Kawamoto S, Horiguchi H, Torigoe D
… +19 more, Wakita M, Ito K, Sugawara S, Zhou X, Mikawa T, Park JH, Jung BK, Okumura Y, Miyagawa H, Maruya M, Hori N, Uemura K, Sugimoto M, Matsuda M, Mochizuki N, Kondoh H, Takahashi A, Oike Y, Hara E
The discovery of the senescence-associated secretory phenotype (SASP) has reshaped our understanding of cellular senescence, shifting its role from a solely tumor-suppressive mechanism to a potential driver of chronic in...The discovery of the senescence-associated secretory phenotype (SASP) has reshaped our understanding of cellular senescence, shifting its role from a solely tumor-suppressive mechanism to a potential driver of chronic inflammation and age-related diseases. Accordingly, senolytic drugs, which selectively eliminate senescent cells, have garnered considerable interest due to promising preclinical studies. However, concerns remain regarding the reproducibility and generalizability of these findings. In this cross-laboratory study, we rigorously tested the senolytic efficacy of a GLS1 inhibitor and an anti-PD-1 antibody-agents previously reported to reduce the burden of p16-positive senescent cells and improve health outcomes in aged mice. Contrary to earlier reports, our study demonstrates that neither GLS1 inhibition nor PD-1 blockade significantly reduced p16-positive cell burden or improved aging-related health parameters. Although we do not seek to discredit prior work, our results underscore the need for rigorous design, standardized protocols, and independent validation to ensure reliable senolytics before clinical translation.
Mitochondrial DNA (mtDNA) is a powerful stimulator of the innate immune system and has been shown to trigger cytosolic DNA-sensing signaling during picornavirus infection. In this study, we observe that EV-A71 infection...Mitochondrial DNA (mtDNA) is a powerful stimulator of the innate immune system and has been shown to trigger cytosolic DNA-sensing signaling during picornavirus infection. In this study, we observe that EV-A71 infection induces mitochondrial damage and leads to the release of mtDNA into the cytoplasm, which was mediated by the viral 2B protein. Despite this release, EV-A71 effectively suppresses the cGAS-STING-mediated type I interferon (IFN-I) response. We identify the nonstructural protein 3AB as a key viral antagonist of mtDNA sensing. Mechanistically, 3AB directly binds cytosolic mtDNA and disrupts cGAS-DNA phase separation, thereby suppressing cGAS-STING-dependent antiviral signaling. The immunosuppressive function of 3AB depends on the "3B + 7" region, with mutations impairing its mtDNA binding and IFN-I suppression. Moreover, the 3AB proteins from coxsackievirus A9 (CVA9) and A16 (CVA16) also exhibit mtDNA-binding ability. This study reveals a novel immune evasion strategy by blocking mtDNA-triggered immune signaling, providing new insights into the interplay between viral infection and mitochondrial immune defense.
Defence systems against genetic mobile elements are highly adaptable, yet their long-term evolutionary stability remains unclear. To address this, we examined the conservation of Piwi-interacting RNA (piRNA)-mediated def...Defence systems against genetic mobile elements are highly adaptable, yet their long-term evolutionary stability remains unclear. To address this, we examined the conservation of Piwi-interacting RNA (piRNA)-mediated defence against envelope-carrying gypsy long terminal repeat (LTR) retrotransposons across insects beyond Drosophila. We show that Aedes aegypti (yellow fever mosquito) and Anopheles stephensi (Asian malaria mosquito), as well as Tetragonula carbonaria (stingless bees), Acheta domesticus (house cricket) and Teleogryllus oceanicus (Pacific field cricket), all produce piRNAs targeting gypsy elements in ovarian somatic cells-the same cellular niche where Drosophila mounts piRNA defence against gypsy-indicating a persistent arms race for more than 400 million years of insect evolution. Notably, in Aedes aegypti, ovarian somatic cells express the same piRNA clusters as other somatic tissues, where they are known to target RNA viruses-suggesting a shared origin of anti-viral and anti-retrotransposon defences. Furthermore, we observe lineage-specific differences in ovarian somatic piRNA biogenesis: slicing-independent phasing appears to dominate in dipterans, ping-pong amplification in bees, and slicing-dependent phasing in crickets. Together, these findings indicate that distinct piRNA pathways have independently evolved at different timepoints to silence the same class of retrotransposons in insect evolution.
