A novel interplay between triglycerides and acute promyelocytic leukemia mediated by the cooperation between PPARα and PML/RARα. [RNA-Seq]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE195777 | GEO | 2022/11/02
REPOSITORIES: GEO
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Project description:Patients with newly diagnosed acute promyelocytic leukemia (APL) are often obese or overweight, accompanied by metabolic disorders, such as dyslipidemia. However, the link between dyslipidemia and leukemia development is obscure. Here, we conducted a retrospective study containing 1,412 medical records (319 APL, 393 non-APL acute myeloid leukemia (AML), and 700 non-tumor controls) and found that APL patients had higher triglyceride levels than non-APL AML and non-tumor controls. We revealed that triglyceride served as a risk factor of early death in APL patients, and there was a positive correlation between high triglyceride levels and high leukocyte counts. RNA-seq analysis on APL patients with high or normal triglyceride levels brought attention to peroxisome proliferator-activated receptor-alpha (PPARα) signaling, a crucial regulator of cell metabolism and a transcription factor involved in cancer development. We demonstrated that PPARα knockdown inhibited the proliferation of APL cells. Chromatin mapping data analysis with CUT&Tag revealed that PPARα coexisted with PML/RARα within the super-enhancer regions to maintain APL. Interventions to PPARα affected the transcription and protein level of FLT3. Moreover, in vivo results in mice having high-fat diet-induced high triglyceride levels supported the connection between high triglyceride levels and the leukemia burden, as well as the involvement of PPARα-mediated-FLT3 activation in the proliferation of APL cells. Our findings shed light on the association between APL cell proliferation and high triglyceride levels and established the contribution of an hyperlipidemia–PPARα–FLT3 axis to APL development.
2022-11-02 | GSE195776 | GEO
Project description:In this series we described the gene expression profiles of 18 APL patients using a high density DNA-oligonucleotide microarray (Agilent) representing about 20.000 genes demonstrating the presence of a very uniform expression pattern of APL cases among which two mainly types of gene profiles were recognized by unsupervised analysis. Relationship between these two subgroups and the different clinical, haematological and molecular APL features, comprising FLT3 status, were investigated. To identify biologically meaningful subsets of APL, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer?s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP and Human Universal Reference (Stratagene) with 3-CTP in each experiment. Samples were hybridized on Agilent Human 1A Oligo Microarray (V2), ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features). Fluorescence data were analysed with Feature Extraction Software v.7.5 (Agilent Technologies). Log10 ratio of the dye-normalized Cy3 and Cy5 channel signals were calculated. Raw signal intensities from each scan were imported into the gene expression analysis software Luminator (Rosetta Biosoftware). Two-dimensional clustering analysis was performed with Rosetta Luminator using an agglomerative algorithm with average link heuristics and correlation with mean subtraction. Supervised classification of APL samples into categories based on gene expression profiles was performed using Bayesian classifier implemented by Rosetta Biosoftware. Resultant gene expression profiles were first analyzed using an unsupervised, agglomerative hierarchical clustering. The matrix view clearly evidenced the high grade of uniformity in gene expression pattern among APL patients being the majority of genes expressed at high (red colour) or low (green colour) levels relative to reference in all APL cases analyzed. This appearance of unsupervised matrix reflects the homogeneous nature of acute promyelocytic leukemia whose gene expression pattern definitely distinguishes it from all other types of acute myeloid leukemia. Beside the homogeneous pattern, subtle differences in gene expression had the strength to distinguish three clusters of APL patients (designed I, II, III). Comparisons between cluster I and cluster II patients clearly revealed a preferential distribution of FLT3 gene mutated cases in cluster I. Again, cluster I was related to microgranular morphology (M3v) (p=0.035) and short-type PML-RAR isoform (bcr3) (p=0.044). Furthermore cluster I was significantly associated with higher presentation circulant blast cell percentage (p=0.030) as well as hyperleucocitosis (p=0.009). To identify those genes distinguishing the FLT3-ITD leukemic cells from FLT3-WT, we applied a Bayesian classifier. 147 genes, significantly different among classes based on t-tests, were selected and included into the classifier. Among them, 92 genes were up-regulated in FLT3-ITD class and 55 were down-regulated. FLT3 internal tandem duplication gene expression signature consisted of several high expressed genes, among them we found genes that are involved in cytoskeleton organization, cell adhesion and migration, in proliferation and coagulation/inflammation pathways as well as down-regulated genes of myeloid granules and differentiation suggesting a role of FLT3 mutations in the pathogenesis and clinical manifestation of an APL subtype. SUPPLEMENTARY DATA:1) Anova gene list ITD, 2)Anova gene list M3 morphology, 3)Anova gene list PML/RARalpha isoforms (bcr), 4)Intersection gene list ITD_M3, 5) Intersection gene list ITD_bcr, 6)Intersection gene list M3_bcr, 7)Bayesian classifier gene list for FLT3-ITD vs FLT3-wt, 8)Bayesian classifier gene list for bcr1 vs bcr3
