scholarly journals Distal Enhancer Elements in ASXL1-Mutant Chronic Myelomonocytic Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2981-2981
Author(s):  
Moritz Binder ◽  
Alexandre Gaspar Maia ◽  
Ryan M. Carr ◽  
Terra Lasho ◽  
Thomas E. Witzig ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Transcriptional Activity ◽  
Chronic Myelomonocytic Leukemia ◽  
Venn Diagram ◽  
Promoter Regions ◽  
Volcano Plot ◽  
Coding Regions ◽  
Dna Accessibility ◽  
Myelomonocytic Leukemia

Introduction: Additional Sex Combs-Like 1 (ASXL1) is a chromatin modifier frequently affected by truncating mutations in myeloid malignancies. These mutations are associated with poor survival outcomes and increased rates of acute leukemic transformation. In chronic myelomonocytic leukemia (CMML), ASXL1 mutations are thought to affect transcriptional activity mainly by modifying histone marks, however additional epigenomic mechanisms have not been fully explored. We interrogated the epigenome of patients with ASXL1-mutant (MT) and -wildtype (WT) CMML using a multiomics approach to define cis-regulatory elements (CREs) such as distal enhancers (DEs). Methods: Bone marrow mononuclear cells from patients with CMML were subjected to targeted NGS of DNA, whole transcriptome shotgun sequencing (RNA-seq), immunoprecipitation (IP) of DNA (hydroxy-)methyl residues (DIP-seq), IP of the histone modifications H3K4me1, H3K4me3, and H3K27me3 (ChIP-seq), and DNA transposase accessibility studies (ATAC-seq). After quality control all samples were sequenced on an Illumina HiSeq 4000 before further processing and data analysis. Global assessments of DNA (hydroxy-)methylation, DNA accessibility, and histone modifications between ASXL1 MT and WT CMML were performed. The samples in the two groups were treated as biological replicates and subjected to a consensus peak calling strategy requiring an overlap of at least 30% between samples and an adjusted p-value < 5x10-5 for a signal peak to be considered statistically significant. Differential gene expression was estimated to define the up-regulated genes in ASXL1 MT CMML. Potential CREs were defined as sites with statistically significant signal peaks overlapping in at least two of the three epigenomic marks: H3K4me1, 5hmC, and ATAC. Potential DEs were defined as CREs in non-coding regions outside promoter regions (defined as transcription start site ±3kb) that were annotated in GeneHancer. Annotated DEs only present in ASXL1 MT but not WT CMML (specific DEs) were intersected with the list of up-regulated genes and the ReMap atlas. Results: Sixteen WHO-defined CMML patients were included, median age 69 years (48 - 77), 63% male; of which 8 patients (50%, all truncating frame shift mutations) were ASXL1 MT and 8 (50%) WT. The burden and spectrum of co-mutations was similar between ASXL1 WT and MT CMML (21 versus 23 per group; p = 0.684; heatmap). There was a predominant up-regulation of gene expression in ASXL1 MT CMML: 707 genes up- and 124 down-regulated (volcano plot, FDR < 0.050 for all genes). There were 64336 potential CREs, the vast majority (97%) being present in both ASXL1 MT and WT CMML (left Venn diagram). These CREs were most commonly located in introns, promoter regions, and distal non-coding regions (bar graph and pie chart). There were 1303 CREs unique to ASXL1 MT CMML (specific DEs), 1161 (90%) of which were annotated in GeneHancer (left Euler diagram). Of these 1161 annotated specific DEs 859 (74%) were located outside promoter regions and 34 (4%) of them were known to be associated with genes up-regulated in ASXL1 MT CMML (Euler diagrams). These specific DEs were characterized by an increase in H3K4me1 occupancy and DNA accessibility (average signal tracks, purple bars indicating annotated DEs, thin bars below peaks indicating statistical significance). We previously observed epigenomic modification of promoter regions in 519 of the 707 up-regulated genes (73%) facilitating transcriptional activity in ASXL1 MT CMML. For 13 of the up-regulated genes (right Venn diagram, blue genes in volcano plot) the specific DEs were the sole identified mechanism, while for the other 21 genes there were additional mechanisms noted in the promoter region. The top five transcription factor candidates binding the 34 specific DEs included JMJD1C, MYC, KDM5B, RCOR1, and HDAC2 (-log10(E) > 40 for all candidates). Conclusions: Using a multiomics approach based on H3K4me1, 5hmC, and ATAC data we identified potential CREs in ASXL1 MT CMML and characterized potential DEs using publicly available annotation data. Specific DEs were associated with up-regulated genes serving as a possible explanation for the observed transcriptional activity, shedding further light on the adverse prognostic impact associated with ASXL1 mutations. Figure 1 Disclosures Patnaik: Stem Line Pharmaceuticals.: Membership on an entity's Board of Directors or advisory committees.

