bims-proteo Biomed News
on Proteostasis
Issue of 2026–06–21
38 papers selected by
Eric Chevet, INSERM



  1. FEBS J. 2026 Jun 16.
      The endoplasmic reticulum (ER) is a cellular organelle frequently subjected to stress under both physiological and pathological circumstances, associated with the accumulation of mis/unfolded proteins in its lumen. To cope with this stress, cells have evolved an adaptive program called the unfolded protein response (UPR), whose primary function is to restore ER proteostasis. When the stress is prolonged, the UPR can also trigger cell death. The UPR controls multiple machineries involved in pre-emptive quality control (QC) of proteins prior to ER entry, ribosome-associated QC, protein folding within the ER, protein degradation through various processes, and export from the ER for secretion. Because the UPR and the machineries it controls play fundamental roles in determining cell fate, they are finely regulated, including through post-translational modifications (PTMs). In this review, we focus on the role of the ubiquitin and ubiquitin-like PTMs in the regulation and mediation of ER proteostasis. We specifically focus on three core processes: the UPR, ER-associated ribosome QC and ER-associated degradation. Lastly, we briefly discuss how Ub and Ubl also control the integrated stress response and the formation of inter-organelle membrane contact sites and thus act as general regulators of responses to cellular stresses beyond ER proteotoxicity.
    Keywords:  ER stress; ERAD; ER‐ribosomal quality control; endoplasmic reticulum; integrated stress response; ubiquitin; ubiquitin‐like; unfolded protein response
    DOI:  https://doi.org/10.1111/febs.70622
  2. Nat Commun. 2026 06 16. pii: 5316. [Epub ahead of print]17(1):
      The Signal Recognition Particle (SRP) targets nascent proteins to the Sec61 translocon for import into the endoplasmic reticulum (ER). However, its range of substrates, point of engagement during targeting, and hence full biological impact remain unclear. Here, we examined SRP interactions with the nascent proteome of S. cerevisiae during translation and membrane targeting. SRP binds effectively to transmembrane domains (TMDs) as they emerge from the ribosomal tunnel, but only to a minority of cleavable signal peptides. We identify nascent chain features that promote SRP binding, allowing to develop a predictive algorithm. We show SRP performs a role in triaging nascent ER proteins into distinct targeting routes and downstream maturation processes. Furthermore, ribosomes frequently dissociate from the membrane before completing translocation, allowing the chaperone Ssb to assist folding of emerging cytosolic domains. Ribosomes translating multipass membrane proteins are retargeted to the translocon through repeated SRP interactions with internal TMDs, emphasizing collaboration between SRP and chaperones in membrane protein biogenesis.
    DOI:  https://doi.org/10.1038/s41467-026-74404-2
  3. Protein Sci. 2026 Jul;35(7): e70682
      Mitochondria import the majority of their proteins from the cytosol, creating a fundamental challenge: precursor proteins must be synthesized, maintained in an import-competent state, and delivered to mitochondrial translocases without premature folding or aggregation. While mitochondrial protein import has been considered a post-translational process, growing evidence shows that a subset of mitochondrial proteins is synthesized in proximity to the organelle. We term this process co-translational targeting, or local translation. It may lead to direct structural coupling of protein synthesis and import, which we term co-translational translocation. New approaches, including selective ribosome profiling, proximity labeling, and RNA imaging, reveal that mitochondrial mRNA localization is highly dynamic and can be driven by both RNA-based and translation-dependent mechanisms. In contrast to the well-defined signal recognition particle pathway at the endoplasmic reticulum, mitochondrial targeting appears to rely on more flexible mechanisms shaped by nascent-chain properties, translation elongation, and coding-sequence features beyond the targeting signal. We discuss how these processes may support mitochondrial biogenesis and proteostasis while also creating vulnerabilities associated with ribosome stalling and precursor quality control. Together, recent findings position mitochondrial protein targeting as an integral part of cellular protein biogenesis and highlight key open questions in the coordination of translation and organelle function.
    Keywords:  NAC; chaperones; co‐translational import; mRNA localization; mitochondria; protein targeting; translation
    DOI:  https://doi.org/10.1002/pro.70682
  4. Nat Commun. 2026 Jun 19.
      The folding of membrane protein cytoplasmic domains on the endoplasmic reticulum (ER) surface, and their coordination with transmembrane and exoplasmic regions, remains poorly understood. Through a genome-wide CRISPR-Cas9 screen, we identified the ER-anchored FK506 binding protein 8 (FKBP8) as a chaperone essential for membrane protein folding and assembly. Using ABC transporters as model substrates, we show that FKBP8 cooperates with Hsp70-Hsp90 machinery to remodel nascent or misfolded cytosolic domains into their native conformations. Cryo-EM analysis reveals that FKBP8 employs a conserved hydrophobic ϕ94ϕ96ϕ97/ϕ158ϕ162 cluster to help form a large client-binding cavity within the FKBP8-Hsp90 complex that captures folding intermediates. FKBP8 deficiency, disruption of this cluster, or disease-associated mutations within FKBP8 abolish substrate maturation, leading to ER retention and degradation. Reconstitution with purified components demonstrates that FKBP8 and Hsp40-Hsp70-HOP-Hsp90 constitute a minimal machinery capable of restoring the native structure of a misfolded ABC transporter. These findings uncover a dedicated folding module at the ER-cytosol interface that bridges cytosolic chaperones with membrane protein quality control, suggesting a broad role for FKBP8 in safeguarding the biogenesis of complex membrane proteins.
    DOI:  https://doi.org/10.1038/s41467-026-74519-6
  5. Nat Commun. 2026 Jun 19.
      The unfolded protein response (UPR) is a critical adaptive program triggered upon cellular stresses that profoundly reshapes the transcriptome and translatome. In the very first minutes of cellular stress, translation blockage, RNA decay and RNA granules formation prompt the synthesis of proteins essential to the stress response. Due to the dynamic nature of these processes, investigating translation upon stress has proven to be challenging; therefore, our understanding of these mechanisms and translatome rewiring upon stress remains limited. Here, we exploit O-Propargyl-puromycin (OPP) labelling of de novo peptides followed by LC-MS/MS to identify de novo proteins translated upon endoplasmic reticulum (ER) stress. Combined with transcriptomic analyses, our approach reveals that ER stress profoundly impacts the synthesis of core splicing factor proteins leading to a significant reshaping of the splicing landscape. We identify a signature of seven splicing events consistently occurring in mammalian cells exposed to ER stress. Using pharmacological, genetic, phosphoproteomic and sequencing approaches, we demonstrate that this specific signature is driven by PERK activation and is dependent on the axis CLK1/SRSF1. Our findings identify PERK/CLK1/SRSF1 -mediated splicing regulation as a new facet of ER stress, defining an ERi-splice signature spanning healthy and malignant tissues.
