation, ion transport, and rRNA were found to be significantly closer to tRNAs than other pathways. These results were consistent across KEGG over-representation analysis (ORA), KEGG Gene Set Enrichment Analysis (GSEA), and Gene Ontology (GO) analysis. Proteasome, ion transport, and RNA are all important aspects of protein production and regulation, suggesting that genes required for the synthesis and quality control of proteins, including tRNAs, are located near each other. Protein regulation is an energetically expensive process, and local co-regulation could increase efficiency and stress impacts on proteins.
    Keywords:  KEGG; gene ontology; genomics; rRNA; ribosome; tRNA; yeast
    DOI:  https://doi.org/10.1093/g3journal/jkag188
  17. Arch Biochem Biophys. 2026 Jul 15. pii: S0003-9861(26)00214-6. [Epub ahead of print] 110943
       BACKGROUND: Sepsis-induced acute kidney injury (S-AKI) is marked by tubular damage, inflammation, and dysregulated autophagy. N6-methyladenosine (m6A) RNA modification has emerged as an important regulator of mRNA stability and cellular stress responses; however, its involvement and related regulatory mechanisms in S-AKI remain incompletely understood.
    METHODS: Human HK-2 proximal tubular epithelial cells were stimulated with LPS to establish an in vitro S-AKI model, while CLP-induced septic C57BL/6J mice were used as an in vivo model. Global m6A levels, METTL3, and FOSL1 expression were assessed by ELISA, qRT-PCR, and Western blot. Functional roles of METTL3 and FOSL1 were evaluated using siRNA-mediated knockdown, plasmid-driven overexpression, and pharmacological inhibitors. MeRIP-qPCR and RIP-qPCR were performed to evaluate m6A-related enrichment and the association between METTL3 and FOSL1 mRNA. Inflammatory cytokines, autophagy-related markers, NF-κB and mTOR signaling alterations, renal function, and histopathological changes were assessed.
    RESULTS: LPS stimulation increased global m6A levels and upregulated METTL3 and FOSL1 expression in HK-2 cells, accompanied by enhanced inflammatory responses and autophagy-related alterations. FOSL1 knockdown attenuated LPS-induced inflammation and autophagy-related changes, whereas METTL3 overexpression increased FOSL1 expression and exacerbated these effects. Further analyses indicated that METTL3 was associated with FOSL1 mRNA stability in an m6A-related manner. Alterations in FOSL1 expression were associated with changes in NF-κB and mTOR-related signaling responses under S-AKI conditions. In CLP-induced S-AKI mice, METTL3 knockdown reduced FOSL1 expression, alleviated inflammatory responses and autophagy-related alterations, and improved renal function and histopathological injury.
    CONCLUSION: Our findings suggest that METTL3/FOSL1-associated regulatory responses may participate in S-AKI through m6A-related regulation, contributing to inflammatory and autophagy-related alterations. These findings provide further insight into the involvement of m6A-related regulation in the pathogenesis of S-AKI.
    Keywords:  Autophagy; FOSL1; METTL3; Sepsis-induced acute kidney injury; m6A RNA methylation
    DOI:  https://doi.org/10.1016/j.abb.2026.110943
  18. Annu Rev Microbiol. 2026 Jul 15.
      The focal site of ribosome assembly and maturation in bacteria is the 5' untranslated region (UTR). Leaderless messenger RNAs (mRNAs) lack a 5' UTR and therefore present a conundrum for translation initiation. Leaderless mRNAs in Escherichia coli are rare and poorly translated, consistent with an inefficient by-product of the canonical mechanism. By contrast, transcription profiling approaches have unexpectedly found that leaderless mRNAs are both abundant and well-translated in certain bacterial clades, identifying those bacteria as leaderless adept. Mycobacteria are leaderless adept and offer multiple experimental model species that collectively broaden conclusions derived from leaderless translation studies. We review criteria derived from native mycobacterial mRNAs and from plasmid reporters expressed in mycobacteria that define leaderless mRNA features. We also look ahead at the unresolved conundrum of how leaderless mRNAs are efficiently translated. We anticipate that mycobacteria, along with diverse leaderless-adept Eubacteria and Archaea, will continue to make fundamental contributions in characterizing this major alternative mode of translation initiation.
    DOI:  https://doi.org/10.1146/annurev-micro-042424-051945
  19. Curr Opin Struct Biol. 2026 Jul 15. pii: S0959-440X(26)00091-6. [Epub ahead of print]99 103309
      Biomolecular condensates play key roles in the cell by organizing and regulating important biochemical processes, including transcriptional regulation, RNA metabolism, ribosome biogenesis, and stress responses. While these assemblies are typically dynamic, some can undergo time-dependent aging into solid assemblies, which in certain cases has been linked to pathologies including neurodegenerative diseases. In this review, we focus on the mechanisms that drive condensate aging. In particular, we discuss how features of protein sequence, such as amino acid composition, interaction motifs, and post-translational modifications, influence condensate aging. We further highlight how interactions with RNA and lipid membranes modulate condensate behavior by altering interaction networks and interfacial properties.
    DOI:  https://doi.org/10.1016/j.sbi.2026.103309
  20. Sci Adv. 2026 Jul 17. 12(29): eaed5708
      Translational control is essential for male germ cell development, yet how post-transcriptional regulation is coupled to chromatin remodeling during spermatogenesis remains poorly understood. Here, we show that the RNA-binding proteins PUMILIO1 (PUM1) and PUMILIO2 (PUM2) promote translation of mRNAs encoding chromatin regulators in the mouse testis. Conditional deletion of Pum1 and Pum2 in germ cells at multiple developmental stages results in spermatogenic failure, defective nuclear shaping, impaired histone-to-protamine exchange, and complete male sterility. Polysome profiling and ribosome sequencing reveal selective reductions in translation efficiency of chromatin regulators, including histone modifiers and nucleosome remodelers, in Pum1/2-deficient testes. Mechanistically, PUM1/2 associate with DAZL and PABPC1 to form a germ cell-specific translational activation complex that enhances protein output with little impact on mRNA stability. Together, these findings redefine mammalian PUM proteins as context-dependent translational activators in the germline and uncover a post-transcriptional mechanism that links RNA regulation to chromatin dynamics during spermatogenesis.
    DOI:  https://doi.org/10.1126/sciadv.aed5708
  21. Proc Natl Acad Sci U S A. 2026 Jul 21. 123(29): e2537017123
      Persistent activation of the integrated stress response (ISR) is a central driver of cognitive decline in both neurodevelopmental and neurodegenerative disorders. However, the cell type-specific mechanisms underlying these deficits remain poorly understood. By integrating single-cell RNA-seq and single-cell assay for transposase-accessible chromatin sequencing, we generated a brain ISR atlas using Ppp1r15bR658C mice, a clinically relevant model of intellectual disability characterized by selective and persistent ISR activation. We find that distinct brain cell types differentially engage transcriptional and chromatin remodeling programs. Notably, selective deletion of the major ISR downstream effector ATF4 in GABAergic neurons, but not in glutamatergic neurons, exacerbates ISR-mediated cognitive decline in Ppp1r15bR658C mice, demonstrating that different neuronal subtypes rely on distinct ISR effectors. We define a molecular single-cell signature of persistent ISR activation that serves as a metric of ISR-mediated cellular vulnerability and as a biomarker for cognitive dysfunction across human cognitive disorders. These findings demonstrate that cell type-specific responses drive cognitive dysfunction during persistent ISR activation.
    Keywords:  cellular homoeostasis; cognitive decline; single-cell ATAC-sequencing; single-cell RNA-sequencing
    DOI:  https://doi.org/10.1073/pnas.2537017123
  22. Am J Cancer Res. 2026 ;16(6): 2355-2366
      Microchromosome maintenance protein 6 (MCM6), a member of the MCM family, is involved in the regulation of various cancer progression. However, the role and related regulatory mechanisms in cervical cancer are unclear. The aim of this study was to investigate the role of MCM6 in cervical cancer and the regulation of MCM6 protein homeostasis by the ubiquitin-conjugating enzyme E2J2 (UBE2J2). To investigate the expression and function of MCM6 in cervical cancer, we used RT-qPCR and Western blot and found that MCM6 was upregulated. Cell function experiments indicate that MCM6 promotes the proliferation and migration of cervical cancer cells. The GEPIA database identified co-expressed genes with MCM6, and KEGG enrichment analysis showed that MCM6 was significantly associated with UBE2J2. We performed molecular docking of proteins and identified amino acid residues involved in the MCM6-UBE2J2 interaction. Using co-immunoprecipitation and Immunofluorescence experiments, we found that MCM6 binds to UBE2J2 and localizes to the nucleus. Ubiquitination experiments demonstrated that UBE2J2 mediates MCM6 ubiquitination. Response experiments showing that UBE2J2-mediated MCM6 ubiquitination modification regulates the proliferation and migration of cervical cancer cells. Our results suggest that the UBE2J2-MCM6 axis plays an important role in regulating cervical cancer proliferation and migration and is a promising therapeutic target for its treatment.
    Keywords:  Cervical cancer (CC); MCM6; UBE2J2; ubiquitination
    DOI:  https://doi.org/10.62347/SHIF8882
  23. FEMS Microbiol Rev. 2026 Jul 15. pii: fuag030. [Epub ahead of print]
      In cyanobacteria, the free-living ancestors of chloroplasts, photosynthesis simultaneously sustains growth and generates reactive oxygen species (ROS) that damage proteins, lipids, and DNA when light capture outpaces carbon fixation. Maintaining redox balance, therefore, requires cells to read photosynthetic electron flow as a signal that continuously tunes gene expression and protein activity. This review traces how these redox signals are transduced to transcription machinery through three routes: membrane-localized sensors, cytoplasmic redox sensors downstream of photosystem I, and ROS generated when electron sinks are saturated. Membrane-bound histidine kinases (two-component systems) relay the redox state of the plastoquinone pool to control photosystem remodeling, pigment biosynthesis, and circadian timing. Cytoplasmic one-component regulators, by contrast, sense redox directly through thiol-disulfide switches, iron-sulfur clusters, and metal-catalyzed oxidation to control photosystem-cofactor, electron-carrier, and transition-metal homeostasis. Because many of these regulators persist in algal and plant chloroplasts, cyanobacteria illuminate principles of redox control across photosynthetic eukaryotes. Post-transcriptional and translational control further shapes redox-dependent gene expression programs through transcript stability, ribosome assembly, and translation initiation, extending redox regulation beyond transcription to every step of protein synthesis and even activity modulation. Finally, we connect redox regulation to photosynthetic physiology, stress resilience, and the rational engineering of cyanobacteria for sustainable bioproduction.