scholarly journals Epigenomic Determinants of Transcriptional Activity in ASXL1-Mutant Chronic Myelomonocytic Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2987-2987
Author(s):  
Moritz Binder ◽  
Alexandre Gaspar Maia ◽  
Ryan M. Carr ◽  
Christopher Pin ◽  
Kurt Berger ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Chronic Myelomonocytic Leukemia ◽  
Regulatory Mechanisms ◽  
Chromatin Conformation ◽  
Disease Phenotype ◽  
Promoter Regions ◽  
Signal Peak ◽  
Proliferative Disease ◽  
Common Signal ◽  
Myelomonocytic Leukemia

Introduction: Truncating mutations in the Additional Sex Combs-Like 1 (ASXL1) gene are associated with a proliferative disease phenotype and poor survival outcomes across the spectrum of myeloid malignancies including chronic myelomonocytic leukemia (CMML). ASXL1 is thought to act as a chromatin modifier regulating transcriptional activity, however the exact mechanisms and resulting chromatin states remain controversial. We interrogated the epigenome of 16 patients with ASXL1-mutant and -wildtype CMML using a multiomics approach. Methods: Bone marrow mononuclear cells from patients with CMML (8 ASXL1-mutant, 8 -wildtype) were subjected to targeted NGS of DNA, whole transcriptome shotgun sequencing (RNA-seq), immunoprecipitation (IP) of DNA (hydroxy-)methyl residues (DIP-seq), IP of the histone modifications H3K4me1, H3K4me3, and H3K27me3 (ChIP-seq), and DNA transposase accessibility studies (ATAC-seq). After quality control all samples were sequenced on an Illumina HiSeq 4000 before further processing and data analysis. Global assessments of DNA (hydroxy-)methylation, DNA accessibility, and histone modifications between ASXL1-mutant and -wildtype CMML were performed. Differential gene expression was performed to define the up-regulated genes in ASXL1-mutant disease. The promoter regions of these up-regulated genes (defined as transcription start site ±3kb) were compared using the aforementioned multiomics approach. Epigenomic modification of the promoter region facilitating up-regulation of transcription was defined as the presence of a signal peak in ASXL1-mutant disease (in the absence of a signal peak in -wildtype disease) or 25% increase in a common signal peak (H3K4me1/3, 5hmC), the presence of a unique signal peak in ASXL1-mutant disease (ATAC), or the absence of a signal peak in ASXL1-mutant disease (in the presence of a signal peak in -wildtype disease), or 25% decrease in a common signal peak (H3K27me3, 5mC). Results: Sixteen patients with CMML, median age 69 years (48 - 77), 63% male, were included. Half of the patients had proliferative disease (pCMML) and half of them had truncating frameshift mutations in ASXL1 (heatmap). All ASXL1 variant allele frequencies were compatible with heterozygosity (31 - 48%). The burden of co-mutations was similar between ASXL1-wildtype and ASXL1-mutant disease (21 versus 23 per group; no difference in the median number of co-mutations, p = 0.684). The spectrum of co-mutations was typical for CMML, involving spliceosome components, epigenetic regulators, chromatin regulators, and cell signaling molecules (heatmap). There was a predominant up-regulation of gene expression in ASXL1-mutant patients: 707 genes up- and 124 down-regulated (volcano plot, FDR < 0.05 for all genes). Functional annotation of the up-regulated genes showed cell division, mitotic nuclear division, sister chromatid cohesion, DNA replication, and G1/S transition to be the 5 most enriched processes (accounting for 29% of all up-regulated genes, FDR < 1x10-10 for all terms). The up-regulated genes included several potential therapeutic targets and HOXA family members (including HOXA9). There were global increases in H3K4me1/3, 5mC, and 5hmC, decreases in H3K27me3, as well as a more relaxed chromatin conformation (bar graphs). Many of these epigenomic changes affected non-coding regions. When focusing on the promoter regions of the 707 up-regulated genes there was evidence of one or more of the interrogated epigenomic mechanisms facilitating transcription for 519 of the genes (73%). The most abundant mechanism was histone modification, followed by changes in DNA (hydroxy-)methylation, and increased chromatin accessibility, with considerable overlap (Venn diagram). For HOXA9, a known driver of leukemogenesis, the data supported a loss of H3K27me3 as the most prominent among the interrogated epigenomic regulatory mechanisms (average signal tracks). Conclusions: The transcriptome and chromatin conformation of ASXL1-mutant CMML are skewed towards proliferation and mirror the aggressive disease phenotype observed in practice. There is evidence of histone modification as well as changes in DNA methylation, and chromatin conformation facilitating transcriptional activity including known leukemogenic drivers. Additional regulatory mechanisms such as gene body methylation and enhancer elements require further exploration. Figure Disclosures Patnaik: Stem Line Pharmaceuticals.: Membership on an entity's Board of Directors or advisory committees.