    DOI:  https://doi.org/10.1038/s41467-026-74397-y
  6. Proc Natl Acad Sci U S A. 2026 Jun 23. 123(25): e2602559123
      Two key enzymes, HMG CoA reductase (HMGCR) and squalene monooxygenase (SM), are subjected to distinct endoplasmic reticulum-associated degradation (ERAD) pathways to maintain cholesterol homeostasis. HMGCR catalyzes conversion of HMG CoA to mevalonate, the first rate-limiting step in cholesterol synthesis. Sterols accelerate ERAD of HMGCR by promoting its binding to Insig proteins, which recruit E3 ubiquitin ligases for ubiquitination and degradation. Downstream, SM catalyzes oxygenation of squalene, committing intermediates to sterol synthesis. Cholesterol stimulates ERAD of SM, but through an Insig-independent mechanism mediated by the E3 ligase MARCH6. Here, we report a mechanism of posttranslational regulation involving a stable complex between HMGCR and SM in sterol-deprived cells. The two enzymes physically interact within ER membranes in an Insig-independent manner, and this interaction protects both proteins from ERAD. Loss of either enzyme destabilizes the other, indicating a costabilization mechanism. These findings uncover a layer of coordination in cholesterol synthesis, suggesting HMGCR and SM function as an integrated complex to ensure synchronization of early and late steps of the pathway.
    Keywords:  ER-associated degradation; cholesterol; isoprenoids; sterols; ubiquitination
    DOI:  https://doi.org/10.1073/pnas.2602559123
  7. Aging Cell. 2026 Jun;25(6): e70587
      Reducing protein synthesis extends lifespan across taxa, but pharmacological strategies to safely attenuate translation remain limited. Tetracyclines are clinically used antibiotics long observed to exert beneficial effects in age-associated diseases and extend lifespan in model organisms, though the underlying mechanisms remain unclear. Here, we systematically profiled commercially available tetracyclines and show that translation attenuation is a general property of the tetracycline class. Importantly, we identify the atypical tetracyclines 4-epiminocycline and 12-aminominocycline, which attenuate translation independently of antibiotic activity and integrated stress response (ISR) activation. These compounds extend lifespan in C. elegans, attenuate translation in human induced neurons, reduce hippocampal protein synthesis in vivo, and protect neurons from ferroptotic stress. Together, our results demonstrate that pharmacological attenuation of translation is sufficient to promote longevity and establish translation attenuation as a druggable longevity mechanism in mammals.
    Keywords:  aging; ferroptosis; integrated stress response; longevity; neuroprotection; proteostasis; tetracyclines; translation inhibition
    DOI:  https://doi.org/10.1111/acel.70587
  8. FEBS J. 2026 Jun 19.
      Insoluble protein aggregates are a hallmark of neurodegenerative diseases like amyotrophic lateral sclerosis (ALS). The ubiquitin-proteasome system (UPS) serves as a neuroprotective quality control mechanism that clears aggregates. PML nuclear bodies (NBs) were proposed to serve as hubs for SUMO-primed ubiquitylation and degradation of misfolded proteins. Georgiadou et al. provide evidence that an ALS-linked NEK1 truncation mutant is recruited to PML NBs, where it likely undergoes SUMOylation and ubiquitylation. In mice, PML loss exacerbates ALS-like symptoms, while induced PML expression delays disease onset. These findings establish PML as a key regulator of proteostasis and highlight PML induction as a potential therapeutic strategy for ALS and related proteinopathies.
    Keywords:  ALS; NEK1; PML; SUMO; SUMO‐targeted ubiquitylation; ubiquitin
    DOI:  https://doi.org/10.1111/febs.70630
  9. Mol Cell. 2026 Jun 19. pii: S1097-2765(26)00385-0. [Epub ahead of print]
      Adaptation to fluctuating nutrient supply is essential for organismal survival, but how human cells monitor the abundance of many critical nutrients remains undefined. Characterizing the conditional degradation of CDO1, the critical enzyme responsible for cysteine catabolism, here we identify a Cullin-RING E3 ligase complex defined by the substrate adaptor LRRC58 that is sensitive to cysteine abundance. When cysteine is replete, LRRC58 activity is restrained through ubiquitination and proteasomal degradation. Upon cysteine deprivation, LRRC58 is stabilized to permit CDO1 degradation. Through saturation mutagenesis stability profiling, we systematically validate a structural model of the CDO1-LRRC58 interaction and identify residues at the LRRC58 C terminus required for cysteine-dependent instability. CDO1 degradation prevents ferroptotic cell death upon cysteine scarcity, and CDO1 mutations causing neurodevelopmental defects in humans encode dominant-active proteins refractory to LRRC58 recognition. Altogether, these data reveal the CDO1-LRRC58 axis as a critical regulator of cysteine homeostasis that safeguards neural development.
    Keywords:  CDO1; Cullin-RING E3 ligase; LRRC58; amino acid sensing; conditional protein degradation; cysteine; cysteine catabolism; ferroptosis; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.014
  10. FEBS J. 2026 Jun 16.
      Gene variants leading to insertions or deletions of amino acid residues (indels) often have detrimental consequences for the folding of the encoded protein. Yet, at some positions, indels are tolerated or result merely in partial unfolding and hypomorphic (reduced function) phenotypes. Typically, unfolded proteins are targeted for protein quality control (PQC) degradation via the ubiquitin-proteasome system, which in yeast is mediated by specific E3 ubiquitin-protein ligases, including Ubr1 and San1. Here, we systematically probed the folding of a library of indel variants in the DHFR protein using a sensitive yeast-based protein folding reporter. We show that deletion of Ubr1 or San1 leads to a greater fraction of folded DHFR indel variants, primarily positioned toward the N- and C-terminal regions in DHFR. Intriguingly, most of the DHFR indels that are structurally stabilized in the E3 knockout strains are also stabilized at lowered temperatures and upon binding the DHFR inhibitor methotrexate. This suggests that blocking PQC degradation can restore sufficient folding and increase function of hypomorph variants, thus providing a potential therapeutic avenue for protein misfolding diseases.
