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Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.

Verfaillie A, Imrichova H, Atak ZK, Dewaele M, Rambow F, Hulselmans G, Christiaens V, Svetlichnyy D, Luciani F, Van den Mooter L, Claerhout S, Fiers M, Journe F, Ghanem GE, Herrmann C, Halder G, Marine JC, Aerts S - Nat Commun (2015)

Bottom Line: This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively.Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors.Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.

ABSTRACT
Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is a critical event at the origin of metastatic spreading. Here we generate transcriptome, open chromatin and histone modification maps of melanoma cultures; and integrate this data with existing transcriptome and DNA methylation profiles from tumour biopsies to gain insight into the mechanisms underlying this key reprogramming event. This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively. Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors. Using regulatory landscapes and in silico analysis, we show that transcriptional reprogramming underlies the distinct cellular states present in melanoma. Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.

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Transcriptome and epigenome profiling in 11 melanoma cell cultures.RNA-seq, FAIRE-seq and ChIP-seq against H3K27Ac and H3K27me3 across 10 short-passage melanoma cultures and one melanoma cell line SK-MEL-5. The SOX10 gene shows high expression and its upstream regions contain high H3K27ac and FAIRE but low H3K27me3 signal in the nine proliferative (blue) samples. In the two invasive (orange) samples, there is no SOX10 expression, no H3K27Ac and FAIRE peaks but high H3K27me3 peaks. Upper panel shows one invasive sample (MM047) and one proliferative sample (MM011). Lower panels showing zoom in around the promoter region of SOX10 with tracks for all 11 samples for each of the four data types. Vertical axes represent normalized coverage for each data track. Arrows indicate regions of interest that are different between proliferative and invasive states. Other genes are illustrated in Supplementary Figs 4 and 5 and in the UCSC Genome Browser using our Melanoma Track Hub (see Methods).
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f2: Transcriptome and epigenome profiling in 11 melanoma cell cultures.RNA-seq, FAIRE-seq and ChIP-seq against H3K27Ac and H3K27me3 across 10 short-passage melanoma cultures and one melanoma cell line SK-MEL-5. The SOX10 gene shows high expression and its upstream regions contain high H3K27ac and FAIRE but low H3K27me3 signal in the nine proliferative (blue) samples. In the two invasive (orange) samples, there is no SOX10 expression, no H3K27Ac and FAIRE peaks but high H3K27me3 peaks. Upper panel shows one invasive sample (MM047) and one proliferative sample (MM011). Lower panels showing zoom in around the promoter region of SOX10 with tracks for all 11 samples for each of the four data types. Vertical axes represent normalized coverage for each data track. Arrows indicate regions of interest that are different between proliferative and invasive states. Other genes are illustrated in Supplementary Figs 4 and 5 and in the UCSC Genome Browser using our Melanoma Track Hub (see Methods).

Mentions: The above findings support in vitro short-term cultures as a valid model system that can be exploited to decipher the chromatin landscapes and regulatory networks underlying these two transcriptional cell states. Therefore, we profiled the transcriptome and chromatin landscape of 10 short-passage melanoma cultures previously described14 and one classical melanoma cell line (SK-MEL-5; see accession code for data availability15). The transcriptome of all 11 samples was compared with publicly available gene expression data from melanoma cultures and with the clusters of tumour biopsies described above using SOMs (Fig. 1c). This comparison indicated that cultures MM047 and MM099 are in an invasive transcriptional state, while the remaining harbour a transcriptome reminiscent of the proliferative state (Supplementary Table 2). This correspondence was further supported by a significant enrichment of the invasive and proliferative gene signatures from Hoek et al.3, and by the high expression of invasive marker genes such as ZEB1, SOX9 and WNT5A (Supplementary Figs 3, 5 and6). In contrast, these samples have undetectable SOX10 and MITF, while the other nine samples express high SOX10 and MITF levels (Fig. 2, Supplementary Figs 3a and 7). Using these data we established a new gene signature for each state, consisting of 772 and 643 genes for the proliferative and invasive phenotypes, respectively (Supplementary Data 1). Comparing our data with the Hoek gene signatures316 identified 100% of Hoek's proliferative genes upregulated in our proliferative samples, while 100% of Hoek's invasive genes are upregulated in our invasive samples (Supplementary Fig. 3a). Importantly, the cells with an invasive transcriptional profile do exhibit enhanced capabilities to invade in a Matrigel assay compared with the cell lines with a transcriptional proliferative state (Supplementary Fig. 8). In addition, similar to the results obtained using the TCGA cohort, the proliferative versus invasive split is not correlated with any specific mutations in known melanoma driver genes, such as BRAF (Supplementary Fig. 9). Again, this is consistent with the view that acquisition of the invasive cell state is likely to be a consequence of transcriptional reprogramming rather than being driven by any specific genetic alterations.


Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.