scholarly journals Gene Body Methylation and Transcriptional Activity in ASXL1-Mutant Chronic Myelomonocytic Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 31-32
Author(s):  
Moritz Binder ◽  
Ryan M. Carr ◽  
Terra Lasho ◽  
Christy Finke ◽  
Abhishek A. Mangaonkar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Promoter Region ◽  
Transcriptional Activity ◽  
Median Number ◽  
Chronic Myelomonocytic Leukemia ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Differential Gene ◽  
Myelomonocytic Leukemia

Introduction: Truncating mutations in Additional Sex Combs-Like 1 (ASXL1) are associated with a high-risk disease phenotype in myeloid malignancies. In chronic myelomonocytic leukemia (CMML), truncating ASXL1 mutations are known to increase transcriptional activity of leukemic driver genes and have been associated with gene body hypermethylation. We interrogated the transcriptome and methylome of patients with ASXL1-mutant (MT) and -wildtype (WT) CMML using a multi-omics approach to test the hypothesis that gene expression is mediated through gene body methylation. Methods: Bone marrow mononuclear cells from patients with ASXL1 WT (n=8) and MT (n=8) CMML were subjected to targeted NGS of DNA, whole transcriptome shotgun sequencing (RNA-seq), and immunoprecipitation of DNA methyl residues (DIP-seq). After quality control all samples were sequenced on an Illumina HiSeq 4000 before further processing and data analysis. Differential gene expression analysis was performed to identify genes up-regulated in MT CMML. The samples in the two groups were treated as biological replicates and subjected to a consensus peak calling strategy requiring an overlap of at least 30% between samples and an adjusted p-value &lt; 5x10-5 for a methylation peak to be considered statistically significant. For validation purposes methylation analysis was performed on 3 ASXL1 MT and 3 WT CMML patients using Illumina Infinium MethylationEPIC microarrays and differentially methylated regions were identified using a bump hunting strategy. Gene body methylation was defined as methylation in gene bodies (outside the promoter region, i.e. transcription start site ±2kb). Gene body methylation was compared between WT and MT CMML for the up-regulated genes and correlated with expression of all genes in MT CMML. Results: Sixteen WHO-defined CMML patients were included, median age 69 years (48-77), 63% male, 50% had truncating ASXL1 frame shift mutations. Abnormal karyotypes were observed in the same number of patients and the burden of co-mutations was similar between the two groups (median number per group 3 vs. 3, p=0.508). This included several modulators of DNA methylation including TET2, DNMT3A, and IDH2 (median number per group 1 vs. 1, p=0.699). There was a predominant up-regulation of gene expression in MT CMML: 707 genes up- and 124 down-regulated (FDR&lt;0.050) without evidence of differential methylation in promoter regions of the differentially expressed genes. There was no difference in the number of genes with consensus methylation peaks in the gene body or the extent of gene body methylation (area under the consensus peaks) between MT and WT CMML for the differentially expressed genes (Figure 1a). We further validated these results using methylation microarrays (Figure 1b). Among the MT CMML patients, there was a curvilinear relationship between gene body methylation and gene expression across all genes with intermediate gene body methylation being associated with the highest gene expression (Figure 1c). As an alternative unbiased approach, we identified 1595 differentially methylated regions (DMR, regions with FDR&lt;0.05) in the validation data set. We mapped all hypermethylated regions to gene bodies requiring that there was no concurrent hypermethylation of the promoter region of the same gene. With this approach we identified one of the 707 up-regulated genes (0.14%) with evidence of isolated gene body hypermethylation (HBZ, log2-fold change in gene expression 4.25, FDR=0.0008, DMR area=1.61, DMR FDR=0.018). Representative examples of up-regulated mitotic kinases without evidence of differential gene body methylation are shown in Figure 1d (pie charts represent the mean β-values of microarray probes, p-values represent the comparisons of mean β-values between MT and WT CMML per gene). Conclusions: Gene body methylation was positively associated with gene expression in MT CMML. However, the lack of differential gene body methylation between WT and MT CMML for the up-regulated genes make it an unlikely explanation for the observed increase in transcriptional activity among patients with MT CMML. Figure 1 Disclosures Ordog: Millipore Sigma: Patents & Royalties.