    Keywords:  E3; PQC, UPS; chaperone; folding; gene variants; misfolding; proteasome; protein stability; proteostasis; ubiquitin; yeast
    DOI:  https://doi.org/10.1111/febs.70625
  11. EMBO Rep. 2026 Jun 15.
      Stress granules (SGs) are transient cytoplasmic biomolecular condensates that play a role in the cellular response to proteotoxic stress. It has been previously shown that ubiquitination regulates SG dynamics; however, the specific mechanisms by which ubiquitin affects SGs are not fully understood. Here, using proximity proteomics, we discover that the recruitment of several E3 ubiquitin ligases, VCP cofactors and HSP70 to SGs is dependent on the activity of the E1 ubiquitin ligase UBA1. The RNA-binding E3 ubiquitin-protein ligase Makorin 2 (MKRN2) is strongly depleted from SGs in the absence of UBA1 function. MKRN2 promotes both the proper formation of SGs and their disassembly following stress recovery, by preventing the accumulation of misfolding-prone defective ribosomal products (DRiPs) within SGs. Therefore, MKRN2 is a novel regulator of SGs that mediates the maintenance of granulostasis.
    DOI:  https://doi.org/10.1038/s44319-026-00832-2
  12. Nat Struct Mol Biol. 2026 Jun;33(6): 962-972
      The ribosome biases the conformations sampled by nascent polypeptide chains along folding pathways toward biologically active states. A hallmark of the cotranslational folding (coTF) of many proteins constitutes highly stable folding intermediates that are absent or only transiently populated off the ribosome, yet persist during translation well beyond complete emergence of the domain from the ribosome exit tunnel. Despite the importance of intermediates for folding fidelity, their structures have remained elusive and cannot be predicted by machine learning methods. Here we obtained structures of two folding intermediates of an immunoglobulin-like domain on the ribosome by developing comprehensive 19F nuclear magnetic resonance analyses using chemical shifts by rational design, paramagnetic relaxation enhancement and protein engineering, integrated with extensive molecular dynamics simulations. The resulting intermediate structures reveal native-like folded cores distinguished by nonnative termini, permitting distinct binding to a molecular chaperone and suggesting parallel folding pathways. The structures of these intermediates are conserved within the protein domain family, in contrast to their in vitro refolding mechanisms. Our detailed structural ensembles of partially folded nascent proteins on the ribosome highlight the diversity of conformations sampled during coTF, providing the ribosome with a passive means to promote efficient protein folding and maintain cellular proteostasis.
    DOI:  https://doi.org/10.1038/s41594-026-01814-7
  13. RNA. 2026 Jun 18. pii: rna.080953.126. [Epub ahead of print]
      The Not proteins of the Ccr4-Not complex regulate translation elongation dynamics, essential for proper folding and assembly of new proteins. In yeast, ribosomes with non-optimal codons in the A-site are enriched within the pool of ribosomes bound by Not4 and Not5. Such ribosomes accumulate in cells lacking Not4 or Not5 that show defects in co-translational assembly and aggregation of new proteins. Recently we observed that depletion of Not1 and Not4 inversely regulate changes in mRNA solubility, correlating with inverse codon-specific changes in A-site ribosome dwelling occupancies (RDOs). Here we describe that mRNAs less soluble upon Not4 depletion are enriched for targets of the RNA-binding protein Puf3. We determine that Puf3 contributes to differential changes of A-site RDOs upon Not1 and Not4 depletion, in particular at rare arginine codons, and it contributes to changes in mRNA solubility in not4Δ Moreover, deletion of Puf3 suppresses temperature sensitivity and protein aggregation in the not4Δ strain, while overexpression of Puf3 is toxic. Interestingly the Puf3 interactome is altered in not4Δ. Taken together, our results associate alterations in Puf3 to not4 mutant phenotypes, in particular to changes in translation elongation dynamics and protein aggregation.
    Keywords:  Not4 and Puf3; Ribosome dwelling and translation elongation; mRNA solubility; protein homeostasis; rare arginine codons
    DOI:  https://doi.org/10.1261/rna.080953.126
  14. Proc Natl Acad Sci U S A. 2026 Jun 23. 123(25): e2610619123
      Protein-protein interactions (PPIs) underpin biological function, yet proteome-scale interaction prediction remains bottlenecked by the quadratic computational complexity of all-vs.-all pairwise comparisons. Here, we present FlashPPI, a contrastive learning framework, grounded in residue-level interactions, that enables linear-time prediction of physical protein interfaces across a microbial proteome. By leveraging a genomic language model that captures cross-protein coevolutionary signals from metagenomic sequences, FlashPPI aligns interacting partners in a shared latent space. We demonstrate a four-fold performance increase over existing sequence-based methods, while reducing proteome-wide screening time from days to minutes. Crucially, FlashPPI achieves comparable screening performance to state-of-the-art structure-folding models at a fraction of the computational cost. Finally, we integrate FlashPPI into an interactive web platform that combines predicted networks with functional annotations and genomic context, making proteome-wide network analysis rapid and accessible for microbial discovery.
    Keywords:  machine learning; microbial genomics; protein–protein interactions
    DOI:  https://doi.org/10.1073/pnas.2610619123
  15. Autophagy. 2026 Jul;22(7): 1441-1443
      The endoplasmic reticulum (ER) is a hub for several essential functions, including lipid metabolism, macroautophagy/autophagy, and innate immune signaling. Excess ER generated during a stress response is degraded by a selective type of autophagy known as ERphagy/reticulophagy. A recent study provides a mechanism by which cholesterol levels regulate ERphagy, STING1 activation, and cholesterol biosynthesis. Elevated ER cholesterol levels suppress ERphagy by reducing RETREG1/FAM134B interactions with the autophagy-related protein MAP1LC3/LC3 and the lysosomal protein LAMP2. The study shows that cholesterol directly binds to RETREG1 and SCAP, facilitating the formation of the RETREG1-SCAP complex. Sequestration of RETREG1 in this manner prevents it from performing its ERphagy functions. Furthermore, RETREG1 also interacts with STING1 and is important for its activation in response to viral infections. SCAP-RETREG1 complex formation also reduces the STING1 response. Thus, this study links lipid metabolism, innate immunity, and autophagy, emphasizing a central role for cholesterol in these processes.
