Genomic binding sites of non-metastatic 2 (NME2) across promoters in lung cancer A549 cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE18284 | GEO | 2011/02/08
SECONDARY ACCESSION(S): PRJNA123513
REPOSITORIES: GEO
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Project description:Non-metastatic 2 (NME2) is one of the first discovered suppressors of metastases. However, the molecular mechanisms underlying its anti-metatsic activity remain insufficiently characterized. We hypothesized that large scale transcriptional potential of NME2 might be at the core of this function. Using a combination of gene expression meta-analysis, and high throughput genomic assays, we explored the transcriptional targets of NME2. Specifically, we found >250 binding sites of NME2 across human gene promoters. Several of the novel targets identified in this way regulated cell adhesion and survival. We subsequently constructed NME2 target gene network which delineated a transcriptional program responsive to NME2 capable of restricting metastasis. Three sets of ChIP vs. mock-ChIP experiments were done. pcDNA plasmid was transfected to lung cancer, A549 cells to express NME2 tagged with MYC epitope which was subsequently immunoprecipitated using anti-MYC antibodies (after 48 hours of transfection). Non-specific IgG was used for mock immunoprecipitation.
2011-02-08 | E-GEOD-18284 | biostudies-arrayexpress
Project description:Non-metastatic 2 (NME2) is an established metastases suppressor in multiple human cancer types. However, the molecular mechanisms of NME2 action remain insufficiently resolved. We recently validated the transcription regulatory activity of NME2 with respect to control of proto-oncogene c-MYC expression. We hypothesized that large scale transcriptional potential of NME2 may be at the core of metastases suppression by NME2. Using a combination of high throughput genomic assays such as chromatin immunoprecipitation coupled to promoter array hybridization (ChIP-chip) and gene expression profiling, we characterized the transcriptional roles of NME2. Specifically, we found a set of NME2 target genes which changed expression upon selective depletion of NME2 in a lung cancer cell line, A549. The analysis of gene expression suggested control of various biological pathways esp. cell adhesion and apoptosis by NME2 target genes which could be important in regulation of metastases.
2011-02-08 | GSE18182 | GEO
Project description:Non-metastatic 2 (NME2) is an established metastases suppressor in multiple human cancer types. However, the molecular mechanisms of NME2 action remain insufficiently resolved. We recently validated the transcription regulatory activity of NME2 with respect to control of proto-oncogene c-MYC expression. We hypothesized that large scale transcriptional potential of NME2 may be at the core of metastases suppression by NME2. Using a combination of high throughput genomic assays such as chromatin immunoprecipitation coupled to promoter array hybridization (ChIP-chip) and gene expression profiling, we characterized the transcriptional roles of NME2. Specifically, we found a set of NME2 target genes which changed expression upon selective depletion of NME2 in a lung cancer cell line, A549. The analysis of gene expression suggested control of various biological pathways esp. cell adhesion and apoptosis by NME2 target genes which could be important in regulation of metastases. For transcriptome analysis, total RNA was purified from A549 cells transiently silenced for NME2 (siRNA duplex against NME2/ NM23 H2(Santa Cruz)) or transfected with control siRNA duplexes. Isolated RNA was converted to cDNA, transcribed in vitro to synthesize biotinylated cRNA, and hybridized to Affymetrix HG-U133 plus 2.0 GeneChip oligonucleotide microarrays, according to manufacturer’s instructions. Three biological replicates were averaged and significance analysis performed using GCOS (P <0.005 of fold change).
2011-02-08 | E-GEOD-18182 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE18182: Expression profile of lung adenocarcinoma, A549 cells following targeted depletion of non metastatic 2 (NME2/NM23 H2) GSE18284: Genomic binding sites of non-metastatic 2 (NME2) across promoters in lung cancer A549 cells Refer to individual Series
2011-02-08 | E-GEOD-18285 | biostudies-arrayexpress
Project description:Our aim was to understand how vesicular NME1 and NME2 released by breast cancer cells influence the tumour microenvironment. As a model, we used human invasive breast carcinoma cells overexpressing NME1 or NME2, and first analysed in detail the presence of both isoforms in EV subtypes by capillaryWestern immunoassay (WES) and immunoelectron microscopy. Data obtained by both methods showed that NME1 was present in medium-sized EVs or microvesicles, whereas NME2 was abundant in both microvesicles and small-sized EVs or exosomes. Next, human skin-derived fibroblasts were treated with NME1 or NME2 containing EVs, and subsequently mRNA expression changes in fibroblasts were examined. RNAseq results showed that the expression of fatty acid and cholesterol metabolism-related genes was decreased significantly in response to NME1 or NME2 containing EV treatment. We found that FASN (fatty acid synthase) and ACSS2 (acyl-coenzyme A synthetase short-chain family member 2), related to fatty acid synthesis and oxidation, were underexpressed in NME1/2-EV-treated fibroblasts. Our data show an emerging link between NME-containing EVs and regulation of tumour metabolism.