    Keywords:  cyanobacteria; iron-sulfur clusters; photosynthetic electron transport; redox regulation; thiol switches; transcription factors
    DOI:  https://doi.org/10.1093/femsre/fuag030
  24. J Pharmacol Exp Ther. 2026 Jun 18. pii: S0022-3565(26)01166-3. [Epub ahead of print]393(8): 104967
      Rett syndrome (RTT) is a neurodevelopmental disorder that is associated with loss-of-function mutations in the methyl CpG binding protein 2 (MECP2) gene. MECP2 regulates transcription both locally and globally, making it challenging to distinguish between genes that are pathogenic and those that constitute transcriptional noise. A rare subpopulation of patients lack MECP2 mutations despite presenting with sufficient symptoms to warrant a clinical diagnosis of RTT. These patients are classified as having atypical and MECP2 mutation-negative forms of the disorder. We hypothesized that identifying pathways with conserved disruption between typical and atypical forms of RTT would be a viable mechanism to reduce transcriptional noise and identify the genes that are most critical to their shared clinical presentation. To test this theory, we conducted differential RNA sequencing using 5 atypical RTT, 6 typical RTT (R255X), and 9 neurotypical control temporal cortex autopsy samples. Pathways associated with heat shock factor 1 (HSF1) signaling were among the most enriched in both RTT populations. Validation studies using 37 patient temporal cortex samples showed that increased HSF1 signaling was enriched in those with classically severe MECP2 mutations. To investigate whether increased HSF1 signaling is compensatory or pathogenic, we conducted in vivo hyperthermia experiments complemented by cellular stress array analyses. These experiments established that RTT model mice exhibit faster and larger induction of cellular stress-associated proteins. Pharmacological induction of HSF1 in Mecp2+/- mice was consistent with hyperthermia experiments, showing seizure-like phenotypes and lethality. Conversely, chronic inhibition of HSF1 signaling improved RTT-like phenotypes in domains of motor learning and general health. Together, these data suggest that promiscuous HSF1 signaling is likely a pathogenic amplifier of severe phenotypes and provide a rationale that inhibiting this pathology may hold therapeutic potential in RTT and related disorders. SIGNIFICANCE STATEMENT: Rett syndrome is a devastating neurodevelopmental disorder with limited therapeutic options. This manuscript identifies heat shock factor 1-signaling as a novel therapeutic target and proposes a molecular mechanism by which cellular stress responses are regulated in Rett syndrome.
    Keywords:  Cellular stress; Heat shock factor 1; MECP2; Rett syndrome
    DOI:  https://doi.org/10.1016/j.jpet.2026.104967
  25. Biochim Biophys Acta Mol Cell Res. 2026 Jul 17. pii: S0167-4889(26)00094-7. [Epub ahead of print] 120195
      The endoplasmic reticulum (ER), a major calcium ion (Ca2+) reservoir, plays a pivotal role in lipid synthesis, protein synthesis, and secretion. Disruption of ER function leads to the accumulation of misfolded proteins, resulting in ER stress. To restore cellular homeostasis, the unfolded protein response (UPR) is activated. However, prolonged or irreversible ER stress can trigger apoptosis and cell death. Cellular dysfunction and apoptosis arising from disrupted ER Ca2+ homeostasis are often implicated in neurodegenerative and metabolic disorders. We investigated the role of LRRC8B, an ER-resident protein previously linked to ER Ca2+ homeostasis, in the ER stress response. LRRC8B expression was upregulated in response to chemically induced ER stress. Overexpression of LRRC8B enhanced the viability of HEK293T cells exposed to the ER stressor tunicamycin, whereas LRRC8B knockdown increased their susceptibility to apoptosis. Furthermore, LRRC8B overexpression reduced protein aggregation during ER stress by upregulating cytoprotective genes associated with the adaptive UPR, including BiP, calnexin, and PDI. Conversely, LRRC8B knockdown decreased BiP expression and elevated the levels of ER stress-induced apoptotic proteins such as CHOP, Bax, and cleaved caspase-3. Co-treatment with the chemical chaperone, 4-PBA, partially rescued the LRRC8B knockdown cells undergoing apoptosis. In Neuro 2a (N2a) cells, LRRC8B overexpression diminished the aggregation of mutant huntingtin protein (HTT-83Q), associated with Huntington's disease, whereas its knockdown exacerbated HTT-83Q aggregation. Taken together, these findings suggest that LRRC8B is a key modulator of the ER stress response and plays a cytoprotective role.
    Keywords:  ER stress; LRRC8B; Protein aggregation; Tunicamycin; UPR
    DOI:  https://doi.org/10.1016/j.bbamcr.2026.120195
  26. Int J Mol Sci. 2026 Jun 23. pii: 5667. [Epub ahead of print]27(13):
      Cyanobacteria, the only prokaryotic oxygenic phototrophs, rely on sophisticated regulatory networks, including those mediated by small RNAs (sRNAs) to cope with environmental fluctuations. Here, we delineate the sRNA landscape of Synechocystis sp. PCC 6803 under short- and long-term ammonium stress, revealing a significant proportion of antisense RNAs (asRNAs). Functional characterization identified three asRNAs (sll0312-as, sll0873-as, and slr1667-as) as key regulators of ammonium stress tolerance, implicating their targets (sll0312, sll0873, and slr1667) as new players in nitrogen fluctuation acclimation. The sll0944-as and sll1515-as were also identified, revealing an additional regulatory layer targeting known carbon/nitrogen metabolism regulators. Mechanistically, we characterized the ammonium-induced asRNA ssr0692-as, demonstrating that it represses pirA translation via direct 5'UTR interaction. This finding, integrated with the known role of the nitrogen limitation-responsive sRNA NsiR4 targeting the same region, supports a synergistic model wherein these two sRNAs precisely modulate PirA protein levels-and thus the downstream nitrogen flux-across varying nitrogen availability. Together, our findings expand the functional repertoire of cyanobacterial sRNAs and elucidate a dynamic post-transcriptional mechanism to fine-tune nitrogen metabolism in response to fluctuating nutrient conditions.
    Keywords:  PirA; Synechocystis; ammonium stress; cyanobacterium; sRNA; ssr0692-as
    DOI:  https://doi.org/10.3390/ijms27135667
  27. Transl Cancer Res. 2026 Jun 30. 15(6): 450
       Background: Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide, and its underlying molecular mechanisms remain incompletely defined. N6-methyladenosine (m6A) RNA modification has emerged as a key epigenetic regulator of tumor metabolic reprogramming. However, the roles of the m6A writer methyltransferase-like 3 (METTL3) and the m6A reader insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) in NSCLC, particularly in lipid metabolic regulation, remain poorly characterized. The present study aimed to investigate the functional significance of METTL3 and IGF2BP1 in NSCLC, with particular focus on their regulation of FADS2 expression and lipid metabolism.
    Methods: Differentially expressed m6A-related genes were identified by analyzing RNA-seq data from The Cancer Genome Atlas (TCGA), followed by validation in 60 paired NSCLC and adjacent normal tissues. Gene and protein expression were examined by qRT-PCR and western blotting, respectively, with immunohistochemistry (IHC) further confirming protein levels in tissue specimens. Functional assays, including colony formation, Transwell migration/invasion, and Oil Red O staining, were performed in A549 and H1299 cells following METTL3, IGF2BP1, or FADS2 perturbation. The m6A modification on FADS2 mRNA was assessed by MeRIP-qPCR, and its association with METTL3 and IGF2BP1 was examined by RIP-qPCR. RNA stability was evaluated via actinomycin D chase assays, and rescue experiments were conducted through co-transfection of shRNA and overexpression constructs. The in vivo role of FADS2 was assessed using a xenograft tumor model.
    Results: METTL3 and IGF2BP1 were significantly upregulated in NSCLC tissues and were associated with poor overall survival. Silencing either gene inhibited NSCLC cell proliferation, migration, and invasion. FADS2 expression was markedly elevated in NSCLC and positively correlated with METTL3 and IGF2BP1 expression. Knockdown of FADS2 reduced lipid droplet accumulation and suppressed malignant phenotypes in vitro, while significantly inhibiting tumor growth in vivo. Mechanistically, m6A modification was enriched within the 3'-UTR of FADS2 mRNA, where both METTL3 and IGF2BP1 were found to bind. Loss of METTL3 or IGF2BP1 accelerated FADS2 mRNA decay, whereas their overexpression enhanced transcript stability. Rescue experiments further confirmed that METTL3 and IGF2BP1 cooperatively regulate FADS2 expression and thereby promote NSCLC progression.
    Conclusions: METTL3-mediated m6A modification of FADS2 transcripts is recognized by IGF2BP1, resulting in enhanced mRNA stability, increased lipid accumulation, and NSCLC progression. Our findings suggest that the METTL3/IGF2BP1-FADS2 axis contributes to lipid metabolic alterations in NSCLC and may serve as a potential therapeutic target.
    Keywords:  FADS2; IGF2BP1; METTL3; N6-methyladenosine (m6A); non-small cell lung cancer (NSCLC)
    DOI:  https://doi.org/10.21037/tcr-2026-1-0380
  28. Mol Cell. 2026 Jul 15. pii: S1097-2765(26)00424-7. [Epub ahead of print]
      The hierarchical, multiphase organization of the nucleolus underlies ribosome biogenesis. Ribonucleoprotein particles that regulate ribosomal subunit assembly are heterogeneously distributed in the nucleolar granular component (GC). However, the molecular origins of the GC's spatial heterogeneity and their link to ribosome subunit assembly remain poorly understood. Here, using super-resolution microscopy in DLD-1 cells, we uncover that key GC biomolecules-NPM1, SURF6, and ribosomal RNA (rRNA)-are heterogeneously localized within GC sub-phases. In vitro reconstitution with E. coli- and human-derived rRNA revealed that these GC biomolecules form multiphase condensates with a SURF6/rRNA-rich core and NPM1-rich shell, providing a mechanistic basis for this heterogeneity. SURF6's association with rRNA weakens upon ribosome subunit assembly, enabling NPM1 to extract assembled subunits from condensates, suggesting an assembly-line-like mechanism of subunit efflux from the GC. Our results establish a framework for understanding the GC's heterogeneous structure and reveal how its distinct sub-phases facilitate ribosome subunit assembly.
    Keywords:  assembly factor; granular component; intrinsically disordered region; multiphase condensate; nucleolus; phase separation; ribonucleoprotein assembly; ribosome biogenesis; spatial heterogeneity; structured illumination microscopy
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.035
  29. Genome Biol. 2026 Jul 17. pii: 229. [Epub ahead of print]27(1):
       BACKGROUND: All organisms experience stress and must rapidly respond to changing conditions. Thus, cells have evolved sophisticated rapid-response mechanisms such as post-translational protein modification to rapidly and reversibly modulate protein activity. One such post-translational modification is reversible lysine acetylation, where proteomic studies have identified thousands of acetylated proteins across diverse organisms. While the sheer size of the 'acetylome' is striking, the function of acetylation for the vast majority of proteins remains largely obscure.
    RESULTS: Here, we find that global acetylation plays a previously unappreciated role in the heat shock response of Saccharomyces cerevisiae. Dysregulated acetylation renders cells heat sensitive, and the acetylome is globally remodeled during heat shock over time, with ~ 400 high-confidence acetyl marks across ~ 200 proteins significantly changing. Proteins with significant acetylome changes strongly overlap with genes induced or repressed by heat shock. Intriguingly, we find nearly 40 proteins with at least two acetyl marks that significantly change in the opposite directions. These proteins are strongly enriched for chaperones and ribosomal proteins, suggesting that these two key processes are coordinately regulated by protein acetylation during heat shock.
    CONCLUSIONS: Our results suggest that protein acetylation helps activate induced proteins and inactivate repressed proteins during heat shock. We hypothesize that the same type of activating and inactivating marks that exist on histones may be a general feature of proteins regulated by acetylation. Overall, this work has identified a new layer of post-translational regulation that likely augments the classic heat shock response.
