Gene expression profile of U2-OS control and NSD3 knockdown cells
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ABSTRACT:
PROVIDER: PRJNA484629 | ENA |
REPOSITORIES: ENA
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Project description:Osteosarcomas (OS) have highly chaotic genomes, yet their cancer drivers are poorly defined. Leveraging cross-species OS genomics we identify the frequent amplification of NSD3, a histone lysine methyltransferase and expose the NSD3-ARID3A axis as a core pathway in osteosarcomagenesis. Loss- and gain-of-function studies with CRISPR-Cas9 and lentivirus systems establish the causal role of NSD3 in OS tumor growth and spontaneous metastasis.
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Project description:U2-OS cells were transfected with scramble siRNA or PKC delta siRNA, then left untreated or treated with 2 ug/ml adriamycin for 8 h.
2011-03-23 | E-MEXP-2643 | biostudies-arrayexpress
Project description:Osteosarcoma (Osteosarcoma) is a type of bone cancer. Eighty percent of this tumor will be metastatic to the lungs or liver, and as a result, patients generally need chemotherapy to improve survival possibility. Recently, anti-tumor activity has been reported in Ocimum gratissimum aqueous extract (OGE), which has been the focus of recent extensive studies on therapeutic strategies due to its antioxidant properties. We used microarrays to identify potential and novel target genes responsive to the anticancer effect in OGE treatment in osteosarcoma cells, We performed pharmacogenomics analyses for the effect of OGE on human osteosarcoma U2-OS and HOS cell growth. Cell viability, Western blot and flow cytometry analysis were performed before performing pharmacogenomics analyses for the effect of OGE on human osteosarcoma U2-OS and HOS cell growth, including cDNA microarray and RT-PCR assays.
2013-06-26 | E-GEOD-48281 | biostudies-arrayexpress
Project description:RNA-sequencing analysis of control (shCon) and NSD3-knockdown (shNSD3) MDA-MB-231 cell lines. NSD3 (also known as WHSC1L1), a histone H3 lysine K36methyltransferase, is highly amplificated in several human cancers, including breast carcinomas. Results provide insight into the transcriptional regulation of NSD3 in breast cancer.
2021-01-01 | GSE152546 | GEO
Project description:The lysine methyltransferase NSD3 is required for the expression of key neural crest transcription factors and the migration of neural crest cells. Nevertheless, a complete view of the genes dependent upon NSD3 for expression and the developmental processes impacted by NSD3 in the neural crest was lacking. We used RNA sequencing (RNA-seq) to profile transcripts differentially expressed after NSD3 knockdown in chick premigratory neural crest cells, identifying 674 genes. Gene Ontology and gene set enrichment analyses further support a requirement for NSD3 during neural crest development and show that NSD3 knockdown also upregulates ribosome biogenesis. To validate our results, we selected three genes not previously associated with neural crest development, Astrotactin-1 (Astn1), Dispatched-3 (Disp3), and Tropomyosin-1 (Tpm1). Using whole mount in situ hybridization, we show that premigratory neural crest cells express these genes and that NSD3 knockdown downregulates (Astn1 and Disp3) and upregulates (Tpm1) their expression, consistent with RNA-seq results. Altogether, this study identifies novel putative regulators of neural crest development and provides insight into the transcriptional consequences of NSD3 in the neural crest, with implications for cancer.
2021-03-04 | GSE161565 | GEO
Project description:Nuclear receptor binding SET domain protein 3 (NSD3), a gene located within the 8p11-p12 amplicon frequently detected in cancers, encodes a chromatin modulator and an attractive onco-target. However, agent that can effectively suppress the NSD3-mediated oncogenic actions is currently lacking. We report an NSD3-targeting proteolysis targeting chimera (PROTAC), termed MS9715, which achieves effective and specific depletion of NSD3 and interacting partners (including cMyc) in tumor cells. MS9715-induced NSD3 degradation relies on BI-9321, an antagonist module binding the PWWP1 domain of NSD3, and VHL, which is chemically conjugated to BI-9321 via a linker and VHL ligand module. Importantly, compared to BI-9321, a recently disclosed NSD3 antagonist, MS9715 is more potent in suppressing growth of the NSD3-dependent hematological cancer including models of MLL-rearranged acute myeloid leukemia (AML) and B-cell acute lymphoblastic leukemia (B-ALL) and multiple myeloma (MM), and uniquely mediate simultaneous depletion of cellular NSD3 and cMyc. Transcriptome profiling further demonstrates effective actions of MS9715 but not BI-9321 in suppressing both NSD3- and cMyc-associated gene-expression programs, a phenomenon reminiscent of the CRISPR/cas9-mediated knockout (KO) of NSD3. Together, this study reports a first-in-class NSD3 PROTAC/degrader suitable for co-suppressing NSD3- and cMyc-related oncogenic nodes in cancer cells, suggesting a novel therapeutic strategy.
