ChIP-seq for PAX8 and histone modifications in Renal Cell Carcinoma cell lines.
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ABSTRACT:
PROVIDER: PRJEB31828 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this experiment we analyzed the genome wide occupancy of PAX8 by ChIP-seq in four Renal Cell Carcinoma cell lines. Additionally we performed ChIP-seq also for histone modifications correlated with transcriptional activity (H3K27ac), enhancers (H3K4me1) and promoters (H3K4me3). Unrelated IgG was used as a background noise control.
2019-06-28 | E-MTAB-7812 | biostudies-arrayexpress
Project description:In this experiment we examined the genes regulated by PAX8 knockdown in four renal cell carcinoma models. Four different cell lines bearing a validated doxycycline (DOX) inducible shRNA against PAX8 were treated with DOX for 96 hours and their gene expression profile analyzed by RNA-seq.
2019-06-28 | E-MTAB-7808 | biostudies-arrayexpress
Project description:RNA-seq upon PAX8 knockdown in Renal Cell Carcinoma cell lines
| PRJEB31824 | ENA
Project description:The oncogenic potential of cancer-associated genetic alterations displays strong tissue-selectivity, the origins of which remain poorly understood. Here, we demonstrate that the lineage transcription factor PAX8 is essential for oncogenic signaling downstream of the most common genetic alterations causing clear cell renal cell carcinoma (ccRCC). Through interaction at a distal enhancer element PAX8 facilitates CCND1 expression by HIF2A, an oncogenic driver that is genetically activated due to VHL loss in ~90% of ccRCCs. PAX8 binding at this enhancer which mediates HIF2A-dependent ccRCC formation is inhibited by the common ccRCC protective allele C at rs7948643. In addition, PAX8 supports MYC expression in ccRCC through HNF1B, another renal lineage factor. Transcriptional lineage factors are thus critical determinants of the tissue-specific cancer risk associated with somatic and inherited genetic variants. Our data also suggest that lineage factors could be targeted for therapeutic inhibition of canonical oncogenic drivers such as MYC and CCND1.
2022-03-11 | GSE163000 | GEO
Project description:The oncogenic potential of cancer-associated genetic alterations displays strong tissue-selectivity, the origins of which remain poorly understood. Here, we demonstrate that the lineage transcription factor PAX8 is essential for oncogenic signaling downstream of the most common genetic alterations causing clear cell renal cell carcinoma (ccRCC). Through interaction at a distal enhancer element PAX8 facilitates CCND1 expression by HIF2A, an oncogenic driver that is genetically activated due to VHL loss in ~90% of ccRCCs. PAX8 binding at this enhancer which mediates HIF2A-dependent ccRCC formation is inhibited by the common ccRCC protective allele C at rs7948643. In addition, PAX8 supports MYC expression in ccRCC through HNF1B, another renal lineage factor. Transcriptional lineage factors are thus critical determinants of the tissue-specific cancer risk associated with somatic and inherited genetic variants. Our data also suggest that lineage factors could be targeted for therapeutic inhibition of canonical oncogenic drivers such as MYC and CCND1.
2022-03-11 | GSE162948 | GEO
Project description:The oncogenic potential of cancer-associated genetic alterations displays strong tissue-selectivity, the origins of which remain poorly understood. Here, we demonstrate that the lineage transcription factor PAX8 is essential for oncogenic signaling downstream of the most common genetic alterations causing clear cell renal cell carcinoma (ccRCC). Through interaction at a distal enhancer element PAX8 facilitates CCND1 expression by HIF2A, an oncogenic driver that is genetically activated due to VHL loss in ~90% of ccRCCs. PAX8 binding at this enhancer which mediates HIF2A-dependent ccRCC formation is inhibited by the common ccRCC protective allele C at rs7948643. In addition, PAX8 supports MYC expression in ccRCC through HNF1B, another renal lineage factor. Transcriptional lineage factors are thus critical determinants of the tissue-specific cancer risk associated with somatic and inherited genetic variants. Our data also suggest that lineage factors could be targeted for therapeutic inhibition of canonical oncogenic drivers such as MYC and CCND1.