    DOI:  https://doi.org/10.1186/s13059-026-04194-9
  30. Oncogene. 2026 Jul 13.
      Prostate cancer progression to advanced disease is accompanied by extensive metabolic rewiring, yet the upstream regulatory mechanisms remain incompletely defined. Here, we showed that the rRNA m6A methyltransferase METTL5 was progressively upregulated during prostate cancer progression and was associated with poor patient survival. Mechanistically, METTL5 catalyzed N6-methyladenosine (m6A) modification at A1832 of 18S rRNA, thereby enhancing overall translational output and promoting prostate cancer cell proliferation in vitro and tumor growth in vivo. Integrative transcriptomic and proteomic analyses further revealed that METTL5-dependent rRNA modification preferentially increased translation of mRNAs harboring a GCACGN(2-4)CC motif within their 5' untranslated regions. Among these targets, the transcription factor IRF7 was selectively upregulated and directly induced DNA2 transcription. DNA2, a mitochondrial nuclease required for mitochondrial DNA maintenance, preserves oxidative phosphorylation capacity in prostate cancer cells. Disruption of the METTL5/IRF7/DNA2 axis led to mitochondrial dysfunction, increased reactive oxygen species, and compensatory mitophagy, ultimately suppressing tumor growth. Notably, neither IRF7 nor METTL5 overexpression rescued the growth defects caused by DNA2 depletion, supporting a hierarchical organization of this pathway with DNA2 as an essential downstream effector. Finally, therapeutic inhibition of METTL5 using locked nucleic acids markedly suppressed prostate cancer growth in vivo without evident systemic toxicity, underscoring translational potential. Collectively, our findings uncover an unappreciated mechanism linking rRNA modification to mitochondrial homeostasis through selective translational control, providing new insights into metabolic regulation and revealing actionable vulnerabilities in advanced prostate cancer.
    DOI:  https://doi.org/10.1038/s41388-026-03867-w
  31. Plant Cell Environ. 2026 Jul 14.
      Although plants are exposed to many environmental stressors (heat, drought, salinity, and pathogen), they survive by rapidly reprogramming their gene expression. Recent findings show that many regulatory mechanisms are maintained within liquid-liquid phase separation (LLPS) formed biomolecular condensates, instead of maintaining these mechanisms within membrane-bound organelles. LLPS has been shown to exist in plant cells; however, the integration of LLPS with functional stress adaptations and gene regulations is still unclear from the studies that have been published thus far. In this review, we discuss recent research that demonstrates how these biomolecular condensates act as dynamic regulatory centers by linking environmental stress perception to transcriptional and post-transcriptional regulation of genes in plants. We describe the biophysical principles that govern the occurrence of LLPS in a plant cellular environment and provide an overview of how both abiotic (e.g., drought, heat) and biotic (i.e., pathogens) stressors initiate the LLPS and remodel nuclear and cytosolic condensate structures. The focus of this work will be on the effects of stress-induced changes (both qualitatively and quantitatively) in the condensate composition and material properties on transcription factor activity (either as an activator or repressor) and the organization of chromatin, RNA stability, and selective translation. We will also discuss post-translational modifications (PTMs) that modulate condensate dynamics and allow for reversibility. Collectively, these findings suggest that LLPS likely contributes significantly to gene regulation and stress adaptation in plants, although the degree of mechanistic validation varies among different condensate systems.
    Keywords:  RNA–protein interactions; gene expression; gene regulation; liquid–liquid phase separation; plant cell biology; plant stress responses; post‐translational modifications; stress adaptation; transcriptional plasticity
    DOI:  https://doi.org/10.1111/pce.70750
  32. Nucleic Acids Res. 2026 Jul 03. pii: gkag680. [Epub ahead of print]54(13):
      Human T-cell leukemia virus type 1 (HTLV-1), an oncogenic retrovirus, uses human tRNAPro to prime reverse transcription. How tRNAPro is annealed to the primer-binding site (PBS), which is embedded in a stable hairpin structure in the genomic RNA, remains unclear. In contrast to human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein, which robustly chaperones transfer RNA (tRNA) annealing to the HIV-1 PBS, HTLV-1 NC protein displays very weak chaperone function. Recombinantly-purified HTLV-1 Gag was only slightly more effective at chaperoning the annealing of tRNAPro to the PBS than NC protein. To identify potential HTLV-1 Gag interacting co-chaperones in cells, we performed affinity tagging/purification-mass spectrometry. Two significant hits, ribosomal protein L7 (RPL7) and DDX21, were validated by reciprocal co-IP studies in cells. Domain mapping revealed that HTLV-1 Gag interacts with RPL7 and DDX21 through the zinc fingers of NC protein in an RNA-independent fashion. Both RPL7 and DDX21 are packaged into virions, and each protein alone was more effective than HTLV-1 Gag at annealing tRNAPro to the PBS. Further synergistic effects were observed for the Gag/RPL7/DDX21 combination in overcoming structural constraints at the PBS to promote tRNAPro annealing. The mechanistic insights gained from these studies may be exploited for the development of new therapeutic strategies aimed at targeting HTLV-1 RT.
    DOI:  https://doi.org/10.1093/nar/gkag680
  33. Biol Psychiatry. 2026 Jul 17. pii: S0006-3223(26)01400-9. [Epub ahead of print]
      Proteostasis is the process by which cells control how much of each protein is made, how long it persists, and when it is removed. In neurons, proteostasis is not merely a housekeeping function, it is actively regulated by neuronal activity. When neurons fire, protein synthesis and degradation are simultaneously and transiently regulated to support synaptic plasticity. In neurodevelopmental disorders (NDDs), neurons lose this capacity to dynamically regulate their proteome in response to stimulation, disrupting synaptic plasticity and leading to cognitive impairments. This review establishes that despite diverse genetic origins, failure of activity-regulated proteostasis is a shared vulnerability across NDDs. This also explains why increasing or blocking protein synthesis or degradation alone under basal condition is insufficient to restore normal function. Our work demonstrates that restoring the coupling between neuronal activity and proteostatic response rescues both molecular and cognitive impairments in NDDs. These findings open new avenues for investigating disease biology and for developing novel therapeutic strategies.
    DOI:  https://doi.org/10.1016/j.biopsych.2026.06.032
  34. Onco Targets Ther. 2026 ;19 600733
      SnoRNAs are regulatory RNAs that play indispensable roles in ribosomal RNA processing and translation. Their distinct structural conformations determine specific protein-binding partners, thereby mediating diverse epigenetic modifications. Most snoRNAs are transcribed from introns of snoRNA host genes (SNHGs). Processed snoRNAs can further yield piwi-interacting RNAs (piRNAs) and snoRNA-derived fragments (sdRNAs). These small RNA products are frequently dysregulated in tumors and exert significant oncogenic functions. In cancer, snoRNA dysregulation stems from DNA-level alterations such as chromosomal aberrations, base mutations, and gene silencing, as well as RNA-level disruptions including aberrant post-transcriptional modifications, degradation, and trafficking. Such dysregulated snoRNAs drive malignant hallmarks-sustained proliferation, invasion and metastasis, angiogenesis, metabolic reprogramming, immune evasion, senescence bypass, epigenetic remodeling, phenotypic plasticity, and microbiome-host crosstalk-through mechanisms spanning histone modifications, nucleic acid epitranscriptomics, and competitive endogenous RNA (ceRNA) networks. Consequently, tumor-associated snoRNAs detectable in body fluids represent promising non-invasive biomarkers for early cancer diagnosis and prognosis prediction. This review systematically summarizes snoRNA biogenesis pathways, elucidates mechanisms underlying their dysregulation in malignancies, summarizes the impact of aberrant snoRNAs on tumorigenesis and progression, and highlights clinically significant snoRNAs for diagnostic and therapeutic applications.
    Keywords:  cancer; competitive endogenous RNA; genetic alterations; non-coding RNAs; snoRNA
    DOI:  https://doi.org/10.2147/OTT.S600733
  35. Epigenetics. 2026 Dec;21(1): 2700836
      Retinal ischemia-reperfusion injury (RIR) is the main pathogenic mechanisms of acute glaucoma, diabetic retinopathy, central retinal vein occlusion. As a common post-transcriptional modification of eukaryotic RNAs, N6-methyladenosine (m6A) is associated with the pathogenesis of different diseases, including angiogenesis, through the regulation of RNA metabolism and functions. The aim of this study was to identify the potential relevance of m6A RNA methylation in pathogenesis of RIR. A total of 10,851 mRNAs and 23,270 associated m6A methylation modified peaks were identified in the RIR group. Similarly, 10,391 mRNAs and 22,935 associated m6A methylation modified peaks were detected in the Sham group. MeRIP-seq identified 3,871 RIR-specific m6A peaks and 3,624 Sham-specific m6A peaks, in addition to 19,399 shared peaks between groups. Gene ontology (GO) analysis showed that hypermethylated mRNAs were enriched in cellular process, cellular anatomical entity, and binding, while hypomethylated mRNAs were enriched in synaptic signaling, synapse, and gated channel activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that hypermethylated mRNAs were involved in tight junction, hippo signaling pathway, and PI3K-Akt signaling pathway, while hypomethylated mRNAs were involved in Neuroactive ligand-receptor interaction, glutamatergic synapses, cholinergic synapses. Joint analysis identified mRNAs with differential m6A methylation and expression simultaneously. Among them, the expression patterns of Irx4, Kdr, and Lyz2 were confirmed by RT-qPCR to be consistent with the sequencing results. The results revealed an altered m6A epitranscriptome in RIR retinas. These methylated RNAs may act as novel modulators and targets in RIR.
    Keywords:  Methylation; mRNA; retina; retinal ischemia-reperfusion
    DOI:  https://doi.org/10.1080/15592294.2026.2700836
  36. Int J Gen Med. 2026 ;19 591732
      The epitranscriptomic landscape defined by reversible post-transcriptional RNA modifications constitutes a sophisticated layer of gene regulatory circuitry that modulates diverse biological processes. As an essential writer enzyme for RNA 5-methylcytosine (m5C), NOP2/Sun RNA methyltransferase 2 (NSUN2) catalyzes site-specific m5C deposition across an extensive repertoire of cellular transcripts spanning messenger RNAs, transfer RNAs and non-coding RNAs, and orchestrates core post-transcriptional events including transcript stabilization, nucleocytoplasmic trafficking, translational tuning and RNA turnover. Accumulating preclinical and clinical evidence corroborates that perturbed NSUN2 expression rewires the physiological m5C epitranscriptomic signature, which functionally contributes to the onset and advancement of numerous human pathological conditions ranging from heterogeneous malignancies and cardiovascular complications to neurodegenerative syndromes, infectious disorders, inflammatory pathologies and systemic metabolic diseases. In this systematic review, we comprehensively consolidate contemporary mechanistic advances underlying NSUN2-dependent m5C modification in governing cellular homeostasis and disease pathogenesis, with focused discussion on its multifaceted functions in modulating oncogenic signaling cascades, mitochondrial fitness, neurodevelopmental progression, immune cell polarization and host-virus interaction. We further highlight prospective therapeutic modalities targeting the NSUN2-m5C regulatory axis and systematically dissect prevailing translational bottlenecks hindering bench-to-bedside transformation of such targeted interventions. Elucidating the conserved and disease-specific regulatory paradigms of NSUN2 therefore provides profound theoretical implications and practical clinical evidence for developing novel diagnostic biomarkers and precision therapeutic regimens across relevant human disorders.
