Dimethylation of H3K36 is the principal catalytic function of NSD2 on histones in cells

Overexpression of NSD2 in 293T cells resulted in increased global H3K36me2 levels, but had no effect on the levels of H3K36me3, H4K20me2, and several other marks (Figure 2A). Next, NSD2 activity was investigated in KMS11 cells, a model t(4;14)⁺ myeloma cell line in which the IgH enhancer drives overexpression of NSD2 (Lauring et al., 2008). RNA interference (RNAi)-mediated knockdown of NSD2 expression in KMS11 cells, using two independent shRNAs (Figure S1A), led to a specific decrease in levels of H3K36me2, but not other histone methyl marks including H4K20me2 and H3K36me3 (Figure 2B). In contrast, global levels of H3K36me3, but not H3K36me2, were decreased in SETD2-depleted KMS11 cells (Figure 2C). In addition, NSD2 depletion in HT1080 and U2OS cancer cell lines decreased H3K36me2 levels without changing H3K36me3 levels (Figure 2D).

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Figure 2

NSD2 generates H3K36me2 in cells

(A) NSD2 overexpression increases global H3K36me2 levels in cells. Western analysis with the indicated antibodies of whole cell extract (WCE) from 293T cells transfected with full-length NSD2 or control vector. Total H3 is shown as a loading control.

(B) Depletion of NSD2 by RNAi specifically decreases global H3K36me2 level in t(4;14)⁺ myeloma cells. Western analysis as in (A) of WCE from t(4;14)⁺ KMS11 myeloma cells stably expressing control shRNA or two independent shRNAs targeting NSD2.

(C) Depletion of SETD2 reduces H3K36me3 levels in myeloma cells. Western analysis of WCE as in (B) from KMS11 cells expressing the indicated shRNAs.

(D) Depletion of NSD2 specifically decreases global H3K36me2 levels in non-myeloma cancer cell lines. Western analysis with the indicated antibodies of WCE from HT1080 (top panel) and U2OS (bottom panel) cells transfected with control siRNA or two independent siRNAs targeting NSD2.

(E) Schematic of KMS11, TKO, and NTKO cell lines (see Lauring et al., 2008). Homologous recombination in t(4;14)⁺ KMS11 cells targeting either inactivation of the t(4;14)-associated NSD2 allele (TKO) or the wild-type NSD2 allele (NTKO).

(F), (G) and (H) Loss of t(4;14)-associated NSD2 expression in myeloma cells leads to depletion of H3K36me2, but not other histone methylation marks. (F) Western analysis of WCE from KMS11, TKO and NTKO cells using the indicated antibodies. (G) Long exposure and quantitation of NSD2 western analysis in the indicated cell lines. (H) Quantitative mass spectrometry of the relative amounts of the indicated methylation events in KMS11 cells versus two independent TKO cell lines. Fold Δ: ratio of KMS11 over TKO samples. ± standard deviation from 2 replicas analyzed in triplicate.

KMS11 cells in which the t(4;14)-driven NSD2 allele has been inactivated by homologous recombination (translocation knock-out (TKO) cells) have attenuated tumorigenicity compared to parental KMS11 cells or cells with targeted inactivation of only the wild-type allele (non-translocation knock-out (NTKO); see Figure 2E) (Lauring et al., 2008). In two independent TKO cell lines, which lack the t(4;14) NSD2 allele, global H3K36me2 levels were lower than in KMS11 and NTKO cells, and no changes in H3K36me3 or H4K20me2 levels were observed (Figure 2F). Accordingly, NSD2 protein abundance was 6 to 7 fold higher in KMS11 cells than in TKO cell lines (Figure 2G and S1G).