scholarly journals Investigating the Role of Methylation in Silencing of VDR Gene Expression in Normal Cells during Hematopoiesis and in Their Leukemic Counterparts

Cells ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1991
Author(s):  
Urszula Nowak ◽  
Sylwia Janik ◽  
Aleksandra Marchwicka ◽  
Agnieszka Łaszkiewicz ◽  
Agnieszka Jakuszak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Blood Cells ◽  
Transcriptional Activity ◽  
Cpg Islands ◽  
Human Umbilical Cord Blood ◽  
Human Umbilical Cord ◽  
Promoter Regions ◽  
Vdr Gene ◽  
Hematopoietic Stem ◽  
Major Mechanism

(1) Background: Vitamin D receptor (VDR) is present in multiple types of blood cells, and its ligand, 1,25-dihydroxyvitamin D (1,25D), is important for the proper functioning of the immune system. Activity of VDR is higher in hematopoietic stem and progenitor cells than in fully differentiated blood cells of mice and humans. In some human acute myeloid leukemia (AML) blasts, the expression of the VDR gene is also high. The mechanism of silencing the VDR gene expression during differentiation of blood cells has been addressed in this work. (2) Methods: The cells have been obtained using fluorescence activated sorting from murine tissues and from human umbilical cord blood (UCB). Then, the expression of the VDR gene and transcriptional activity of the VDR protein has been tested in real-time polymerase chain reaction (PCR). Eventually, the methylation of VDR promoter regions was tested using bisulfite sequencing. (3) Results: The CpG islands in VDR promoters were not methylated in the cells studied both in mice and in humans. The use of hypomethylating agents had no effect toward expression of human VDR transcripts, but it increased expression of the VDR-target gene, CYP24A1. (4) Conclusions: The expression of the VDR gene and transcriptional activity of the VDR protein varies at successive stages of hematopoietic differentiation in humans and mice, and in blasts from AML patients. The experiments presented in this case indicate that methylation of the promoter region of the VDR gene is not the major mechanism responsible for these differences.

scholarly journals Molecular Alterations in Chronic Myelomonocytic Leukemia Monocytes: Transcriptional and Methylation Profiling

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3889-3889
Author(s):  
Anca Franzini ◽  
Jamshid S Khorashad ◽  
Hein Than ◽  
Anthony D. Pomicter ◽  
Dongqing Yan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dna Damage ◽  
Transcription Factors ◽  
Chronic Myelomonocytic Leukemia ◽  
Healthy Controls ◽  
Age Related ◽  
Dna Methylation Profiling ◽  
Myelomonocytic Leukemia ◽  
Methylation Profiling

