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NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation

View Article: PubMed Central - PubMed

ABSTRACT

The histone methyltransferase NSD2/WHSC1/MMSET is overexpressed in a number of solid tumors but its contribution to the biology of these tumors is not well understood. Here, we describe that NSD2 contributes to the proliferation of a subset of lung cancer cell lines by supporting oncogenic RAS transcriptional responses. NSD2 knock down combined with MEK or BRD4 inhibitors causes co-operative inhibitory responses on cell growth. However, while MEK and BRD4 inhibitors converge in the downregulation of genes associated with cancer-acquired super-enhancers, NSD2 inhibition affects the expression of clusters of genes embedded in megabase-scale regions marked with H3K36me2 and that contribute to the RAS transcription program. Thus, combinatorial therapies using MEK or BRD4 inhibitors together with NSD2 inhibition are likely to be needed to ensure a more comprehensive inhibition of oncogenic RAS-driven transcription programs in lung cancers with NSD2 overexpression.

No MeSH data available.


Chromosomal domains with coordinated loss of H3K36me2 and gene expression.(a) Smoothed H3K36me2 signal ratio (H3K36me2) and gene expression changes (FPKM) in doxycycline versus vehicle treated cells along chromosomes most enriched in top H3K36me2 islands (shown in red). Regions of retention of H3K36me2 are shown in dark blue and loss in light blue. Upregulated genes are shown in black and downregulated genes in grey. (b) H3K27ac and H3K36me3 levels and RNA Pol II occupancy at top H3K36me2 islands and the indicated flanking sites in H1299. (c) Levels of H3K27me3 at top H3K36me2 islands and flanking sites in H1299 and normal human lung fibroblasts (NHLF). (d) Model of NSD2 action in cell lines with RAS activating mutations. RAS signaling contributes to the establishment of super-enhancers. In the presence of low levels of NSD2, H3K36me2 is confined to enhancer regions. When levels of NSD2 are high the H3K36me2 mark spreads along regions of low H3K27me3 levels and low gene content, increasing the expression of genes located on these areas.
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f6: Chromosomal domains with coordinated loss of H3K36me2 and gene expression.(a) Smoothed H3K36me2 signal ratio (H3K36me2) and gene expression changes (FPKM) in doxycycline versus vehicle treated cells along chromosomes most enriched in top H3K36me2 islands (shown in red). Regions of retention of H3K36me2 are shown in dark blue and loss in light blue. Upregulated genes are shown in black and downregulated genes in grey. (b) H3K27ac and H3K36me3 levels and RNA Pol II occupancy at top H3K36me2 islands and the indicated flanking sites in H1299. (c) Levels of H3K27me3 at top H3K36me2 islands and flanking sites in H1299 and normal human lung fibroblasts (NHLF). (d) Model of NSD2 action in cell lines with RAS activating mutations. RAS signaling contributes to the establishment of super-enhancers. In the presence of low levels of NSD2, H3K36me2 is confined to enhancer regions. When levels of NSD2 are high the H3K36me2 mark spreads along regions of low H3K27me3 levels and low gene content, increasing the expression of genes located on these areas.

Mentions: Interestingly, we noticed that top H3K36me2 islands were not evenly spread along the genome but clustered in certain locations, mainly on the large arms of several chromosomes (Supplementary Fig. 11). These regions are often coincident with large areas of strong H3K36me2 depletion that correlate with large domains of downregulated gene expression after NSD2 knock down (Fig. 6a). We next asked which features might be promoting the accumulation of these long domains at these particular genomic locations in cancer cells. Top H3K36me2 regions contained twice less CpG islands and 3.5 less genes per Kb than regions with low H3K36me2, suggesting that the absence of CpG islands and gene bodies might favor the spread of this mark in cancer cells that express high levels of NSD2. In accordance with this hypothesis we found that the boundaries of top H3K36me2 islands were enriched in proximal promoter regions (p-value: 4.7 × 10−15) and features associated with active promoters (H3K27ac, H3K36me3 and Pol II occupancy) (Fig. 6b). As expected from the negative correlation found between H3K36me2 and H3K27me3 signals, levels of H3K27me3 were low along the H3K36me2 islands compared to flanking regions (Fig. 6c). This pattern was found both in H1299 cells and normal human lung fibroblast (NHLF) that express low levels of NSD2, suggesting that low levels of H3K27me3 at certain genomic locations might facilitate the spreading of the H3K36me2 mark rather than being the consequence of the H3K36me2 spread.


NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation
Chromosomal domains with coordinated loss of H3K36me2 and gene expression.(a) Smoothed H3K36me2 signal ratio (H3K36me2) and gene expression changes (FPKM) in doxycycline versus vehicle treated cells along chromosomes most enriched in top H3K36me2 islands (shown in red). Regions of retention of H3K36me2 are shown in dark blue and loss in light blue. Upregulated genes are shown in black and downregulated genes in grey. (b) H3K27ac and H3K36me3 levels and RNA Pol II occupancy at top H3K36me2 islands and the indicated flanking sites in H1299. (c) Levels of H3K27me3 at top H3K36me2 islands and flanking sites in H1299 and normal human lung fibroblasts (NHLF). (d) Model of NSD2 action in cell lines with RAS activating mutations. RAS signaling contributes to the establishment of super-enhancers. In the presence of low levels of NSD2, H3K36me2 is confined to enhancer regions. When levels of NSD2 are high the H3K36me2 mark spreads along regions of low H3K27me3 levels and low gene content, increasing the expression of genes located on these areas.
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Related In: Results  -  Collection

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f6: Chromosomal domains with coordinated loss of H3K36me2 and gene expression.(a) Smoothed H3K36me2 signal ratio (H3K36me2) and gene expression changes (FPKM) in doxycycline versus vehicle treated cells along chromosomes most enriched in top H3K36me2 islands (shown in red). Regions of retention of H3K36me2 are shown in dark blue and loss in light blue. Upregulated genes are shown in black and downregulated genes in grey. (b) H3K27ac and H3K36me3 levels and RNA Pol II occupancy at top H3K36me2 islands and the indicated flanking sites in H1299. (c) Levels of H3K27me3 at top H3K36me2 islands and flanking sites in H1299 and normal human lung fibroblasts (NHLF). (d) Model of NSD2 action in cell lines with RAS activating mutations. RAS signaling contributes to the establishment of super-enhancers. In the presence of low levels of NSD2, H3K36me2 is confined to enhancer regions. When levels of NSD2 are high the H3K36me2 mark spreads along regions of low H3K27me3 levels and low gene content, increasing the expression of genes located on these areas.
Mentions: Interestingly, we noticed that top H3K36me2 islands were not evenly spread along the genome but clustered in certain locations, mainly on the large arms of several chromosomes (Supplementary Fig. 11). These regions are often coincident with large areas of strong H3K36me2 depletion that correlate with large domains of downregulated gene expression after NSD2 knock down (Fig. 6a). We next asked which features might be promoting the accumulation of these long domains at these particular genomic locations in cancer cells. Top H3K36me2 regions contained twice less CpG islands and 3.5 less genes per Kb than regions with low H3K36me2, suggesting that the absence of CpG islands and gene bodies might favor the spread of this mark in cancer cells that express high levels of NSD2. In accordance with this hypothesis we found that the boundaries of top H3K36me2 islands were enriched in proximal promoter regions (p-value: 4.7 × 10−15) and features associated with active promoters (H3K27ac, H3K36me3 and Pol II occupancy) (Fig. 6b). As expected from the negative correlation found between H3K36me2 and H3K27me3 signals, levels of H3K27me3 were low along the H3K36me2 islands compared to flanking regions (Fig. 6c). This pattern was found both in H1299 cells and normal human lung fibroblast (NHLF) that express low levels of NSD2, suggesting that low levels of H3K27me3 at certain genomic locations might facilitate the spreading of the H3K36me2 mark rather than being the consequence of the H3K36me2 spread.

View Article: PubMed Central - PubMed

ABSTRACT

The histone methyltransferase NSD2/WHSC1/MMSET is overexpressed in a number of solid tumors but its contribution to the biology of these tumors is not well understood. Here, we describe that NSD2 contributes to the proliferation of a subset of lung cancer cell lines by supporting oncogenic RAS transcriptional responses. NSD2 knock down combined with MEK or BRD4 inhibitors causes co-operative inhibitory responses on cell growth. However, while MEK and BRD4 inhibitors converge in the downregulation of genes associated with cancer-acquired super-enhancers, NSD2 inhibition affects the expression of clusters of genes embedded in megabase-scale regions marked with H3K36me2 and that contribute to the RAS transcription program. Thus, combinatorial therapies using MEK or BRD4 inhibitors together with NSD2 inhibition are likely to be needed to ensure a more comprehensive inhibition of oncogenic RAS-driven transcription programs in lung cancers with NSD2 overexpression.

No MeSH data available.