    Keywords:  5-methylcytosine; NSUN2; RNA methylation; epitranscriptome; human disease; therapeutic target
    DOI:  https://doi.org/10.2147/IJGM.S591732
  37. NAR Mol Med. 2026 Jul;3(3): ugag034
      Targets of RNA-binding proteins (RBPs) are often investigated by implementing variants of cross-linking and immunoprecipitation methodology, which can yield several disadvantages in target detection. The RBP and N6-methyladenosine (m6A) reader insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2/IMP2) exerts an essential pathophysiological role as a metabolic regulator and tumor promoter, impacting the stability, localization, and translation of its targets. Here, we employed HyperTRIBE as a method to identify RBP targets in native cells in vivo and identified targets of IMP2 in murine hepatocytes. IMP2-associated adenosine-to-inosine editing sites were identified by hydrodynamic transfection of mouse livers using an IMP2-ADAR (adenosine deaminase acting on RNA) construct. Functional enrichment and motif analysis results suggest IMP2-facilitated target stabilization and confirm presence of m6A-binding motifs. In addition, the overlap with data of a TRIBE experiment employing murine embryonic fibroblasts and with those of differential gene expression was investigated. Comparative transcriptomics between IMP2, wild-type, and control samples (mCherry-ADAR) revealed an enrichment of IMP2-bound mRNAs associated with autophagy, which could be validated by RNA immunoprecipitation in a human liver cancer cell line. A functional knockdown of IMP2 demonstrated an increased autophagic flux, providing further evidence for the involvement of IMP2 in autophagy.
    DOI:  https://doi.org/10.1093/narmme/ugag034
  38. Mol Biol Rep. 2026 Jul 15. pii: 1160. [Epub ahead of print]53(1):
       BACKGROUND: Synonymous variants are often overlooked during genetic screening, however current reports forecasted their significant biological impact and inevitably considered pathogenic. These silent changes in genome significantly affect the mRNA structure and stability and hence, alter the protein expression and function. IRX4 is an essential transcription factor for cardiogenesis and reported to be associated with congenital heart disease (CHD).
    METHODS AND RESULTS: We have performed genetic screening of IRX4 in 205 isolated cases of CHD. Five synonymous variants c.90A > C; Gly30=, c.240G > A; Ser80=, c.381A > G; Pro127=, c.1281G > A; Ala427=, and c.1509C > T; Gly503=, six intronic variants c.1-139G > A, c.21-107G > C, c.46-107G > C, c.297 + 6T > G, c.815-130 C > A, c.1638 + 62 C > T were identified. A computed analysis by diverse tools namely RNAfold, MutaRNA, Human Splicing Finder (HSF), and RNA22 was applied to predict the substantial effect on downstream function. RNAfold analysis indicated that all five variants impacted RNA structure and stability. Further, notable changes in the base-pairing probability and RNA accessibility were induced by c.90A > C, c.240G > A, c.381A > G, c.1281G > A, and c.1509C > T variants as shown by MutaRNA. Moreover, the effect on the cis-acting regulatory element of splicing was speculated due to c.1281G > A variant only. Likewise, various modes of the RNA22 tool indicated changes in miRNA binding sites, showing that 61.5% of targets were altered and 38.5% were completely lost as a result of the c.1281G > A variant.
    CONCLUSIONS: Our findings provide an insight into the molecular effect on mRNA structure and stability, splicing and miRNA target binding sites that potentially impair the transcription and translation and consequently might be associated with the pathogenesis of CHD.
    Keywords:   IRX4 ; in-silico ; Congenital heart disease; Isolated; Synonymous; mRNA; variations
    DOI:  https://doi.org/10.1007/s11033-026-12304-w
  39. Plant Sci. 2026 Jul 16. pii: S0168-9452(26)00356-0. [Epub ahead of print] 113328
      Plastid ribosomes are composed of large (50S) and small (30S) subunits, each made up of ribosomal RNAs (rRNA) and plastid ribosomal proteins (PRPs). While numerous PRPs have been characterized, the functions of several PRPs remain elusive. We followed a reverse genetics approach in Arabidopsis to functionally characterize nuclear genes encoding PRPs for which no viable mutant alleles had been described. We report here the characterization of 50S subunit PRP bL31c. Its gene, RPL31, was previously identified as essential for embryo development (EMB2184), but viable alleles were unavailable. RPL31 is a single-copy gene and we confirmed that rpl31-1 and emb2184 (renamed rpl31-2) are allelic. rpl31 mutants display reduced growth, paleness, pointed rosette leaves with toothed margins, loosely packed and small mesophyll cells with abnormal chloroplasts, and disrupted cotyledon venation. Chloroplast targeting of the bL31c protein was confirmed using an RPL31pro:RPL31-GFP construct. RPL31 loss of function affects transcript and protein accumulation from nuclear and plastid genes and modifies the abundances of rRNAs, suggesting defects in plastid ribosome biogenesis and/or translation. Remarkably, rpl31 mutants show altered expression of the auxin activity markers DR5pro:GUS and DR5pro:GFP, as well as auxin-related genes, and exhibit reduced sensitivity to the synthetic auxin 2,4-D. These findings and the abnormalities in venation and leaf morphology suggest compromised auxin homeostasis in rpl31 mutants. RPL31-mediated leaf margin development depends on CUP-SHAPED COTYLEDON2 and the rpl31-1 mutation synergistically interacts with others affecting regulators of plastid gene expression. Overall, our results demonstrate that besides embryo development, RPL31 plays a key role in leaf morphogenesis, highlighting its broader developmental significance.
    Keywords:  Arabidopsis; auxin; chloroplast; plant development; plastid ribosomal proteins
    DOI:  https://doi.org/10.1016/j.plantsci.2026.113328
  40. PLoS Biol. 2026 Jul 17. 24(7): e3003887
      The complex life cycle of the human parasite Leishmania mexicana requires rapid translational adaptation for survival in two distinct environments: the insect vector and the mammalian host. These protists lack conventional transcriptional control due to their unusual genome organization. Consequently, tRNA modifications may represent an additional mechanism for post-transcriptional regulation of gene expression. One such modification is queuosine (Q), which is incorporated at the anticodon wobble position 34 of specific tRNAs. Here, we demonstrate that Q-tRNA levels increase substantially during Leishmania differentiation from the insect stage to the mammalian-infective stage, implying an important role for virulence. Hence, we generated mutant cells lacking the enzyme responsible for Q incorporation, tRNA-guanine transglycosylase (TGT), which exhibited substantial changes in the proteome during differentiation in vitro. Specifically, downregulated proteins were enriched in NAU codons, whereas upregulated proteins predominantly contained NAC codons. Although LmxTGT knockout parasites exhibited normal growth and differentiation in vitro, they demonstrated impaired survival within macrophages and reduced pathogenicity in mice, highlighting the role of the Q-tRNAs under stress conditions. To our knowledge, we present here the first direct evidence that queuosine tRNA modification controls the infectivity of Leishmania via codon-biased translation. To date, gene expression regulation in Leishmania and other trypanosomatids has been attributed mostly to RNA stability and processing; however, our findings demonstrate that tRNA modifications also play a key regulatory role. Specifically, the Q-tRNA modification provides a novel layer of gene expression regulation, maintaining translational balance and supporting the parasite's ability to adapt to changing environments, and contributing to Leishmania virulence.
    DOI:  https://doi.org/10.1371/journal.pbio.3003887
  41. Eng Microbiol. 2026 Sep;6(3): 100280
      Hydrogenotrophic methanogens are promising biocatalysts for biomethanation and carbon dioxide utilization, yet their robustness under bioprocess perturbations remains insufficiently defined. We quantified robustness in a Methanothermobacter archaeal strain with proven potential for industrial application across temperature shifts, oxidative exposure, nitrogen depletion, and hydrogen starvation, measured five key cellular functions in batch culture, and derived a Fano factor based robustness metric that links data dispersion to functional stability. Thermal and oxidative stress were the primary constraints on robustness, most notably for methane productivity and lag phase duration, whereas hydrogen starvation increased productivity in some cases without large losses in robustness, and nitrogen depletion had limited effects. Global proteomics revealed coordinated changes consistent with these patterns, including increased ribosomal proteins, trehalose synthesis, chaperones, and redox regulators under thermal stress, and enrichment of PAS and histidine kinase domain proteins under oxidative stress. Structure-guided predictions using Alpha Fold 3 supported the hypothesis that stress responsive proteins may associate with canonical methanogenesis core subunits, as FmdE was predicted to associate with FmdE-like paralogs under thermal stress, while several Mtr subunits decreased in abundance. The combined results identify actionable targets for engineering robustness in methanogenic archaea, including stabilizing multi subunit methanogenesis complexes such as Mtr, tuning PAS and HK sensors to improve redox response, and modulating chaperone and osmoprotection capacity to regulate metabolic functions during temperature fluctuations. As derived future work, mapping protein interactions with abundance profiling may help move proteomics from description to prediction, providing network-informed design rules that complement conventional genome-centered proteomics and guide strain optimization of robust archaeal biocatalysts for biomethanation.
    Keywords:  Biomethanation; Bottom-up proteomics; Methanogenic archaea; Methanothermobacter; Microbial robustness; Protein-protein interactions
    DOI:  https://doi.org/10.1016/j.engmic.2026.100280
  42. Cancers (Basel). 2026 Jun 23. pii: 2033. [Epub ahead of print]18(13):
      Cancer is a genetic disease driven by the accumulation of mutations that disrupt normal cellular growth. Among the most frequently mutated families are protein kinases, inositol polyphosphate kinases, and GTPases, which together function as central molecular switches controlling proliferation, survival, and metabolism. In cancer, activating mutations in protein kinases, such as EGFR and BRAF, lead to uncontrolled downstream signaling by locking these enzymes in a constitutively active state. Similarly, mutations affecting inositol kinases, notably PI3KCA, hyperactivate the PI3K/AKT pathway, promoting relentless cell survival and resistance to apoptosis. GTPases, particularly Ras family members (KRAS, NRAS, HRAS), are classical oncogenes where single amino acid substitutions impair their intrinsic GTP hydrolysis activity, trapping them in a persistently GTP-bound "on" state. This unleashes continuous mitogenic signaling independently of external growth factors. Collectively, these mutations are not random but converge on a limited set of core pathways, making them key drivers of tumor initiation and progression. Understanding the specific molecular consequences of kinase and GTPase mutations has directly informed the development of targeted therapies, including small molecule inhibitors and monoclonal antibodies, now used in routine clinical practice.
    Keywords:  GTPases; cancers; inositol polyphosphate kinases; leukemias; mutations; protein kinases
    DOI:  https://doi.org/10.3390/cancers18132033
  43. Plant Cell Physiol. 2026 Jul 16. pii: pcag096. [Epub ahead of print]
      When ribosome biogenesis or function is perturbed, plant cells undergo ribosomal stress, leading to growth defects and developmental alterations. The plant ribosomal stress response has recently gained recognition, but its molecular mechanism remains elusive. Here, we characterized this response in Arabidopsis thaliana using ribosome biogenesis-impairing mutations (rid2 and rid3) and ribosome biogenesis/function-interfering drugs (5-fluorouracil and puromycin) as ribosomal stressors. These stressors repressed cell proliferation and increased ploidy levels indicative of endoreduplication. Under the ribosomal stress conditions, a subset of NAC transcription factor genes and CDK inhibitor genes were upregulated, while they tended to downregulate G2/M-specific genes. Overexpression of ANAC082, which encodes a NAC factor implicated in the ribosomal stress response pathway, phenocopied the ribosomal stress response in the cellular behavior and gene expression. These results together indicated that, predominantly mediated by ANAC082, ribosomal stress arrests the cell cycle at G2 and promotes endoreduplication. Comparison of gene expressions and genetic relations between the ribosomal and DNA damage stress responses, focusing on ANAC082 and the DNA damage stress response-mediating NAC factor SOG1, revealed that these stress response pathways are distinct and largely independent from each other, although they have similar outputs in the control of cell proliferation and endoreduplication.