The heterogeneity of dermal mesenchymal cells, including perivascular mesenchymal cells and papillary and reticular fibroblasts, plays critical roles in skin homeostasis. Herein, we present human skin equivalents (HSEs),...The heterogeneity of dermal mesenchymal cells, including perivascular mesenchymal cells and papillary and reticular fibroblasts, plays critical roles in skin homeostasis. Herein, we present human skin equivalents (HSEs), in which pericytes, papillary fibroblasts, and reticular fibroblasts are spatially organized through autonomous three-cell interactions among epidermal keratinocytes, dermal fibroblasts, and vascular endothelial cells. The replication of dermal mesenchymal cell heterogeneity enhances skin functions, including epithelialization, epidermal barrier formation, and dermal elasticity, enabling in vitro evaluation of drug efficacy. Furthermore, ascorbic acid-induced epidermal turnover and synthesis of well-aligned extracellular matrix via perivascular niche cells play crucial roles in improving skin barrier function and elasticity. Therefore, HSEs with heterogeneous dermal mesenchymal cells may improve our understanding of the mechanisms underlying skin homeostasis through cell-to-cell communication and serve as a model to animal experiments for developing precision medicine.
Organ functionality requires the precise coordination of diverse tissues during development. Halfway through Drosophila embryogenesis, two lateral epidermal sheets stretch to fuse at the dorsal midline; concomitant with...Organ functionality requires the precise coordination of diverse tissues during development. Halfway through Drosophila embryogenesis, two lateral epidermal sheets stretch to fuse at the dorsal midline; concomitant with this, the main tubes of the respiratory system also shift dorsally. Here, we demonstrate that these processes occur simultaneously and are coordinated by the adhesion of the epidermal sheets and a subset of cells of the tracheal trunks to a common extracellular matrix (ECM) that separates them. We also show that during dorsal closure, tracheal trunk cells extend protrusions towards the ECM underneath the epidermis. These protrusions are under tension, suggesting that they have a mechanical function. Additionally, perturbing adhesion between tracheal cells and the epidermis affects the development of both tissues. Altogether, our findings uncover a mechanism used for tissue coordination during development, one that is based on tissue adhesion towards a common ECM capable of transmitting mechanical forces across the embryo.
Notch signaling is an evolutionarily conserved pathway known to orchestrate neurogenesis by regulating the transition from progenitors to neurons and glia, and by directing neurite outgrowth and axon guidance in many spe...Notch signaling is an evolutionarily conserved pathway known to orchestrate neurogenesis by regulating the transition from progenitors to neurons and glia, and by directing neurite outgrowth and axon guidance in many species. Although extensively studied in vertebrates and ecdysozoans, the role of Notch in spiralians remains unexplored, limiting our understanding of its conserved functions across bilaterians. Here we focus on the segmented annelid Platynereis dumerilii, a model organism in neurobiology and regeneration, to investigate Notch signaling functions during post-embryonic developmental processes. We show that Notch pathway components are expressed in neurogenic territories during both posterior elongation and regeneration, two processes requiring sustained neurogenesis. Through chemical inhibitions of the pathway and RNA-seq profiling, we find that Notch signaling regulates neural progenitor specification, differentiation, and overall neurogenic balance in the regenerating and elongating posterior part. Disruption of Notch signaling activity leads to severe defects in pygidial and central nervous system organization. Altogether, our results support the hypothesis that Notch has multifaceted conserved functions in neurogenesis across bilaterians, shedding light on the ancestral functions of this critical pathway.