An unbiased quantitative mass spectrometry screen, comparing levels of histone methyl marks between KMS11 and TKO cells, revealed that H3K36me2 levels are 3-fold higher in KMS11 cells versus TKO cells (Figure 2H). Conversely, levels of unmethylated H3K36 and H3K36me1 are lower by a factor of two in KMS11 cells relative to TKO cells, suggesting conversion of these marks to H3K36me2 in KMS11 cells (Figure 2H). No other significant differences in histone methylation were observed (Figure 2H). Thus, we conclude that NSD2 does not trimethylate H3K36 or dimethylate H4K20, and NSD2 is required for the majority of H3K36me2 present in several cancer cell types, including t(4;14)⁺ myeloma cells.

t(4;14)⁺-driven NSD2 overexpression triggers genome-wide reprogramming of H3K36me2

We next used ChIP-seq (chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing) to determine the genomic distribution of H3K36me2 in the absence or presence of the t(4;14) translocation (TKO2 and KMS11 cells, respectively). In TKO2 cells, which express NSD2 only from one wild-type allele (see Figure 2E, 2G, S1G), H3K36me2 signal was preferentially enriched in intragenic versus intergenic regions on a representative chromosome (Figure 3A, bottom panel for higher resolution image). In contrast, in t(4;14)⁺ KMS11 cells the H3K36me2 signal does not map to gene bodies but rather is dispersed throughout the chromosome (Figure 3A). On a genome-wide scale, in two independent H3K36me2 ChIP-seq experiments, the majority of H3K36me2 peaks in TKO2 cells map to intragenic regions, whereas in KMS11 cells, H3K36me2 peaks are largely found within intergenic regions (Figure 3B; Figure S2A; independent biological ChIP-seq replica are shown in Supplementary Figures). Despite the high global levels of H3K36me2 in KMS11 cells, peak-calling programs identified relatively few peaks due to the widespread enrichment of H3K36me2 throughout the KMS11 genome (e.g. on chromosome 21, 35 peaks in KMS11 cells versus 236 peaks in TKO cells (Figure 3A)). To circumvent potential computational bias in calling peaks, the genomic distribution of the raw number of H3K36me2-associated reads per nucleotide was determined. As shown in Figure 3C, independent of read numbers, H3K36me2-bound nucleotides in KMS11 cells are found dispersed throughout the genome, with an intergenic/intragenic ratio paralleling the intergenic/intragenic composition of the whole genome (Figure 3C; Figure S2B). In contrast, in TKO2 cells, H3K36me2-bound nucleotides, like H3K36me2 peaks, preferentially map within gene bodies (Figure 3C; Figure S2B).

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Figure 3

t(4;14)-driven NSD2 overexpression obliterates the normal genome-wide and gene-specific distribution of H3K36me2

(A), (B) and (C) t(4;14)-associated NSD2 overexpression obliterates the normal genome-wide distribution of H3K36me2. (A) H3K36me2 ChIP-seq signals from KMS11 and TKO2 cells across a representative chromosome are shown. Top two insets: H3K36me2 distribution on chromosome 21 in the indicated cell lines. H3K36me2 peak #s are indicated. Bottom two insets: Higher resolution track of H3K36me2 ChIP signal from 23–29 megabasepairs (mb) on chromosome 21. Genes are marked below the track. (B) Percent of H3K36me2-enriched peaks localized to either intergenic (yellow) or intragenic (purple) regions throughout the genome in KMS11 and TKO2 cells. Number of H3K36me2 peaks in each cell line is shown. (C) Distribution of nucleotides associated with the indicated number of H3K36me2 ChIP-seq reads mapping to intergenic (yellow) and intragenic (purple) regions in KMS11 and TKO2 cells. p-values are calculated for the indicated read thresholds. The intergenic versus intragenic composition of the whole genome is shown.

(D) Normal H3K36me2 distribution within genes is abolished in t(4;14)⁺ myeloma cells. Average H3K36me2 ChIP signal across 20,910 annotated genes in KMS11 (left; blue) and TKO2 (right; red) cells. The transcribed bodies of all genes were normalized to 15 kilobasepairs (kb). The arrow in the schematic illustrates the TSS.