    Keywords:  Autophagy; ER-phagy; FAM134B/RETREG1; SCAP; STING; cholesterol
    DOI:  https://doi.org/10.1080/15548627.2026.2639645
  16. FEBS J. 2026 Jun 15.
      IRE1α (hereafter referred to as IRE1) is one of the sensors implicated in the unfolded protein response that controls the ER protein homeostasis (also known as proteostasis). Alteration of proteostasis is observed in many diseases, making IRE1 a central element of cell adaptability upon disease onset and progression. Upon ER stress, IRE1 initially promotes cell adaptation. Conversely, when proteostasis cannot be restored, IRE1 activation can lead to cell death. IRE1 activity mainly regulates two pathways: the formation of the transcription factor XBP1s; and the regulated IRE1-dependent decay (RIDD) of RNA, which can contribute to both cell adaptation and death. Hence, on one hand, IRE1 favors gene expression, while on the other hand it induces transcript degradation. We have recently identified two genes, CD95 and UBE2D3, which are targeted by both signaling branches downstream of IRE1 RNase's activity, resulting in a dual and opposing regulation of their expression. We propose naming these targets 'DIT' for Dual IRE1 Targets. Interestingly, other IRE1 targets, such as BiP and DGAT2, have previously been reported to be regulated by XBP1s and RIDD in separate studies. We hypothesize that regulation of DIT could be crucial to tilt the balance between the pro-adaptative and pro-death outcomes of IRE1, especially in pathological contexts. Therefore, understanding this regulation could be key to unraveling the IRE1/XBP1s/RIDD signaling network. Here, we explore these hypotheses by highlighting various aspects of the regulation of IRE1 branches, and reviewing the DIT identified in the literature so far.
    Keywords:  CD95; ER stress; IRE1; RIDD; UBE2D3; XBP1s; cancer; dual IRE1 target; proteostasis
    DOI:  https://doi.org/10.1111/febs.70624
  17. iScience. 2026 Jun 19. 29(6): 116290
      The unfolded protein response (UPR) maintains cellular homeostasis during ER stress. In this process, activating transcription factor 6α (ATF6α) is activated through several multi-step processes, including transport to the Golgi apparatus, and plays an important role as a UPR sensor. Disulfide bond-mediated dimerization of ATF6α contributes to efficient transport to the Golgi apparatus. However, this regulatory mechanism remains unclear. Here, we show that ER-resident oxidoreductases, including ERdj5 and PDIR, promote C467 dimerization, whereas ERp18 inhibits this process. In particular, ERdj5 facilitates C467 dimerization via Trx2 and reduces C618 dimerization via Trx3, supporting ATF6α activation. Furthermore, ATF6α dimerization stabilizes its structure and prevents its degradation by ER-associated degradation (ERAD). Our findings reveal that multiple oxidoreductases participate in the regulation of ATF6α activation during ER stress.
    Keywords:  molecular interaction; molecular network; protein
    DOI:  https://doi.org/10.1016/j.isci.2026.116290
  18. Autophagy. 2026 Jun 18. 1-3
      Optineurin (OPTN) is widely recognized as a multifunctional selective autophagy receptor involved in cargo turnover. However, our recent findings uncover an unexpected function of OPTN that challenges the conventional view of autophagy adaptors. In dendritic cells (DCs), OPTN binds to and stabilizes Rictor, a key component of the mTORC2 complex. Loss of OPTN leads to depletion of Rictor, reduced Akt2 activity, and activation of the mTORC1/p70S6K1 pathway, culminating in enhanced phosphorylation of STAT3 at Ser727. Activated STAT3 transcriptionally induces the E3 ubiquitin ligase MARCH1, which promotes MHC II internalization, resulting in a striking inverse relationship between MARCH1 and MHC II expression in Optn-deficient cells. Together, these findings identify an unexpected signaling function of OPTN, independent of its canonical autophagy activities. By stabilizing Rictor and maintaining mTORC2-Akt2 signaling, OPTN links a classical autophagy adaptor to the regulation of antigen presentation and adaptive immunity. More broadly, our findings raise the possibility that selective autophagy receptors preserve cellular homeostasis not only through cargo clearance but also through context-dependent, non-degradative regulation of protein stability and signaling networks.Abbreviation: OPTN: Optineurin; mTORC1: mammalian target of rapamycin complex 1; mTORC2: mammalian target of rapamycin complex 1; Rictor: Rapamycin-Insensitive Companion of mTOR.
    Keywords:  Antigen presentation; MHC II; mTOR signaling; optineurin; protein stabilization
    DOI:  https://doi.org/10.1080/15548627.2026.2689040
  19. Infect Immun. 2026 Jun 15. e0017826
      Many intracellular pathogens stimulate host cell stress by directly or indirectly causing an imbalance in host nutrients. Depletion of amino acid pools, in particular, can act as a danger signal to infected cells. Using a restrictive host model of Salmonella enterica serovar Typhi (S. Typhi) infection, we identify early induction of the integrated stress response (ISR) by viable bacteria, but not by heat-killed bacteria. Genetic deletion of the amino acid-sensing ISR kinase GCN2 (also known as EIF2AK4) prevented early ISR activation during S. Typhi infection and murine macrophages lacking GCN2 show impaired bacterial clearance and decreased cytokine output. Supplementation of wild-type C57BL/6 murine macrophages with only the non-essential amino acid asparagine was sufficient to suppress S. Typhi-induced ISR activation, and deletion of S. Typhi ansB, encoding an asparaginase, prevented ISR activation during infection. Pharmacological inhibition of mammalian target of rapamycin (mTOR), the other major amino acid-sensing pathway in eukaryotic cells, prevented GCN2 activation and ISR induction in murine macrophages, indicating an upstream role for mTOR in signaling to GCN2. These findings suggest a role for the ISR in macrophage innate immune responses to S. Typhi infection and highlight a potential difference in nutrient-dependent signaling between the S. Typhi-susceptible human host and the restrictive murine host centered around asparagine, mTOR, and GCN2.
