GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 2)
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ABSTRACT:
PROVIDER: PRJNA417694 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6269560_1.fastq.gz | Fastqsanger.gz | |||
| SRR6269560_2.fastq.gz | Fastqsanger.gz | |||
| SRR6269551_1.fastq.gz | Fastqsanger.gz | |||
| SRR6269551_2.fastq.gz | Fastqsanger.gz | |||
| SRR6269561_1.fastq.gz | Fastqsanger.gz |
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Project description:The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity. The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model. Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences. The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome. This SuperSeries is composed of the SubSeries listed below.
2017-11-20 | GSE106695 | GEO
Project description:The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity. The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model. Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences. The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.
2018-04-13 | GSE113092 | GEO
Project description:The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity. The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model. Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences. The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.
2017-12-16 | GSE108167 | GEO
Project description:The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity. The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model. Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences. The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.
2017-11-20 | GSE106694 | GEO
Project description:The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. Considering what is known about the complex mechanisms that contribute to the development of resistance it is likely that further development of ER-modulators will yield only incremental improvements. Thus, with the view that resistance is inevitable, we undertook the development of a new approach to treat ER-positive breast cancer by identifying and exploiting targetable vulnerabilities that emerge in endocrine therapy resistant disease. Genomic discovery platforms, including DNASeq, ChIPSeq and RNASeq were used to assess the epigenome, targeting global transcription factor binding profile, and transcriptome in cellular models of endocrine therapy sensitive and resistant disease. DNASeq was first used to identify the chromatin state, with a focus on differences, between these two models. Motif enrichment analysis indicated FOXA1 was a candidate transcription factor influencing the chromatin architecture, which was consistent with previously published studies. This led to the examination of the FOXA1 chromatin binding profile in these models. FOXA1 has previously been described to bind at enhancers. Furthermore, the relative transcription activity of specific enhancers has been shown to be indicated by the epigenomic marks on histones flanking transcription factor binding sites. For this reason, we assessed the specific pattern of histone 3 lysine 4 methylation to confirm enhancer status and histone 3 lysine 27 acetylation as an indicator of transcriptional activity. The specific patterns and distribution of FOXA1 binding was then integrated with this epigenomic information to reveal a subset of enhancers that became activated and another subset that gained enhanced activation in the tamoxifen resistant setting relative to the tamoxifen sensitive model from which it was derived. These results were integrated with the differential transcriptome, or genes shown to be differential expressed based on RNASeq, in the TAMR model as compared to its parental cell line, MCF7-WS8, and confirmed that the active enhancers were in fact associated with genes that were expressed more highly, on average, in the TAMR model. Motif enrichment at these two subgroups of enhancers indicated that another transcription factor, GRHL2, likely interacts with FOXA1 at these active sites. These results were again integrated with the “differential transcriptome” based on RNASeq and confirmed that the active enhancers, and indicated an even stronger enrichment of genes that were expressed more highly, on average, in the TAMR model relative to the MCF7-WS8 model. The GRHL2 transcriptome was then further defined by both GRHL2 ChIPSeq as well as RNASeq by comparing TAMR samples in which downregulation of GRHL2 expression had been achieved via siRNA as compared to control siRNA sequences. The collection of these data defined a subset of genes, the GRHL2 dependent transcriptome, that demonstrated increased expression in TAMR. The results of these cell lines studies were corroborated by assessing the transcriptome of xenograft mouse models of endocrine therapy sensitive and resistant disease. Integrative analysis of these data identified a collateral ER-independent signaling pathway in endocrine therapy resistant tumors that converges upon and modulates the FOXA1 and GRHL2 cistrome/transcriptome.
2017-11-20 | GSE106681 | GEO
Project description:GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer
| PRJNA417687 | ENA
Project description:GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer [ChIP-seq]
| PRJNA449958 | ENA
Project description:GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer [DNase hypersensitivity]
| PRJNA422625 | ENA
Project description:GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 1)
| PRJNA417666 | ENA
Project description:Notwithstanding the positive clinical impact of endocrine therapies in estrogen receptor-alpha (ER?)-positive breast cancer, de novo and acquired resistance limits the therapeutic lifespan of existing drugs. Taking the position that resistance is nearly inevitable, we undertook a study to identify and exploit targetable vulnerabilities that were manifest in endocrine therapy-resistant disease. Using cellular and mouse models of endocrine therapy-sensitive and endocrine therapy-resistant breast cancer, together with contemporary discovery platforms, we identified a targetable pathway that is composed of the transcription factors FOXA1 and GRHL2, a coregulated target gene, the membrane receptor LYPD3, and the LYPD3 ligand, AGR2. Inhibition of the activity of this pathway using blocking antibodies directed against LYPD3 or AGR2 inhibits the growth of endocrine therapy-resistant tumors in mice, providing the rationale for near-term clinical development of humanized antibodies directed against these proteins.
| S-EPMC6874102 | biostudies-literature