To specifically investigate H3K36me2 distribution within gene bodies, the average signal of H3K36me2 across 20,910 annotated genes was determined in TKO2 and KMS11 cells. In TKO2 cells, H3K36me2 signal is modest in the promoter regions, peaks proximal to the transcription start site (TSS), and gradually decays downstream into the transcribed body away from the TSS (Figure 3D, right inset; Figure S2C). In contrast, in KMS11 cells, there is no prominent TSS-proximal area of H3K36me2 enrichment and little overall variance in H3K36me2 signal intensity across the average gene unit (Figure 3D, left inset; Figure S2C). The results in TKO2 cells are consistent with a ChIP-chip-based genome-wide binding study in Drosophila of H3K36me2 distribution (Bell et al., 2007). Thus, in mammalian cells we propose that H3K36me2 normally maps to gene bodies, and t(4;14)-driven overexpression of NSD2 disrupts the physiologic genomic organization of H3K36me2.

NSD2 promotes transcription

Previous studies have implicated NSD2 as a negative regulator of transcription (Kim et al., 2008; Marango et al., 2008; Nimura et al., 2009), though H3K36me2 is generally associated with gene activation (Bannister et al., 2005; Kizer et al., 2005; Krogan et al., 2003). To investigate the relationship between NSD2 and transcription, comparative gene expression analysis between KMS11 cells and TKO cells and between KMS11 cells stably expressing control shRNA or two independent NSD2-targeting shRNAs were determined (Figure 4A and S3A). Employing a linear model statistical analysis (Smyth et al., 2003), NSD2 expression correlated with upregulation for the large majority of genes displaying statistically significant expression changes (Figure 4A and S3A). Real-time PCR independently confirmed the differential expression of a number of genes identified in the microarray analyses (Figure S3B). Based on these data we conclude that NSD2 expression is linked to transcription activation.

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Figure 4

NSD2 activates transcription and promotes an oncogenic program in KMS11 cells

(A) Depletion of NSD2 by targeted inactivation of t(4;14)-associated NSD2 allele in KMS11 cells correlates with global downregulation of transcription. Genome-wide expression profiling of KMS11 cells in comparison to the two TKO cell lines. Top: heatmap representation of differentially expressed genes in TKO2 versus KMS11 cells (n=3). Numerical expression values for each gene were median centered and scaled to range from −1.0 (blue; low expression) to 1.0 (yellow; high expression). Bottom: overlap of differentially expressed genes between the two TKO cell lines. Activated: upregulated in KMS11/TKO cells; repressed: downregulated in KMS11/TKO cells. p-values: statistical significance of the overlap.

(B) Positive correlation between H3K36me2 enrichment and gene expression is abolished by NSD2 overexpression. Average H3K36me2 profile in the indicated cell lines across the 20,910 annotated genes separated into three groups based on absolute expression units from the datasets described in (A).

(C) In KMS11 cells, H3K36me2 levels are elevated at NSD2-dependent upregulated genes. The average H3K36me2 profile in the indicated cell lines across the top 500 genes upregulated in KMS11/TKO2 cells (Group A: blue) and the top 500 genes downregulated in KMS11/TKO2 cells (Group B: green).

(D) NSD2 promotes expression of normally silent genes. Top: scatter plot of absolute gene transcript levels for 20,910 annotated genes in KMS11 versus TKO2 cells. The percent of Group A (blue) and Group B (green) genes that fall within the 3 expression quantile categories (low, medium, and high) is shown at right.

(E) t(4;14)-driven NSD2 overexpression promotes expression of genes involved in cancer-signaling pathways. KEGG pathway analysis of group A and group B genes using p-value cutoff=0.1 and sorted by the percentage of genes within a functional group.

(F) Genes upregulated in t(4;14)⁺ myeloma cells constitute a common signature in diverse cancers. Oncomine cancer concept analysis of group A and B genes with genes overexpressed in different cancers using Q-value cutoff=0.05 and odds ratio cutoff=3. Significant cancer concepts sorted by the odds ratio.

(G) Genes upregulated in t(4;14)⁺ KMS11 cells are co-expressed with NSD2 in myeloma patient samples. Table: number of genes that positively (276) or negatively (203) correlate with NSD2 expression in the Multiple Myeloma Research Consortium patient sample database and the overlap with group A and B genes. p-values: statistical significance of the overlap.

