Cell reports最新文献

Although recurrent mutations of MLL3 are reported in various cancers, and MLL3 represents one of the most commonly mutated cancer genes, a pan-cancer-wide portrait of this high-frequency mutational event is still lacking. Here, we report that the genetic alterations in MLL3 in 33 cancer types are primarily driven by point mutations or small insertions and deletions (indels) and exhibit lineage-specific variations. These variations spontaneously yet heterogeneously impinge on the clinical behaviors of cancers and are intrinsically linked to hot tumor microenvironments, especially in uterine corpus endometrial carcinoma (UCEC) and colon adenocarcinoma (COAD), where MLL3 aberrances predict better overall survival and favorable response to immunochemotherapy. Concurrent mutations of MLL3 and POLE in UCEC signify a better immune response, which is validated in mouse models with Mll3-ablated colon cancer. Our study provides a pan-cancer spectrum of the MLL3 mutational event and will contribute to the understanding of the genetic evolution and disease management of cancers.

While most genes are equivalently expressed on both alleles, genes with random monoallelic expression (RME) stably maintain expression from only one allele, but the mechanisms and consequences of RME remain unclear. We performed allele-specific RNA sequencing (RNA-seq) on ∼100 F₁ hybrid neural progenitor cell (NPC) clonal lines to reveal the extent of autosomal RME (aRME). Of the 287 aRME genes, Pvt1, an oncogenic long non-coding RNA, is an aRME with a genetic bias. In the absence of genetic differences, Pvt1 undergoes balanced aRME. Pvt1 monoallelic expression is maintained by allele-specific active and repressive histone modifications, opposed to DNA methylation. Additionally, we provide a two-step mechanism for the initiation of aRME and demonstrate that Pvt1 monoallelic expression results in a growth phenotype due to the interplay with Myc. These findings provide insight into how genetic differences can skew a stochastic process, resulting in monoallelic expression with a phenotypic consequence in early development.

Polygonaceae, with ecological versatility and global distribution, is an ideal system for investigating plant adaptation. However, the genomic mechanisms underlying its karyotype evolution and environmental resilience remain unclear. We herein present chromosome-level genomes of 11 species from 10 Polygonaceae genera. Our analyses reveal that Gypsy retrotransposons are key drivers of genome size variations in Polygonaceae. We reconstructed a Polygonaceae ancestral karyotype comprising 28 proto-chromosomes and elucidated evolutionary trajectories via extensive chromosomal rearrangements. Furthermore, we constructed a cross-genus super pan-genome for Polygonaceae, identifying 80,055 gene families, of which 9,845 (12.30%) are core gene families. Private genes are found to contribute significantly to interspecific differences in adaptability. Notably, gene copy number variations are identified as a critical factor influencing adaptations to diverse niches involving species-specific increases in metabolic pathways. This study provides a genomic framework for Polygonaceae karyotype plasticity and adaptive innovation, offering insights into plant evolution under environmental challenges.

RNA-DNA hybrids and R-loops can lead to extensive DNA damage and loss of genomic integrity if not regulated in a timely manner. Although RNase H1 overexpression is frequently used as a tool to resolve R-loops, the regulation of RNase H1, overexpressed or endogenous, remains poorly characterized. We reveal that in yeast, overexpressed RNase H1 (RNH1) has no effect on gene expression, cell growth, or RNA-DNA hybrid resolution in wild-type cells. Overexpressed RNase H1 does, however, remove RNA-DNA hybrids in mutants where hybrids have become dysregulated. Endogenous RNase H1 becomes up-regulated and chromatin-associated in the absence of Sen1 in a DNA replication checkpoint-dependent manner. Rnh1 gets recruited to genomic loci where RNA-DNA hybrids accumulate following the loss of Sen1. Rnh1, together with Sen1, promotes DNA replication at sites of transcription-replication conflict. Hence, RNase H1, overexpressed or endogenous, responds to unscheduled, stress-inducing RNA-DNA hybrids.

Fibrillarin (FBL) is a nucleolar protein critical for rRNA biogenesis. We show that FBL is essential for the maintenance of epithelial integrity through its regulation of cell-cell adhesion proteins. RNA-seq analyses upon FBL depletion revealed deregulation of adhesion- and apical membrane organization-associated pathways. FBL loss deregulates cell polarity via increased deposition of H3K27me3 on the SCRIB promoter, driven by the localization of a subpopulation of EZH2 from the nucleolus to the nucleoplasm. Disrupting the FBL-EZH2 interaction increases cell migration, underscoring a requirement for retaining EZH2 also in the nucleolus. Furthermore, FBL depletion induces EMT in breast epithelial cells, owing to increased levels of mesenchymal factors (Snail1, Twist1, and Zeb1) and activation of Akt. Since Scribble tethers PHLPP1 and PTEN to antagonize Akt, repression of Scribble induces EMT. In summary, FBL safeguards epithelial integrity, by regulating the expression of Scribble, uncovering an FBL-EZH2 axis in EMT and metastasis.

