Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA120777 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mantle Cell Lymphoma (MCL) is a mostly incurable malignancy arising from naïve B cells (NBC) in the mantle zone of lymph node follicles. We analyzed genome-wide methylation in MCL patients using the HELP (Hpa II tiny fragment Enrichment by Ligation mediated PCR) assay and found significant aberrancy in promoter methylation patterns as compared to normal NBCs. Using biological and stringent statistical criteria, we further identified four hypermethylated genes CDKN2B, MLF-1, PCDH8, HOXD8 and four hypomethylated genes CD37, HDAC1, NOTCH1 and CDK5 where aberrant methylation was associated with inverse changes in mRNA levels. MassArray Epityper analysis confirmed the presence of differential methylation at the promoter region of these genes. Immunohistochemical analysis of an independent cohort of 14 MCL patient samples, confirmed CD37 surface expression in 93% of patients, validating its selection as a target for MCL therapy. Treatment of MCL cell lines with a novel small modular immunopharmaceutical(CD37-SMIP) resulted in significant loss of viability in cell lines with intense surface CD37 expression. Treatment of MCL cell lines with the DNA methyltransferase inhibitor decitabine resulted in reversal of aberrant hypermethylation and synergized with the HDAC inhibitor SAHA in induction of the four hypermethylated genes CDKN2B, MLF-1, PCDH8 and HOXD8. The combination of Decitabine and SAHA also resulted in potent and synergistic anti-MCL cytotoxicity as compared to either drug alone. In conclusion, our analysis shows prominent and aberrant methylation of the MCL genome and identifies novel differentially methylated and expressed genes in MCL cell lines and patient samples. Furthermore, our data suggest that differentially methylated genes can be targeted for therapeutic benefit in MCL. Gene expression profiling by array comprised of 8 mantle cell lymphoma (MCL) cell lines and 8 leukemic blast from blood from patients newly diagnosed with MCL. Unbiased genome-wide analysis of DNA methylation in leukemic blast from peripheral blood or pheresis products from 22 patients newly diagnosed with mantle cell lymphoma (MCL) prior to any treatment. 10 IgD+ Na ve B cells from specimens from healthy donors undergoing routine tonsillectomy were used as appropriate controls. Methylation patterns of 13 MCL cell lines were also compared.
2010-07-30 | E-GEOD-19243 | biostudies-arrayexpress
Project description:Identification of potential tumor suppressor genes using the GINI strategy in Mantle Cell Lymphoma cell lines Keywords: response to drug treatment
2007-12-31 | GSE6728 | GEO
Project description:DNA methylation profiling from 70 Mantle Cell Lymphoma cases
| EGAD00010001877 | EGA
Project description:BLUEPRINT DNA Methylation 450K data of mantle cell lymphoma
| EGAD00010001012 | EGA
Project description:MCL-1 plays a central role in B-cell lymphoma progression and drug resistance. Pharmacologically targeting MCL-1, therefore, represents an attractive strategy to combat these lymphomas. S63845, a MCL1 inhibitor, was shown to have high response rates in mantle cell lymphoma (MCL) and burkitt lymphoma.
2022-12-02 | GSE160742 | GEO
Project description:8-amino-adenosine (8-NH2-Ado) inhibits RNA synthesis and specifically inhibits synthesis of mRNAs with short half-lives. We hypothesize that the mRNAs affected code for proteins important in apoptosis and glucose metabolism. Gene Expression Arrays will help us understand which gene families may be affected by this drug and give us a better understanding of mechanism of action of this drug 1. MM.1S cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (myeloma cells sensitive to the drug) 2. U266 cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (myeloma cells resistant to the drug). 3. Jeko cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (Mantle cell lymphoma cells sensitive to drug) 4. Granta cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (Mantle cell lymphoma cells resistant to drug).
2012-05-31 | E-GEOD-38145 | biostudies-arrayexpress
Project description:Mantle Cell Lymphoma (MCL) is a mostly incurable malignancy arising from naïve B cells (NBC) in the mantle zone of lymph node follicles. We analyzed genome-wide methylation in MCL patients using the HELP (Hpa II tiny fragment Enrichment by Ligation mediated PCR) assay and found significant aberrancy in promoter methylation patterns as compared to normal NBCs. Using biological and stringent statistical criteria, we further identified four hypermethylated genes CDKN2B, MLF-1, PCDH8, HOXD8 and four hypomethylated genes CD37, HDAC1, NOTCH1 and CDK5 where aberrant methylation was associated with inverse changes in mRNA levels. MassArray Epityper analysis confirmed the presence of differential methylation at the promoter region of these genes. Immunohistochemical analysis of an independent cohort of 14 MCL patient samples, confirmed CD37 surface expression in 93% of patients, validating its selection as a target for MCL therapy. Treatment of MCL cell lines with a novel small modular immunopharmaceutical(CD37-SMIP) resulted in significant loss of viability in cell lines with intense surface CD37 expression. Treatment of MCL cell lines with the DNA methyltransferase inhibitor decitabine resulted in reversal of aberrant hypermethylation and synergized with the HDAC inhibitor SAHA in induction of the four hypermethylated genes CDKN2B, MLF-1, PCDH8 and HOXD8. The combination of Decitabine and SAHA also resulted in potent and synergistic anti-MCL cytotoxicity as compared to either drug alone. In conclusion, our analysis shows prominent and aberrant methylation of the MCL genome and identifies novel differentially methylated and expressed genes in MCL cell lines and patient samples. Furthermore, our data suggest that differentially methylated genes can be targeted for therapeutic benefit in MCL.
2010-07-31 | GSE19243 | GEO
Project description:High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (RNA-Seq)
| PRJNA227025 | ENA
Project description:High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (ChIP-Seq)
| PRJNA227024 | ENA