(H) NSD2 directly binds at target genes. ChIP analysis of NSD2 occupancy across the TGFA and PAK1 genes in KMS11 and TKO2 cells. Top: schematics of the two genes. Arrow indicates the TSS and numbers the location of ChIP primer pairs. Middle: snapshot of H3K36me2 ChIP-seq signal at TGFA and PAK1 in the indicated cell lines. Bottom: NSD2 ChIP signals at the indicated primer pairs. Protein A beads used in control ChIP. Error bars indicate the standard error of the mean (s.e.m.) from 3 experiments.

We next determined the relationship between NSD2-mediated H3K36me2 enrichment and gene expression level. Using the expression profiles obtained from KMS11 and TKO2 cells, the 20,910 annotated genes present in the data sets were partitioned into high, medium, and low expression groups based upon absolute expression level and the average H3K36me2 distribution for each group was determined. In TKO2 cells, a clear correlation was observed between H3K36me2 and gene expression: the most highly expressed genes have the highest H3K36me2 signal and the lowest expressed genes have little H3K36me2 enrichment (Figure 4B, bottom panel; Figure S3C). These results provide genome-wide evidence that H3K36me2 localization at gene bodies positively correlates with transcription levels in mammalian cells.

In KMS11 cells, high H3K36me2 signal did not correlate with gene expression, indicating that H3K36me2 is not strictly required for transcription (Figure 4B, top panel; Figure S3C). However, the observation of t(4;14)-dependent changes in cellular transcription profiles suggests that at a subset of genes, localized H3K36me2 enrichment is sufficient to activate expression. We therefore analyzed H3K36me2 distribution within genes that are differentially expressed in KMS11 cells relative to TKO2 cells, grouped into the top 500 upregulated genes (group A) or the top 500 downregulated genes (group B). As shown in Figure 4C, within KMS11 cells the average H3K36me2 signal is higher in group A than group B, and within TKO2 cells the average H3K36me2 signal is higher in group B than group A (also see Figure S3D). These findings indicate that in KMS11 cells, H3K36me2 enrichment at a distinct set of genes positively correlates with transcription (i.e. group A versus group B). Further, a scatter plot comparing absolute expression levels for all 20,910 genes in KMS11 versus TKO2 cells revealed that a large fraction of group A genes are expressed at low levels in TKO2 cells (Figure 4D). Together, these results argue that (i) H3K36me2 is sufficient but not necessary to induce transcription, and (ii) in KMS11 cells, NSD2-mediated localized elevation of H3K36me2 induces transcription at normally inert genes.

NSD2 promotes an oncogenic gene expression program

Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was employed to characterize the biological signaling pathways associated with t(4;14)-driven NSD2 overexpression. The top functional categories of group A genes included cancer-associated and cell migration signaling pathways (Figure 4E). In contrast, group B genes are associated with immunologic-related B cell functions (Figure 4E). Moreover, the signature of upregulated genes comprising group A, but not group B genes, overlaps with the transcriptional signature of several cancers present in the Oncomine Concept Database (Figure 4F). Finally, group A genes show significant overlap with genes that are co-upregulated with NSD2 in myeloma patient samples (Figure 4G and Figure S3E). Thus, NSD2 overexpression in KMS11 cells might alter the balance of transcriptional programs away from normal plasma cell gene expression pathways to activation of pathways that promote myelomagenesis.

Next, a systematic quantitative direct ChIP strategy was used to determine if group A genes are direct targets of NSD2. In all regions spanning four oncogenes (TGFA, PAK1, MET, and RRAS2) that have greater H3K36me2 signal in KMS11 cells than in TKO2 cells, NSD2 binding was significantly higher in KMS11 cells than in TKO2 cells (Figure 4H; Figure S3F). Together, these data argue for a model in which t(4;14)-driven NSD2 overexpression leads to aberrant enrichment of H3K36me2 at normally silent cancer-associated genes, triggering increased expression of these oncogenes.