Verfaillie A, Imrichova H, Atak ZK, Dewaele M, Rambow F, Hulselmans G, Christiaens V, Svetlichnyy D, Luciani F, Van den Mooter L, Claerhout S, Fiers M, Journe F, Ghanem GE, Herrmann C, Halder G, Marine JC, Aerts S - Nat Commun (2015)

Transcriptome and epigenome profiling in 11 melanoma cell cultures.RNA-seq, FAIRE-seq and ChIP-seq against H3K27Ac and H3K27me3 across 10 short-passage melanoma cultures and one melanoma cell line SK-MEL-5. The SOX10 gene shows high expression and its upstream regions contain high H3K27ac and FAIRE but low H3K27me3 signal in the nine proliferative (blue) samples. In the two invasive (orange) samples, there is no SOX10 expression, no H3K27Ac and FAIRE peaks but high H3K27me3 peaks. Upper panel shows one invasive sample (MM047) and one proliferative sample (MM011). Lower panels showing zoom in around the promoter region of SOX10 with tracks for all 11 samples for each of the four data types. Vertical axes represent normalized coverage for each data track. Arrows indicate regions of interest that are different between proliferative and invasive states. Other genes are illustrated in Supplementary Figs 4 and 5 and in the UCSC Genome Browser using our Melanoma Track Hub (see Methods).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403341&req=5

f2: Transcriptome and epigenome profiling in 11 melanoma cell cultures.RNA-seq, FAIRE-seq and ChIP-seq against H3K27Ac and H3K27me3 across 10 short-passage melanoma cultures and one melanoma cell line SK-MEL-5. The SOX10 gene shows high expression and its upstream regions contain high H3K27ac and FAIRE but low H3K27me3 signal in the nine proliferative (blue) samples. In the two invasive (orange) samples, there is no SOX10 expression, no H3K27Ac and FAIRE peaks but high H3K27me3 peaks. Upper panel shows one invasive sample (MM047) and one proliferative sample (MM011). Lower panels showing zoom in around the promoter region of SOX10 with tracks for all 11 samples for each of the four data types. Vertical axes represent normalized coverage for each data track. Arrows indicate regions of interest that are different between proliferative and invasive states. Other genes are illustrated in Supplementary Figs 4 and 5 and in the UCSC Genome Browser using our Melanoma Track Hub (see Methods).
Mentions: The above findings support in vitro short-term cultures as a valid model system that can be exploited to decipher the chromatin landscapes and regulatory networks underlying these two transcriptional cell states. Therefore, we profiled the transcriptome and chromatin landscape of 10 short-passage melanoma cultures previously described14 and one classical melanoma cell line (SK-MEL-5; see accession code for data availability15). The transcriptome of all 11 samples was compared with publicly available gene expression data from melanoma cultures and with the clusters of tumour biopsies described above using SOMs (Fig. 1c). This comparison indicated that cultures MM047 and MM099 are in an invasive transcriptional state, while the remaining harbour a transcriptome reminiscent of the proliferative state (Supplementary Table 2). This correspondence was further supported by a significant enrichment of the invasive and proliferative gene signatures from Hoek et al.3, and by the high expression of invasive marker genes such as ZEB1, SOX9 and WNT5A (Supplementary Figs 3, 5 and6). In contrast, these samples have undetectable SOX10 and MITF, while the other nine samples express high SOX10 and MITF levels (Fig. 2, Supplementary Figs 3a and 7). Using these data we established a new gene signature for each state, consisting of 772 and 643 genes for the proliferative and invasive phenotypes, respectively (Supplementary Data 1). Comparing our data with the Hoek gene signatures316 identified 100% of Hoek's proliferative genes upregulated in our proliferative samples, while 100% of Hoek's invasive genes are upregulated in our invasive samples (Supplementary Fig. 3a). Importantly, the cells with an invasive transcriptional profile do exhibit enhanced capabilities to invade in a Matrigel assay compared with the cell lines with a transcriptional proliferative state (Supplementary Fig. 8). In addition, similar to the results obtained using the TCGA cohort, the proliferative versus invasive split is not correlated with any specific mutations in known melanoma driver genes, such as BRAF (Supplementary Fig. 9). Again, this is consistent with the view that acquisition of the invasive cell state is likely to be a consequence of transcriptional reprogramming rather than being driven by any specific genetic alterations.

Bottom Line: This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively.Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors.Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.

ABSTRACT
Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is a critical event at the origin of metastatic spreading. Here we generate transcriptome, open chromatin and histone modification maps of melanoma cultures; and integrate this data with existing transcriptome and DNA methylation profiles from tumour biopsies to gain insight into the mechanisms underlying this key reprogramming event. This shows thousands of genomic regulatory regions underlying the proliferative and invasive states, identifying SOX10/MITF and AP-1/TEAD as regulators, respectively. Knockdown of TEADs shows a previously unrecognized role in the invasive gene network and establishes a causative link between these transcription factors, cell invasion and sensitivity to MAPK inhibitors. Using regulatory landscapes and in silico analysis, we show that transcriptional reprogramming underlies the distinct cellular states present in melanoma. Furthermore, it reveals an essential role for the TEADs, linking it to clinically relevant mechanisms such as invasion and resistance.

Show MeSH
Related in: MedlinePlus