Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA106357 | ENA |
REPOSITORIES: ENA
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Project description:The role of microRNAs (miRNAs) in multiple myeloma (MM) has yet to be fully elucidated. To identify miRNAs that are potentially deregulated in MM, we investigated those mapping within transcription units, based on evidence that intronic miRNAs are frequently coexpressed with their host genes. To this end, we monitored host transcript expression values in a panel of 20 human MM cell lines (HMCLs) profiled on Affymetrix U133A oligonucleotide microarrays and focused on transcripts whose expression varied significantly across the dataset. We identified transcripts specific to six miRNA host genes (CCPG1, GULP1, EVL, TACSTD1, MEST, and TNIK) whose average changes in expression varied at least 2-fold from the mean of the examined dataset. We evaluated the expression levels of the corresponding intronic miRNAs by quantitative real-time RT-PCR. There was a significant correlation between the expression levels of MEST, EVL, and GULP1 and those of the corresponding miRNAs miR-335, miR-342-3p, and miR-561, respectively. Genome-wide profiling of the 20 HMCLs with the Affymetrix GeneChip human mapping 250K array set indicated that the increased expression of the three host genes and their corresponding intronic miRNAs was not correlated with local copy number variations. Notably, miRNAs and their host genes were overexpressed in a fraction of primary tumors with respect to normal plasma cells; however, this finding was not correlated with known molecular myeloma groups. The predicted putative miRNA targets, as well as the transcriptional profiles associated with the primary tumors, suggest that MEST/miR-335 and EVL/miR-342-3p may play a role in plasma cell homing and/or interactions with the bone marrow microenvironment. Our data support the idea that intronic miRNAs and their host genes are regulated dependently, and may contribute to the understanding of their biological roles in cancer. To our knowledge, this is the first evidence of deregulated miRNA expression in MM, providing insights that may lead to the identification of new biomarkers and altered molecular pathways of the disease. Keywords: integrative genomic analysis of miR-335, miR-342, and miR-561 in multiple myeloma
2008-11-11 | GSE11522 | GEO
Project description:The role of microRNAs (miRNAs) in multiple myeloma (MM) has yet to be fully elucidated. To identify miRNAs that are potentially deregulated in MM, we investigated those mapping within transcription units, based on evidence that intronic miRNAs are frequently coexpressed with their host genes. To this end, we monitored host transcript expression values in a panel of 20 human MM cell lines (HMCLs) profiled on Affymetrix U133A oligonucleotide microarrays and focused on transcripts whose expression varied significantly across the dataset. We identified transcripts specific to six miRNA host genes (CCPG1, GULP1, EVL, TACSTD1, MEST, and TNIK) whose average changes in expression varied at least 2-fold from the mean of the examined dataset. We evaluated the expression levels of the corresponding intronic miRNAs by quantitative real-time RT-PCR. There was a significant correlation between the expression levels of MEST, EVL, and GULP1 and those of the corresponding miRNAs miR-335, miR-342-3p, and miR-561, respectively. Genome-wide profiling of the 20 HMCLs with the Affymetrix GeneChip human mapping 250K array set indicated that the increased expression of the three host genes and their corresponding intronic miRNAs was not correlated with local copy number variations. Notably, miRNAs and their host genes were overexpressed in a fraction of primary tumors with respect to normal plasma cells; however, this finding was not correlated with known molecular myeloma groups. The predicted putative miRNA targets, as well as the transcriptional profiles associated with the primary tumors, suggest that MEST/miR-335 and EVL/miR-342-3p may play a role in plasma cell homing and/or interactions with the bone marrow microenvironment. Our data support the idea that intronic miRNAs and their host genes are regulated dependently, and may contribute to the understanding of their biological roles in cancer. To our knowledge, this is the first evidence of deregulated miRNA expression in MM, providing insights that may lead to the identification of new biomarkers and altered molecular pathways of the disease. Keywords: integrative genomic analysis of miR-335, miR-342, and miR-561 in multiple myeloma This series of microarray experiments contains the genome-wide profiles of 20 HMCLs. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labelled DNA were hybridized on GeneChip® Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip® Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Raw data were extracted using the Hidden Markov Model Genomic Smoothing window was set to 0. After the preprocessing, piecewise constant estimates of the underlying local DNA CN variation was calculated using the DNA copy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).