2022-08-21 | GSE211556 | GEO
Project description:Purpose: Herein we demonstrate that UV-induced melanomas of low metastatic potential in mice that overexpress HGF and harbor deletion of the Ink4a/p16 locus (HP strain) are converted to highly metastatic forms by virtue of hemizygous deletion of the metastasis suppressor genes Nme1 and Nme2 (HPN strain). The striking difference in metastatic activity between HP and HPN melanomas strains provided a powerful system for identifying molecular profiles associated with metastatic activity. Methods: Primary and metastatic melanoma RNAseq profiling. Results: RNA-seq analysis of primary melanomas identified a 32-gene expression signature that was strongly associated with the HPN genotype and lung metastatic activity (HPN lung metastasis signature, or HPN-LMS). Expression of the HPN-LMS was highly predictive of overall survival in human cohorts of cutaneous melanoma (SKCM) and uveal melanoma (UVM) patients of The Cancer Genome Atlas (TCGA). Conclusions: Three HPN-LMS genes (ARRDC3, NYNRIN, RND3) associated with longer survival in SKCM and/or UVM patients exhibited strong anti-invasion activity in human melanoma cells, consistent with roles as effectors of the metastasis suppressor functions of Nme1 and Nme2. The HP/HPN mouse paradigm has thus yielded a network of potential therapeutic targets and prognostic markers for clinical management of metastatic melanoma.
2021-08-02 | GSE181207 | GEO
Project description:It is widely believed that reorganization of nucleosomes result in availability of binding sites that engage transcription factors during eukaryotic gene regulation. Recent findings, on the other hand, suggest that transcription factors induced as a result of physiological perturbations directly (or in association with chromatin modifiers) may alter nucleosome occupancy to facilitate DNA binding. Although, together these suggest a close relationship between transcription factor binding and nucleosome reorganization, the nature of the inter-dependency, or to what extent it influences regulatory transcription is not clear. Moreover, since most studies used physiolgical pertubations that induced multiple transcription factor chromatin modifiers, the relatively local (or direct) effect of transcription factor binding on nucleosome occupancy remains unclear. With these in mind, we used a single transcription factor to induce physiological changes, representing metastatic (aggressive cancer) and the corresponding non-metastatic state, in human cancer cells. Following characterization of the two states (before and after induction of the transcription factor) we determined: (a) genome wide binding sites of the transcription factor, (b) promoter nucleosome occupancy and (c) transcriptome profiles, independently in both conditions. Interestingly, we find only ~20% of TF binding results from nucleosome reorganization - however, almost all corresponding genes were transcriptionally altered. Whereas, in cases where TF-occupancy was independent of nucleosome repositioning (in close vicinity), or co-occurred with nucleosomes, only a small fraction of the corresponding genes were expressed/repressed. Together, these indicate a model where TF occupancy only when coupled with nucleosome repositioning in close proximity is transcriptionally active. This, to our knowledge, for the first time also helps explain why genome wide TF occupancy (e.g., from ChIP-seq) is typically associated with only a small fraction of genes that change expression. For expression profiling of cells in NME2-induced conditions, A549 cells were transfected with pcDNA-NME2-MYC or pcDNA-MYC (control). RNA was isolated from the cells 48h after transfection using the trizol method (Sigma) as per manufacturerM-bM-^@M-^Ys protocol. Total RNA was processed to hybridize to Illumina Human HT-12 v4 Expression BeadChip as per manufacturerM-bM-^@M-^Ys instructions. Three biological replicates were averaged and data was analyzed using BeadStudio (P <0.05 of fold change).
2014-08-04 | E-GEOD-40194 | biostudies-arrayexpress
Project description:In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi’s sarcoma associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68), which encode an mRNA endonuclease that initiates widespread RNA decay. Here, we show that MHV68-induced mRNA decay leads to a genome-wide reduction of Pol II occupancy at mammalian promoters. Viral genes, despite the fact that they require Pol II for transcription, escape this transcriptional repression. Protection is not governed by viral promoter sequences; instead, location on the viral genome is both necessary and sufficient to escape the transcriptional repression effects of mRNA decay. We hypothesize that the ability to escape from transcriptional repression is linked to the localization of viral DNA in replication compartments, providing a means for these viruses to counteract decay-induced viral transcript loss.
2019-12-10 | PXD015786 | Pride
Project description:Fatty acid homeostasis is critical for normal cellular physiology and leads to severe diseases when deregulated. Here we report Nucleoside-Diphosphate Kinase 1 and 2 (NME1/2) as major cellular co-enzyme A (CoA) and acetyl-CoA binding proteins and negative regulators of de novo lipogenesis (DNL). Structural studies demonstrate that Nme1 recognizes CoA through its nucleotide moiety, which competes for binding with ADP/ATP. By using a Nme2 ko mouse model, we observe that NME2 is required for the gene transcriptional response to a high fat diet (HFD) in liver cells, leading to a repression of lipogenesis and the activation of a protective gene response. Nme2 ko mice submitted to a HFD challenge are unable to repress key lipogenic genes, resulting in an excessive triglyceride synthesis and liver steatosis. Mechanistically, the NME2-dependent down-regulation of DNL in response to HFD changes the balance for the use of acetyl-CoA between the competing paths of acetylation and DNL, thereby increasing TSS-targeted histone acetylation and gene activation. A structure-guided generation of a NME1 mutant, with intact NDK activity, but unable to bind CoA, directly demonstrates the functional impact of acetyl-CoA/CoA binding by NME1/2 in repressing DNL. Taken together, these findings highlight a yet unknow protective liver response to HFD, regulated by multi-ligand binding proteins which act as direct sensors for the cellular levels of NDP/NTP and CoA/acetyl-CoA.
2023-08-01 | GSE198687 | GEO