Integrated analysis of the human hematopoietic non-coding RNA landscape reveals lncRNA-stem cell signature in AML
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE98854 | GEO | 2017/06/30
SECONDARY ACCESSION(S): PRJNA386456
REPOSITORIES: GEO
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Project description:Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation. shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis.
2017-05-31 | GSE98830 | GEO
Project description:Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation. shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis.
2017-05-31 | GSE98791 | GEO
Project description:Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation. shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis.
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Project description:Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation. shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis. This series only contains the RNAseq data obtained from successive stages of human granulocytic differentiation (myeloblasts, promyelocytes, metamyelocytes and neutrophils) which was obtained to validate the differentiation-dependent expression of LINC00173 in human granulopoiesis. To access the microarray data see GSE98633 and GSE98791.
2017-08-21 | GSE98946 | GEO
Project description:Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. We predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. In addition, both shRNA and CRISPR-KRAB mediated knock-down of LINC00173 showed reduced cell proliferation in stem cells and NB4 cells (2-3-fold, p≤0.01). Here we assess early effects of LINC00173 knockdown in human HSPC subjected to myeloid differentiation conditions.
2017-05-31 | GSE98829 | GEO
Project description:Epigenetic dysregulation is a common feature of acute myeloid leukemia (AML). Recently it has become clear that long noncoding RNAs (lncRNAs) can play a key role in epigenetic regulation, and consequently also dysregulation. Currently, our understanding of the requirements and roles of lncRNAs in AML is still limited. Using CRISPRi screening, we identified the lncRNA SGOL1-AS1 as an essential regulator of survival in THP-1 AML cells. We use RNA affinity purification using a biotinylated bait to pull down binding partners of the lncRNA, SGOL1-AS1. The identified proteins show a signficant enrichment for chromatin-modifying proteins involved in gene repression and chromosome organization.
2023-06-12 | PXD034329 | Pride
Project description:Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides located within the intergenic stretches or overlapping antisense transcripts of protein coding genes. LncRNAs are involved in numerous biological roles including imprinting, epigenetic regulation, apoptosis and cell-cycle. To determine whether lncRNAs are associated with clinical features and recurrent mutations in older patients (aged M-bM-^IM-%60 years) with cytogenetically normal (CN) acute myeloid leukemia (AML), we evaluated lncRNA expression in 148 untreated older CN-AML cases using a custom microarray platform. We analyzed 148 older cytogenetically normal(CN)-AML patients samples using a custom microarray platform and describe the expression of lncRNAs among the AML samples.
2014-11-26 | E-GEOD-63614 | biostudies-arrayexpress
Project description:Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and the second most common form of leukemia in children. Multiple lncRNAs participate in normal and may be implicated in malignant hematopoiesis associated with blood cell cancers, such as leukemia. Currently, the expression profile of lncRNAs in pediatric AML is unclear. In this study, we evaluated the lncRNA expression profile in the tissue of three pediatric AML patients with lncRNA microarray techniques. In order to gain insight into the function of targets of lncRNAs, GO term and KEGG pathway annotation were applied to the target gene pool. qPCR was performed to evaluate the expression patterns of dys-regulated lncRNAs.
2015-12-31 | GSE65263 | GEO
Project description:Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-transcriptome of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors, which we correlated with the ncRNA expression profile of 48 pediatric AML samples to establish a core lncRNA stem cell signature in AML.Linear (PCA) and nonlinear (t-SNE) dimensionality reduction of 46 pediatric AML samples including Down syndrome AMKL, core-binding factor AMLs (inv[16] or t[8;21]) and MLL-rearranged leukemias mapped most samples to a space between HSCs and differentiated cells together with the myeloid progenitors. A subset of AML-samples mapped closely to healthy HSCs, including most of the DS-AMKLs and MLL-AMLs. Following the incorporation of acute myeloid leukemia (AML) samples into the landscape, we further uncover prognostically relevant ncRNA stem cell signatures shared between AML blasts and healthy hematopoietic stem cells.
2017-05-31 | GSE98697 | GEO
Project description:Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and the second most common form of leukemia in children. Multiple lncRNAs participate in normal and may be implicated in malignant hematopoiesis associated with blood cell cancers, such as leukemia. Currently, the expression profile of lncRNAs in pediatric AML is unclear. In this study, we evaluated the lncRNA expression profile in the tissue of three pediatric AML patients with lncRNA microarray techniques. In order to gain insight into the function of targets of lncRNAs, GO term and KEGG pathway annotation were applied to the target gene pool. qPCR was performed to evaluate the expression patterns of dys-regulated lncRNAs. Bone marrow specimens were obtained at the time of diagnosis during routine clinical assessment of 3 pediatric patients with AML, who presented at the Department of Hematology and Oncology, Children's Hospital of Soochow University between 2000 and 2011. Additionally, bone marrow samples from 3 healthy donors were analyzed as controls. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturerâs standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY⢠Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3â bias utilizing a random priming method. The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 6 samples have flags in Present or Marginal (âAll Targets Valueâ) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.
2015-12-31 | E-GEOD-65263 | biostudies-arrayexpress