Abstract Chronic myelomonocytic leukemia (CMML) is a genetically heterogeneous hematopoietic stem cell disorder that combines features of a myelodysplastic syndrome and a myeloproliferative neoplasm and exhibits a strong bias towards older age. The prognosis of CMML is poor, with overall survival of less than 3 years in most studies, however recurrent somatic mutations explain only 15-24% of the clinical heterogeneity of CMML (Elena C. et al. Blood 128:1408-17, 2016). The extreme skewing of the CMML age distribution suggests that CMML reflects the malignant conversion of the myelomonocytic-biased differentiation characteristic of an aged hematopoietic system. We hypothesized that separating the contribution of the normal aging process from bona fide CMML-specific alterations will improve the molecular characterization and biological understanding of CMML. We decided to focus on monocytes as the phenotypic minimal common denominator of genetically heterogeneous diseases. CD14+ monocytes were sorted from the blood of untreated CMML patients (N=12, median age 77 years, range 61-90), age-matched healthy controls (old controls: N=12, median age 68 years, range 62-74) and young healthy controls (young controls: N=16, median age 29 years, range 24-44) and subjected to RNA sequencing and DNA methylation profiling. Differentially expressed genes in CMML monocytes compared to healthy controls were identified with DESeq2 using a 1% false discovery rate (FDR) and a fold-change cutoff set at >│2│ (Figure 1A). We identified the 2480 CMML-specific genes by subtracting all genes with significant differences in the young controls vs. old controls comparison from the CMML vs. old controls comparison. The top-25 most significantly upregulated genes (Figure 1B) included transcription factors, TNFα signaling genes, genes that regulate genomic stability, and genes involved in apoptosis. The most significantly downregulated transcripts were genes involved in response to DNA damage, RNA binding, monocyte differentiation and mediators of inflammatory process. To link these observations to function, we imputed the 2480 CMML-specific differentially expressed genes into the ingenuity pathway analysis (IPA) application. This analysis uncovered significant enrichment of pathways involved in: mitotic roles of Polo-like kinase, G2/M DNA damage checkpoint regulation, lymphotoxin β receptor signaling, IL-6 signaling and ATM signaling (Figure 1C). DNA methylation profiling revealed 909 differentially methylated regions (DMRs) between CMML and age-matched controls, with most regions being hypermethylated in CMML monocytes. Of these, 37% of the DMRs were intronic, 22% were exonic, 14 % were in the promoter region (Figure 1D), 10% were downstream, 10% were upstream, the remainder were 3' and 5'-overlaps. We also performed integrated analysis using the promoter DMRs and the gene expression profile to identify CMML-associated genes that are likely to be regulated by specific changes in methylation. We observed concomitant changes in CMML-specific mRNA transcripts and DNA methylation promoter regions in the CMML vs. old controls contrast for 10 genes (Figure 1E). AOAH, SERINC5, TAF3 and AHCYL1 were downregulated and hypermethylated; MS4A3, TNF, VCAM1, and IFT80, were upregulated and hypermethylated; TUBA1B was upregulated and hypomethylated and PITPNA was downregulated and hypomethylated. Our study is the first to combine transcriptional and methylation profiling for molecular characterization of CMML monocytes. Conclusions: (i) age-related gene expression changes contribute significantly to the CMML transcriptome; (ii) the CMML-specific transcriptome is characterized by differential regulation of transcription factors, inflammatory response genes and anti-apoptotic pathway genes; (iii) differences in promoter methylation represent only a small proportion of overall differences in methylation, suggesting that intragenic or intronic methylation is a major contributor to the leukemic phenotype; (iv) age-related changes may be necessary, but are not sufficient to realize the CMML phenotype. Figure 1. Figure 1. Disclosures Deininger: Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Blueprint: Consultancy.

Distinct patterns of histone modifications at cardiac-specific gene promoters between cardiac stem cells and mesenchymal stem cells

2013 ◽  
Vol 304 (11) ◽  
pp. C1080-C1090 ◽  
Author(s):  
Meijing Wang ◽  
Qing Yu ◽  
Lina Wang ◽  
Hongmei Gu
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Histone Acetylation ◽  
Histone Modifications ◽  
Specific Gene ◽  
Cardiac Stem Cells ◽  
Gene Promoters ◽  
Promoter Regions ◽  
Specific Gene Expression

