Aberrant NUP98 condensates activate leukemogenic genes via discrete genomic engagement
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1041477 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26856226_1.fastq.gz | Fastqsanger.gz | |||
| SRR26856226_2.fastq.gz | Fastqsanger.gz | |||
| SRR26856227_1.fastq.gz | Fastqsanger.gz | |||
| SRR26856227_2.fastq.gz | Fastqsanger.gz | |||
| SRR26856228_1.fastq.gz | Fastqsanger.gz |
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Project description:NUP98 FG repeats trigger hematopoietic malignancies when aberrantly fused to various DNA/chromatin binding domains. However, how these heterogeneous NUP98 fusions drive oncogenesis remains unclear. Here we fuse different NUP98 FG repeat compositions to dCas9 and establish that NUP98 FG repeats are sufficient to activate human genes via cooperative activity at human endogenous promoters. Further, we find that NUP98-FG repeats spontaneously undergo liquid-liquid phase separation and co-condensate with other transcriptional coactivators in human cells, which we show is indispensable for transcriptional activation. We also define a threshold of NUP98 FG repeat numbers required for biomolecular condensation and gene activation that is consistent with NUP98 FG repeat lengths observed across clinical cohorts. Using ChIP-seq and live cell imaging, we further demonstrate that although NUP98 FG repeats can robustly shuttle into cell nuclei, engagement with the human genome is directed solely through fusion partner. Interestingly, two frequent oncogenic fusions, NUP98-HOXA9 and NUP98-KDM5A exhibit discrete genomic engagement landscapes and gene-regulatory modes in that NUP98-HOXA9 initiates strong transcription via intragenic super enhancer-like binding and increased intrachromosomal contacts, while NUP98-KDM5A activates genes via strict localization to promoters. Additionally, in primary human HSCs, NUP98-HOXA9 and NUP98-KDM5A globally dysregulate transcription in a largely non-overlapping manner. Nevertheless, both oncogenic fusion proteins directly drive the inappropriate activation of core leukemia-associated oncogenes, which occurs coincident with the downregulation of genes associated with HSC lineage commitment. Altogether, our studies point toward a conserved core set of potential therapeutic targets driving NUP98-associated cancers and clarify the transcriptional and oncogenic role of aberrant NUP98 condensates.
2025-02-19 | GSE248061 | GEO
Project description:Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remains poorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the disordered FG-repeats-rich region of NUP98 and the H3K4me3/2-binding PHD finger domain of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD domain targets condensates to H3K4me3/2-demarcated developmental genes while the FG repeats determine condensate composition and gene activation. The FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the KMT2/MLL family of H3K4 methyltransferases, histone acetyltransferases and BRD4. The FG repeats are sufficient to partition these transcriptional regulators and activate a reporter when tethered to a locus. NUP98-PHF23 assembles the chromatin-bound condensates that partition multiple positive regulators, initiating a feed-forward loop of reading-and-writing active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.
2024-12-31 | PXD056948 | Pride
Project description:Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remainspoorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the FG-repeat region of NUP98 and the H3K4me3-binding PHD finger of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD finger targets condensates to H3K4me3-demarcated developmental genes and the FG repeats determine condensate composition and gene activation. The FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the MLL family of H3K4 methylation-writing enzymes and BRD4. The FG repeats are sufficient, when tethered to the genome, to partition these transcriptional regulators and activate genes. NUP98-PHF23 assembles chromatin-bound condensates that partition multiple positive regulators, initiating a feed-forward loop of reading-and-writing active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.
2025-01-30 | GSE280397 | GEO
Project description:Cancer-associated genetic aberrations, such as the nucleoporin 98 (NUP98) gene rearrangement detected in human leukemias, often produce condensates, a type of membrane-less biomolecular assemblies. How exactly the cancer-related condensation contributes to oncogenesis remains far from clear. Here, we investigate NUP98-PHF23, a leukemia-causing chimeric protein that fuses NUP98’s sequence enriched in phenylalanine-and-glycine repeats (FG repeats, also known as intrinsically disordered region [IDR]) in-frame with PHF23’s PHD finger, a domain that specifically ‘reads’ and binds H3K4 trimethylation (H3K4me3). Our integrated analyses using protein module mutagenesis, cell imaging, genomic profiling and condensation reconstitution collectively demonstrate a multifaced role for NUP98’s FG repeats in driving fusion condensation while recruiting and co-mixing with a set of histone modifiers and chromatin remodelers, notably the MLL family of H3K4 methylation-‘writing’ enzymes. The H3K4me3-‘reading’ PHD finger and NUP98’s IDR are cooperative in mediating efficient targeting of NUP98-PHF23 and its coactivators onto leukemic genes, leading to active transcription. Together, we show that NUP98-PHF23 coordinates a set of homotypic and heterotypic interactions (IDR:IDR, IDR:coactivator and PHD:histone) to organize formation of the chromatin-bound multi-component condensates, wherein a feedforward loop involving the ‘reading’ and ‘writing’ of H3K4 methylation acts to enforce an open chromatin landscape at leukemogenic loci, thereby driving oncogenic transformation.
