Which dataset would you like to analyze?

Use the form below to search 9,145 publicly available datasets published in the Gene Expression Omnibus database and processed by ARCHS4.

 
Mutant p53R270H drives altered metabolism and increased invasion in pancreatic ductal adenocarcinoma
GSE106853
12 samples
Published September 2018
Summary
Pancreatic cancer is characterized by nearly universal activating mutations in KRAS. Among other somatic mutations, TP53 is mutated in more than 75% of human pancreatic tumors. Genetically engineered mice have proven instrumental in studies of the contribution of individual genes to carcinogenesis. Oncogenic Kras mutations occur early during pancreatic carcinogenesis and are considered an initiating event. In contrast, mutations in p53 occur later during tumor progression. In our model, we recapitulated the order of mutations of the human disease, with p53 mutation following expression of oncogenic Kras. Further, using an inducible and reversible expression allele for mutant p53, we inactivated its expression at different stages of carcinogenesis. Notably, the function of mutant p53 changes at different stages of carcinogenesis. Our work establishes a requirement for mutant p53 for the formation and maintenance of pancreatic cancer precursor lesions. In tumors, mutant p53 becomes dispensable for growth. However, it maintains the altered metabolism that characterizes pancreatic cancer and mediates its malignant potential. Further, mutant p53 promotes epithelial-mesenchymal transition (EMT) and cancer cell invasion. This work generates new mouse models that mimic human pancreatic cancer and expands our understanding of the role of p53 mutation, common in the majority of human malignancies.
Organism
Mus musculus
Replicated transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]
GSE70466
6 samples
Published September 2018
Summary
To identify differentially expressed transcripts in Cancer and Normal Prostate cells global transcript abundance was assayed by replicated (n=3) stranded RNA-Sequencing
Organism
Homo sapiens
RNA profiling of 6xAOM induced colon tumors from wt, miR-34a IEC deficient, p53 IEC deficient and miR-34a/p53 IEC deficient mice
GSE99452
12 samples
Published August 2018
Summary
P53 induced Mir34a is a tumor suppressor microRNA that plays important roles in cancer related processes such as proliferation, invasion and metastasis. Simultaneous loss of Mir34a and p53 is often observed in CRC. Here we show that, combined deletion of Mir34a and p53 has synergistic effects in suppressing tumor initiation, progression, invasion and metastasis in CRC by using mice lacking Mir34a and p53 in their intestinal epithelium. By in vivo inhibition of IL6R and SERPINE1, which we identified as up-regulated Mir34a targets in tumors of Mir34a/p53 deficient mice, we obtained preclinical evidence for their therapeutic value for treatment of sporadic CRC.
Organism
Mus musculus
Genome-wide Mapping of Lamin B1 Reveals the Existence of Dynamic and Functional Euchromatin Lamin B1 Domains (eLADs) at the onset of the Epithelial to Mesenchymal Transition
GSE96033
18 samples
Published August 2018
Summary
Lamins (A/C and B) are type V intermediate filaments and constitute the major cytoskeleton component of nuclei. They are assembled forming a filamentous meshwork that is mainly located between the inner nuclear membrane and the peripheral chromatin in where they form structural and conserved elements called lamin-associated domains (LADs) that cover around 40% of the mammalian genome. However, a small fraction of lamins are also located in the nucleoplasm although is still unclear if represents a fraction that is in transit towards the nuclear membrane, a reservoir for protein turnover or they have specific functions in nuclear organization6. Here we mapped genome-wide the localization of lamin B1 from an enriched euchromatin fraction. Our analysis show for the first time that lamin B1 can be also associated with active euchromatin forming domains of about half a megabase on average in size. These euchromatin lamin B1 domains (eLADs) are constituted by active and accessible euchromatin showed by RNAseq and ATACseq. Importantly, we have analyzed its behavior at the onset of the epithelial to mesenchymal transition (EMT), a cellular transformation process essential during development and reactivated in cancer cells. Our results suggest that eLADs are dynamic and functional during EMT. Finally, Hi-C data during this cellular transformation showed changes in the frequency of chromatin contacts around the TSS in genes enriched in lamin B1 before the generation of new regulatory elements in the mesenchymal state. Taken together, these results demonstrate that not only heterochromatin but euchromatin is organized into lamin domains as well. Moreover, these eLADs are dynamic, functional and essential for chromatin organization and gene regulation during the EMT.
Organism
Mus musculus
Gene expression changes in fibroblasts with constitutively active Nrf2 reflect a senescence-associated secretory phenotype (SASP)
GSE106097
6 samples
Published August 2018
Summary
Nrf2 is a key regulator of the cellular antioxidant defense system, and pharmacological Nrf2 activation is a promising strategy for cancer prevention. Here we discovered a novel role of Nrf2 as a regulator of the matrisome. Activation of Nrf2 in fibroblasts induced early onset of cellular senescence. Mechanistically, this resulted from Nrf2-mediated transcription of matrix and matrix-remodeling genes. Fibroblasts with activated Nrf2 deposited a senescence-promoting matrix, with plasminogen-activator inhibitor being the key inducer of the senescence program. In vivo, this promoted keratinocyte proliferation and re-epithelialization during wound healing, but also skin tumorigenesis. Analysis of the gene expression profile of fibroblasts with activated Nrf2 and published data sets revealed that Nrf2 activates genes characteristic for cancer-associated fibroblasts. These data identify Nrf2 as a key player in the control of the cancer-associated fibroblast phenotype and highlight the need for careful use of Nrf2-activating pharmaceuticals.