2021-08-27 | PXD021901 | Pride
Project description:Nuclear receptor binding SET domain protein 3 (NSD3), a gene located within the 8p11-p12 amplicon frequently detected in human cancers, encodes a chromatin modulator and an attractive onco-target. However, agent that can effectively suppress the NSD3-mediated oncogenic actions is currently lacking. Here, we report an NSD3-targeting proteolysis targeting chimera (PROTAC), termed MS9715, which achieves effective and specific depletion of NSD3 and interacting partners (including cMyc) in tumor cells. We show that MS9715-induced NSD3 degradation relies on BI-9321, an antagonist module binding the PWWP1 domain of NSD3, and VHL, which is chemically conjugated to BI-9321 via a linker and a VHL ligand. Importantly, compared to BI-9321, a recently disclosed NSD3 antagonist, MS9715 is more potent in suppressing growth of the NSD3-dependent hematological cancer including models of MLL-rearranged acute myeloid leukemia (AML) and B-cell acute lymphoblastic leukemia (B-ALL) and multiple myeloma (MM), and uniquely mediates simultaneous depletion of cellular NSD3 and cMyc. Transcriptome profiling further demonstrates effective actions of MS9715 but not BI-9321 in suppressing both the NSD3- and cMyc-mediated gene-expression programs, a phenomenon reminiscent of the CRISPR/cas9-mediated knockout (KO) of NSD3. Together, this study reports a first-in-class NSD3 degrader suitable for co-suppressing NSD3- and cMyc-related oncogenic nodes in cancer, suggesting a novel therapeutic strategy,
2021-08-31 | GSE158296 | GEO
Project description:Analysis of changes in the phosphoproteome upon transient siRNA-mediated knockdown of ABL1/ABL2 or DDR1 for 48 hours. CILAC phosphoproteome analysis was conducted after 48hrs using human U-2 OS cells.
2023-10-24 | PXD023146 | Pride
Project description:Burkholderia pseudomallei OS strain:OS Genome sequencing and assembly
| PRJNA188496 | ENA
Project description:Amplification of chromosomal region 8p11-12 is a frequent genetic alteration implicated in the etiology of lung squamous cell carcinoma (LUSC). FGFR1 (fibroblast growth factor receptor 1) is the main candidate driver within this region. However, clinical trials evaluating FGFR1 inhibition as a targeted therapy have been unsuccessful. Here we identify the H3K36 methyltransferase NSD3 (nuclear receptor binding SET domain protein 3), an 8p11-12-localized gene, as a key regulator of LUSC tumorigenesis. In contrast to other 8p11-12 candidate LUSC drivers, increased NSD3 expression strongly correlates with gene amplification. Ablation of NSD3, but not FGFR1, attenuates tumor growth and extends survival in a potent LUSC mouse model. We identify NSD3T1232A as an LUSC-associated variant that increases H3K36 dimethylation (H3K36me2) catalytic activity in vitro and in vivo. Structural dynamic analyses reveal that the T1232A substitution elicits localized mobility changes throughout NSD3’s catalytic domain to relieve auto-inhibition and increase H3 substrate accessibility. NSD3T1232A expression in vivo in LUSC mouse models accelerates tumorigenesis and decreases overall survival. Pathologic generation of H3K36me2 by NSD3T1232A rewires the chromatin landscape to promote oncogenic gene expression programming. Accordingly, depletion of NSD3 and H3K36me2 in patient derived xenografts (PDXs) from primary LUSC harboring NSD3 amplification or the NSD3T1232A variant attenuate neoplastic growth. Finally, NSD3-regulated LUSC PDXs are markedly and selectively sensitive to bromodomain inhibition (BETi). Together, our work identifies NSD3 as a principal 8p11-12 amplicon-associated oncogenic driver in LUSC and suggests that NSD3-dependency renders LUSC therapeutically vulnerable to BETi.
2020-11-24 | GSE149272 | GEO