    Keywords:  gram-negative bacteria; innate immunity; nutritional immunity
    DOI:  https://doi.org/10.1128/iai.00178-26
  20. Nat Cell Biol. 2026 Jun 15.
      Tumour progression towards dedifferentiated cell clusters plays a critical role in intratumour heterogeneity and therapy resistance. While tumour microenvironmental stress has been implicated, the underlying mechanisms remain poorly defined. Using mouse models of lung adenocarcinoma, we demonstrate that activation of the integrated stress response (ISR)-marked by phosphorylation of eIF2 (p-eIF2) and ATF4 induction-drives tumour heterogeneity. ISR activation facilitates the emergence of high-plasticity, undifferentiated and pre-epithelial-to-mesenchymal transition clusters characterized by elevated ATF4 and MYC activity. This process is MYC dependent and involves ISR-mediated repression of NKX2-1, a key determinant of alveolar identity, and induction of CHCHD10, a regulator of mitochondrial integrity and metabolic fitness. Disruption of the p-eIF2-ATF4 axis induces mitochondrial dysfunction, limits dedifferentiation and suppresses tumour growth. In human lung adenocarcinoma, ISR-driven dedifferentiation correlates with advanced disease and poor prognosis, identifying the ISR as a central driver of lineage reprogramming and metabolic fitness in tumour progression.
    DOI:  https://doi.org/10.1038/s41556-026-01991-z
  21. Cell Metab. 2026 Jun 16. pii: S1550-4131(26)00221-4. [Epub ahead of print]
      Fibroblast growth factor 21 (FGF21) is an endocrine hormone with broad metabolic actions at supraphysiological concentrations but unclear physiological function, related to endoplasmic reticulum (ER) stress. ER stress activates the unfolded protein response (UPR), a cellular repair mechanism that maintains cellular homeostasis during protein folding stress. Using proximity labeling, we assessed the intracellular action of FGF21 at its receptor β-klotho (KLB) and discovered associations with protein folding in the ER, ER stress, and H2S production. We found that FGF21 increases enzymatic sulfide production and enhances, but does not initiate, the UPR. This FGF21 action is blunted by genetic or pharmacological inhibition of sulfide signaling and is phenocopied by an H2S donor in vivo. FGF21 modulating the UPR requires KLB, and even physiological levels of FGF21 modulate the UPR via increased hepatic H2S production. Collectively, we reveal a novel physiological role of FGF21 as an endocrine stress hormone that enhances the UPR via increased sulfide signaling.
    Keywords:  ER stress; FGF21; H(2)S; ISR, β-klotho, KLB; UPR; integrated stress response; sulfide signaling; unfolded protein response
    DOI:  https://doi.org/10.1016/j.cmet.2026.05.011
  22. J Cell Sci. 2026 Jun 17. pii: jcs.264610. [Epub ahead of print]
      The pathogenic yeast Candida albicans relies on morphogenesis-the transition from spherical yeast to filamentous hyphal forms-for infection. While morphogenesis requires Ire1, a transmembrane protein that canonically initiates the Unfolded Protein Response (UPR) through HAC1 mRNA splicing, the specific mechanisms linking Ire1 to filamentation remain unclear. Using transcriptome analysis, we found that the Ire1-dependent transcriptional response driving morphogenesis is fundamentally distinct from the canonical UPR response to proteotoxic stress, with minimal overlap between programs. Morphogenesis is associated with only limited HAC1 splicing compared to robust splicing during proteotoxic stress, and HAC1 deletion only partially impairs filamentation, unlike the near-complete loss observed with IRE1 deletion. These findings establish that Ire1 regulates hyphal development through previously uncharacterized HAC1-independent pathways. We identify cell wall integrity as a key HAC1-independent mechanism, with Ire1-but not Hac1-essential for cell wall stress tolerance and upregulation of cell wall biosynthesis genes during filamentation. Our data also reveal Ire1-dependent decreases in transcripts encoding secretory proteins during both proteotoxic stress and morphogenesis, consistent with a possible role for Ire1-mediated mRNA degradation in these processes. Given Ire1's essential role in pathogenesis and extensive development of Ire1-targeting compounds for mammalian systems, our findings position Ire1 as a highly promising druggable target for novel antifungal therapeutics and development of fungal-specific inhibitors.
    Keywords:  Candida albicans; Endoplasmic reticulum; Morphogenesis; UPR
    DOI:  https://doi.org/10.1242/jcs.264610
  23. RNA. 2026 Jun 15. pii: rna.081011.126. [Epub ahead of print]
      Processing bodies (P-bodies) are cytoplasmic granules that regulate mRNA storage, repression, and decay, yet how their internal organization supports selective mRNA regulation remains poorly understood. Here, we show that the conserved LSm protein Trailer Hitch (Tral) is a key organizer of P-body architecture and function in Drosophila melanogaster nurse cells. Using quantitative confocal imaging, super-resolution microscopy, and chemical perturbation of intermolecular interactions, we demonstrate that Tral coordinates the incorporation and spatial organization of the core P-body proteins Me31B and Cup. Loss of Tral alters their partitioning into P-bodies, promotes demixing into distinct subdomains, and shifts condensates toward a less dynamic, structurally heterogeneous state. These organizational changes have functional consequences for mRNA storage: Tral depletion selectively releases maternal mRNA bicoid, while nanos mRNA remains P-body associated and stable. We further identify twinstar mRNA, encoding the actin regulator Cofilin, as a Tral-dependent P-body client whose localization and organization within P-bodies requires Tral:RNA interactions and electrostatic forces. Reduced twinstar mRNA levels in the absence of Tral are associated with decreased nuclear G-actin and altered transcription of me31B and cup, revealing a potential feedback mechanism that links cytoplasmic P-body organization to nuclear gene expression. Together, these findings establish Tral as a central regulator of P-body architecture that couples condensate organization to selective mRNA regulation and transcriptional homeostasis in D. melanogaster nurse cells.