2008-11-10 | E-GEOD-11522 | biostudies-arrayexpress
Project description:Analyzing the influence of the protein-coding gene Evl or it's intronic miR-342 on hematopoietic stem and progenitor cells on gene expression level. Evl drives lymphopoiesis, whereas miR-342 deregulates myeloid signaling pathways.
2021-06-08 | GSE109600 | GEO
Project description:A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide dosage effect on gene and microRNA expression This SuperSeries is composed of the following subset Series: GSE13591: Integrated genomics approach to detect allelic imbalances in multiple myeloma GSE16121: Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data Refer to individual Series
2009-05-16 | E-GEOD-16122 | biostudies-arrayexpress
Project description:Accumulating evidence indicates that altered miRNA expression is crucially involved in lung cancer development, but only little has been elucidated about how MYC, an archetypical oncogene, is regulated by miRNAs, especially through a mechanism involving the MYC cofactor(s). In this study, we aimed at identifying miRNAs involved in the regulation of MYC transcriptional activity in lung cancers. To this end, we have taken an integrative approach with combinatorial usage of miRNA and mRNA expression profile datasets of patientsâ?? tumor tissues as well as those of MYC-inducible cell lines in vitro. We report here that in addition to miRNAs previously reported to be directly regulating or regulated by MYC including let-7 and miR-17-92, our strategy allowed us to identify miR-342-3p as the one capable of indirectly regulating MYC activity through direct repression of a MYC-cooperating molecule, E2F1. Furthermore, the miR-342-3p module activity, which we defined as a gene set reflecting experimentally substantiated influence of miR-342-3p on mRNA expression, was found to be inversely correlated with MYC activity reflected in the MYC module activity in three independent datasets of lung adenocarcinoma patients obtained by the Directorâ??s Challenge Consortium of the United States (P=1.94x10-73), the National Cancer Center of Japan (P=9.05x10-34) and our own in this study (P=3.37x10-6). Our integrative approach thus appears to be useful to elucidate inter-regulatory relationships between miRNAs and a protein coding-gene of interest, even those present in tumor tissues in patients, which still remains a challenge to better understand the pathogenesis of this devastating disease. Microarray analysis using a SurePrint G3 Human GE 8 x 60K Microarray G4851A (Agilent) was conducted. Tai, MeiChee
2016-01-06 | E-GEOD-66758 | biostudies-arrayexpress
Project description:Accumulating evidence indicates that altered miRNA expression is crucially involved in lung cancer development, but only little has been elucidated about how MYC, an archetypical oncogene, is regulated by miRNAs, especially through a mechanism involving the MYC cofactor(s). In this study, we aimed at identifying miRNAs involved in the regulation of MYC transcriptional activity in lung cancers. To this end, we have taken an integrative approach with combinatorial usage of miRNA and mRNA expression profile datasets of patientsâ tumor tissues as well as those of MYC-inducible cell lines in vitro. We report here that in addition to miRNAs previously reported to be directly regulating or regulated by MYC including let-7 and miR-17-92, our strategy allowed us to identify miR-342-3p as the one capable of indirectly regulating MYC activity through direct repression of a MYC-cooperating molecule, E2F1. Furthermore, the miR-342-3p module activity, which we defined as a gene set reflecting experimentally substantiated influence of miR-342-3p on mRNA expression, was found to be inversely correlated with MYC activity reflected in the MYC module activity in three independent datasets of lung adenocarcinoma patients obtained by the Directorâs Challenge Consortium of the United States (P=1.94x10-73), the National Cancer Center of Japan (P=9.05x10-34) and our own in this study (P=3.37x10-6). Our integrative approach thus appears to be useful to elucidate inter-regulatory relationships between miRNAs and a protein coding-gene of interest, even those present in tumor tissues in patients, which still remains a challenge to better understand the pathogenesis of this devastating disease. Microarray analysis using a SurePrint G3 Human GE 8 x 60K Microarray G4851A (Agilent) was conducted.
