bioRxiv. 2023 Sep 16. pii: 2023.09.14.557228. [Epub ahead of print]
Katherine A Alexander,
Ruofan Yu,
Nicolas Skuli,
Nathan J Coffey,
Son Nguyen,
Christine Faunce,
Hua Huang,
Ian P Dardani,
Austin L Good,
Joan Lim,
Catherine Li,
Nicholas Biddle,
Eric F Joyce,
Arjun Raj,
Daniel Lee,
Brian Keith,
M Celeste Simon,
Shelley L Berger.
Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of its s peckle targeting m otifs (STMs)-defined in this study-led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.HIGHLIGHTS: - Nuclear speckles shown to reproducibly vary in cancer, predicting patient survival in ccRCC- HIF-2α drives DNA/gene-speckle contacts dependent on identified speckle targeting motifs within HIF-2α- Putative speckle targeting motifs are highly enriched among regulators of gene expression- Partitioning of transcription factor functional programs may be a major biological function of nuclear speckles.