    Keywords:  Drosophila melanogaster; Nuclear Actin; P-bodies; RNA; oogenesis
    DOI:  https://doi.org/10.1261/rna.081011.126
  24. Dev Cell. 2026 Jun 16. pii: S1534-5807(26)00195-4. [Epub ahead of print]
      Δ1-Pyrroline-5-carboxylate synthase (P5CS), therate-limiting enzyme in the proline biosynthesis, has been implicated in diverse physiology and pathology, including cancer. However, whether P5CS exerts functions beyond its enzymatic activity has remained unclear. Here, we identify P5CS as a non-canonical RNA-binding protein that inhibits cancer cell growth and metastasis by inhibiting translation initiation in an enzyme-activity-independent manner in human cancer cells and cell-derived xenograft mouse models. Mechanistically, P5CS binds to the 5' untranslated region (UTR) of oncogenic mRNAs and disrupts the recruitment of eukaryotic translation initiation factor (eIF) 3a/3d-containing 43S preinitiation complex to cap-binding complex eIF4F, thereby blocking 48S assembly and subsequent global protein synthesis. Loss of P5CS accelerates the translational efficiency of IGF1R and promotes tumor progression. Collectively, our study highlights a non-canonical function of P5CS in translational regulation and the emerging non-metabolic functions of metabolic enzymes in tumorigenesis.
    Keywords:  43/48S; P5CS; RNA-binding protein; eIF3a/3d; translation regulation
    DOI:  https://doi.org/10.1016/j.devcel.2026.05.011
  25. Nat Commun. 2026 Jun 19.
      The type I Interferon (IFN-I)-induced ubiquitin-like modifier Interferon-Stimulated Gene 15 (ISG15) plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade, called ISGylation. While ubiquitin-specific protease 18 (USP18) serves as the major deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Here, we identify USP24 as an ISG15 cross-reactive DUB through activity-based protein profiling. USP24 processes pro-ISG15 and ISG15-linked substrates in vitro, and its depletion increases ISG15 conjugates following interferon stimulation in cells without altering canonical IFN-I signaling. USP24 knockout cells show increased IFN-β and ISG expression upon activation of cytosolic RNA sensing via viral mimicry. Proteomic analysis identifies RNA helicase Moloney leukemia virus 10 (MOV10) as a specific target of USP24 for deISGylation. Our data revealed that ISGylation of MOV10 promotes MOV10 interaction with IFIT3 and enhances IFN-β production/secretion in response to viral stimuli. This process is negatively regulated by USP24, which directly deISGylates MOV10. Our data highlight USP24's role in modulating ISGylation and IFN-I production, suggesting USP24 as a potential therapeutic agent for infectious and inflammatory diseases.
    DOI:  https://doi.org/10.1038/s41467-026-74490-2
  26. J Med Chem. 2026 Jun 17.
      Proteolysis-targeting chimeras (PROTACs) have emerged as a novel drug modality, but their development currently relies on a limited number of E3 ligase ligands, primarily targeting CRBN and VHL. Conversely, current validation studies on novel E3 ligase ligands are typically limited to a few highly degradable targets, like BRD4. Here, we used our previously established workflow for E3 ligase ligand validation, employing promiscuous kinase PROTACs, to evaluate the potential of recruiting DCAF1 for PROTAC development. Our study revealed the DCAF1-dependent degradation of a diverse set of kinases, which were validated in orthogonal assays. In a comparative analysis, we identified a significant overlap between the degradable kinome of DCAF1- versus CRBN-recruiting PROTACs, suggesting alternative design strategies for PROTACs using available structurally diverse DCAF1 ligands. Moreover, ubiquitinomics analysis of the PROTAC-induced ubiquitination patterns provided insight into substrate- and isoform-selective degradation. The presented data will establish DCAF1-recruiting PROTACs as a versatile design strategy for future degrader development.
    DOI:  https://doi.org/10.1021/acs.jmedchem.6c00383
  27. J Clin Invest. 2026 Jun 16. pii: e196687. [Epub ahead of print]
      Most mitochondrial proteins are nuclear encoded, translated in the cytosol, and imported into the mitochondria. Through gene expression analysis and functional assays, we demonstrated that mitochondrial protein import is increased in acute myeloid leukemia (AML) cells compared to normal hematopoietic cells. Increased mitochondrial protein import was positively correlated with increased mitochondrial unfolded protein response (UPRmt), a stress activated pathway of mitochondrial proteases and chaperones that maintains protein solubility and prevents the formation of toxic aggregates. The UPRmt protease LONP1 (Lon Peptidase 1) was upregulated in AML and positively correlated with increased mitochondrial protein import and UPRmt. Genetically or chemically inhibiting the LONP1 ATPase domain induced mitochondrial protein aggregation and selectively killed AML cells with high LONP1 expression while sparing AML cells with low LONP1 expression and normal hematopoietic cells in vitro and in vivo. Thus, we uncovered a critical role of the UPRmt protease LONP1 in buffering stress from mitochondrial protein import in AML.
    Keywords:  Cancer; Cell biology; Metabolism; Oncology
    DOI:  https://doi.org/10.1172/JCI196687
  28. Nat Commun. 2026 Jun 15.
      Posttranslational modifications with ubiquitin-like modifiers (UBLs) are critical for genome maintenance, yet many remain mechanistically uncharacterised. Here, we identify UFM1 as a key regulator of non-homologous end-joining (NHEJ), a major DNA double-strand break repair pathway. Using a structure-guided chemical biology approach, we develop a photo-crosslinkable UFM1 probe and, in combination with NMR, map non-canonical UFM1-binding interfaces in core NHEJ factors, including the disordered XRCC4 tail. Mechanistically, proximity-dependent proteomics and functional assays identify Ku70 as a crucial UFMylation substrate and reveal a UFM1-dependent axis in which XRCC4 engages UFMylated Ku70 to stabilise NHEJ complex assembly on chromatin. Disruption of this molecular mechanism via UFSP2 depletion or a hypomorphic UBA5 variant in patient-derived cells impairs NHEJ function, linking UFMylation defects to compromised genome integrity processes. Our findings define a complete UFM1 signalling module in DNA repair and establish a generalisable framework for dissecting low-affinity UBL networks with broad functional and disease relevance.