    Keywords:  ANAC082; CDK inhibitor; Cell cycle; DNA damage; Endoreduplication; Ribosomal stress
    DOI:  https://doi.org/10.1093/pcp/pcag096
  44. EMBO Rep. 2026 Jul 17.
      RNA localization to organelles is emerging as a key mechanism for regulating protein expression at the subcellular level in neurons. Although certain transcripts associate with endosomes, the functional significance remains poorly understood. Using APEX-seq, we identify a broad set of mRNAs localized to endosomes. We focus on the autophagy-related lc3b mRNA and confirm its endosomal association in cultured cells and Xenopus neuronal axons. In axons, lc3b mRNA is translated at endosomes, where the resulting LC3B protein also colocalizes, suggesting a tight spatial coupling between transcript localization and protein function. Impairment of LC3B membrane insertion via expression of a mutant ATG7 leads to the accumulation of enlarged axonal endosomes. Moreover, RAB5 overactivation promotes the formation of dysfunctional endosomes in axons that are targeted and cleared by LC3B-mediated autophagy. Finally, chloroquine-induced damage to axonal endosomes triggers their targeting by LC3B in a translation-dependent manner. Collectively, our findings expand the catalog of endosome-associated transcripts and reveal a functional link between autophagy and endosomal turnover in axons.
    DOI:  https://doi.org/10.1038/s44319-026-00867-5
  45. FASEB J. 2026 Jul 31. 40(14): e72112
      The activation of endoplasmic reticulum stress (ERS), specifically the PERK/eIF2α/CHOP signaling, is a recognized consequence of ischemic stroke. However, the roles and mechanisms of CRM-1 regulating ERS in stroke are poorly elucidated. A murine model of stroke was generated via transient middle cerebral artery occlusion (MCAO). The endpoints included TTC-derived infarct volume, H&E/TUNEL histopathology, p-PERK immunohistochemistry, and Western blot. Oxygen-glucose deprivation/reoxygenation (OGD/R) was employed in HT22 neurons. The CRM1-ALKBH5 interaction and subcellular distribution were assessed by co-immunoprecipitation (co-IP), cytoplasm-nucleus fractionation, and confocal microscopy. m6A regulation of BANF1 was examined using MeRIP-qPCR, RIP-qPCR, and a dual-luciferase reporter assay. Knockdown of CRM-1 reduced the infarct size, decreased ER stress activation, decreased apoptosis in vivo, and improved cell viability after OGD/R. CRM-1 was attached to ALKBH5 and promoted its export from the nucleus, which increased m6A modification and expression on BANF1. IGF2BP2 and YTHDF1, respectively, enhanced the stability and translation of BANF1 mRNA, thereby upregulating its expression. BANF1 overexpression restored PERK/eIF2α/CHOP activation and apoptosis in the CRM-1 knockdown context. CRM-1 exacerbated ischemic stroke injury by exporting ALKBH5 to upregulate BANF1 in an m6A-IGF2BP2/YTHDF1-dependent manner. This cascade subsequently activated the PERK/eIF2α/CHOP ERS pathway.
    Keywords:  ALKBH5; BANF1; CRM‐1; PERK/eIF2α/CHOP pathway; ischemic stroke
    DOI:  https://doi.org/10.1096/fj.202601304R
  46. EMBO J. 2026 Jul 11.
      Anabolic and catabolic processes are coordinated by a conserved regulatory network, which includes the nutrient-sensing protein kinase mTOR complex 1 (mTORC1) and the insulin- and stress-responsive transcription factor FoxO. In a physiological setting, these regulators align growth, storage, reproduction, and aging with nutrient availability. Here, we identify transcription factor Spalt-related (Salr), previously implicated in organogenesis, as a negative regulator of growth and lipid storage in Drosophila melanogaster. Salr activates catabolic gene expression and restricts mTORC1-mediated cell growth in the Drosophila fat body. The genomic binding of Salr overlaps extensively with that of FoxO, and a similar convergence is observed for their mammalian homologs, SALL1 and FOXO1. Both Salr and FoxO are activated upon fasting, but respond to distinct cues: while FoxO displays transient activation and is responsive to AKT inhibition, Salr is activated in a slow and sustained manner through the integrated stress response. Once activated, Salr counters nuclear localization of FoxO. Taken together, we show that Salr and FoxO are growth-inhibitory transcription factors that act in a convergent manner to respond to nutrient stress through distinct cues.
    DOI:  https://doi.org/10.1038/s44318-026-00858-1
  47. Biochimie. 2026 Jul 17. pii: S0300-9084(26)00167-7. [Epub ahead of print]
      The endoplasmic reticulum (ER) is the principal site of glycerolipid synthesis in eukaryotic cells. The continuous production of lipid intermediates, including phosphatidic acid (PA), diacylglycerol (DAG), and triacylglycerol (TAG), destabilizes the ER membrane when they accumulate. To maintain bilayer integrity, cells deploy two sequential strategies: enzymatic conversion of these intermediates into membrane-compatible phospholipids, and their physical sequestration into lipid droplets (LDs), ER-derived organelles whose biogenesis is actively regulated by the seipin complex. LD growth is further sustained by the relocalization of TAG-synthesizing enzymes to the LD surface and by bridge-like lipid transfer proteins at ER-LD contact sites. When these mechanisms are overwhelmed, the accumulation of non-bilayer lipids drives ER stress and lipotoxicity, thereby contributing to the development of metabolic diseases. Here, we review the molecular logic of ER lipid quality control, from intermediate-driven membrane stress to the regulated responses that neutralize it.
    Keywords:  Diacylglycerol; Kennedy pathway; endoplasmic reticulum; ferroptosis; lipid droplets; lipid quality control; lipotoxicity
    DOI:  https://doi.org/10.1016/j.biochi.2026.07.007
  48. Res Sq. 2026 Jul 08. pii: rs.3.rs-9580737. [Epub ahead of print]
      Background: Protein post-translational modification (PTM) plays a pivotal role in cellular activities and biological processes. Although several databases curate PTM information, most cover only a limited number of PTMs. Although the scientific literature continues to accumulate a vast amount of PTM-related knowledge, these databases are not updated regularly. This growing information gap highlights the need for automated information extraction (IE) systems that can identify modified proteins and their specific amino acid sites directly from the literature. While numerous PTMs have been reported in scientific articles, most existing tools are designed only for a few specific PTMs, and developing separate systems for every PTM is not feasible. Methods: To address this challenge, we developed GenPTM, a generalized and adaptable IE tool that identifies modified proteins and sites from PubMed abstracts using a unified text representation strategy. GenPTM replaces PTMspecific modification and chemical group mentions with generic placeholders, allowing the model to focus on shared textual patterns that express modification events. A BiomedBERT-based classifier is fine-tuned to determine whether a candidate protein or site is truly modified, and a post-processing module assembles the final protein, site, or protein-site pair predictions. Results: Trained on five major PTM types (e.g., Ubiquitination, Phosphorylation) and evaluated on eight additional PTMs, including PTMs that are not frequently mentioned (e.g., Citrullination, AMPylation), GenPTM achieves F1- scores ranging from 92% to 96% across all PTMs for three different evaluation categories. Conclusions: These results exhibit strong generalization capability of GenPTM by providing a viable solution for PTM-agnostic IE and automated PTM knowledge discovery in proteomics.
    DOI:  https://doi.org/10.21203/rs.3.rs-9580737/v1
  49. bioRxiv. 2026 Jul 09. pii: 2026.07.08.737257. [Epub ahead of print]
      RNA-based sensors offer powerful and programmable control of gene expression, yet our understanding of the structural principles that govern their potential design space remains incomplete. Here, we challenged a community of designers to generate novel riboregulators capable of activating translation in response to specific RNA targets. Participants submitted diverse sequence architectures, which were synthesized and evaluated in a cell-free transcription-translation system. Across 100 designs, community-generated riboregulators displayed wide variability in activation dynamics, fold change, and structural features, outperforming some canonical toehold-switch designs and achieving up to 80-fold activation. Structural ensemble analyses identified accessibility patterns near the ribosome binding site that distinguish high- from low-performing regulators, highlighting the central role of RBS sequestration and release in modulating expression. Together, we demonstrate community-driven design can expand the accessible structural space of riboregulators and uncover mechanistic features governing translational activation. Our findings establish quantitative links between RNA folding energetics and gene expression output, providing design principles for next-generation programmable RNA sensors.
    DOI:  https://doi.org/10.64898/2026.07.08.737257
  50. Biochem Biophys Res Commun. 2026 Jul 09. pii: S0006-291X(26)00966-6. [Epub ahead of print]830 154202
      3-Hydroxy-3-methylglutaryl-CoA reductase (HMGR) catalyzes the committed step of the mevalonate pathway and is encoded by multigene families in plants. However, the functional specialization of individual isoforms in abiotic stress remains poorly understood in legumes. Here, we characterize three HMGR isoforms from chickpea (Cicer arietinum) and demonstrate that CaHMGR2 and CaHMGR3 function as stress-inducible isoforms with structural and regulatory divergence from the constitutively expressed CaHMGR1. Quantitative expression profiling revealed strong induction of CaHMGR2 and CaHMGR3 under drought, salinity, and cold stress. Promoter analysis identified enrichment of abiotic stress-responsive cis-elements exclusively in these isoforms. Structural comparison uncovered conserved substitutions within the dimerization motif, transmembrane regions, and residues proximal to the regulatory serine, suggesting altered regulatory properties. Subcellular localization further distinguished CaHMGR2 and CaHMGR3, which associate with both endoplasmic reticulum and nuclear envelope. Functional validation using overexpression lines demonstrated enhanced germination, root growth, reduced water loss, and improved recovery under stress. Metabolic profiling and KEGG pathway enrichment revealed selective metabolic re-programming associated with branched chain amino acid and fatty acid metabolism. Together, these findings establish functional specialization of HMGR isoforms and their role in abiotic stress resilience in chickpea.
    Keywords:  Abiotic stress; Chickpea; HMGR; Isoform specialization; Metabolic reprogramming; Mevalonate pathway
    DOI:  https://doi.org/10.1016/j.bbrc.2026.154202
  51. bioRxiv. 2026 Jul 09. pii: 2025.09.13.676059. [Epub ahead of print]
      RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment into Ebola virus condensates under basal and IFN-stimulated states. We find that in the basal state, cellular RNAs with minimally folded coding regions are selectively recruited. Under IFN-stimulation, however, interferon-stimulated genes (ISGs) with structured 3'UTRs concentrate in viral condensates. We find that both features, minimally folded coding regions and structured 3'UTRs, are conserved in the viral RNA genome, supporting viral genome retention in condensates. In parallel, for cellular mRNAs, we find that partitioning into condensates escapes decay, prolonging RNA-half-life, and amplifying rather than dampening ISG expression. Fruit bats, which do not experience severe disease for RNA viruses, instead have ISGs with reduced 3'UTR folding, and may evade condensate-sequestration, enabling balanced antiviral responses. This selective stabilization links condensate function to RNA regulation as a molecular determinant of viral and host co-evolution and disease pathogenesis.