2016-01-06 | E-GEOD-66759 | biostudies-arrayexpress
Project description:Recent development of integrative therapy against melanoma combines surgery, radiotherapy, targeted therapy, and immunotherapy; however, the clinical outcomes of advanced stage and recurrent melanoma are poor. As a skin cancer, melanoma is generally resistant to radiotherapy. Hence, there is an urgent need for evaluation of the mechanisms of radioresistance. The present study identified miR-335 as one of the differential expression of miRNAs in recurrent melanoma biopsies post-radiotherapy. The expression of miR-335 declined in melanoma tissues compared to the adjacent tissues. Moreover, miR-335 expression correlated with advanced stages of melanoma negatively. Consistent with the prediction of STARBASE and miRDB database, miR-335 targeted ROCK1 via binding with 3’-UTR of ROCK1 directly, resulting in attenuation of proliferation, migration and radioresistance of melanoma cells. The authors validated that overexpression of miR-335 enhanced X-ray-induced tumor regression by B16 mouse models. Briefly, the present findings gained insights into miR-335/ROCK1-mediated radiosensitivity and provided a promising therapeutic strategy for improving radiotherapy against melanoma. miRNAs profiling by array
2020-02-13 | GSE143777 | GEO
Project description:Accumulating evidence indicates that altered miRNA expression is crucially involved in lung cancer development, but only little has been elucidated about how MYC, an archetypical oncogene, is regulated by miRNAs, especially through a mechanism involving the MYC cofactor(s). In this study, we aimed at identifying miRNAs involved in the regulation of MYC transcriptional activity in lung cancers. To this end, we have taken an integrative approach with combinatorial usage of miRNA and mRNA expression profile datasets of patients’ tumor tissues as well as those of MYC-inducible cell lines in vitro. We report here that in addition to miRNAs previously reported to be directly regulating or regulated by MYC including let-7 and miR-17-92, our strategy allowed us to identify miR-342-3p as the one capable of indirectly regulating MYC activity through direct repression of a MYC-cooperating molecule, E2F1. Furthermore, the miR-342-3p module activity, which we defined as a gene set reflecting experimentally substantiated influence of miR-342-3p on mRNA expression, was found to be inversely correlated with MYC activity reflected in the MYC module activity in three independent datasets of lung adenocarcinoma patients obtained by the Director’s Challenge Consortium of the United States (P=1.94x10-73), the National Cancer Center of Japan (P=9.05x10-34) and our own in this study (P=3.37x10-6). Our integrative approach thus appears to be useful to elucidate inter-regulatory relationships between miRNAs and a protein coding-gene of interest, even those present in tumor tissues in patients, which still remains a challenge to better understand the pathogenesis of this devastating disease.
2016-01-06 | GSE66759 | GEO
Project description:Accumulating evidence indicates that altered miRNA expression is crucially involved in lung cancer development, but only little has been elucidated about how MYC, an archetypical oncogene, is regulated by miRNAs, especially through a mechanism involving the MYC cofactor(s). In this study, we aimed at identifying miRNAs involved in the regulation of MYC transcriptional activity in lung cancers. To this end, we have taken an integrative approach with combinatorial usage of miRNA and mRNA expression profile datasets of patients’ tumor tissues as well as those of MYC-inducible cell lines in vitro. We report here that in addition to miRNAs previously reported to be directly regulating or regulated by MYC including let-7 and miR-17-92, our strategy allowed us to identify miR-342-3p as the one capable of indirectly regulating MYC activity through direct repression of a MYC-cooperating molecule, E2F1. Furthermore, the miR-342-3p module activity, which we defined as a gene set reflecting experimentally substantiated influence of miR-342-3p on mRNA expression, was found to be inversely correlated with MYC activity reflected in the MYC module activity in three independent datasets of lung adenocarcinoma patients obtained by the Director’s Challenge Consortium of the United States (P=1.94x10-73), the National Cancer Center of Japan (P=9.05x10-34) and our own in this study (P=3.37x10-6). Our integrative approach thus appears to be useful to elucidate inter-regulatory relationships between miRNAs and a protein coding-gene of interest, even those present in tumor tissues in patients, which still remains a challenge to better understand the pathogenesis of this devastating disease. Microarray analysis using a SurePrint G3 Human GE 8 x 60K Microarray G4851A (Agilent) was conducted.
2016-01-06 | GSE66758 | GEO
Project description:Precision Medicine for Relapsed Multiple Myeloma Based on an Integrative Multi-Omics Approach
| PRJNA474747 | ENA