Cells decode mechanical cues to direct fate decisions through nuclear remodeling, yet nuclear adaptors to mechanical signals remain elusive. Here, we show that soft matrix suppresses myoblast differentiation and induces...Cells decode mechanical cues to direct fate decisions through nuclear remodeling, yet nuclear adaptors to mechanical signals remain elusive. Here, we show that soft matrix suppresses myoblast differentiation and induces nuclear abnormality within 30 min, accompanied by a greater than 60% reduction in lamin B1 proteins levels. Mechanistically, midnolin interacts with lamin B1 and mediates ubiquitination-independent degradation of lamin B1 on soft matrix, through the Catch domain of midnolin engaging a β-strand within lamin B1's Ig-like domain. Functionally, moderate lamin B1 expression is essential for myoblast differentiation initiation, as its depletion either by siRNA or CRISPR knockout abolishes myogenic capacity. Our findings reveal that the midnolin-proteasome axis directly converts mechanical inputs into lineage commitment by triggering lamin B1 degradation, defining a novel nuclear mechano-adaptation pathway.
Type I interferons (IFNs) play crucial roles in antiviral defence, autoinflammation and cancer immunity. The human genome encodes 17 different type I IFNs that all signal through the same receptor. Non-redundant function...Type I interferons (IFNs) play crucial roles in antiviral defence, autoinflammation and cancer immunity. The human genome encodes 17 different type I IFNs that all signal through the same receptor. Non-redundant functions have been reported for some type I IFNs. However, whether different type I IFNs induce different responses remains largely unknown. Here, we stimulate human peripheral blood mononuclear cells (PBMCs) with recombinant type I IFNs to address this question in multiple types of primary cells. We analyse signalling responses by mass cytometry and changes in gene expression by bulk and single-cell RNA sequencing. We find cell-type specific changes in the phosphorylation of STAT transcription factors and in the gene sets induced and repressed upon type I IFN exposure. We further report that the magnitude of these responses varies between different type I IFNs, while qualitatively different responses to type I IFN subtypes are not apparent. Taken together, we provide a rich resource mapping signalling responses and IFN-regulated genes in immune cells.
While both common and rare variants contribute to the genetic etiology of complex traits, whether their impacts manifest through the same effector genes and molecular mechanisms is not well understood. Here, we systemati...While both common and rare variants contribute to the genetic etiology of complex traits, whether their impacts manifest through the same effector genes and molecular mechanisms is not well understood. Here, we systematically analyze common and rare variants associated with each of 373 phenotypic traits within a large biological knowledge network of gene and protein interactions. While common and rare variants implicate few shared genes, they converge on shared molecular networks for more than 75% of traits. We demonstrate that the strength of this convergence is influenced by core factors such as trait heritability, gene selective constraint, and tissue specificity. Using neuropsychiatric traits as examples, we show that common and rare variants impact genes with shared functions across multiple levels of biological organization. These findings underscore the importance of integrating variants across the frequency spectrum and establish a foundation for network-based investigations of the genetics of diverse human diseases and phenotypes.
Abraham E, Roule T, Douglas A
… +13 more, Megill E, Pericak OM, Howe JE, Choya-Foces C, Garbincius JF, Cohen HM, Roig-Flórez P, Zubillaga M, Andrake MD, Kim S, Elrod JW, Akizu N, Estaras C
YAP1 signaling is essential for development but its specific roles in early embryogenesis remain poorly understood. To shed light on this, we analyze YAP1's role in regulating the pluripotency of the mammalian epiblast,...YAP1 signaling is essential for development but its specific roles in early embryogenesis remain poorly understood. To shed light on this, we analyze YAP1's role in regulating the pluripotency of the mammalian epiblast, using scRNAseq approaches. Conditional deletion of Yap1 in the mouse epiblast (Sox2-Cre) alters the expression of signaling genes, including Nodal, Wnt3, and Fgf8. Accordingly, Yap1 loss leads to enhanced differentiation of the epiblast toward primitive streak lineages, as evidenced by the upregulation of T/Brachyury and Eomes genes. A proximity labeling assay in human pluripotent stem cells, followed by biochemical assays and molecular modeling predictions, reveals that YAP1 cooperates with QSER1 protein to regulate lineage genes. Our analysis shows that YAP1:TEAD4 enhancers recruit QSER1 to prevent RNA Polymerase II recruitment. QSER1 depletion, similar to YAP1, increases NODAL gene expression and leads to hyperactive NODAL signaling during human embryonic stem cells differentiation. Overall, our findings define a role of YAP1 in the epiblast in vivo and uncover an interplay with QSER1 controlling the activity of developmental signaling pathways in pluripotent cells.
