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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.


Related in: MedlinePlus

Loss of H3K36me2 correlates with downregulated genes after NSD2 knock down.(a) Top H3K36me2 islands in vehicle treated cells identified using ROSE. (b) Gene tracks of H3K36me2 signal in presence (dox) or absence (vehicle) of doxycycline. Ratio of H3K36me2 signal in doxycycline minus vehicle treated cells is also shown (Negative light blue values represent loss of signal caused by doxycycline, positive dark blue values represent remaining signal after doxycycline treatment). H3K36me3, H3K27ac signal and CpG islands are also shown. (c) Log2 of fold change (doxycycline vs. vehicle) of H3K36me2 signal at different genomic features located in top H3K36me2 islands. Significance to the fold change was tested using paired two-tailed t test; P = 8.63 × 10−15 in top H3K36me2 islands (islands), P = 5.68 × 10−34 for intergenic regions (intergenic) P = 1.76 × 10−19 for lamina associated domains (LADs), P = 1.44 × 10−15 for coding regions without H3K36me3 (CDS_wo_K36me3), P = 6.531 × 10−101 for regions marked with H3K27ac located at TSSs (K27ac_TSS), P = 1.70 × 10−155 for H3K27ac marked regions not coincident with TSSs (K27ac_enhancers) and P = 4.81 × 10−09 for coding regions with H3K36me3 (CDS_K36me3). (d) Metagene representation of average H3K36me2 density at top H3K36me2 identified in A in the presence of vehicle or doxycycline. The x axis shows the average size of the top H3K36me2 islands flanked by 5 Kb up and down. See Supplementary Table 4 for comparison of H3K36me2 densities at each island in the presence of vehicle or doxycycline. (e) Average density of H3K36me2 −/+20 Kbs around the center of H3K27 acetylated regions not coincident with TSSs (enhancers) in top H3K36me2 islands in H1299 cells transduced with sh3 and treated with doxycycline (Dox) or vehicle. (f ) Gene set enrichment analysis (GSEA) plot showing significant enrichment of top H3K36me2 islands downregulated by dox-associated gene signature (H3K36me2_Signature; Supplementary Table 3) and genes downregulated by doxycycline. (g) Expression of genes on the leading edge of panel F after different treatments. ***p-value < 0.0005 determined by paired t-test comparing each treatment to control (DMSO).
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f5: Loss of H3K36me2 correlates with downregulated genes after NSD2 knock down.(a) Top H3K36me2 islands in vehicle treated cells identified using ROSE. (b) Gene tracks of H3K36me2 signal in presence (dox) or absence (vehicle) of doxycycline. Ratio of H3K36me2 signal in doxycycline minus vehicle treated cells is also shown (Negative light blue values represent loss of signal caused by doxycycline, positive dark blue values represent remaining signal after doxycycline treatment). H3K36me3, H3K27ac signal and CpG islands are also shown. (c) Log2 of fold change (doxycycline vs. vehicle) of H3K36me2 signal at different genomic features located in top H3K36me2 islands. Significance to the fold change was tested using paired two-tailed t test; P = 8.63 × 10−15 in top H3K36me2 islands (islands), P = 5.68 × 10−34 for intergenic regions (intergenic) P = 1.76 × 10−19 for lamina associated domains (LADs), P = 1.44 × 10−15 for coding regions without H3K36me3 (CDS_wo_K36me3), P = 6.531 × 10−101 for regions marked with H3K27ac located at TSSs (K27ac_TSS), P = 1.70 × 10−155 for H3K27ac marked regions not coincident with TSSs (K27ac_enhancers) and P = 4.81 × 10−09 for coding regions with H3K36me3 (CDS_K36me3). (d) Metagene representation of average H3K36me2 density at top H3K36me2 identified in A in the presence of vehicle or doxycycline. The x axis shows the average size of the top H3K36me2 islands flanked by 5 Kb up and down. See Supplementary Table 4 for comparison of H3K36me2 densities at each island in the presence of vehicle or doxycycline. (e) Average density of H3K36me2 −/+20 Kbs around the center of H3K27 acetylated regions not coincident with TSSs (enhancers) in top H3K36me2 islands in H1299 cells transduced with sh3 and treated with doxycycline (Dox) or vehicle. (f ) Gene set enrichment analysis (GSEA) plot showing significant enrichment of top H3K36me2 islands downregulated by dox-associated gene signature (H3K36me2_Signature; Supplementary Table 3) and genes downregulated by doxycycline. (g) Expression of genes on the leading edge of panel F after different treatments. ***p-value < 0.0005 determined by paired t-test comparing each treatment to control (DMSO).

Mentions: Similar to the analysis done to identify regions with top levels of H3K27ac, we used ROSE to rank the H3K36me2 density signal in vehicle treated cells (Fig. 5a). This analysis revealed that certain genomic locations display very high levels of H3K36me2. After stitching together H3K36me2 intervals separated less than 12.5 Kb, 402 top H3K36me2 regions were identified with an average size of 800 Kb and a maximum size of 5 Mb (Supplementary Table 4). Therefore, in the presence of high levels of NSD2 H3K36me2 regions extended long domains (that we called H3K36me2 islands) that typically embedded several genes, including well known clusters of genes such as the histone cluster (38 genes covered by a single island) or the metalloproteinase cluster. This broad distribution might be expected from an abundant modification described to mark up to 40% of histone H3 in mammalian cells38.


NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation
Loss of H3K36me2 correlates with downregulated genes after NSD2 knock down.(a) Top H3K36me2 islands in vehicle treated cells identified using ROSE. (b) Gene tracks of H3K36me2 signal in presence (dox) or absence (vehicle) of doxycycline. Ratio of H3K36me2 signal in doxycycline minus vehicle treated cells is also shown (Negative light blue values represent loss of signal caused by doxycycline, positive dark blue values represent remaining signal after doxycycline treatment). H3K36me3, H3K27ac signal and CpG islands are also shown. (c) Log2 of fold change (doxycycline vs. vehicle) of H3K36me2 signal at different genomic features located in top H3K36me2 islands. Significance to the fold change was tested using paired two-tailed t test; P = 8.63 × 10−15 in top H3K36me2 islands (islands), P = 5.68 × 10−34 for intergenic regions (intergenic) P = 1.76 × 10−19 for lamina associated domains (LADs), P = 1.44 × 10−15 for coding regions without H3K36me3 (CDS_wo_K36me3), P = 6.531 × 10−101 for regions marked with H3K27ac located at TSSs (K27ac_TSS), P = 1.70 × 10−155 for H3K27ac marked regions not coincident with TSSs (K27ac_enhancers) and P = 4.81 × 10−09 for coding regions with H3K36me3 (CDS_K36me3). (d) Metagene representation of average H3K36me2 density at top H3K36me2 identified in A in the presence of vehicle or doxycycline. The x axis shows the average size of the top H3K36me2 islands flanked by 5 Kb up and down. See Supplementary Table 4 for comparison of H3K36me2 densities at each island in the presence of vehicle or doxycycline. (e) Average density of H3K36me2 −/+20 Kbs around the center of H3K27 acetylated regions not coincident with TSSs (enhancers) in top H3K36me2 islands in H1299 cells transduced with sh3 and treated with doxycycline (Dox) or vehicle. (f ) Gene set enrichment analysis (GSEA) plot showing significant enrichment of top H3K36me2 islands downregulated by dox-associated gene signature (H3K36me2_Signature; Supplementary Table 3) and genes downregulated by doxycycline. (g) Expression of genes on the leading edge of panel F after different treatments. ***p-value < 0.0005 determined by paired t-test comparing each treatment to control (DMSO).
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f5: Loss of H3K36me2 correlates with downregulated genes after NSD2 knock down.(a) Top H3K36me2 islands in vehicle treated cells identified using ROSE. (b) Gene tracks of H3K36me2 signal in presence (dox) or absence (vehicle) of doxycycline. Ratio of H3K36me2 signal in doxycycline minus vehicle treated cells is also shown (Negative light blue values represent loss of signal caused by doxycycline, positive dark blue values represent remaining signal after doxycycline treatment). H3K36me3, H3K27ac signal and CpG islands are also shown. (c) Log2 of fold change (doxycycline vs. vehicle) of H3K36me2 signal at different genomic features located in top H3K36me2 islands. Significance to the fold change was tested using paired two-tailed t test; P = 8.63 × 10−15 in top H3K36me2 islands (islands), P = 5.68 × 10−34 for intergenic regions (intergenic) P = 1.76 × 10−19 for lamina associated domains (LADs), P = 1.44 × 10−15 for coding regions without H3K36me3 (CDS_wo_K36me3), P = 6.531 × 10−101 for regions marked with H3K27ac located at TSSs (K27ac_TSS), P = 1.70 × 10−155 for H3K27ac marked regions not coincident with TSSs (K27ac_enhancers) and P = 4.81 × 10−09 for coding regions with H3K36me3 (CDS_K36me3). (d) Metagene representation of average H3K36me2 density at top H3K36me2 identified in A in the presence of vehicle or doxycycline. The x axis shows the average size of the top H3K36me2 islands flanked by 5 Kb up and down. See Supplementary Table 4 for comparison of H3K36me2 densities at each island in the presence of vehicle or doxycycline. (e) Average density of H3K36me2 −/+20 Kbs around the center of H3K27 acetylated regions not coincident with TSSs (enhancers) in top H3K36me2 islands in H1299 cells transduced with sh3 and treated with doxycycline (Dox) or vehicle. (f ) Gene set enrichment analysis (GSEA) plot showing significant enrichment of top H3K36me2 islands downregulated by dox-associated gene signature (H3K36me2_Signature; Supplementary Table 3) and genes downregulated by doxycycline. (g) Expression of genes on the leading edge of panel F after different treatments. ***p-value < 0.0005 determined by paired t-test comparing each treatment to control (DMSO).
Mentions: Similar to the analysis done to identify regions with top levels of H3K27ac, we used ROSE to rank the H3K36me2 density signal in vehicle treated cells (Fig. 5a). This analysis revealed that certain genomic locations display very high levels of H3K36me2. After stitching together H3K36me2 intervals separated less than 12.5 Kb, 402 top H3K36me2 regions were identified with an average size of 800 Kb and a maximum size of 5 Mb (Supplementary Table 4). Therefore, in the presence of high levels of NSD2 H3K36me2 regions extended long domains (that we called H3K36me2 islands) that typically embedded several genes, including well known clusters of genes such as the histone cluster (38 genes covered by a single island) or the metalloproteinase cluster. This broad distribution might be expected from an abundant modification described to mark up to 40% of histone H3 in mammalian cells38.

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.


Related in: MedlinePlus