    DOI:  https://doi.org/10.1038/s41467-026-73882-8
  29. Mol Cell Proteomics. 2026 Jun 16. pii: S1535-9476(26)00098-8. [Epub ahead of print] 101602
      USP7 is a pleiotropic deubiquitylating enzyme that is involved in tumor suppression, (neuro)development, chromatin regulation and the DNA damage response. How USP7 regulates these diverse pathways is still unclear. Here, we report data-independent acquisition and label free quantitation mass spectrometry (DIA-LFQ-MS) to profile the proteome-wide impact of USP7 on substrate de-ubiquitylation and overall protein abundance. First, we identified proteins associated with endogenous USP7 by immunopurification followed by DIA-LFQ-MS. Integration of our new results with earlier interactomes of epitope-tagged USP7 yielded a consensus set of high-confidence protein targets. Domain mapping analysis revealed that, in addition to the TRAF domain, the ubiquitin-like domains of USP7 play a key role in substrate selection. Using specific enrichment of tryptic K-ε-GG peptides, we mapped proteome-wide changes in ubiquitinome dynamics following inhibition of USP7. Combining unbiased proteome-wide and targeted quantitative mass spectrometry revealed that deubiquitylation by USP7 can have different effects on the stability of distinct substrates, and suggests that USP7's activity profile is substrate-dependent rather than an intrinsic enzymatic property. Thus, in addition to providing a proteome-wide map of USP7 target sites, our multi-angle proteomics approach reveals that the effects of USP7-mediated deubiquitylation on its targets are remarkably variable and substrate-specific. Finally, based on these detailed molecular insights we show how USP7 connects various neurodevelopmental syndromes and tumor suppression pathways.
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101602
  30. Nat Commun. 2026 Jun 18.
      Serine/threonine phosphoprotein phosphatases (PPPs) are conserved metalloenzymes and key regulators of intracellular signaling. Here, we systematically map the components and residues required for PP2A-like phosphatase (PP2A/PP4/PP6) function using genome-wide CRISPR knockout and focused base editing screens and provide this as a comprehensive resource. We uncover the reductase CYB5R4 as an evolutionarily conserved activator of PP4 and PP6, but not PP2A. We demonstrate that PP4 and PP6 are redox sensitive and require CYB5R4 to reduce the active site metal ions for activation. Mechanistically, this involves the selective binding of PP4 and PP6 through binding elements in the N-terminal tail of CYB5R4 and CYB5R4-bound heme serving as an electron donor for the active site. We further show that this activation is critical for regulating the response to DNA damage. Our work hints that active site metal ion redox regulation mediates crosstalk between the oxidative state of the cell and specific phosphatase activities.
    DOI:  https://doi.org/10.1038/s41467-026-74262-y
  31. J Clin Invest. 2026 06 15. pii: e207335. [Epub ahead of print]136(12):
      Cancer proteogenomics has revealed that RNA abundance often poorly predicts protein output, highlighting translation as a central determinant of malignant identity. In this issue of JCI, Mishra et al. showed that pharmacologic inhibition of eIF4E cap binding selectively rewired the prostate cancer translatome, suppressing basal keratin translation while promoting luminal features and renewed sensitivity to hormone therapy. More broadly, the study illustrates how tumors exploit selective translation to maintain lineage plasticity, survival, and therapeutic resistance. Targeting translational dependencies may therefore offer a powerful strategy to dismantle cancer-specific proteomic programs and convert resistant cell states into druggable vulnerabilities.
    DOI:  https://doi.org/10.1172/JCI207335
  32. ACS Nano. 2026 Jun 17.
      Recently, targeted protein degradation (TPD) strategies have emerged as an effective tool for addressing undruggable targets in both biomedical research and the pharmaceutical industry, selectively binding proteins of interest and targeting them to the intracellular degradation machinery for degradation. However, the targeting of extracellular proteins with current degradation tools requires a tedious, case-specific selection and design process based on lysosomal trafficking of cell surface receptors. Here, we introduce Macropinocytosis-Targeting Chimeras (MapTACs), a TPD platform that exploits macropinocytosis, a receptor-independent endocytic process, to deliver extracellular proteins to lysosomes for degradation. Using dextran as a versatile scaffold conjugated to protein-binding aptamers or antibodies, we demonstrate that MapTACs efficiently degrade monocyte chemotactic protein-1 (MCP-1) in a time-, dose-, and macropinocytosis-dependent manner. Importantly, without the need for receptor-specific modifications, MapTACs exhibit broad applicability to a variety of cell types and extracellular protein targets (MCP-1, tumor necrosis factor-α, and interferon-γ). In vivo, TNF-α-targeting MapTACs effectively and specifically reduce the levels of TNF-α in an LPS-induced acute inflammation model, attenuating lung injury, with a half-life of approximately 0.72 h and predominant accumulation in the liver and lung, where F4/80-positive monocytes/macrophages serve as the primary uptake cells. By overcoming the limitations of the receptor-based TPD strategy, MapTAC provides a universal, cost-effective, and scalable platform for extracellular protein degradation, facilitating the development of targeted protein degradation tools and opening opportunities for therapeutic intervention in cancer, inflammation, and other diseases.
    Keywords:  MapTAC; TPD; dextran; lysosome; macropinocytosis
    DOI:  https://doi.org/10.1021/acsnano.6c07737
  33. Nat Commun. 2026 Jun 18.
      Abnormal accumulation of Poly(ADP-ribose) polymerase 1 (PARP1) promotes cancer progression, yet its stabilization mechanisms remain unclear. Here, we identify E3 ubiquitin ligase tripartite motif-containing 21 (TRIM21) as a PARP1-binding partner. PARP1 interacts directly with TRIM21 via its 662-908 domain, while the PRY-SPRY domain of TRIM21 is essential for this binding. TRIM21 facilitates PARP1 polyubiquitination at residue K654, leading to its degradation. In small cell lung cancer (SCLC), TRIM21 is significantly downregulated, and its tumor-suppressive function is partly mediated through the degradation of PARP1, supporting genomic stability. Additionally, the PI3K/AKT pathway transcriptionally suppresses TRIM21 via transcription factor STAT5A, thereby stabilizing PARP1. Importantly, combining the PI3K/AKT inhibitor PKI-587 with the PARP inhibitor BMN673 synergistically inhibits tumor growth across multiple SCLC models, including cell lines, patient-derived organoids, and xenograft models. Collectively, our findings define a "PI3K/AKT-STAT5A-TRIM21-PARP1" axis critical for SCLC progression and propose its dual inhibition as a promising therapeutic strategy.