Mesenchymal stem cells (MSCs) and cardiac stem cells (CSCs) possess different potential to develop into cardiomyocytes. The mechanism underlying cardiomyogenic capacity of MSCs and CSCs remains elusive. It is well established that histone modifications correlate with gene expression and contribute to cell fate commitment. Here we hypothesize that specific histone modifications accompany cardiac-specific gene expression, thus determining the differentiation capacity of MSCs and CSCs toward heart cells. Our results indicate that, at the promoter regions of cardiac-specific genes ( Myh6, Myl2, Actc1, Tnni3, and Tnnt2), the levels of histone acetylation of H3 (acH3) and H4 (acH4), as a mark indicative of gene activation, were higher in CSCs (Sca-1+CD29+) than MSCs. Additionally, lower binding levels of histone deacetylase (HDAC) 1 and HDAC2 at promoter regions of cardiac-specific genes were noticed in CSCs than MSCs. Treatment with trichostatin A, an HDAC inhibitor, upregulated cardiac-specific gene expression in MSCs. Suppression of HDAC1 or HDAC2 expression by small interfering RNAs led to increased cardiac gene expression and was accompanied by enhanced acH3 and acH4 levels at gene loci. We conclude that greater levels of histone acetylation at cardiac-specific gene loci in CSCs than MSCs reflect a stronger potential for CSCs to develop into cardiomyocytes. These lineage-differential histone modifications are likely due to less HDAC recruitment at cardiac-specific gene promoters in CSCs than MSCs.

scholarly journals Gene expression profiling separates chronic myelomonocytic leukemia in two molecular subtypes

Leukemia ◽  
2007 ◽  
Vol 21 (11) ◽  
pp. 2359-2362 ◽  
Author(s):  
V Gelsi-Boyer ◽  
N Cervera ◽  
F Bertucci ◽  
V Trouplin ◽  
V Remy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Molecular Subtypes ◽  
Chronic Myelomonocytic Leukemia ◽  
Myelomonocytic Leukemia

scholarly journals Patient-Derived Induced Pluripotent Stem Cells Identified SLITRK4 As a Causative Gene of Chronic Myelomonocytic Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1134-1134
Author(s):  
Sho Yamazaki ◽  
Kazuki Taoka ◽  
Shunya Arai ◽  
Masashi Miyauchi ◽  
Keisuke Kataoka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Stem Cells ◽  
Candidate Gene ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
Chronic Myelomonocytic Leukemia ◽  
Leukemic Cells ◽  
Induced Pluripotent ◽  
Myelomonocytic Leukemia

Abstract Chronic myelomonocytic leukemia (CMML), the most frequent disease entity of myelodysplastic syndrome/myeloproliferative neoplasm is a clonal hematopoietic malignancy that is characterized by persistent monocytosis, morphologic myeloid dysplasia, and progression to acute myeloid leukemia. The pathogenesis of CMML remains entirely elusive because of the lack of suitable mouse models and the difficulties in the establishment of CMML cell lines. We have previously reported that we established induced pluripotent stem cells (iPSC) from CMML CD34 positive leukemic cells (CMML-iPSC) as a new disease model. Co-cultured with C3H10T1/2 stromal cells in the presence of vascular endothelial growth factor, CMML-iPSC generated CD34 CD43 double-positive hematopoietic progenitor cells (CMML-HPC). CMML-HPC have recapitulated important disease features of parental CMML cells in terms of genetic abnormalities, acceleration of cell proliferation, and aberrant surface markers expression. In addition, a novel human CMML xenograft mouse model has been established through secondary transplantation of human HPCs from CMML-iPSC-derived teratomas. This model produced HPCs that mimicked the properties of CMML in vivo. To identify key molecular abnormalities that contribute to the pathophysiology of CMML, we conducted comprehensive gene expression and DNA methylation profiling analyses of normal and CMML parental CD34 positive cells, iPSC, and their hematopoietic progenies, respectively. Correlation analysis revealed that gene expression and DNA methylation status between normal and CMML iPSC-derived HPC exhibited similar pattern (R2 = 0.92 and 0.96, respectively), although normal and CMML parental CD34 positive cells were quite different (R2 = 0.72 and 0.90, respectively), indicating that reprogramming followed by re-differentiation may enable to obtain more homogenous population of normal and CMML cells that reside in almost the same differentiation stage. These results allowed us to determine the difference in the genetic and epigenetic status between normal and CMML iPSC-derived HPC, which remained through reprogramming and re-differentiation, in order to find out causative genes in the pathogenesis of CMML. Using these combined omics platforms, we identified SLIT and NTRK like family member 4 (SLITRK4) as a candidate gene involving in pathogenesis of CMML, whose expression was enhanced and whose promoters were hypo-methylated in CMML-HPC. In other CMML patients' CD34 positive leukemic cells, the expression of SLITRK4 was up-regulated compared to healthy CD34 positive bone marrow cells and other leukemia cells. In addition, we revealed SLITRK4 had pro-proliferative activity as the knockdown of SLITRK4 inhibited proliferation of leukemic cell lines OCI-AML3. To elucidate whether SLITRK4 exert any biological functions in CMML, we established CMML-iPSC clones harboring hetero-knockout (wt/-) or homo-knockout (-/-) of SLITRK4 gene by CRISPR/Cas9 system. Although SLITRK4 (wt/-) and (-/-) clones did not exhibit any morphological and proliferative difference in CMML-iPSC, the production of HPC from CMML-iPSC was dramatically attenuated in SLITRK4-dependent manner. Therefore, while little has been known about the roles of SLITRK molecules in tumorigenesis, we demonstrated SLITRK4 was indispensable for generation of CMML leukemic cells and suggested the possibility of novel molecular therapy targeting SLITRK4, based on the findings obtained from our combined omics platforms. In summary, we identified SLITRK4 as a novel candidate gene responsible for the pathogenesis of CMML through our combined omics platform using patient-derived iPSC. This platform may provide a potential to trace causative genes in a variety of diseases. Disclosures Kataoka: Kyowa Hakko Kirin: Honoraria; Boehringer Ingelheim: Honoraria; Yakult: Honoraria.