NSD2 catalytic activity promotes transcriptional activation at oncogenic loci

To test the specific role of NSD2 methylation activity in aberrant oncogene induction, we screened for NSD2 catalytic mutants based on sequence homology with other SET domain-containing proteins (Dillon et al., 2005)(Figure S1A). NSD2 proteins harboring several amino acid substitutions reported in the literature to inactivate NSD2 (Marango et al., 2008; Martinez-Garcia et al., 2011; Pei et al., 2011) retained robust methylation activity (Figure S4A; data not shown). Instead, a tyrosine to alanine substitution at amino acid Y1092 or Y1179 (Y1092A and Y1179A, respectively) abolished NSD2 methylation of nucleosomes in vitro (Figure 5A). To model t(4;14)-driven expression of NSD2, a reconstitution system was established in which TKO2 cells were complemented with NSD2_WT, NSD2_Y1092A, or NSD2_Y1179A (cell lines named NSD2_WT, NSD2_Y1092A, or NSD2_Y1179A, respectively; see schematic Figure 5B) to restore NSD2 amounts to those detected in KMS11 cells (Figure 5C). Only NSD2_WT, but not the NSD2 catalytic mutants, reconstituted global H3K36me2 signal to the amounts detected in KMS11 cells (Figure 5C).

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Figure 5

NSD2 catalytic activity is required for transcriptional activation at oncogenic loci

(A) Identification of catalytically inactive NSD2 mutants. Top: autoradiogram of in vitro methylation assay with NSD2_SET and the two mutants (Y1092A and Y1179A) on native nucleosomes. Coomassie stain of NSD2_SET proteins (middle panel) and nucleosomes (bottom panel) is shown.

(B) Schematic of NSD2 cellular reconstitution system. Full-length NSD2 or catalytically inactive NSD2 (NSD2_Y1092A, and NSD2_Y1179A) were introduced into TKO2 cells by lentiviral transduction.

(C) Complementation of TKO2 cells with NSD2_WT but not catalytically inactive NSD2 increases global H3K36me2 to KMS11 levels. Western analysis of WCE from KMS11 cells, TKO2 cells, and TKO2 cells stably transduced with wild-type or catalytically inactive NSD2.

(D and E) Complementation of TKO2 cells with NSD2_WT but not with catalytic mutants increases H3K36me2 levels at target oncogenes and activates expression of these genes. (D) ChIP analyses of NSD2 occupancy (top; y axis: %input) and H3K36me2 signal (bottom; y axis: H3K36me2/H3) at four genes at the location indicated in Figures 4H and S3F: TGFA (#4), MET (#2), PAK1 (#2) and RRAS2 (#5). Error bars indicate s.e.m. from 3 experiments. (E) ChIP analyses of H3K4me3 levels at promoter regions (top) and quantitative RT-PCR analysis of mRNA transcripts (bottom) of the genes in (D).

At chromatin, NSD2 occupancy at t(4;14)-associated NSD2-target genes TGFA, MET, PAK1 and RRAS2 was partially to fully reconstituted in NSD2_WT, NSD2_Y1092A, or NSD2_Y1092A cell lines (Figure 5D). However, only NSD2_WT, but not the catalytic mutants, reconstituted H3K36me2 ChIP signal at the four genes to levels approaching those observed in KMS11 cells (Figure 5D). Moreover, co-occurrence of NSD2 binding and H3K36me2 elevation was associated with H3K4me3 promoter enrichment and transcription of the NSD2-target genes (Figure 5E). These data further support a direct role for NSD2 dimethylation of H3K36 in activating transcription and argue that NSD2 overexpression can change the state of chromatin from an inert to active form that promotes transcription.

Catalytically active NSD2 restores tumorigenicity of t(4;14)-negative myeloma cells

KMS11 cells proliferate more rapidly and grow more aptly in an anchorage-independent environment relative to TKO2 cells (Lauring et al., 2008). Moreover, proliferation of RNAi-mediated NSD2-depleted KMS11 cells is attenuated relative to control cells, suggesting NSD2 dosage regulates cancer cell phenotypes (Figure S4B). Consistent with the RNAi results, complementation of TKO2 cells with NSD2_WT, but not the NSD2 catalytic mutants, increased the cellular proliferation rate to match that of KMS11 cells (Figure 6A). In addition, NSD2_WT cells, but not TKO2 and NSD2_Y1179A cells, form colonies in methylcellulose (a measure of anchorage-independent growth) with efficiency comparable to KMS11 cells (Figure 6B).