    DOI:  https://doi.org/10.1101/2025.09.13.676059
  52. Arch Physiol Biochem. 2026 Jul 17. 1-15
      Background: Acute Respiratory Distress Syndrome (ARDS) is a life-threatening condition associated with high morbidity and mortality, characterized by severe inflammation, oxidative stress, impaired gas exchange, and progressive lung injury. Disruption of cellular redox homeostasis plays a central role in ARDS pathogenesis, making redox-regulatory mechanisms attractive therapeutic targets. Methods: This review evaluates experimental evidence on protein-mediated regulation of oxidative stress pathways in ARDS, focusing on proteins involved in antioxidant defense, reactive oxygen species (ROS) generation, mitochondrial signaling, and maintenance of cellular redox homeostasis. Results: Current evidence indicates that key regulatory proteins modulate oxidative stress by activating endogenous antioxidant defense systems, regulating ROS production, and influencing mitochondrial signaling pathways. These mechanisms reduce oxidative damage and pulmonary inflammation while preserving cellular redox balance. Experimental studies further demonstrate that modulation of specific protein regulators enhances cellular resilience under hypoxic and inflammatory conditions characteristic of ARDS. Conclusions: Protein-mediated regulation of redox signaling represents a promising therapeutic strategy for ARDS. Targeting redox-regulatory proteins may attenuate oxidative stress, reduce lung inflammation, and improve cellular survival, supporting their potential as novel therapeutic targets. Further preclinical and clinical studies are needed to validate these findings and facilitate their translation into clinical practice.
    Keywords:  Acute respiratory distress syndrome (ARDS); antioxidant defense; lung injury; mitochondrial function; oxidative stress; protein regulation; reactive oxygen species (ROS); redox metabolism
    DOI:  https://doi.org/10.1080/13813455.2026.2701306
  53. Brain. 2026 Jul 16. pii: awag245. [Epub ahead of print]
      The process of neurodevelopment and neuropathology can be influenced by RNA binding proteins. The RNA binding protein ZC3H14 (also referred to as MSUT2) is of particular interest for two reasons. First, homozygous loss-of function alleles in ZC3H14 are associated with an inherited form of intellectual disability. Second, in model systems, loss of ZC3H14 can suppress the toxicity of tau aggregates, which are hallmark diagnostic features of Alzheimer's disease and other neurodegenerative diseases referred to as "tauopathies". In this review, we discuss both the normal functions of ZC3H14 and how alterations in these functions may affect cognitive function or tau pathology. Although not fully understood, an emerging theme is that alterations in RNA regulation due to ZC3H14 loss can affect neuronal function.
    Keywords:  Alzheimer’s disease; RNA; RNA binding protein; ZC3H14; neurodevelopment; tau
    DOI:  https://doi.org/10.1093/brain/awag245
  54. Nat Commun. 2026 Jul 17.
      Defects in ribosome biogenesis cause ribosomopathies, but the pathogenic role of malformed preribosomes remains unclear. Using preribosome fractionation, live-cell and confocal microscopy, and automated imaging screens, we tracked abortive preribosomes following depletion of the 33 small-subunit ribosomal proteins (RPSs). We found that all RPS deficiencies lead to accumulation of nucleolar preribosome materials in the nucleoplasm, regardless of the affected 40S subunit maturation stage. These aberrant particles appear as dispersed complexes or persistent aggregates arising during nucleolar reassembly in late mitosis. Although nucleolar morphology remains largely intact, their accumulation impairs recycling of nucleolar factors and disrupts nucleolar-nucleoplasmic proteostasis. Distinct RPS deficiencies produce different preribosome behaviors, indicating maturation-specific properties. Notably, depletion of RPS19, the protein encoded by the most frequently mutated gene in Diamond-Blackfan anemia, causes particularly severe defects. Our findings identify nucleoplasmic preribosome aggregation and dispersion as common consequences of RPS deficits and potential contributors to 40S ribosomopathy pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-026-75682-6
  55. Front Cell Dev Biol. 2026 ;14 1898234
      Intervertebral disc degeneration (IVDD) is commonly framed as the cumulative result of extracellular matrix loss, inflammatory activation, oxidative damage, cellular senescence and cell death. This formulation is useful, but it also fragments the disease into parallel mechanisms and obscures a central paradox: nucleus pulposus and annulus fibrosus cells normally reside in a microenvironment that would be hostile to most mammalian cells. The healthy disc is avascular, diffusion limited, hypoxic, glycolytic, relatively acidic and mechanically loaded. These features are not simply pathological insults; they are defining ecological constraints to which disc cells are continuously adapted. Here we propose that IVDD can be productively reframed as a process of stress-response exhaustion. In this view, degeneration begins when the adaptive systems that maintain disc cell viability and matrix homeostasis under chronic microenvironmental stress lose amplitude, flexibility or recovery capacity. Hypoxia-inducible factor signalling, AMPK-mTOR metabolic sensing, autophagy and mitophagy, unfolded-protein and integrated stress responses, and redox buffering are initially protective. With ageing, endplate dysfunction, nutrient diffusion failure, acidosis, abnormal mechanical loading and organelle damage, these same systems can become insufficient or maladaptive, creating a degenerative tipping point. Downstream consequences include senescence, sterile inflammation, cell death, matrix collapse and neuroimmune conversion to painful disease. This framework does not replace established mechanisms of IVDD; rather, it orders them along a temporal axis from adaptation to exhaustion. It also suggests stage-specific therapeutic logic: preserve adaptive reserve early, prevent stress-response collapse, suppress senescence and sterile inflammation, and target neuroimmune sensitization in painful degeneration.
    Keywords:  adaptive reserve; autophagy; cartilage endplate; cellular stress response; discogenic pain; intervertebral disc degeneration; senescence
    DOI:  https://doi.org/10.3389/fcell.2026.1898234
  56. Nat Commun. 2026 Jul 13.
      The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We find two 2'-O-methylated positions that are differentially modified during the parasite's two life stages. The deposition of these modifications is guided by snoRNAs. When we perform cytosine base-editing of the snoRNA responsible for guiding one of the two stage-regulated modifications, Am479, we fail to detect ribosomes lacking this modification, suggesting that it is essential. To better understand the role of the snoRNA and its guided modification, we determine the cryo-EM structures of ribosomes from cells overexpressing the guiding snoRNA and compare them to ribosomes from the parental strain. We do not find structural changes around Am479 or in the small subunit rRNA, but observe a difference in H68 of the large subunit rRNA due to a second base-pairing interaction, suggesting a potential chaperone activity for the snoRNA. Based on these results, translatome and tRNA analysis, we propose a mechanism whereby changes in ribosome structure affect the release of specific tRNAs, which correlate with changes in translation of only a subset of mRNAs.
    DOI:  https://doi.org/10.1038/s41467-026-75486-8
  57. Aging Cell. 2026 Jul;25(7): e70634
      Aging is often framed as the gradual erosion of proteostasis, driven by declining chaperone capacity, impaired degradation, and dysregulated protein synthesis. Yet this view implicitly assumes that proteins fail primarily because they misfold or escape clearance. Increasing evidence instead points to a more fundamental problem: aging disrupts the spatial management of the proteome. Gradually, proteins are misplaced, signaling pathways are uncoupled from their compartments, and condensates that were once dynamic become pathological. At the center of this spatial collapse lies nucleocytoplasmic protein partitioning. Nucleocytoplasmic protein transport has long been treated as a background housekeeping process, that is, essential but largely passive. However, this assumption is no longer reasonable. Karyopherins, the importins, exportins and biportins that mediate selective transport across the nuclear pore complex (NPC), are emerging as active regulators of proteostasis, phase behavior, and signaling fidelity. Rather than simply responding to cargo demand, karyopherins shape intracellular protein solubility, suppress aberrant condensation, and buffer age-associated stress. Their dysfunction therefore constitutes a primary, not secondary, driver of aging phenotypes. Here, I argue that karyopherins should be repositioned at the core of aging biology. I propose that age-dependent failure of karyopherin-mediated transport represents a unifying mechanism linking proteostasis collapse, altered gene regulation, and the emergence of age-associated diseases. This perspective redefines nucleocytoplasmic protein transport from a logistics challenge into a central regulatory layer and highlights karyopherins as emerging targets for aging interventions.
    DOI:  https://doi.org/10.1111/acel.70634
  58. J Assist Reprod Genet. 2026 Jul 17.
      N6-methyladenosine (m6A), the dominant internal RNA modification in eukaryotic mRNA, plays an important regulatory role in female reproductive physiology and associated pathologies. This review systematically outlines the precise regulatory mechanisms exerted by m6A writers, erasers, and readers in core processes including germ cell development, early embryogenesis, and hormone signaling. We further elaborate on how aberrant m6A modifications contribute to the pathogenesis of various female reproductive disorders, such as gynecological cancer, polycystic ovary syndrome, and preeclampsia. In addition, we conducted a rigorous assessment of the therapeutic and diagnostic potential targeting the m6A mechanism. By synthesizing mechanistic insights from both neoplastic and non-neoplastic diseases, this review provides a comprehensive framework for understanding the epitranscriptomic governance of female reproductive health and proposes new directions for future research and clinical translation.
    Keywords:  Epigenetic modification; Female reproductive development; Female reproductive diseases; M6A detection technology; N6-methyladenosine (m6a); Treatment strategy
    DOI:  https://doi.org/10.1007/s10815-026-03953-8
  59. Cell Death Dis. 2026 Jul 17.
      Human cytoplasmic leucyl-tRNA synthetase (LARS) is known to catalyze the ligation of leucine to tRNALeu during protein biosynthesis. However, LARS also acts as a nutrient sensor in a non-canonical activity to regulate cell growth. In this investigation, LARS was determined to be expressed at high levels in human liver cancer, which correlated with poor clinical outcomes in patients. Knockdown of LARS in HepG2 liver cancer cells suppressed cell proliferation and growth, yet promoted cell migration, without affecting global protein translation. Using data from RNA sequencing, differentially expressed genes in response to LARS knockdown were significantly clustered in the cellular senescence pathway. Elevated p21 and p16 expression with increased senescence-associated β-galactosidase activity was observed in LARS knockdown HepG2 cells. In addition, autophagy with increasing autophagic flux was triggered in LARS knockdown HepG2 cells. Furthermore, the depletion of LARS induced oxidative stress with increased production of reactive oxygen species and decreased mitochondrial membrane potential. Importantly, re-expression of shRNA-resistant LARS largely rescued the senescence, autophagy, and oxidative stress caused by LARS knockdown, confirming the specificity of these effects. These findings suggest that LARS plays a role in regulating liver cancer cell proliferation via multiple cellular responses and may serve as a promising therapeutic target in liver cancer.