Hepatocellular carcinoma (HCC) is a primary liver malignancy with high rates of morbidity and mortality, yet effective treatment options remain limited. Accumulating evidence indicates that large tumour suppressor kinase...Hepatocellular carcinoma (HCC) is a primary liver malignancy with high rates of morbidity and mortality, yet effective treatment options remain limited. Accumulating evidence indicates that large tumour suppressor kinase 1 (LATS1), a core kinase in the Hippo pathway, mediates the phosphorylation of downstream YAP/TAZ, thereby suppressing HCC progression. Although LATS1 protein stability has been reported to be modulated by ubiquitination, the specific mechanism controlling LATS1 kinase activity remains unknown. Here, we identify USP25 as a deubiquitinase that regulates LATS1 activity, independent of LATS1 protein stability. We demonstrated that USP25 is overexpressed in HCC and that USP25 depletion significantly suppresses HCC cell and tumour growth. Mechanistically, USP25 catalyses the removal of K63-linked ubiquitin at K688 of LATS1, which disrupts LATS1-MOB1 complex formation and promotes YAP-mediated transcriptional activation. Furthermore, we successfully developed a cell-penetrating peptide that disrupts the USP25-LATS1 interaction, which increases p-YAP expression and synergizes with chemotherapy in xenograft and patient-derived organoid and xenograft models. Collectively, our findings reveal a mechanism through which USP25 regulates LATS1 activity and provide a potential therapeutic strategy for HCC treatment.
Cystinosis is a systemic lysosomal storage disease resulting from mutations in the CTNS gene encoding the lysosomal cystine transporter cystinosin, leading to cystine accumulation in all organs. Despite cystinosin's ubiq...Cystinosis is a systemic lysosomal storage disease resulting from mutations in the CTNS gene encoding the lysosomal cystine transporter cystinosin, leading to cystine accumulation in all organs. Despite cystinosin's ubiquitous expression, renal Fanconi syndrome (FS) is the first clinical manifestation of cystinosis, which is not prevented by cystine reduction therapy with cysteamine. Here, we report a novel interaction of cystinosin and sodium/hydrogen (Na/H) exchanger proteins in the endosomes of yeast and mammalian cells. NHE3 is a major absorptive sodium transporter at the apical membrane of proximal tubular cells (PTCs). Cystinosin is required for the correct subcellular localization and trafficking of NHE3 and for sodium uptake. Introducing CTNS successfully rescues these defects in CTNS- deficient PTCs, whereas CTNS-LKG, encoding the lysosomal and plasma membrane isoform of cystinosin, did not. NHE3 mislocalization was confirmed in Ctns mice and cystinosis patient kidney. Transplantation of wild-type hematopoietic stem and progenitor cells in Ctns mice restores NHE3 expression at the brush border membrane and improves FS-related phenotypes. This study uncovers an evolutionary conserved novel role of cystinosin in NHE3 trafficking, offering insights into FS pathogenesis and potential new therapeutic avenues.
DNA replication timing (RT) often correlates with transcription during cell fate transitions, yet notable exceptions indicate a complex relationship. Using a reductionist system in mouse embryonic stem cells, we manipula...DNA replication timing (RT) often correlates with transcription during cell fate transitions, yet notable exceptions indicate a complex relationship. Using a reductionist system in mouse embryonic stem cells, we manipulate transcriptional length and strength at a single locus upstream of the silent, late-replicating Pleiotrophin (Ptn) gene. Small reporter genes driven by two of four promoters advance RT, whereas all promoters advance RT when driving the 96-kb endogenous Ptn gene. Inducible transcription of Ptn, but not the reporter, triggers a rapid and reversible RT advance, providing a system to manipulate RT independent of differentiation. Strikingly, deletion of the Ptn promoter and enhancers abolishes transcription yet does not prevent the developmental RT switch to early replication during neural differentiation. These findings, supported by parallel genome-wide analyses during differentiation, demonstrate that transcriptional elongation can causally advance RT in a rate-dependent and context-specific manner, but that transcription is neither necessary nor sufficient for RT advancement. Our results provide a solid empirical base with which to re-evaluate decades of seemingly contradictory literature.
