Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA315856 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Although 90% of children with acute lymphoblastic leukemia (ALL) are now cured, the prognosis of infant-ALL (diagnosis within the first year of life) remains dismal. Infant-ALL is usually caused by a single genetic hit that arises in utero: rearrangement of the MLL/KMT2A gene (MLL-r). This is sufficient to give rise to a uniquely aggressive and treatment-refractory leukemia compared to older children with the same MLL-r. The reasons for disparate outcomes in patients of different ages with identical molecular drivers are unknown. This paper addresses the hypothesis that fetal-specific gene expression programs co-operate with MLL-AF4 to initiate and maintain infant-ALL. Using direct comparison of fetal and adult HSC and progenitor transcriptomes we identify fetal-specific gene expression programs in primary human cells. We show that MLL-AF4-driven infant-ALL, but not MLL-AF4 childhood-ALL, displays expression of fetal-specific genes. In a direct test of this observation, we find that CRISPR-Cas9 gene editing of primary human fetal liver cells (to produce a t(4;11)/MLL-AF4 translocation) replicates the clinical features of infant-ALL and drives infant-ALL-specific and fetal-specific gene expression programs. These data strongly support the hypothesis that fetal-specific gene expression programs co-operate with MLL-AF4 to initiate and maintain the distinct biology of infant ALL.
2021-10-25 | GSE162034 | GEO
Project description:Acute Lymphoblastic Leukemia (ALL) caused by chromosomal translocation involving the Mixed Lineage Leukemia (MLL) gene remains a poor prognosis disease, especially in infants. The most common MLL-rearrangement in infant ALL (iALL), MLL-AF4, originates in utero where the properties of fetal target cells likely provide a permissive landscape for transformation. We describe the first faithful MLL-AF4 iALL model derived by CRISPR-Cas9 genome editing of primary human fetal liver (FL) cells. Using this model, we demonstrate that H3K79me2/3 is increased during transformation as a direct consequence of MLL-AF4 binding, but correlates weakly with changes in gene expression. DOT1L, the only known H3K79 methyltransferase, does not form part of the MLL-AF4 complex. Instead, we identify PAF1 as a key protein recruited by the MLL-AF4 complex, which in turn can recruit DOT1L. These results explain the previously unclear link between MLL-AF4 binding and increased H3K79me2/3, and introduce an iALL-specific model for future drug studies.
2021-10-25 | GSE162032 | GEO
Project description:The prognosis of infant B-cell acute lymphoblastic leukemia (iB-ALL) remains dismal, especially in patients harboring the MLL-AF4 (KTM2A-AFF1) rearrangement, which arises prenatally in early hematopoietic stem/progenitor cells (HSPCs). MLL-AF4+ B-ALL shows a bimodal localization of the MLL gene breakpoint within the MLL break cluster region, and two subgroups of patients based on the gene expression pattern of the HOXA/MEIS cluster have been identified. The pathogenic mechanisms in MLL-AF4+ B-ALL are challenging to study functionally due to the absence of faithful human cellular models recapitulating the disease phenotype and latency. Here, we assess the molecular contribution and leukemogenic capacity of MLL breakpoints occurring in either intron 10 (MLLi10, centromeric) or intron 12 (MLLi12, telomeric) in ontogenically-different human HSPCs sourced prenatally (fetal liver) and neonatally (cord blood). CRISPR-Cas9-induced MLL-AF4 (MA) targeting either MLLi10 (Mi10A) or MLLi12 (Mi12A) causes MA-driven in vitro myeloid immortalization in both fetal liver- and cord blood-CD34+ HSPCs. The cellular ontogeny and the location of the MLL breakpoint influenced the capacity of MLL-edited CD34+ HSPCs to initiate pro-B-ALL in vivo, which faithfully recapitulated the molecular, transcriptomic and methylome profiles of patients with primary MA+ iB-ALL. This dataset contains the DNA methylation information (Illumina MethylationEPIC Beadchip platform) of MLL-edited CD34+ cells (i10 or i12). BCPs, used as controls, were obtained from E-MTAB-8505
2023-10-29 | E-MTAB-12806 | biostudies-arrayexpress
Project description:B-cell acute lymphoblastic leukemia (B-ALL) is the most prevailing childhood cancer. As predicated by its prenatal origin, infant B-ALL (iB-ALL) show a silent mutational landscape irrespective of the MLL rearrangement/status, suggesting that other regulatory mechanisms might be impaired in the context of the disease. Here we used the most recent Illumina MethylationEPIC Beadchip platform to describe the genome-wide DNA methylation changes observed in a total of 69 de novo MLL-AF4+, MLL-AF9+ and non-rearranged MLL iB-ALL leukemias uniformly treated according to Interfant 99/06 protocol. Please note that samples X8 and X9 (pool of B cells and BCP) correspond to samples 200340580160_R08C01 and 200340580161_R07C01 from study E-MTAB-6315, respectively.