2022-03-11 | GSE163485 | GEO
Project description:The oncogenic potential of cancer-associated genetic alterations displays strong tissue-selectivity, the origins of which remain poorly understood. Here, we demonstrate that the lineage transcription factor PAX8 is essential for oncogenic signaling downstream of the most common genetic alterations causing clear cell renal cell carcinoma (ccRCC). Through interaction at a distal enhancer element PAX8 facilitates CCND1 expression by HIF2A, an oncogenic driver that is genetically activated due to VHL loss in ~90% of ccRCCs. PAX8 binding at this enhancer which mediates HIF2A-dependent ccRCC formation is inhibited by the common ccRCC protective allele C at rs7948643. In addition, PAX8 supports MYC expression in ccRCC through HNF1B, another renal lineage factor. Transcriptional lineage factors are thus critical determinants of the tissue-specific cancer risk associated with somatic and inherited genetic variants. Our data also suggest that lineage factors could be targeted for therapeutic inhibition of canonical oncogenic drivers such as MYC and CCND1.
2022-03-11 | GSE163487 | GEO
Project description:Background: The mammalian kidneys maintain salt and water homeostasis for proper electrolyte balance and hydration. As the glomerular filtrate passes through the nephron and into the renal medulla, electrolytes, water, and urea are reabsorbed through the concerted actions of solute carrier channels and aquaporins located at various positions along the nephron and in the outer and inner medulla. Renal epithelial cells develop from Pax2 positive proliferating stem cells that suppress Pax2 expression once differentiated into mature proximal and distal tubules, but continue to express the related Pax8 protein. The collecting tubules and renal medulla are derived from a Pax2 positive ureteric bud epithelia that continue to express Pax2 and Pax8 in adult kidneys. Despite the necessity for Pax2 in renal development, functions for Pax2 or Pax8 in adult renal epithelia have not been established. Methods: In this report, we deleted either Pax2, Pax8, or both genes in adult mice and examined the phenotypes and changes in gene expression patterns. The mechanism of Pax8 mediated activation of potential target genes was described in inner medullary collecting duct cells. Results: Mice with induced deletions of both Pax2 and Pax8 exhibit severe polyuria that can be attributed to significant changes in the expression of solute carriers, such as the urea transporter UTA1, and aquaporins within the inner and outer medulla. Furthermore, Pax8 expression is induced by high salt in collecting duct cells and activates the UTA1 gene by recruiting a histone methyltransferase complex to the promoter. Conclusions: These data uncover novel functions for Pax proteins, in adult renal epithelia, that are essential for retaining water and concentrating urine.
2019-12-05 | GSE141455 | GEO
Project description:The proteome of clinical tissue samples diagnosed with clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (pRCC) were evaluated analyzed along with the dataset identifier PXD022018 to establish a potential discriminative biomarker panel of proteins for these tumors subtypes.
2021-12-15 | PXD023296 | Pride
Project description:Renal cell carcinoma comprises several histological types with different clinical behavior. Accurate pathological characterization is important in the clinical management of these tumors. We describe gene expression profiles in 41 renal tumors determined by using DNA microarrays containing 22,648 unique cDNAs representing 17,083 different UniGene Clusters, including 7230 characterized human genes. Differences in the patterns of gene expression among the different tumor types were readily apparent; hierarchical cluster analysis of the tumor samples segregated histologically distinct tumor types solely based on their gene expression patterns. Conventional renal cell carcinomas with clear cells showed a highly distinctive pattern of gene expression. Papillary carcinomas formed a tightly clustered group, as did tumors arising from the distal nephron and the normal kidney samples. Surprisingly, conventional renal cell carcinomas with granular cytoplasm were heterogeneous, and did not resemble any of the conventional carcinomas with clear cytoplasm in their pattern of gene expression. Characterization of renal cell carcinomas based on gene expression patterns provides a revised classification of these tumors and has the potential to supply significant biological and clinical insights. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Computed
2006-01-31 | E-GEOD-4125 | biostudies-arrayexpress