Men have a higher risk of developing cutaneous squamous cell carcinoma (SCC) compared with women, but models and comprehensive analyses of signaling pathways highlighting this sexual dimorphism are missing. Here, we use...Men have a higher risk of developing cutaneous squamous cell carcinoma (SCC) compared with women, but models and comprehensive analyses of signaling pathways highlighting this sexual dimorphism are missing. Here, we use a UV-induced SCC model in hairless mice recapitulating this sex difference, with enhanced SCC development in males. While UV-induced DNA damage is similar between sexes, we uncover sex-specific responses in epidermal proliferation and differentiation. Global transcriptional profiling identifies E2F transcription factors as key sex-specific markers of the proliferative response to UV. E2F1/2 and their target gene CDKN3 are selectively downregulated in female mouse and human epidermis following UV exposure, and this is mediated by estrogen receptors. CDKN3 depletion impairs SCC cell progression into S-phase and reduces tumor growth in xenograft models. Consistently, low CDKN3 expression in head and neck SCC occurs exclusively in female patients and correlates with better prognosis. We thus reveal a mechanism protecting women from carcinogen-induced cancer formation, which could lead to better sex-targeted preventive and therapeutic strategies in SCC.
Microtubules perform a variety of cellular functions, including regulation of mitotic cell division, cilia formation, and neurite extension. Post-translational modifications controlled by the TTLL-family of enzymes confe...Microtubules perform a variety of cellular functions, including regulation of mitotic cell division, cilia formation, and neurite extension. Post-translational modifications controlled by the TTLL-family of enzymes confer a host of properties that affect microtubule dynamics and function. Specifically, polyglutamylation of tubulin C-terminal tails plays an important role in regulating microtubule dynamics and function within specific cellular contexts. In this study, we examined contributions from and potential regulators of polyglutamylation during mitosis, focusing on the microtubule remodeling that occurs in telophase once the mitotic spindle has completed chromosome separation. We demonstrate that the anaphase-to-telophase transition is accompanied by an increase in short-chain polyglutamylation of central spindle microtubules. We also show that TTLL1 and TPGS1, subunits of the tubulin polyglutamylation complex, are targeted to the intracellular bridge and midbody during cell progression through telophase. Finally, we demonstrate that loss of TPGS1 leads to defects in remodeling of the central spindle during telophase and impacts the cell's ability to complete mitotic cell division.
N-Methyladenosine (mA) is the most abundant internal modification of eukaryotic mRNAs and regulates target transcripts throughout the mRNA life cycle. Although changes in mA have been reported in human cancers, technical...N-Methyladenosine (mA) is the most abundant internal modification of eukaryotic mRNAs and regulates target transcripts throughout the mRNA life cycle. Although changes in mA have been reported in human cancers, technical limitations have hindered a comprehensive understanding of the cancer-associated mA landscape. Here, we use GLORI-sequencing to establish the first transcriptome-wide, single-nucleotide resolution maps of mA in bladder cancer. Comparing bladder cancer and healthy bladder samples, we discover two key mA signatures: a global dilution of methylation and a focal hypermethylation at 3'-UTRs. The global methylation dilution results from an increased expression of unmethylated transcripts and a decreased expression of methylated transcripts. In contrast, focal 3'-UTR hypermethylation is associated with the overexpression of VIRMA, a component of the mA writer complex. A functional role of VIRMA is confirmed in knockdown experiments that reveal reduced 3'-UTR methylation and oncogenic phenotypes of bladder cancer cells. Our study is the first to describe the mA epitranscriptomic landscape of cancer at single-base resolution and provides first insights into the processes that generate its characteristic signatures.
