Expression profiling of TNBCs following atRA treatment [Affymetrix II]
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PROVIDER: PRJNA483988 | ENA |
REPOSITORIES: ENA
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Project description:Expression profiling of TNBCs following atRA treatment [Affymetrix I]
| PRJNA482563 | ENA
Project description:All-trans retinoic acid (atRA) regulates gene expression and is used to treat acute promyelocytic leukemia. Attempts to use atRA for breast cancer treatment without a stratification strategy have resulted in limited overall effectiveness. To identify biomarkers for the treatment of triple-negative breast cancer (TNBC) with atRA, we characterized the effects of atRA on the tumor growth of 13 TNBC cell lines. This resulted in a range of tumor growth effects that was not predictable based on the levels of retinoid signaling molecules and transcriptional responses that were mostly independent of retinoic acid response elements. Given the importance of DNA methylation in regulating gene expression, we hypothesized that differential DNA methylation could predict the response of TNBCs to atRA. We identified over 1400 CpG sites that were differentially methylated between atRA resistant and sensitive cell lines. These CpG sites predicted the response of four TNBC patient-derived xenografts to atRA treatment and we utilized these xenografts to refine the profile to 6 CpGs. We identify as many as 17% of TNBC patients who could benefit from atRA treatment. These data illustrate that differential DNA methylation of specific sites may predict the response of patient tumors to atRA treatment. This study characterizes the gene expression of 2 triple-negative patient-derived breast cancer xenografts
2018-10-22 | GSE118002 | GEO
Project description:All-trans retinoic acid (atRA) regulates gene expression and is used to treat acute promyelocytic leukemia. Attempts to use atRA for breast cancer treatment without a stratification strategy have resulted in limited overall effectiveness. To identify biomarkers for the treatment of triple-negative breast cancer (TNBC) with atRA, we characterized the effects of atRA on the tumor growth of 13 TNBC cell lines. This resulted in a range of tumor growth effects that was not predictable based on the levels of retinoid signaling molecules and transcriptional responses that were mostly independent of retinoic acid response elements. Given the importance of DNA methylation in regulating gene expression, we hypothesized that differential DNA methylation could predict the response of TNBCs to atRA. We identified over 1400 CpG sites that were differentially methylated between atRA resistant and sensitive cell lines. These CpG sites predicted the response of four TNBC patient-derived xenografts to atRA treatment and we utilized these xenografts to refine the profile to 6 CpGs. We identify as many as 17% of TNBC patients who could benefit from atRA treatment. These data illustrate that differential DNA methylation of specific sites may predict the response of patient tumors to atRA treatment.
2018-10-22 | GSE117579 | GEO
Project description:Following treatment with the de-methylating agent 5-aza-deoxycytidine (DAC), the gene expression profiles of neuroblastoma cell lines Kelly, SK-N-AS and NGP were analysed in order to examine the relationship between transcriptional re-activation and promoter region DNA methylation.<br>In addition, the neuroblastoma cell line SK-N-BE was treated with all-trans-retinoic acid (ATRA) in order to examine the impact this differentiation agent has on DNA methylation status.
2010-11-03 | E-MEXP-2557 | biostudies-arrayexpress
Project description:We analysed the dynamics of the HL60 nuclear proteome after the ATRA treatment in different time points in 0, 3, 6, 9, 12 and 72 h.
2023-08-16 | MSV000092670 | MassIVE
Project description:Searching for new strategies of acute myeloid leukemia (AML) treatment is of particular interest. Cell lines, e. g. HL-60 and NB4, represent model systems to study molecular features of leukemic cells. The all-trans-retinoic acid (ATRA) has proven itself to be an effective treatment for one of AML subtypes, i.e., acute promyelocytic leukemia (APL). At the same time, ATRA causes granulocytic differentiation of non-APL leukemic cells in vitro. Combination of new therapeutics with ATRA could improve efficiency of treatment. Studying the proteome perturbation in leukemic cells under the ATRA treatment allows to determine potential regulatory molecules that could be affected pharmacologically. Thus, the TMT-based proteomic profiles of HL-60, NB4, and K562 cell lines under the ATRA treatment were obtained at 0, 3, 12, 24, and 72 h after the ATRA treatment.
2024-06-23 | PXD050317 | Pride
Project description:Acute myeloid leukemia (AML) is characterized by the accumulation of immature leukemic blasts. The application of all-trans retinoic acid (ATRA) treatments have markedly transformed acute promyelocytic leukemia (APL, the M3 subtype of AML) to a highly manageable disease, and research strategies that seek to extend the application of ATRA-based treatment to other AML subtypes are an important area of investigation. Here, we found CASP1/GSDMD was lower expressed in APL and most other subtypes of primary de novo AML patients and increased in ATRA-treated APL cells. We showed that ATRA increased and activated CASP1 to trigger pyroptosis and differentiation of APL cells. Mechanistically, ATRA could induce CASP1 expression via IFNγ/STAT1 in APL and non-APL AML cells, while do not activate CASP1 in non-APL AML cells. Accordingly, pharmacological activation of CASP1 by Val-boroPro (DPP8/9 inhibitor) enhanced pyroptosis and differentiation induced by ATRA in AML cells. Moreover, the combination of ATRA and Val-boroPro enhanced anti-leukemia activity in primary AML cells. Our study demonstrates that the ATRA-mediated anti-leukemia effect requires a functional activated CASP1 and provides a highly attractive therapeutic strategy for the treatment of AML.
2024-12-01 | GSE190341 | GEO
Project description:We used microarrays to detail the global programme of gene expression in embryonic stem cells, early differentiated embrioid bodies and effect of short-term ATRA treatment. Expression data from undifferentiated mouse embryonic stem cells (D3), four-day old aggregated embrioid bodies and 12h atRA or DMSO treated embrioid bodies. Three replicates each.
2010-07-16 | E-GEOD-20919 | biostudies-arrayexpress