    DOI:  https://doi.org/10.1038/s41467-026-73271-1
  34. Nat Commun. 2026 06 17. pii: 5359. [Epub ahead of print]17(1):
      Recent advances in mitochondrial network dynamic and signalling highlight mitochondria as key therapeutic targets across diverse diseases. Yet, high drug development failure rates reflect an incomplete understanding of upstream molecular regulators of mitochondrial fate. Here, we address this gap by reverse engineering of the BH3-only protein BNIP3. Structural modelling and sequence-function analyses of its N-terminus identify a critical functional domain and amino acid hotspots that directly activate BCL-2 executioner proteins, triggering mitochondrial cell death. Leveraging these insights, we develop a BNIP3 antagonist peptide (B-017) that disrupts interactions between BNIP3 and BCL-2 executioner proteins, preserving mitochondrial integrity. B-017 demonstrates target specificity, a favourable safety profile, and robust suppression of cell death signalling in human cells. In clinically relevant animal models, it reduces tissue damage in the heart, brain, and liver. Together, these findings position B-017 as a promising therapeutic candidate targeting mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s41467-026-73993-2
  35. Neoplasia. 2026 Jun 16. pii: S1476-5586(26)00059-X. [Epub ahead of print]79 101329
      Endoplasmic reticulum (ER) stress contributes to hepatocellular carcinoma (HCC) progression and promotes the development of a pro-tumorigenic microenvironment. Here, we demonstrate that selective inhibition of the ER-stress sensor PERK using AMG-PERK substantially restrains tumor development when administered during early carcinogenesis in a chemically induced HCC model. PERK inhibition reduced tumor burden, proliferation, and cell viability in vivo, and impaired the growth of HCC cells and patient-derived organoids in vitro. In parallel, AMG-PERK markedly reduced stromal activation, fibrosis, and inflammatory signaling within the tumor microenvironment. Mechanistic analyses indicated that ER-stress enhances tumor-stromal communication in part through increased secretion of the glycoprotein GP73, which can activate hepatic stellate cells via GRP78-dependent signaling. Blocking PERK or using GRP78-targeting antibodies reduced stellate cell activation and fibrogenic responses. Single-cell RNA sequencing and patient biopsies showed that PERK/EIF2AK3 and GP73/GOLM1 are upregulated in malignant hepatocytes and associated with poor clinical outcomes. Transcriptomic profiling further revealed that ER-stress drives oncogenic programs, including MYC signaling, epithelial-to-mesenchymal transition, and inflammatory pathway activation, all of which were affected by pharmacological PERK inhibition. Together, these findings identify PERK signaling as a potential driver of malignant progression and microenvironmental remodeling in HCC and establish PERK inhibition as a promising therapeutic strategy to target both tumor cells and their stromal interactions during the initial stages of hepatocarcinogenesis.
    Keywords:  Endoplasmic reticulum stress; GP73; Hepatocellular carcinoma; PERK pathway; Tumor-stromal interactions
    DOI:  https://doi.org/10.1016/j.neo.2026.101329
  36. FEBS Lett. 2026 Jun 15.
      To sustain rapid proliferation, cancer cells increase protein synthesis, intensifying reliance on protein disulfide isomerase A1 (PDIA1). It is largely unknown whether disulfide bond formation of PDIA1 substrates is driven by one or both CGHC motifs. Using active-site trapping mutants in prostate cancer cells combined with mass spectrometry, we identified 29 proteins uniquely bound to the C53GHC56 domain and 20 proteins uniquely bound to the C397GHC400 domain. Hyaluronan-mediated motility receptor (HMMR) was validated as a PDIA1 C397GHC400-specific substrate, with PDIA1 catalysing disulfide bond formation between Cys242 and Cys293. PDIA1 knockdown induced HMMR ubiquitination, blocked androgen receptor nuclear translocation, and suppressed prostate cancer cell growth, survival, and migration. These findings reveal a previously unknown role of PDIA1 in prostate cancer biology.
    Keywords:  HMMR; PDIA1; androgen receptor; prostate cancer
    DOI:  https://doi.org/10.1002/1873-3468.70377
  37. Trends Genet. 2026 Jun 15. pii: S0168-9525(26)00141-1. [Epub ahead of print]
      Protein language models compress protein sequences into high-dimensional embeddings that capture biochemical, structural, and functional constraints without explicit supervision. We highlight that these embeddings encode rich evolutionary information, enabling new geometry-based views of homology, divergence, and convergence, and calling for a synthesis between classical molecular evolution and systematic evolutionary embedding analysis.
    Keywords:  deep learning; evolutionary bioinformatics; genomics; machine learning; phylogenetics; protein language models
    DOI:  https://doi.org/10.1016/j.tig.2026.05.014
  38. Sci Data. 2026 Jun 13.
      Valosin-containing protein (VCP), a conserved AAA ATPase hexamer, participates in multiple biological processes including ERAD, ubiquitin-dependent degradation by extracting misfolded proteins for proteasomal degradation. Although its interactions with cofactors are well-characterized, and its dysregulation is implicated in multisystem proteinopathy, amyotrophic lateral sclerosis, and cancer, the tissue-specific VCP interactomes underlying its functional versatility remain elusive. Here, we generated HA-N-tagged VCP knock-in mice via CRISPR/Cas9 strategy and performed affinity purification coupled with data-independent acquisition (DIA) mass spectrometry to systematically profile VCP interactors across eight mouse tissues, yielding a high-confidence dataset. We identified 923 robust VCP-binding partners, including established interactors (UBX2B, UFD1, proteasomal subunits) and novel candidates implicated in energy metabolism (TCA cycle, oxidative phosphorylation) and protein quality control (proteasome, ERAD). Notably, we validated the interaction of VCP to two hepatic candidate proteins, DAXX and PRKAG2 (AMPK γ2 regulatory subunit), using HepG2 cells. This study establishes the first in vivo atlas of the VCP interaction network, providing mechanistic insights into its tissue-specific roles and highlighting potential therapeutic avenues for VCP-related disorders.
    DOI:  https://doi.org/10.1038/s41597-026-07626-0