SETD2 is a methyltransferase responsible for depositing histone H3 lysine 36 trimethylation (H3K36me3). Loss of its enzymatic activity occurs in some cancers, including renal cell carcinoma. SETD2 mutations have been lin...SETD2 is a methyltransferase responsible for depositing histone H3 lysine 36 trimethylation (H3K36me3). Loss of its enzymatic activity occurs in some cancers, including renal cell carcinoma. SETD2 mutations have been linked to delayed transcription termination but have not been explored in depth. Here, using nascent transcriptomics in SETD2 knockout and patient-derived cells, we reveal a dichotomy in SETD2 functions depending on the affected protein-coding gene. The majority of genes, named class I, are dependent on SETD2 function for transcription initiation, yet terminate transcription in the usual locations. In contrast, for class II genes, corresponding to 15-25% of active protein-coding genes, transcription initiation is robust in absence of SETD2 activity; however, widespread transcriptional readthrough occurs. Defective termination following SETD2 loss/mutation is associated with increased cryptic transcription initiation and impaired 3' pre-mRNA cleavage. Additionally, alternative polyadenylation upon SETD2 activity loss is highly cell type specific, and no relationship with transcription readthrough was observed. We demonstrate that methyltransferase activity of SETD2 stimulates proper initiation, prevents cryptic initiation and promotes efficient 3' end processing, however, it does so indirectly.
Educators in the life sciences can be challenged by students who disagree with Darwin’s theory of evolution. This article analyses the history of Creationist’s attempts to introduce alternative explanations to Darwinian...Educators in the life sciences can be challenged by students who disagree with Darwin’s theory of evolution. This article analyses the history of Creationist’s attempts to introduce alternative explanations to Darwinian evolution and makes recommendations on how to prepare for such situations. [Image: see text]
Phase separation (PS) of biomolecular condensates is often assumed to be driven by interactions involving nucleic acids and intrinsically disordered regions (IDRs) of proteins. PGL-3 is a component of P granules, biomole...Phase separation (PS) of biomolecular condensates is often assumed to be driven by interactions involving nucleic acids and intrinsically disordered regions (IDRs) of proteins. PGL-3 is a component of P granules, biomolecular condensates in C. elegans, that contains two structured domains (D1-D2), an internal IDR, and a C-terminal IDR rich in RGG motifs. Theoretical and in vitro studies implicated the internal IDR and RGG motifs in driving PGL-3 PS via self-interactions and binding to RNA. Studies in cells, however, implicated the D1 and D2 domains. Here, we investigate the molecular basis of PGL-3 PS in vitro using microscopy, crosslinking mass spectrometry, and biophysical measurements. We find that D1-D2 forms oligomers and is necessary and sufficient for PS. The terminal RGG region interacts with D1-D2 in a manner that enhances PS even in the absence of RNA. In contrast, the internal IDR is neither necessary nor sufficient for PS. These findings support an alternative model for PGL-3 PS that does not require RNA and is driven by oligomerization of structured domains that interact with RGG repeats.
Basak D, Ghosh P, Gautam A
… +14 more, Sarkar I, Bhoumik A, Chowdhury S, Mahanti S, Mandal A, Chakraborty R, Kar A, Chowdhury S, Kumar K, Barman S, Ganesan SK, Chakrabarti S, Paul S, Chatterjee S
Sphingosine-1-phosphate receptor 1 (S1PR1) signaling has been linked to the regulation of immunosuppressive cell populations within the tumor microenvironment (TME); however, its role in shaping anti-tumor CD8⁺ T cell re...Sphingosine-1-phosphate receptor 1 (S1PR1) signaling has been linked to the regulation of immunosuppressive cell populations within the tumor microenvironment (TME); however, its role in shaping anti-tumor CD8⁺ T cell responses remains poorly defined. Herein, we demonstrate that intratumoral CD8⁺ T cells express S1PR1, with expression predominantly enriched in the terminally exhausted subset. Transcriptomic profiling, combined with pharmacological inhibition and genetic knockdown, reveals that S1PR1-S1P signaling activates the PERK (protein kinase R (PKR)-like endoplasmic reticulum kinase)-CHOP (C/EBP homologous protein) axis of the endoplasmic reticulum stress response. CHOP, in turn, upregulates transcription of Map3k13 and Map3k15, triggering downstream MAPK signaling and culminating in activation of p38MAPK. Activation of this pathway impairs CD8⁺ T cell metabolism and effector function while increasing apoptotic susceptibility. This ultimately limits the persistence and accumulation of functional CD8⁺ T cells within the TME, thereby compromising their responsiveness to anti-PD-1 therapy. Targeting the S1PR1-S1P axis or its downstream effectors offers a promising strategy to improve cancer immunotherapy outcomes.