Nucleoporin 98-rearranged (NUP98-r) acute myeloid leukemia (AML) is associated with poor outcomes and remains a major therapeutic challenge due to the absence of strategies that directly eliminate NUP98 fusion oncoproteins. Targeted degradation of cancer-driving oncofusions is an attractive approach, but the molecular mechanisms controlling NUP98 oncofusion stability are unknown. Using a CRISPR-Cas9 screen, we identify the E3 ligase Speckle-type POZ protein (SPOP) as a direct regulator of NUP98 fusion oncoprotein stability and a novel tumor suppressor in NUP98-r AML. Loss of SPOP increases NUP98 oncofusion levels and promotes leukemia cell proliferation. Exploiting this specificity, we demonstrate that induced proximity of SPOP and NUP98::lysine-specific demethylase 5A (KDM5A) through a biological proteolysis-targeting chimera (bioPROTAC) induces full clearance of the fusion oncoprotein, driving terminal differentiation and apoptosis of NUP98-r leukemia cells in vitro and in vivo. This study identifies SPOP as a direct regulator of NUP98 oncofusion stability and outlines a strategy to redirect the ubiquitin-proteasome system against oncogenic fusions.

We discovered that Plakophilin 3 (PKP3) was expressed only at the apical membrane of duct cells in the pancreas, and its expression was induced in acinar-to-ductal metaplasia (ADM), pancreatic intraepithelial neoplasia (PanIN), and pancreatic ductal adenocarcinoma (PDAC) cells. PKP3 was predominantly localized on the cell membrane in ADM and both in the membrane and cytoplasm in PanIN, while PDAC cells expressed PKP3 in the nucleus rather than in the cytoplasm or membrane. PKP3 expression transformed acinar cells into duct-like cells and promoted the malignant behavior of PDAC cells. Mechanistically, PKP3 upregulated FOXM1 expression by inhibiting FOXM1 ubiquitylation. Genetic ablation of PKP3 blocked ADM formation, PanIN and PDAC. Increased PKP3 expression predicted poor survival of patients with PDAC disease. Thus, PKP3 is transformed from a desmosomal protein into an oncogenic molecule that promotes PDAC development through FOXM1 stabilization. This PKP3-FOXM1 signaling axis is a potential target for intervention in early-stage PDAC.

Extracellular vesicles and particles (EVPs) serve as functional mediators delivering their cargoes to specific destinations. Exomeres (EMs) represent a newly discovered subset of nanoparticles, with limited understanding of their biophysical characteristics and functionalities. Here, we isolated and studied EMs from different normal and cancer cell lines. Proteomic analysis reveals distinctive features of EMs compared to small extracellular vesicles (sEVs) and identifies galactosamine (N-acetyl)-6-sulfatase (GALNS) and mannosidase alpha class 2B member 1 (MAN2B1) to be expressed in EMs, indicating their potential as specific EM molecular markers. Subsequent investigations into tumor-derived EMs demonstrate their oncogenic properties to support cancer growth and metastasis. Furthermore, analysis of murine hepatocellular carcinoma-derived EM reveals their ability to induce cell cycle progression and metabolic alterations. Collectively, our data highlight the distinct nature of EMs as a nanoparticle subpopulation different from sEVs, with cancer-derived EMs significantly contributing to tumor growth and dissemination.

Neuronal response to changes in nutrient availability is critical for maintaining metabolic homeostasis and organismal survival. Nevertheless, we know little about the molecular players that regulate and maintain neurotransmission under nutritional stress. We demonstrate that, under acute amino acid restriction, the maintenance of normal synaptic strength at the Drosophila larval neuromuscular junction critically depends on the integrated stress response (ISR) machinery. Our findings indicate that amino acid restriction triggers a non-canonical ISR cascade in muscle via GCN2 and eIF2α phosphorylation but independently of ATF4. We have identified Still life (Sif), an ortholog of human TIAM1, as a translational target of the ISR and show that it is required in muscle for mediating the action of the ISR. Our results reveal an intricate non-canonical ISR signaling cascade at the synapse and offer a new framework to separate the role of the ISR in proteostasis from its synaptic actions.