2008-05-07 | E-GEOD-2550 | biostudies-arrayexpress
Project description:In this series we described the gene expression profiles of 18 APL patients using a high density DNA-oligonucleotide microarray (Agilent) representing about 20.000 genes demonstrating the presence of a very uniform expression pattern of APL cases among which two mainly types of gene profiles were recognized by unsupervised analysis. Relationship between these two subgroups and the different clinical, haematological and molecular APL features, comprising FLT3 status, were investigated. To identify biologically meaningful subsets of APL, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer?s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP and Human Universal Reference (Stratagene) with 3-CTP in each experiment. Samples were hybridized on Agilent Human 1A Oligo Microarray (V2), ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features). Fluorescence data were analysed with Feature Extraction Software v.7.5 (Agilent Technologies). Log10 ratio of the dye-normalized Cy3 and Cy5 channel signals were calculated. Raw signal intensities from each scan were imported into the gene expression analysis software Luminator (Rosetta Biosoftware). Two-dimensional clustering analysis was performed with Rosetta Luminator using an agglomerative algorithm with average link heuristics and correlation with mean subtraction. Supervised classification of APL samples into categories based on gene expression profiles was performed using Bayesian classifier implemented by Rosetta Biosoftware. Resultant gene expression profiles were first analyzed using an unsupervised, agglomerative hierarchical clustering. The matrix view clearly evidenced the high grade of uniformity in gene expression pattern among APL patients being the majority of genes expressed at high (red colour) or low (green colour) levels relative to reference in all APL cases analyzed. This appearance of unsupervised matrix reflects the homogeneous nature of acute promyelocytic leukemia whose gene expression pattern definitely distinguishes it from all other types of acute myeloid leukemia. Beside the homogeneous pattern, subtle differences in gene expression had the strength to distinguish three clusters of APL patients (designed I, II, III). Comparisons between cluster I and cluster II patients clearly revealed a preferential distribution of FLT3 gene mutated cases in cluster I. Again, cluster I was related to microgranular morphology (M3v) (p=0.035) and short-type PML-RAR isoform (bcr3) (p=0.044). Furthermore cluster I was significantly associated with higher presentation circulant blast cell percentage (p=0.030) as well as hyperleucocitosis (p=0.009). To identify those genes distinguishing the FLT3-ITD leukemic cells from FLT3-WT, we applied a Bayesian classifier. 147 genes, significantly different among classes based on t-tests, were selected and included into the classifier. Among them, 92 genes were up-regulated in FLT3-ITD class and 55 were down-regulated. FLT3 internal tandem duplication gene expression signature consisted of several high expressed genes, among them we found genes that are involved in cytoskeleton organization, cell adhesion and migration, in proliferation and coagulation/inflammation pathways as well as down-regulated genes of myeloid granules and differentiation suggesting a role of FLT3 mutations in the pathogenesis and clinical manifestation of an APL subtype. SUPPLEMENTARY DATA:1) Anova gene list ITD, 2)Anova gene list M3 morphology, 3)Anova gene list PML/RARalpha isoforms (bcr), 4)Intersection gene list ITD_M3, 5) Intersection gene list ITD_bcr, 6)Intersection gene list M3_bcr, 7)Bayesian classifier gene list for FLT3-ITD vs FLT3-wt, 8)Bayesian classifier gene list for bcr1 vs bcr3 Keywords = APL Keywords = FLT3 Keywords = ITD Keywords = mutation Keywords = expression profiling Keywords: other
2005-10-06 | GSE2550 | GEO
Project description:Combined all trans retinoic acid (ATRA) / arsenic regimen cures virtually all acute promyelocytic leukemi (APL) patients. However, APL is often associated with activating FLT3-internal tandem duplication (ITD) mutation and the molecular bases for this effect remain unknown. Using mouse APL models, we demonstrate the FLT3-ITD severely blunts ATRA response.
