Identification of UNC1999-responsive gene signatures in NK92MI cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE184127 | GEO | 2021/09/15
REPOSITORIES: GEO
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Project description:Identification of UNC1999-responsive gene signatures in NK92MI cells
| PRJNA763222 | ENA
Project description:Ezh2 and EZH1 are histone H3 lysine 27 specific methyltransferase. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia cell lines. UNC2400, a di-methylated derivative of UNC1999, is employed an inactive analog compound for assessment of off-target effects. EED knockdown was used to demonstrate gene targets of PRC2. Here we performed microarray analysis in MLL-AF9 transformed acute leukemia cells following treatment with DMSO, UNC2400 or UNC1999, or after induction of EED shRNA (Renilla shRNA as control). This study allows us to identify UNC1999-responsive gene signatures as well as their overlap with PRC2 targets in MLL-AF9-bearing leukemia cells. We analyzed 5 of DMSO-treated, 5 of UNC2400 (inactive analog of UN1999)-treated, and 6 of UNC1999-treated MLL-AF9 leukemia cell samples to identify UNC1999-responsive gene signatures. We also performed microarray in 3 of shRNA control lines (Renilla or Ren) and 3 of shEED lines to identify downstream targets of PRC2 complex in MLL-AF9 leukemia cells.
2014-10-10 | E-GEOD-62198 | biostudies-arrayexpress
Project description:Ezh2 and EZH1 are histone H3 lysine 27 specific methyltransferase. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia cell lines. UNC2400, a di-methylated derivative of UNC1999, is employed an inactive analog compound for assessment of off-target effects. EED knockdown was used to demonstrate gene targets of PRC2. Here we performed microarray analysis in MLL-AF9 transformed acute leukemia cells following treatment with DMSO, UNC2400 or UNC1999, or after induction of EED shRNA (Renilla shRNA as control). This study allows us to identify UNC1999-responsive gene signatures as well as their overlap with PRC2 targets in MLL-AF9-bearing leukemia cells.
2014-10-10 | GSE62198 | GEO
Project description:Background: MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development, and stress responses. With more copper (Cu) and copper-containing compounds used as bactericides and fungicides in viticulture, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, many Cu-responsive miRNAs have been detected in several plant species. However, there have been few reports about the grapevine miRNAs in response to Cu. Results: Here, two small RNA libraries were constructed from Cu-treated and water-treated (control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, 158 known vvi-miRNAs and 98 novel vvi-miRNAs were identified in the two libraries. Among these, 24 could only be detected in the treatment, and 63 were only detected in the control. Additionally, 100 known vvi-miRNAs were found to be clearly responsive to Cu, among which 96 were down-regulated and four were up-regulated; 47 novel vvi-miRNAs were found to be clearly responsive to Cu, among which 35 were down-regulated and 12 were up-regulated. Subsequently, expression patterns of a set of Cu-responsive vvi-miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive vvi-miRNAs between high-throughput sequencing and qRT-PCR assays. In addition, 92 putative targets for 79 known vvi-miRNAs and 51 putative targets for 22 novel vvi-miRNAs were predicted, and most of the targets are involved in multiple biological processes including transcriptional regulation and response to biotic and abiotic stresses. Conclusions: In this study, 147 Cu-responsive vvi-miRNAs were identified using high-throughput sequencing, and their target genes were predicted, which will be helpful to understanding the molecular mechanisms of miRNAs in response to Cu stress. Furthermore, this work can also provide a foundation for further study of the networks of miRNAs involved in grapevine plant growth and breeding some Cu-tolerant grapevine cultivars. Mixed 'Summer Black' grapevine young leaves (2 weeks old), large leaves (5 weeks old), and old leaves (9 week old) in randomly-selected plants from both the Cu-treated and control groups were collected for high-throughput sequencing. Subsequently, we carried out the analysis of Solexa sequencing data, and performed the research of regulatory modes of grapevine miRNAs on their target genes during Cu stress.
2016-02-20 | E-GEOD-78133 | biostudies-arrayexpress
Project description:Increased expression of chemokines in UNC1999-treated tumor tissues were successfully checked out through chemokines profiles screening of a total 25 different mouse chemokines using control and UNC1999-treated tumor tissues.