2025-01-30 | GSE255868 | GEO
Project description:Cancer-associated genetic aberrations, such as the nucleoporin 98 (NUP98) gene rearrangement detected in human leukemias, often produce condensates, a type of membrane-less biomolecular assemblies. How exactly the cancer-related condensation contributes to oncogenesis remains far from clear. Here, we investigate NUP98-PHF23, a leukemia-causing chimeric protein that fuses NUP98’s sequence enriched in phenylalanine-and-glycine repeats (FG repeats, also known as intrinsically disordered region [IDR]) in-frame with PHF23’s PHD finger, a domain that specifically ‘reads’ and binds H3K4 trimethylation (H3K4me3). Our integrated analyses using protein module mutagenesis, cell imaging, genomic profiling and condensation reconstitution collectively demonstrate a multifaced role for NUP98’s FG repeats in driving fusion condensation while recruiting and co-mixing with a set of histone modifiers and chromatin remodelers, notably the MLL family of H3K4 methylation-‘writing’ enzymes. The H3K4me3-‘reading’ PHD finger and NUP98’s IDR are cooperative in mediating efficient targeting of NUP98-PHF23 and its coactivators onto leukemic genes, leading to active transcription. Together, we show that NUP98-PHF23 coordinates a set of homotypic and heterotypic interactions (IDR:IDR, IDR:coactivator and PHD:histone) to organize formation of the chromatin-bound multi-component condensates, wherein a feedforward loop involving the ‘reading’ and ‘writing’ of H3K4 methylation acts to enforce an open chromatin landscape at leukemogenic loci, thereby driving oncogenic transformation.
2025-01-30 | GSE255508 | GEO
Project description:NUP98-fusion proteins cause leukemia via unknown molecular mechanisms. All NUP98-fusion proteins share an intrinsically disordered region (IDR) featuring >35 repeats of Phenylalanine-Glycine (FG) in the NUP98 N-terminus. Conversely, C-terminal NUP98-fusion partners often have critical functions in gene control. Given these structural features we hypothesized that mechanisms of oncogenic transformation by NUP98-fusion proteins are hard-wired in their protein interactomes. Affinity purification coupled to mass spectrometry and confocal imaging of five distinct NUP98-fusion proteins revealed that conserved interactors were enriched for proteins involved in biomolecular condensation and that they co-localized with NUP98-fusion proteins in nuclear puncta. We developed biotinylated isoxazole-mediated condensome mass spectrometry (biCon-MS) to show that NUP98-fusion proteins alter the global composition of biomolecular condensates. An artificial FG-repeat-containing fusion protein phenocopied the nuclear localization patterns of NUP98-fusion proteins and their capability to drive oncogenic gene expression programs. Thus, we propose that IDR-containing fusion proteins uniquely combine biomolecular condensation with transcriptional control to induce cancer.
2020-12-23 | PXD022518 | Pride
Project description:NUP98-fusion proteins cause acute myeloid leukemia via unknown molecular mechanisms. All NUP98-fusion proteins share an intrinsically disordered region (IDR) featuring >35 repeats of Phenylalanine-Glycine (FG) in the NUP98 N-terminus. Conversely, different C-terminal NUP98-fusion partners are often transcriptional and epigenetic regulators. Given these structural features we hypothesized that mechanisms of oncogenic transformation by NUP98-fusion proteins are hard-wired in their protein interactomes. Affinity purification coupled to mass spectrometry of five distinct NUP98-fusion proteins revealed a conserved set of interactors that was highly enriched for proteins involved in biomolecular condensation. We developed biotinylated isoxazole-mediated condensome mass spectrometry (biCon-MS) to show that NUP98-fusion proteins alter the global composition of biomolecular condensates. In addition, an artificial FG-repeat containing fusion protein was able to phenocopy the induction of leukemic gene expression as mediated by NUP98-KDM5A. Thus, we propose that IDR-containing fusion proteins have evolved to uniquely combine biomolecular condensation with gene control to induce cancer.
2021-02-16 | GSE159037 | GEO
Project description:Nuclear Condensation of NUP98-Fusion Proteins drives leukemogenic gene expression
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Project description:Using mouse and human models of NUP98-rearrranged leukemia, we demonstrate that inhibition of MLL-Menin impairs leukemogenic gene expression and disrupts chromatin binding of MLL1 and NUP98 fusion proteins at a critical subset of genes that is essential for sustaining the undifferentiated leukemia phenotype.
2022-06-01 | GSE175596 | GEO
Project description:Using mouse and human models of NUP98-rearrranged leukemia, we demonstrate that inhibition of MLL-Menin impairs leukemogenic gene expression and disrupts chromatin binding of MLL1 and NUP98 fusion proteins at a critical subset of genes that is essential for sustaining the undifferentiated leukemia phenotype.
2022-06-01 | GSE175595 | GEO