    DOI:  https://doi.org/10.1038/s41419-026-09114-0
  60. RSC Chem Biol. 2026 Jul 01.
      Biomolecular liquid-liquid phase separation, which forms droplets in living cells, plays a crucial role in the regulation of gene expression. Dysfunction of liquid-liquid phase separation leads to aberrant aggregates that sequester RNA-binding proteins, thereby impairing their functions, which potentially leads to the onset of neurodegenerative diseases. Preventing and reversing the sequestration of RNA-binding proteins from droplets represent a promising therapeutic approach. Noteworthily, the G-quadruplex, a non-canonical secondary structure of nucleic acids formed by a guanine-rich sequence, is an essential structural motif that triggers liquid-liquid phase separation with a partner protein. Thus, a G-quadruplex ligand, which selectively binds and stabilizes the G-quadruplex, can be promising for controlling liquid-liquid phase separation of G-quadruplexes and partner proteins. In this study, we investigated the effects of G-quadruplex ligands on the liquid-liquid phase separation of RNA G-quadruplexes and RGG domain-derived cationic peptides. It was found that G-quadruplex ligands formed aggregates with the target G-quadruplexes and excluded the G-quadruplex-binding peptides from these aggregates. Moreover, structure-selective G-quadruplex ligands induced aggregates only with the G-quadruplex but not with other secondary structures. These findings demonstrate for the first time that the structure-selectivity of G-quadruplex ligands plays a key role in modulating condensates.
    DOI:  https://doi.org/10.1039/d6cb00020g
  61. Transl Cancer Res. 2026 Jun 30. 15(6): 471
       Background: XBP1s, a key downstream molecule of endoplasmic reticulum stress (ERS), is widely involved in processes such as proliferation, invasion, and apoptosis in cancer. However, the role and underlying mechanism of XBP1s in colorectal cancer (CRC) remain poorly understood. We hypothesize that XBP1s plays a critical role in promoting CRC proliferation through the regulation of autophagy. Therefore, this study aims to investigate the expression, biological functions, and underlying mechanisms of XBP1s in colorectal cancer, opening up new directions for targeted tumor therapy.
    Methods: Based on The Cancer Genome Atlas (TCGA) database, the expression of XBP1 in pan-cancer tissues and CRC tissues was analyzed. Western blotting (WB) and immunohistochemistry (IHC) were used to validate the protein expression level of XBP1s in clinical CRC tissues, and its correlation with clinicopathological characteristics and patient prognosis was assessed. The effects of XBP1s on CRC cells were examined using in vitro cell experiments. Furthermore, bioinformatics analyses, including Gene Ontology (GO) functional annotation and gene set enrichment analysis (GSEA) pathway enrichment, were employed to predict downstream pathways associated with XBP1s, which were subsequently validated through follow-up experiments. Therefore, this study aims to investigate the expression, biological functions, and underlying mechanisms of XBP1s in colorectal cancer, opening up new directions for targeted tumor therapy.
    Results: The expression of XBP1s was significantly higher in CRC tissues compared to normal tissues and was significantly associated with poor prognosis in CRC patients. Knockdown of XBP1s expression ex vivo markedly inhibited CRC cell proliferation and promoted apoptosis. GO and GSEA enrichment analyses revealed a close association between XBP1 and the autophagy signaling pathway. Consequently, by utilizing inhibitors and establishing an ERS model, it was demonstrated that XBP1s might promote CRC growth and proliferation by activating autophagy.
    Conclusions: Our findings indicate that interference with XBP1s expression can inhibit the malignant proliferation of CRC by suppressing the autophagy signaling pathway. Targeting XBP1s may represent a novel therapeutic strategy for the diagnosis and treatment of CRC patients.
    Keywords:  XBP1s; autophagy; colorectal cancer (CRC); endoplasmic reticulum stress (ERS); unfolded protein response
    DOI:  https://doi.org/10.21037/tcr-2026-0428
  62. Sci Adv. 2026 Jul 17. 12(29): eaee9999
      Medullary thymic epithelial cells (mTECs) establish central immune tolerance by expressing diverse tissue-restricted antigens and eliminating self-reactive thymocytes. Here, we show that fibroblast growth factor 21 (FGF21), although predominantly produced in the liver, is also expressed locally by mature mTECs and contributes to central tolerance. Fgf21-deficient mice exhibited exacerbated peripheral autoimmune responses. FGF21 supported the number and function of mTECs and promoted clonal deletion in cooperation with thymic dendritic cells. In mature mTECs, endoplasmic reticulum stress induced FGF21 expression through unfolded protein response pathways, with FGF21 acting preferentially within the mature mTEC compartment as a stress-responsive metabolic regulator downstream of the integrated stress response. By limiting sustained stress and preserving protein homeostasis, FGF21 maintained mTEC integrity and central tolerance. These findings identify FGF21 as a key regulator of thymic immune homeostasis and as a potential therapeutic target for autoimmune disease.
    DOI:  https://doi.org/10.1126/sciadv.aee9999
  63. bioRxiv. 2026 Jul 08. pii: 2026.07.06.736874. [Epub ahead of print]
      Chronic microglial inflammation and cellular senescence are hallmarks of the aging brain, yet the molecular events that lock microglia into durable inflammatory states remain poorly understood. Prior studies using genetic manipulation of METTL3 have implicated the RNA modification N6-methyladenosine (m6A) in senescence. However, because METTL3 also has m6A-independent functions, loss-of-function approaches cannot distinguish whether senescence arises from reduced m6A itself or from broader disruption of METTL3-dependent pathways. This question is further complicated in microglia, where METTL3 has been reported to promote acute inflammatory activation, suggesting that m6A may have context-dependent effects on immune state. Whether sustained reduction of m6A is sufficient to drive microglial senescence has therefore remained unresolved. Here, we show that selective catalytic inhibition of METTL3 with STM2457 lowers global m6A and is sufficient to induce a senescence-like inflammatory state in human HMC3 microglia. This state includes increased senescence-associated β-galactosidase activity, elongated cellular morphology, reduced proliferation, Lamin B1 loss, and remodeling of nuclear architecture. Transcriptomic profiling revealed suppression of mitotic gene programs together with a SASP-like inflammatory output marked by NF-κB and interferon signatures. Rather than causing broad transposable-element derepression, m6A inhibition promoted cytoplasmic double-stranded RNA accumulation and a selective HERVK-associated response. These findings support a model in which m6A helps preserve microglial homeostasis by limiting immunogenic RNA accumulation and senescence-associated inflammatory remodeling. Together, our study identifies m6A as a safeguard against microglial senescence and suggests that reduced m6A-dependent RNA regulation may contribute to chronic inflammatory remodeling in the aging brain.
    DOI:  https://doi.org/10.64898/2026.07.06.736874
  64. Biomed Khim. 2026 Jul;72(3): 220-229
      Renalase (RNLS) is a protein exhibiting various functions inside and outside cells. A series of synthetic peptides, corresponding to the fragments of the RNLS amino acid sequence, may reproduce the effects of the full-length RNLS. In this study we have investigated the interaction of proteins in the mitochondrial brain fraction of rats with the full-length RNLS and its peptides RP211-223 (peptide 1) and RP224-232 (peptide 2) immobilized on CNBr-activated Sepharose. Proteomic profiles of proteins bound to the full-length RNLS and its peptide RP211-223 were significantly different, whereas RP224-232 bound a small number of proteins (6), similar to those bound to the full-length RNLS. However, most proteins bound to RNLS and its peptides were multifunctional and associated with neurodegenerative pathology (Alzheimer's and Parkinson's diseases, etc.).
    Keywords:  neurodegeneration; proteomic profiling; rat brain mitochondria; renalase; renalase peptides RP211-223 and RP224-232
    DOI:  https://doi.org/10.18097/PBMCR1704
  65. Cell Mol Life Sci. 2026 Jul 13.
      Podocyte injury is a central driver of proteinuria and progressive kidney dysfunction. Although podocytes are continuously exposed to diverse stressors in both physiological and pathological contexts, the dynamic processes underlying their adaptation and eventual failure remain poorly defined. Here, we performed integrative single-nucleus RNA sequencing of kidney tissues from patients with six types of representative chronic glomerulonephritis, capturing a spectrum of podocyte injury states. We identified distinct podocyte subpopulations and reconstructed a dynamic trajectory characterized by an initial adaptive activation followed by progressive functional decline. Integration with time-resolved transcriptomics identified 778 candidate genes associated with podocyte stress responses. To distinguish putative functional drivers from secondary transcriptional changes, we integrated these candidates with a genome-wide CRISPR-Cas9 knockout screen, prioritizing genes required for podocyte survival under stress conditions. Subsequent siRNA-mediated validation of five representative candidates-BST1, TALDO1, ATP6V1E1, PPP2R1A and CHL1-showed that knockdown of these genes significantly compromised cell viability and accelerated apoptosis, highlighting a coordinated survival network spanning metabolic regulation, autophagy, and cytoskeletal stability. Our findings define a dynamic framework of podocyte stress adaptation and failure, and suggest that targeting stress-response pathways may prolong podocyte survival, thereby extending the therapeutic window for intervention in chronic kidney disease.
    Keywords:  CRISPR screening; Podocyte; Single-nucleus RNA sequencing; Stress
    DOI:  https://doi.org/10.1007/s00018-026-06335-6
  66. Ageing Res Rev. 2026 Jul 17. pii: S1568-1637(26)00253-9. [Epub ahead of print] 103261
      Cardiovascular aging is a major contributor to the development of cardiovascular diseases (CVDs), yet the mechanisms linking metabolic imbalance to age-related cardiovascular dysfunction remain unclear. Protein palmitoylation, a reversible lipid post-translational modification, regulates protein localization, stability, and signaling, but its role in cardiovascular aging has not been systematically defined. Importantly, protein palmitoylation appears to act as a double-edged sword: whereas its physiological regulation is indispensable for cardiovascular homeostasis, aberrant palmitoylation under metabolic stress may drive aging and disease progression. In this review, we summarize current evidence indicating that dysregulated palmitoylation contributes to key features of cardiovascular aging, including mitochondrial dysfunction, impaired autophagy, oxidative stress, and cellular senescence. We further integrate findings across cardiomyocytes, endothelial cells, fibroblasts, and immune cells to highlight the role of palmitoylation in coordinating cellular dysfunction and intercellular communication during cardiovascular aging and disease. We propose a "palmitoylation-driven metabolic vicious cycle" that links metabolic disorders to enhanced palmitoylation and progressive cardiovascular injury. In addition, we discuss emerging detection approaches and therapeutic strategies targeting palmitoylation. Overall, this review provides a mechanistic framework linking palmitoylation to cardiovascular aging and disease and identifies potential targets for intervention in aging-related CVDs.
    Keywords:  Palmitoylation; cardiovascular aging; cardiovascular diseases; metabolic dysregulation; therapeutic targets
    DOI:  https://doi.org/10.1016/j.arr.2026.103261
  67. Curr Cancer Drug Targets. 2026 Jul 07.
       INTRODUCTION: Mitochondria continuously undergo fission and fusion processes, and this dynamic balance is essential for maintaining proper cellular function. Disruption of this balance can lead to cellular dysfunction, making cancer cells more resistant, increasing their metastatic potential, and promoting tumor growth. In this review, we examine how dysregulation of proteins involved in mitochondrial dynamics contributes to drug resistance. We also discuss emerging therapeutic strategies aimed at correcting mitochondrial dysfunction to enhance the effectiveness of cancer therapies.
    METHODS: This review synthesizes recent research on mitochondrial dynamics in cancer. It focuses on key proteins DRP1, MFN1, MFN2, and OPA1 and their roles in mitochondrial fission, fusion, and clearance. The review also integrates current understanding of these processes at the cellular level with emerging findings from studies on drug-resistant cancers.
