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WES Coding Mutations

Supplementary Methods

Drug Resistant POS Cells Emerge Following Chronic Trametinib Treatment.

Triple-negative breast cancers contain a spectrum of epithelial and mesenchymal phenotypes. SUM-229PE cells represent a model for this heterogeneity, maintaining both epithelial and mesenchymal subpopulations that are genomically similar but distinct in gene expression profiles. We identified differential regions of open chromatin in epithelial and mesenchymal cells that were strongly correlated with regions of H3K27ac. Motif analysis of these regions identified consensus sequences for transcription factors that regulate cell identity. Treatment with the MEK inhibitor trametinib induced enhancer remodeling that is associated with transcriptional regulation of genes in epithelial and mesenchymal cells. Motif analysis of enhancer peaks downregulated in response to chronic treatment with trametinib identified AP-1 motif enrichment in both epithelial and mesenchymal subpopulations. Chromatin immunoprecipitation sequencing (ChIP-seq) of JUNB identified subpopulation-specific localization, which was significantly enriched at regions of open chromatin. These results indicate that cell identity controls localization of transcription factors and chromatin-modifying enzymes to enhancers for differential control of gene expression. We identified increased H3K27ac at an enhancer region proximal to CXCR7, a G-protein–coupled receptor that increased 15-fold in expression in the epithelial subpopulation during chronic treatment. RNAi knockdown of CXCR7 inhibited proliferation in trametinib-resistant cells. Thus, adaptive resistance to chronic trametinib treatment contributes to proliferation in the presence of the drug. Acquired amplification of KRAS following trametinib dose escalation further contributed to POS cell proliferation. Adaptive followed by acquired gene expression changes contributed to proliferation in trametinib-resistant cells, suggesting inhibition of early transcriptional reprogramming could prevent resistance and the bypass of targeted therapy.Implications:We defined the differential responses to trametinib in subpopulations of a clinically relevant in vitro model of TNBC, and identified both adaptive and acquired elements that contribute to the emergence of drug resistance mediated by increased expression of CXCR7 and amplification of KRAS.

Chromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis is not well understood. Interestingly, some translocation-driven cancers exhibit dramatic clinical responses to therapy, such as radiotherapy, although the precise mechanism has not been elucidated. Here we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable sensitivity of myxoid liposarcomas to radiation therapy. FUS-CHOP interacted with chromatin remodeling complexes to regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, colocalized with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylated the prion-like domain of FUS-CHOP to impede these protein–protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupted oncogenic targeting of chromatin remodelers required for FUS-CHOP–driven sarcomagenesis. This mechanism of disruption links phosphorylation of the prion-like domain of an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma.Significance:Prion-like domains, which are frequently translocated in cancers as oncogenic fusion proteins that drive global epigenetic changes, confer sensitivity to radiation via disruption of oncogenic interactions.

Supplementary data figures, tables, and methods.

Chromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis is not well understood. Interestingly, some translocation-driven cancers exhibit dramatic clinical responses to therapy, such as radiotherapy, although the precise mechanism has not been elucidated. Here we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable sensitivity of myxoid liposarcomas to radiation therapy. FUS-CHOP interacted with chromatin remodeling complexes to regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, colocalized with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylated the prion-like domain of FUS-CHOP to impede these protein–protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupted oncogenic targeting of chromatin remodelers required for FUS-CHOP–driven sarcomagenesis. This mechanism of disruption links phosphorylation of the prion-like domain of an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma. Significance: Prion-like domains, which are frequently translocated in cancers as oncogenic fusion proteins that drive global epigenetic changes, confer sensitivity to radiation via disruption of oncogenic interactions.

Triple-negative breast cancers contain a spectrum of epithelial and mesenchymal phenotypes. SUM-229PE cells represent a model for this heterogeneity, maintaining both epithelial and mesenchymal subpopulations that are genomically similar but distinct in gene expression profiles. We identified differential regions of open chromatin in epithelial and mesenchymal cells that were strongly correlated with regions of H3K27ac. Motif analysis of these regions identified consensus sequences for transcription factors that regulate cell identity. Treatment with the MEK inhibitor trametinib induced enhancer remodeling that is associated with transcriptional regulation of genes in epithelial and mesenchymal cells. Motif analysis of enhancer peaks downregulated in response to chronic treatment with trametinib identified AP-1 motif enrichment in both epithelial and mesenchymal subpopulations. Chromatin immunoprecipitation sequencing (ChIP-seq) of JUNB identified subpopulation-specific localization, which was significantly enriched at regions of open chromatin. These results indicate that cell identity controls localization of transcription factors and chromatin-modifying enzymes to enhancers for differential control of gene expression. We identified increased H3K27ac at an enhancer region proximal to CXCR7, a G-protein–coupled receptor that increased 15-fold in expression in the epithelial subpopulation during chronic treatment. RNAi knockdown of CXCR7 inhibited proliferation in trametinib-resistant cells. Thus, adaptive resistance to chronic trametinib treatment contributes to proliferation in the presence of the drug. Acquired amplification of KRAS following trametinib dose escalation further contributed to POS cell proliferation. Adaptive followed by acquired gene expression changes contributed to proliferation in trametinib-resistant cells, suggesting inhibition of early transcriptional reprogramming could prevent resistance and the bypass of targeted therapy. Implications: We defined the differential responses to trametinib in subpopulations of a clinically relevant in vitro model of TNBC, and identified both adaptive and acquired elements that contribute to the emergence of drug resistance mediated by increased expression of CXCR7 and amplification of KRAS.

SummaryChromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis and the effect of cancer therapies on their function are not well understood. Here, we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable radiation sensitivity of myxoid liposarcomas. We identified novel interactions between FUS-CHOP and chromatin remodeling complexes that regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, co-localizes with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylate the prion-like domain of FUS-CHOP to impede these protein-protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupts oncogenic targeting of chromatin remodelers required for FUS-CHOP-driven sarcomagenesis.SignificancePrion-like domains translocated in cancer have been shown to drive global epigenetic changes that are oncogenic. However, some translocation-driven cancers exhibit dramatic clinical responses to therapy, though the mechanism for these responses are not well-understood. Here we show that ionizing radiation can disrupt oncogenic interactions between a fusion oncoprotein and a chromatin remodeling complex, ISWI. This mechanism of disruption links phosphorylation of the prion-like domain in an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma.

Though hematopoietic stem cell transplantation (HSCT) is the preferred treatment for a variety of blood malignancies, its use is limited by the development of acute graft-versus-host disease (aGvHD). Type II innate lymphoid cells (ILC2s) are immune cells that play an important role in maintaining mucosal homeostasis, and our lab has previously shown that ILC2s in the gastrointestinal tract (GI) are sensitive to conditioning therapy prior to HSCT. Strikingly, we have demonstrated that the infusion of activated donor ILC2s markedly reduces aGvHD-associated mortality. We therefore wanted to investigate the mechanism of the loss of protective ILC2s from the GI tract. We hypothesized that ILC2s fail to repopulate the gut after HSCT due to inflammatory environmental cues that convert ILC2 precursors to an alternate, ILC1- or ILC3-like fate. Thus, we evaluated the impact of cytokines associated with commitment on murine ILC2s by exposing them to cytokines that may promote differentiation to an ILC1 or ILC3 fate (IL-1b/IL-12/IFN-γ and TGF-b/IL-6/IL-23, respectively). We found ILC2 cells acquired the ability to secrete TNF and IL-17 after in vitro skewing (with these lineage-defining cytokines. To test the ability of these "ex-ILC2" cells to home to other tissues in vivo, GFP-ILC2s were infused into recipients at the time of transplantation. We tracked GFP-ILC2s to the liver and spleen, where they made IFN-g and IL-17 and expressed transcription factors associated with the ILC1 and ILC3 lineages (Figure 1). Next we assessed the ability of cytokines alter ILC2 fate via epigenetic reprogramming by using ChIP-sequencing to evaluate the presence of histone marks that may underlie cellular plasticity. We show that these changes are associated with alterations in epigenetic marks around pioneer, lineage-determining factors. We therefore chose to test a screen of compounds known to modulate a variety of epigenetic targets to ask if they can maintain or convert ILC2s to alternate fates and identified a number of compounds that target bromodomains, methyltransferases, and histonedeacetylases, respectively, that alter the viability and differentiation of ILC2s into an "ex-ILC2"-like phenotype. Preliminary work suggests that maintenance ofG9a expression is able to rescue the loss of ILC2s, which is being tested in vivo. Taken together, these data provide new insights into mechanisms by which innate lymphoid cell precursors are epigenetically regulated, providing novel approaches to treating aGvHD following HSCT. Figure 1 Disclosures Davis: Triangle Biotechnology: Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Pattenden:Triangle Biotechnology, Inc.: Equity Ownership, Other: Inventor on intellectual property. Serody:Merck: Research Funding; GlaxoSmithKline: Research Funding.

The essential oil of catmint, Nepeta cataria L., contains nepetalactones, that, on hydrogenation, yield the corresponding dihydronepetalactone (DHN) diastereomers. The DHN diastereomer (4R,4aR,7S,7aS)-4,7-dimethylhexahydrocyclopenta[c]pyran-1(3H)-one, DHN 1) was evaluated as mosquito repellent, as was the mixture of diastereomers {mostly (4S,4aR,7S,7aR)-4,7-dimethylhexahydrocyclopenta[c]pyran-1(3H)-one, DHN 2} present after hydrogenation of catmint oil itself. The repellency of these materials to Aedes aegypti L. and Anopheles albimanus Wiedemann mosquitoes was tested in vitro and found to be comparable to that obtained with the well-known insect repellent active ingredient N,N-diethyl-3-methylbenzamide (DEET). DHN 1 and DHN 2 also repelled the stable fly, Stomoxys calcitrans L., in this study. DHN 1, DHN 2, and p-menthane-3,8-diol (PMD), another natural monoterpenoid repellent, gave comparable levels of repellency against An. albimanus and S. calcitrans. Laboratory testing of DHN 1 and DHN 2 using human subjects with An. albimanus mosquitoes was carried out. Both DHN 1 and DHN 2 at 10% (wt:vol) conferred complete protection from bites for significant periods of time (3.5 and 5 h, respectively), with DHN2 conferring protection statistically equivalent to DEET. The DHN 1 and DHN 2 diastereomers were also efficaceous against black-legged tick (Ixodes scapularis Say) nymphs.