Expression profiling in extracellular miRNAs of CML patients after imatinib discontinuation (STOP-IM)
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tomohiro Umezu
PROVIDER: E-GEOD-75392 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:An approximately 40% of chronic myeloid leukemia (CML) patients who discontinued imatinib (IM) therapy maintained undetectable minimal residual disease (UMRD) for more than one year (STOP-IM). We therefore set out to examine exosomal miRNAs expression in CML patients who could discontinue IM, to seek the possible distinguishable biomarker in STOP-IM CML patients. We compared CML patients who sustained UMRD for more than one year after discontinuation of imatinib (STOP-IM group) with healthy volunteers (controls). In 7 patients who had discontinued IM with sustained UMRD for more than 6 months (STOP-IM group), samples were collected when IM was stopped. Seven healthy volunteers served as control. Plasma samples were harvested form 2ml of whole blood. Exosoms were isolated from plasma using a Total exosome isolation kit for plasma (Life Technologies). Isolation of total RNA was performed using the mirVana PARIS kit (Ambion, Austin, TX, USA). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). Synthetic ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerâs recommended program. With the use of SDS2.2 software and Data Assist (Thermo Fisher Sciences), the expression of plasma miRNAs was calculated based on cycle threshold (Ct) values normalized by those of ath-miR-159, which was spiked in each plasma sample. Data analysis was done using GeneSiferâ software (Perkin Elmer, Waltham, MA, USA). The Benjamini-Hochberg algorithm was used for estimation of false discovery rates.
2016-03-31 | E-GEOD-75389 | biostudies-arrayexpress
Project description:An approximately 40% of chronic myeloid leukemia (CML) patients who discontinued imatinib (IM) therapy maintained undetectable minimal residual disease (UMRD) for more than one year (STOP-IM). We set out to examine plasma miRNAs expression in CML patients who could discontinue IM, to seek the possible distinguishable biomarker in STOP-IM CML patients. We compared CML patients who sustained UMRD for more than one year after discontinuation of imatinib (STOP-IM group) with healthy volunteers (controls). In 7 patients who had discontinued IM with sustained UMRD for more than 6 months (STOP-IM group), samples were collected when IM was stopped. Seven healthy volunteers served as control. Plasma samples were harvested form 2ml of whole blood. Isolation of total RNA was performed using the mirVana PARIS kit (Ambion, Austin, TX, USA). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). Synthetic ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerâ??s recommended program. With the use of SDS2.2 software and Data Assist (Thermo Fisher Sciences), the expression of plasma miRNAs was calculated based on cycle threshold (Ct) values normalized by those of ath-miR-159, which was spiked in each plasma sample. Data analysis was done using GeneSiferâ?? software (Perkin Elmer, Waltham, MA, USA). The Benjamini-Hochberg algorithm was used for estimation of false discovery rates.
2016-03-31 | E-GEOD-75391 | biostudies-arrayexpress
Project description:The aging of bone marrow stromal cells (BMSCs) lead to decreased ability to maintain hematopoiesis, however, effects of aging on BMSC-derived exosomes in bone marrow microenvironment remain unclear. The aim of this study is therefore to determine the age-related change of BMSC-derived exosomal miRNAs. Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors: 62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. The exosomes from culture medium of BM-MSCs were isolated by Total Exosome Isolation Reagent (Invitrogen). Exosomal miRNA profiling was done using a TaqMan low-density array (ABI), and Studentâ??s t-test was used to determine statistical significance for comparisons between young and old groups using R software.
2017-05-12 | E-GEOD-78865 | biostudies-arrayexpress
Project description:Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used SUDHL4 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from SUDHL4 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from SUDHL4 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). SUDHL4 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2013-12-03 | E-GEOD-45387 | biostudies-arrayexpress
Project description:Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used RPMI8226 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from RPMI8226 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from RPMI8226 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in RPMI8226 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). RPMI8226 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2013-12-03 | E-GEOD-45388 | biostudies-arrayexpress
Project description:Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used K562 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from K562 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from K562 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from K562 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in K562 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). K562 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2013-12-03 | E-GEOD-45289 | biostudies-arrayexpress
Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, KMS-11-HR, derived from KMS-11 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used KMS-11 cells and KMS-11-HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from KMS-11 cells (normoxia or hypoxia) and exosomes derived from KMS-11-HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the KMS-11-HR cells significantly increased tube formation of HUVECs than those from KMS-11 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in KMS-11 cells and KMS-11-HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). KMS-11 cells and KMS-11-HR cells were cultured for 24 hours under hypoxic conditions (1% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2014-10-15 | E-GEOD-48908 | biostudies-arrayexpress
Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, U266HR, derived from U266 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used U266 cells and U266HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from U266 cells (normoxia or hypoxia) and exosomes derived from U266HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the U266HR cells significantly increased tube formation of HUVECs than those from U266 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in U266 cells and U266HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). U266 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2014-10-15 | E-GEOD-48910 | biostudies-arrayexpress
Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, RPMI8226HR, derived from RPMI8226 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used RPMI8226 cells and RPMI8226HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells (normoxia or hypoxia) and exosomes derived from RPMI8226HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the RPMI8226HR cells significantly increased tube formation of HUVECs than those from RPMI8226 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in RPMI8226 cells and RPMI8226HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). RPMI8226 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2014-10-15 | E-GEOD-48909 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-10-15 | E-GEOD-48983 | biostudies-arrayexpress