2019-03-18 | E-MTAB-7566 | biostudies-arrayexpress
Project description:Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17) leading to formation of PML-RARA fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations which cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational landscape using whole-exome (n=12) and subsequent targeted sequencing of 398 genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an average of eight non-silent somatic mutations per exome. We observed recurrent alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, while mutations in other genes commonly mutated in myeloid leukemia were rarely detected. The molecular signature of APL relapse was characterized by emergence of frequent mutations in PML and RARA genes. Our sequencing data also demonstrates incidence of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A, both of which encode for key components of the SWI/SNF complex. We show that knockdown of ARID1B in APL cell line, NB4, results in large scale activation of gene expression and reduced in vitro differentiation potential. Studying the effects of silensing ARID1B gene in NB4 cell lines
2016-02-17 | E-GEOD-77946 | biostudies-arrayexpress
Project description:Acute promyelocytic leukemia (APL) is a hematopoietic malignant disease characterized by the chromosomal translocation t(15;17), resulting in the formation of the PML-RARA gene. Here, 47 t(15;17) APL samples were analyzed with high-density single-nucleotide polymorphism microarray (50K and 250K SNP-chips) using the new algorithm AsCNAR (allele-specific copy-number analysis using anonymous references). Copy-number-neutral loss of heterozygosity (CNN-LOH) was identified at chromosome 10q (3 cases), 11p (3 cases) and 19q (1 case). Twenty-eight samples (60%) did not have an obvious alteration (normal-copy-number [NC] group). Nineteen samples (40%) showed either one or more genomic abnormalities: 8 samples (17%) had trisomy 8 either with or without an additional duplication, deletion, or CNN-LOH (+8 group); and 11 samples (23%) had genomic abnormalities without trisomy 8 (other abnormalities group). These chromosomal abnormalities were acquired somatic mutations. Interestingly, FLT3-ITD mutations (11/47 cases) only occurred in the group with no genomic alteration (NC group). Taken together, these results suggest that the pathway of development of APL differs in each group: FLT3-ITD, trisomy 8, and other genomic changes. Here, we showed for the first time hidden abnormalities and novel disease-related genomic changes in t(15;17) APL. Keywords: SNP-chip To identify oncogenic lesions in APL, we performed a genome-wide analysis of primary APL samples using high-density SNP arrays (Affymetrix GeneChip).
2010-04-03 | E-GEOD-14016 | biostudies-arrayexpress
Project description:Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17) leading to formation of PML-RARA fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations which cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational landscape using whole-exome (n=12) and subsequent targeted sequencing of 398 genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an average of eight non-silent somatic mutations per exome. We observed recurrent alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, while mutations in other genes commonly mutated in myeloid leukemia were rarely detected. The molecular signature of APL relapse was characterized by emergence of frequent mutations in PML and RARA genes. Our sequencing data also demonstrates incidence of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A, both of which encode for key components of the SWI/SNF complex. We show that knockdown of ARID1B in APL cell line, NB4, results in large scale activation of gene expression and reduced in vitro differentiation potential.