2022-08-25 | GSE211880 | GEO
Project description:Background: MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development, and stress responses. With more copper (Cu) and copper-containing compounds used as bactericides and fungicides in viticulture, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, many Cu-responsive miRNAs have been detected in several plant species. However, there have been few reports about the grapevine miRNAs in response to Cu. Results: Here, two small RNA libraries were constructed from Cu-treated and water-treated (control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, 158 known vvi-miRNAs and 98 novel vvi-miRNAs were identified in the two libraries. Among these, 24 could only be detected in the treatment, and 63 were only detected in the control. Additionally, 100 known vvi-miRNAs were found to be clearly responsive to Cu, among which 96 were down-regulated and four were up-regulated; 47 novel vvi-miRNAs were found to be clearly responsive to Cu, among which 35 were down-regulated and 12 were up-regulated. Subsequently, expression patterns of a set of Cu-responsive vvi-miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive vvi-miRNAs between high-throughput sequencing and qRT-PCR assays. In addition, 92 putative targets for 79 known vvi-miRNAs and 51 putative targets for 22 novel vvi-miRNAs were predicted, and most of the targets are involved in multiple biological processes including transcriptional regulation and response to biotic and abiotic stresses. Conclusions: In this study, 147 Cu-responsive vvi-miRNAs were identified using high-throughput sequencing, and their target genes were predicted, which will be helpful to understanding the molecular mechanisms of miRNAs in response to Cu stress. Furthermore, this work can also provide a foundation for further study of the networks of miRNAs involved in grapevine plant growth and breeding some Cu-tolerant grapevine cultivars.
2016-02-20 | GSE78133 | GEO
Project description:Fibromyalgia is a chronic pain syndrome characterized by widespread pain. The pathophysiology of fibromyalgia is not clearly understood and there are no specific biomarkers available for accurate diagnosis. Here we define genomic signatures using high throughput RNA sequencing on 96 fibromyalgia and 93 matched controls. Our findings revealed two major fibromyalgia-associated expression signatures. The first group included 44 patients with a signature enriched for gene expression associated with extracellular matrix and downregulation of RhoGDI signaling pathway. The second group included 31 patients and showed a profound reduction in the expression of inflammatory mediators with an increased expression of genes involved in the CLEAR signaling pathway. These results suggest defective tissue homeostasis associated with the extra-cellular matrix and cellular program that regulates lysosomal biogenesis and participates in macromolecule clearance in fibromyalgia. Further elucidation of these pathways will lead to development of accurate diagnostic markers, and effective therapeutic options for fibromyalgia.
2024-02-21 | GSE221921 | GEO
Project description:To characterize plant heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, the transcriptome analysis of rice was conducted using microarray. Rice (Oryza sativa L. cv. Nipponbare) were grown in plastic pots filled with nutrient soil for 2 weeks with a 12 h light (28°C)/12 h dark (25°C) regimen (ca. 1500 μmol photons mâ2 sâ1) and were treated for 30 min at 42°C.
2017-02-23 | E-MTAB-4503 | biostudies-arrayexpress
Project description:To characterize heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, transcriptome analysis of soybean was conducted using microarray. Soybean (Glycine max cv. Williams82) were grown in plastic pots filled with nutrient soil for 2 weeks with a 12 h light (28°C)/12 h dark (25°C) regimen (ca. 1500 μmol photons mâ2 sâ1) and were treated for 30 min at 42°C.
2017-02-23 | E-MTAB-4504 | biostudies-arrayexpress
Project description:The goal of this experiment was to identify the early responsive genes activated by the 22 amino acid peptide of bacterial flagellin (flg22) in Arabidopsis seedlings that are involved in the initial responses important for plant innate immunity. We used the microarrays to detail the global program of gene expression underlying intial cellular and molecular responses to microbial associated molecualr patterns (MAMPs). Arabidopsis seedlings were treated with 2 nM flg22 for 30 min and 60 min. Transcript profiles were analyzed and compared between control and treated cells to identify early flg22 responsive genes.
2010-03-18 | E-GEOD-17382 | biostudies-arrayexpress