scholarly journals NUP98-HBO1–fusion generates phenotypically and genetically relevant chronic myelomonocytic leukemia pathogenesis

2019 ◽  
Vol 3 (7) ◽  
pp. 1047-1060 ◽  
Author(s):  
Yoshihiro Hayashi ◽  
Yuka Harada ◽  
Yuki Kagiyama ◽  
Sayuri Nishikawa ◽  
Ye Ding ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Acetylation ◽  
Cell Fate ◽  
Therapeutic Potential ◽  
Macrocytic Anemia ◽  
Chronic Myelomonocytic Leukemia ◽  
Disease Development ◽  
Monocytic Cell ◽  
Hematopoietic Stem ◽  
Myelomonocytic Leukemia

Abstract Chronic myelomonocytic leukemia (CMML) constitutes a hematopoietic stem cell (HSC) disorder characterized by prominent monocytosis and myelodysplasia. Although genome sequencing has revealed the CMML mutation profile, the mechanism of disease development remains unclear. Here we show that aberrant histone acetylation by nucleoporin-98 (NUP98)-HBO1, a newly identified fusion in a patient with CMML, is sufficient to generate clinically relevant CMML pathogenesis. Overexpression of NUP98-HBO1 in murine HSC/progenitors (HSC/Ps) induced diverse CMML phenotypes, such as severe leukocytosis, increased CD115+ Ly6Chigh monocytes (an equivalent subpopulation to human classical CD14+ CD16− monocytes), macrocytic anemia, thrombocytopenia, megakaryocyte-lineage dysplasia, splenomegaly, and cachexia. A NUP98-HBO1–mediated transcriptional signature in human CD34+ cells was specifically activated in HSC/Ps from a CMML patient cohort. Besides critical determinants of monocytic cell fate choice in HSC/Ps, an oncogenic HOXA9 signature was significantly activated by NUP98-HBO1 fusion through aberrant histone acetylation. Increased HOXA9 gene expression level with disease progression was confirmed in our CMML cohort. Genetic disruption of NUP98-HBO1 histone acetyltransferase activity abrogated its leukemogenic potential and disease development in human cells and a mouse model. Furthermore, treatment of azacytidine was effective in our CMML mice. The recapitulation of CMML clinical phenotypes and gene expression profile by the HBO1 fusion suggests our new model as a useful platform for elucidating the central downstream mediators underlying diverse CMML-related mutations and testing multiple compounds, providing novel therapeutic potential.

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