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Figure 6

Catalytically active NSD2 confers tumorigenicity upon t(4;14)⁻ negative cells

(A) Complementation with NSD2_WT but not catalytically inactive NSD2 accelerates the proliferation rate of TKO2 cells. Cell numbers in the indicated lines were determined over 9 days. Error bars indicate s.e.m. from 3 independent experiments.

(B) Complementation of TKO2 cells with NSD2_WT but not with NSD2_Y1179A promotes anchorage-independent growth. The ability of the indicated cells lines to grow colonies in methylcellulose is shown. Bar graph indicates # of colonies/per field 21 days after seeding. Error bars indicate s.e.m. from 3 independent experiments.

(C and D) Catalytically active NSD2 confers xenograft tumor formation and invasion capacity upon t(4;14)-negative cells. (C) KMS11, TKO2, NSD2, and NSD2_Y1179A cell lines stably expressing GFP-luciferase biomarkers were introduced into SCID/Beige mice via intraperitoneal injection. Top: western analysis of WCE using anti-GFP antibodies. Total H3 is shown as a loading control. Middle: # of tumor-bearing mice at day 28 from 2 independent experiments. Bottom: representative bioluminescent images of mice 4 weeks after injection. (D) Cell lines as in (C) were introduced into non-irradiated SCID/Beige mice via intravenous tail vein injection. Top: western analysis of WCE as in (C). Middle: # of tumor-bearing mice at day 28. Bottom: representative bioluminescent images of mice 4 weeks after injection.

A mouse xenograft model system was used to assess the role of NSD2 methylation activity in tumor formation in vivo. SCID/Beige mice were injected intraperitoneally with KMS11, TKO2, NSD2_WT, and NSD2_Y1179A cells stably expressing GFP-luciferase biomarkers to allow for in vivo live-cell imaging (Creusot et al., 2008). 28 days after injection – in two independent experiments and in multiple mice – KMS11 and NSD2_WT cells formed tumors in the peritoneal cavity, whereas TKO2 and NSD2_Y1179A cells failed to grow (Figure 6C). In myeloma disease, proliferation of malignant plasma cells within the bone marrow (BM) compartment eventually overwhelms and disrupts normal BM function (Anderson and Carrasco, 2011). The role of NSD2 in BM seeding and invasion was determined in non-irradiated SCID/Beige mice injected intravenously with the biomarked cell lines. In multiple mice, the signal from both TKO2 and NSD2_Y1179A cells was not detected one week after injection (Figure 6D and S4C). In contrast, in 5/5 injections with KMS11 cells and 4/5 injections with NSD2_WT cells, the signal grew stronger over time and was consistent with the cells seeding in the BM of major bones such as femur and pelvis (Figure 6D; Figure S4C). Immunohistochemical staining of bone marrow sections confirmed the presence of KMS11 cells in the femur medullary cavities (data not shown). Thus, we conclude that catalytically active NSD2 directly promotes neoplastic growth in vivo.

Xenograft mouse model

10^6 cells stably expressing GFP-luciferase fusion protein were directly injected into the peritoneal cavities or tail veins of SCID/Beige mice. Tumor growth was measured weekly by bioluminescence imaging. All mice were treated in accordance with AAALAC approved guidelines at Stanford University (protocol number: 15066).

We thank D. Reinberg for NSD2 and SETD2 antibody. This work was supported in part by grants from the NIH to O.G. (R01 GM079641), W.L. (U01DA025956) and B.A.G. (DP2OD007447), GlaxoSmithKline to OG, the DOD to W.L. (PC094421), an ASMS Research Award, and NJCCR SEED grant to B.A.G, a Genentech Foundation Predoctoral Fellowship for A.J.K. and a NSF Fellowship to B.M.Z.. W.L. is a recipient of a Duncan Scholar Award. O.G. is a recipient of an Ellison Senior Scholar in Aging Award.