2016-02-17 | GSE77946 | GEO
Project description:The origin of aberrant DNA methylation in cancer remains largely unknown. In this study, we elucidated the DNA methylome in primary Acute Promyelocytic Leukemia (APL) and the role of PML-RARa in establishing these patterns. APL patients showed increased genome-wide DNA methylation with higher variability than healthy CD34+ cells, promyelocytes and remission bone marrow. A core set of differentially methylated regions in APL was identified. Age at diagnosis, Sanz score and Flt3-mutation status characterized methylation subtypes. Transcription factor binding sites, e.g. c-myc binding sites were associated with low methylation. SUZ12 and REST binding sites identified in embryonic stem cells were, however, preferentially DNA hypermethylated in APL. Unexpectedly, PML-RARa binding sites were also protected from aberrant DNA methylation in APL. In line, myeloid cells from pre-leukemic PML-RARa knock-in mice did not show altered DNA methylation and expression of PML-RARa in hematopoietic progenitor cells prevented differentiation without affecting DNA methylation. ATRA treatment of APL blasts did also not result in DNA methylation changes. These results suggest that aberrant DNA methylation is associated with leukemia phenotype but not required for PML-RARa-mediated initiation of leukemogenesis. Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2012-11-08 | E-GEOD-42118 | biostudies-arrayexpress
Project description:In order to facilitate inter-tissue communication and exchange of proteins, lipoproteins, and metabolites with the circulation, hepatocytes have an intricate and efficient intracellular trafficking system regulated by small Rab GTPases. Rab30, a putative Golgi-localized Rab GTPase, is induced in the mouse liver by fasting and its expression is further amplified in liver-specific carnitine palmitoyltransferase 2 knockout mice (Cpt2L-/-) that lack the ability to oxidize fatty acids in a Pparα-dependent manner. Live-cell super-resolution imaging and biochemical in vivo proximity labeling demonstrated that Rab30-marked vesicles are highly dynamic and interact with proteins throughout the secretory pathway. Rab30 whole-body, liver-specific, and Rab30;Cpt2 liver-specific double knockout (DKO) mice are viable and display intact Golgi ultrastructure. However, the loss of Rab30 in Rab30;Cpt2 DKO mice suppresses serum dyslipidemia observed in Cpt2L-/- single knockout mice. Corresponding with decreased serum triglyceride and cholesterol levels, Rab30;Cpt2 DKO mice exhibit decreased circulating but not hepatic ApoA4 protein, indicative of a trafficking defect. Together, these data suggest a role for Rab30 in the selective sorting of lipoproteins to influence hepatocyte and circulating triglyceride levels particularly during times of excessive lipid burden.
2023-09-12 | PXD044528 | Pride
Project description:In order to facilitate inter-tissue communication and exchange of proteins, lipoproteins, and metabolites with the circulation, hepatocytes have an intricate and efficient intracellular trafficking system regulated by small Rab GTPases. Rab30, a putative Golgi-localized Rab GTPase, is induced in the mouse liver by fasting and its expression is further amplified in liver-specific carnitine palmitoyltransferase 2 knockout mice (Cpt2L-/-) that lack the ability to oxidize fatty acids in a Pparα-dependent manner. Live-cell super-resolution imaging and biochemical in vivo proximity labeling demonstrated that Rab30-marked vesicles are highly dynamic and interact with proteins throughout the secretory pathway. Rab30 whole-body, liver-specific, and Rab30;Cpt2 liver-specific double knockout (DKO) mice are viable and display intact Golgi ultrastructure. However, the loss of Rab30 in Rab30;Cpt2 DKO mice suppresses serum dyslipidemia observed in Cpt2L-/- single knockout mice. Corresponding with decreased serum triglyceride and cholesterol levels, Rab30;Cpt2 DKO mice exhibit decreased circulating but not hepatic ApoA4 protein, indicative of a trafficking defect. Together, these data suggest a role for Rab30 in the selective sorting of lipoproteins to influence hepatocyte and circulating triglyceride levels particularly during times of excessive lipid burden.
2024-05-04 | PXD050376 | Pride