    RESULTS: When proteins such as DRP1, MFN1, MFN2, and OPA1 are dysregulated, cancer cells develop mechanisms to survive treatments. These cells alter mitochondrial function, affecting energy production, reactive oxygen species management, and susceptibility to apoptosis. In drug-resistant tumors, mitochondria undergo dynamic remodeling, fusing or dividing depending on cellular requirements. Additionally, mitophagy removes damaged mitochondria while preserving functional ones, further enhancing the survival and resilience of these cells.
    DISCUSSION: When mitochondria undergo such adaptations, cancer cells can survive hostile environments and evade conventional therapies. Targeting these processes offers therapeutic opportunities: inhibitors of DRP1 can prevent abnormal mitochondrial fission, while modulation of OPA1 or other fusion proteins can restore healthy mitochondrial structure and promote apoptosis. By focusing on mitochondrial dynamics, new strategies emerge to overcome drug resistance by disrupting cancer cell metabolism and organelle homeostasis.
    CONCLUSION: This review underscores the potential of mitochondrial dynamics as a promising new target in cancer therapy. Examining the regulation of mitochondrial fission and fusion, the clearance of damaged mitochondria, and the dysregulation of key proteins reveals potential therapeutic opportunities. Furthermore, recent drugs that modulate these processes offer strategies to enhance the durability of cancer treatments and overcome drug resistance.
    Keywords:  Mitochondria; ROS.; apoptosis; cancer drugs; fission; fusion
    DOI:  https://doi.org/10.2174/0115680096460139260618104458
  68. PLoS Biol. 2026 Jul 17. 24(7): e3003863
      The RNA-binding protein Sex-lethal (Sxl) is classically known as a master regulator of sex determination and mRNA splicing in Drosophila melanogaster. However, this role is not conserved across species, and functions beyond the canonical pathway remain poorly understood. In this study, we uncover a splicing-independent role for Sxl at the chromatin level in the Drosophila brain. Using Targeted DamID (TaDa) profiling in neurons, we identify widespread binding of Sxl to promoter regions, independent of sex or RNA binding activity. Notably, Sxl chromatin occupancy exhibits near-complete overlap with Polr3E (RPC37), an RNA Polymerase III subunit, with Sxl binding abolished upon Polr3E knockdown. Depletion of Sxl in mature male neurons induces widespread transcriptional changes, particularly in metabolic genes, and improves negative geotaxis during aging, phenotypes that closely mirror Polr3E knockdown. Conversely, overexpression of the brain-specific SxlRAC transcript leads to severe climbing deficits and upregulated gene expression associated with metabolism and translation. Manipulating Sxl levels in the brain significantly impacts select tRNA production and global protein synthesis rates. Together, these findings reveal a previously unrecognized role for Sxl in regulating Pol III activity via Polr3E, modulating tRNA synthesis and supporting neuronal metabolism. Given the emerging tie between Pol III regulation and neuronal aging, our study highlights Sxl as a novel factor in neuronal homeostasis.
    DOI:  https://doi.org/10.1371/journal.pbio.3003863
  69. Transl Cancer Res. 2026 Jun 30. 15(6): 480
       Background: Lung cancer (LC) remains a leading cause of cancer-related death globally. The methyltransferase METTL3, a core writer of RNA N6-methyladenosine (m6A) modification, is a key regulator in cancer. However, its systematic regulatory network, particularly in contexts where it exerts tumor-suppressive functions, remains to be fully elucidated. In this study, we aimed to systematically investigate the transcriptomic and epitranscriptomic remodeling induced by METTL3 overexpression in A549 lung cancer cells to uncover its potential tumor-suppressive mechanisms.
    Methods: Bioinformatics analysis of public databases was performed to evaluate METTL3 expression and prognostic significance in LC. Cell biology assays were conducted to assess phenotypic changes (proliferation, migration/invasion apoptosis) induced by METTL3 overexpression (METTL3-OE). RNA-sequencing (RNA-seq) was performed for METTL3-OE and negative control (NC) A549 cells. Publicly available methylated RNA immunoprecipitation sequencing (MeRIP-seq) datasets of LC cell line and tissues (GSE117299, GSE76367) were downloaded from the Gene Expression Omnibus (GEO) database. Bioinformatics analysis was performed to identify m6A-modified targets and infer their potential function. Key differentially expressed genes (DEGs) and alternative splicing events (ASEs) were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR).
    Results: Analysis of public databases indicated that METTL3 was downregulated in LC tissues and its higher expression correlated with better patient prognosis. Functionally, METTL3 overexpression in A549 cells inhibited proliferation, migration, and invasion, while promoting apoptosis (P<0.05). RNA-seq identified 240 DEGs (227 up-/13 down-regulated). Upregulated DEGs were significantly enriched in antiviral response and antigen presentation pathways. METTL3-OE also altered 1,305 ASEs, with affected genes enriched in cell migration and apoptosis. Integrated analysis identified 22 genes (e.g., HLA-A/B/C, MYD88) that were upregulated by METTL3 overexpression and have been reported to harbor m6A modifications reported in LC tissues and A549 cells. Furthermore, analysis revealed an overlap of 222 genes between those undergoing METTL3-regulated splicing changes and genes documented as m6A-modified in the same LC datasets. RT-qPCR confirmed the upregulation of the immune-related genes (MYD88, HLA-A/B/C, IFIT1, IFIT3, OAS1, ISG20) and the altered splicing of NCOR2 and SIRT7 and AURKB (P<0.05).
    Conclusions: Our study demonstrates that METTL3 overexpression exerts tumor-suppressive effects in A549 cells and suggests that METTL3 may be involved in a multi-layered transcriptional and post-transcriptional response. This response includes the upregulation of immune-related genes-many of which are known m6A targets in LC-and the modulation of splicing in genes controlling cell fate, collectively contributing to the suppression of malignant phenotypes.
    Keywords:  Lung cancer (LC); METTL3; N6-methyladenosine (m6A); alternative splicing (AS); immune response
    DOI:  https://doi.org/10.21037/tcr-2026-1-0354
  70. Antimicrob Agents Chemother. 2026 Jul 15. e0050726
      Drug resistance hampers malaria treatment and control. Resistance to nearly all clinically used antimalarials has emerged and spread globally. With multi-drug-resistant parasites now on the rise, understanding resistance mechanisms and their ability to spread is crucial for optimal treatment and control strategies. Clindamycin is an apicoplast-targeting antimalarial used as a partner compound in second-line treatment combinations, but mechanisms of clindamycin resistance remain largely unexplored, and it is unclear whether resistant parasites could spread readily. We selected in vitro for clindamycin resistance in African and Southeast Asian strains of Plasmodium falciparum. All resistant lines carried mutations in the apicoplast-encoded large ribosomal subunit RNA (23S rRNA), reminiscent of clindamycin resistance mechanisms found in bacteria. We recovered three different mutations, all located in the peptidyl transferase region of apicoplast 23S rRNA. Each 23S rRNA mutation was associated with >20-fold resistance, although some mutants grew extremely poorly in vitro and therefore may lack clinical relevance in vivo. We assessed how well our most vigorously growing 23S rRNA mutant could infect Anopheles mosquitoes and found a modest reduction in vector infectivity, indicating that high-level clindamycin resistance is likely to be transmissible in the field. This is in contrast to atovaquone resistance, which exhibits a total block to transmission (and hence spread), but is more pronounced than P. falciparum azithromycin resistance, which does not significantly impair development in the mosquito.
    Keywords:  apicoplast translation; clindamycin; drug resistance; large ribosomal RNA; malaria transmission
    DOI:  https://doi.org/10.1128/aac.00507-26
  71. J Exp Bot. 2026 Jul 17. pii: erag355. [Epub ahead of print]
      Heat stress disrupts protein homeostasis, triggering the heat shock response (HSR) to maintain cellular proteostasis. A key aspect of this response is the release of heat shock factors (HSFs) from HSP70-mediated attenuation under heat shock conditions, making HSP70 a central regulator of HSR. However, the role of HSP70 co-chaperones in this process remains largely unexplored in plants. Our study identifies AtDJB3, a heat-inducible class II J-domain protein (JDP), as a critical modulator of HSR. Microscopy and cell fractionation show that loss of AtDJB3 impairs HSC70-1 recruitment to heat-induced protein aggregates, maintaining HSFA1d bound to HSC70-1 in the cytoplasm. Chromatin immunoprecipitation (ChIP) and promoter luciferase assays revealed that AtDJB3 is required for HSFA1d enrichment at promoters of key heat-inducible genes, linking AtDJB3 to transcriptional activation of genes, including HSC70-1, HSP90, HSP17.6, FES1A, and HOP3. Consistent with this, atdjb3 mutants displayed compromised thermotolerance, evidenced by their inability to survive prolonged heat stress of 37°C. Conversely, overexpression of AtDJB3 conferred enhanced thermotolerance, supporting its positive regulatory role in HSR. We propose that AtDJB3 not only contributes to the solubilization of heat-induced protein aggregates but also promotes HSFA1d activation by diverting HSC70-1 to aggregates, thereby releasing HSFA1d to drive the transcriptional heat shock response.
    Keywords:   Arabidopsis thaliana ; AtDJB3; HSC70-1; HSFA1d; heat shock response (HSR); protein aggregates; thermotolerance
    DOI:  https://doi.org/10.1093/jxb/erag355
  72. J Thorac Cardiovasc Surg. 2026 Jul 15. pii: S0022-5223(26)01151-7. [Epub ahead of print]
       OBJECTIVE: Post-cardiopulmonary bypass (post-CPB) vasoplegia syndrome (VS) is associated with a dysregulated inflammatory response and a higher morbidity and mortality, but the molecular pathways involved have been incompletely identified. We used multiplexed proteomic and transcriptomic analyses and targeted biochemical assays to identify the inflammatory and metabolic mediators that characterize post-CPB VS.
    METHODS: 16 matched pairs of VS+ and VS- patients were analyzed pre-CPB and post-CPB for comparative proteomic and transcriptomic differences, with gene ontology (GO) pathway enrichment. Circulating NO metabolites (NOx), acetylcholine (ACh), and choline acetyltransferase (ChAT) levels were measured and correlated with VS.
    RESULTS: Baseline proteomic analysis demonstrated elevated TNF, IL-1R1 and IL-17RA in VS+ patients, with the activation of inflammatory cytokine, leukocyte activation, and NO biosynthesis pathways. Analysis of temporal pre-to-post-CPB proteomic changes in VS+ patients demonstrated post-CPB elevation IL17A, CXCL2, and VEGFR/FLT, and decreased immune resolving proteins. Post-CPB proteomic analysis demonstrated differential activation of leukocyte trafficking, T-cell differentiation, IL-6, and IL-17 pathways in VS+ patients. Transcriptomic analysis demonstrated post-CPB activation of cellular response to hypoxia, cellular stress response, and decreased response to angiotensin pathways. Circulating NOx, ACh, and ChAT levels were elevated pre-CPB in VS+ patients and increased further post-CPB. Pre-CPB ACh had a 99% AUC correlation with post-CPB VS+.
    CONCLUSIONS: We demonstrated increased baseline cardiovascular inflammation in VS+ patients, which predisposed them to a dysregulated response to CPB, and we identified CPB-induced activation of IL-17 skewed multi-cytokine inflammatory pathways and endothelial activation as mechanistic mediators of post-CPB VS. Circulating ACh was identified as a potential biomarker.
    DOI:  https://doi.org/10.1016/j.jtcvs.2026.06.026