EMBO Reports最新文献

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.

N⁶-Methyladenosine (m⁶A) is the most abundant internal modification of eukaryotic mRNAs and regulates target transcripts throughout the mRNA life cycle. Although changes in m⁶A have been reported in human cancers, technical limitations have hindered a comprehensive understanding of the cancer-associated m⁶A landscape. Here, we use GLORI-sequencing to establish the first transcriptome-wide, single-nucleotide resolution maps of m⁶A in bladder cancer. Comparing bladder cancer and healthy bladder samples, we discover two key m⁶A 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 m⁶A 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 m⁶A 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 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.

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.

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.

Memory-like or precursor exhausted (Tpex) CD8⁺ T cells are a critical reservoir in chronic infections and cancer, yet the signals sustaining their cytokine production remain unclear. Here, we identify KLRF1 as part of a CD4-CD8 communication axis that supports cytokine production in late-differentiated human CD8⁺ T cells. KLRF1 is upregulated in late-differentiated CD8⁺ T cells, and neutralizing KLRF1 reduces TNF and IFN-γ production. Differentiated CD4⁺ T cells express the KLRF1 ligand AICL, and in co-culture only AICL⁺ - not AICL⁻ - CD4⁺ T cells enhance cytokine output in CD8⁺ T cells. Using spatial proteomics of lung adenocarcinoma and adjacent tissue, we found that CD4⁺ AICL⁺ and CD8⁺ KLRF1⁺ T cells are enriched and spatially interacting in non-tumor regions, whereas both populations are reduced within tumor tissue. Single-cell RNA-seq of tissue samples and scRNA/ATAC analyses of circulating immune cells further showed that CD8⁺KLRF1⁺ T cells display a Tpex-like transcriptional and chromatin-accessibility profile. Together, these data identify the AICL-KLRF1 axis as a CD4⁺-CD8⁺ communication pathway that supports cytokine competence in late-differentiated CD8⁺ T cells.

The social behaviors of microbes provide unique opportunities for testing social evolution theories. How can altruistic behaviors arise by natural selection is a central challenge in biology. Green-beard effect has been proposed as a basic mechanism for the evolution of altruistic behaviors. Yet, green-beard genes are generally thought to be rare. Here, we find that the Schizosaccharomyces pombe gsf2 gene mediates flocculation-like aggregation, and flocculation is triggered by acid stresses. gsf2-expressing cells preferentially adhere to each other. The expression of gsf2 is costly, but gsf2-expressing cells preferentially adhere to each other and protect each other from external stress. Gsf2 is highly variable in natural populations, likely contributing to different flocculation intensity. These findings suggest that gsf2 is a gradient green-beard gene that drives the altruism among gsf2 carriers. Moreover, we find that gsf2 is a new gene that originated very recently. Our results provide insights into the origin and evolution of green-beard genes.

Paneth cells, intestine-originated innate immune-like cells, are important for maintenance of the intestinal stem cell niche, gut microbiota, and gastrointestinal barrier. Dysfunctional Paneth cells under pathological conditions are a site of origin for intestinal inflammation. However, mechanisms underlying stress-induced Paneth cell dysregulation remain unclear. Here, we report that SIRT1, the most conserved mammalian NAD⁺-dependent protein deacetylase and a well-known genetic repressor of inflammation, cell-autonomously suppresses Paneth cell function and sensitizes the gut epithelium to environmental stress. Specifically, deletion of Paneth cell SIRT1 in mice elevates Wnt signaling and ATF4/endoplasmic reticulum stress pathway in Paneth cells. These molecular alterations are coupled with increased Paneth cell abundance and enhanced anti-microbial peptide production in young mice, improved protection against intestinal immune cell expansion in aged mice, and increased resistance to chemically induced colitis. Using microbiota-depleted mice with or without fecal transplantation, we further demonstrate that Paneth cell SIRT1 deficiency ameliorates colitis by interacting with the gut microbiota. Collectively, our findings uncover an unanticipated function of Paneth cell SIRT1 in conferring stress sensitivity in the gut epithelium.