Organism
Mus musculus
Polycomb complexes associate with enhancers to promote oncogenic transcriptional programs in cancer
GSE107176
16 samples
Published August 2018
Summary
The Polycomb repressive complexes PRC1 and PRC2 play an essential role in cell fate decisions, embryonic development and gene regulation. While the functions of PRC2 in cancer are under intense study, the function of PRC1 in cancer remains largely unexplored. Here, we show that RNF2, the gene encoding RING1B, and canonical PRC1 (cPRC1) genes are amplified and overexpressed in breast cancer. Specifically, in estrogen receptor positive (ER+) breast cancer cells, cPRC1 is functionally associated with enhancers and genes regulated by ERa, while in triple negative breast cancer (TNBC) cells, a different cPRC1 variant is recruited to enhancers and promoters occupied by the bromodomain protein BRD4. Mechanistically, cPRC1 complexes are recruited to active enhancers independently of PRC2 and RING1B enzymatic activity. Moreover, RING1B has a dual role in regulating enhancer activity and gene transcription as it is recruited to enhancers to maintain and promote gene expression of breast cancer oncogenes. We also show that RING1B regulates chromatin accessibility of oncogenic transcription factors. Finally, we provide evidence that association of PRC1 to active enhancers is not restricted to breast cancer, demonstrating that RING1B recruitment to transcriptionally active sites occurs in multiple cancer types. Our work highlights a non-classical function of cPRC1 complexes in regulating specific oncogenic programs in cancer through its association with enhancer regions.
Organism
Homo sapiens
Comparing oestrogen-responsive genes in endometrial and breast cancer cell lines
GSE107693
12 samples
Published August 2018
Summary
Up to 80% of endometrial and breast cancers express the oestrogen receptor ERa. Unlike breast cancer, anti-oestrogen therapy has had limited success in endometrial cancer, raising the possibility that oestrogen has different effects in the two cancer types. We investigated the role of oestrogen in endometrial and breast cancers using cell lines and found that oestrogen-responsive genes were predominantly unique between the two cancer types.
Organism
Homo sapiens
Regulators of cellular heterogeneity in basal-like breast cancer influence symmetric versus asymmetric division rates (shRNA targeting)
GSE84143
15 samples
Published August 2018
Summary
Differentiation events contribute to cellular heterogeneity within tumors and influence disease progression and response to therapy. Here we dissect the mechanisms controlling intratumoral heterogeneity within basal-like breast cancers. We show that cancer cells can transition between a differentiation state related to that of normal luminal progenitors and a state closer to that of mature luminal cells, and that this occurs through asymmetric cell divisions. The Polycomb factor EZH2 and the Notch pathway act to increase the rates of symmetric divisions that produce progenitor-like cells, while the FOXA1 transcription factor promotes asymmetric divisions that reduce the numbers of such cells. Through functional screening, we identified a group of regulators that control cancer cell differentiation state and the relative proportions of tumor cell subpopulations. Our findings highlight the regulation of asymmetric cell divisions as a mechanism controlling intratumoral heterogeneity, and identify molecular pathways that control breast cancer cellular composition.
Organism
Homo sapiens
RNA sequencing of lncRNAs knockdown in human pancreatic cancer cell lines
GSE96931
13 samples
Published August 2018
Summary
We report the transcriptome changes that result from the transient knockdown of FAM83H-AS1 in Aspc1 cells and transient knockdown of LINC00673 in Panc1 cells.
Organism
Homo sapiens
RNAseq data from SCCOHT1 and OVCAR8 ovarian cancer cells treated with BET inhibitors
GSE102908
10 samples
Published August 2018
Summary
The antitumor activity of bromodomain inhibitors (BETi) has been demonstrated across numerous types of cancer. As such, these inhibitors are currently undergoing widespread clinical evaluation. However, predictive biomarkers allowing the stratification of tumors into responders and non-responders to BETi are lacking. Here, we show significant anti-proliferative effects of BETi in vitro and in vivo against aggressive SCCOHT1 ovarian cancer models lacking the SWI/SNF-related, SMARCA4 protein . Transcriptomic analysis revealed that exposure to BETi potently down-regulated the oncogenic receptor tyrosine kinase HER3 in SCCOHT1 but not in resistant OVCAR8 cells. Repression of this pathway is found to be an important determinant of response to BETi in cells harboring a loss of SMARCA4. Overall, we propose that BETi represent a rational therapeutic strategy in poor prognosis, SMARCA4 deficient cancers.
Organism
Homo sapiens