2021-03-12 | E-MTAB-8505 | biostudies-arrayexpress
Project description:Malignant transformation in a multipotential precursor has recently been shown to underlie mixed phenotype acute leukaemias. In contrast, and despite the conclusive demonstration that MLL-AF4 infant ALL arises in utero. In order to address this we purified haematopoietic stem/progenitor cell (HSPC) populations from four non-lineage switching presentation infant ALL cases and one ALL presentation which went on to lineage switch at relapse. The specific MLL-AF4 fusion event was determined in unsorted samples by LDI-PCR and identified in purified populations by nested PCR. In three cases where non-lineage restricted populations were able to be purified, MLL-AF4 was identified in the CD34+CD38-CD45RA+ population (LK228, LK230, LS01), the CD34+CD38-CD45RA-CD90- multipotential progenitor population (MPP, LS01) and even a candidate CD34+CD38-CD45RA-CD90+ haematopoietic stem cell (HSC) population (LK228) Interestingly, in a single non-switched MLL-AF9 case analysed for external comparison, the fusion was only identified in CD19+ blast/B cell populations, not in any HSPC population. Unexpectedly, we were also able to identify the presence of the MLL-AF4 fusion in apparently normally differentiated CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells from the peripheral blood/bone marrow of 4/5 cases examined. This finding was further supported by single cell analysis of LS01PALL which identified the fusion in 2/22 CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells analysed. Furthermore, the matched AML sample (LS01RAML) also contained MLL-AF4 positive mature T lymphoid cells. These data imply that MLL-AF4 does not impose a complete block on normal haematopoietic differentiation, and raise the question of what additional factors contribute to leukaemic lineage determination in the setting of the MLL-AF4 translocation. To examine the functional capacity of MLL-AF4 transformed precursor cells we generated a patient-derived xenograft model using NOD-scid/IL2Rγ-/- (NSG) mice. Serial xenotransplantation identified an MLL-AF4 positive clone persisting within the human CD34+CD38-CD45RA-CD90+ compartment across four generations of mice, confirming self-renewal of this population. Together these data identify an early multipotent progenitor or HSC as the putative cell of origin for MLL-AF4 ALL. Furthermore, they demonstrate that MLL-AF4, uniquely amongst MLL fusion genes, imposes a profound lymphoid bias on the developing leukemia but without completely abolishing broader, non-malignant, haematopoietic differentiation.
2020-04-21 | GSE130142 | GEO
Project description:Malignant transformation in a multipotential precursor has recently been shown to underlie mixed phenotype acute leukaemias. In contrast, and despite the conclusive demonstration that MLL-AF4 infant ALL arises in utero. In order to address this we purified haematopoietic stem/progenitor cell (HSPC) populations from four non-lineage switching presentation infant ALL cases and one ALL presentation which went on to lineage switch at relapse. The specific MLL-AF4 fusion event was determined in unsorted samples by LDI-PCR and identified in purified populations by nested PCR. In three cases where non-lineage restricted populations were able to be purified, MLL-AF4 was identified in the CD34+CD38-CD45RA+ population (LK228, LK230, LS01), the CD34+CD38-CD45RA-CD90- multipotential progenitor population (MPP, LS01) and even a candidate CD34+CD38-CD45RA-CD90+ haematopoietic stem cell (HSC) population (LK228) Interestingly, in a single non-switched MLL-AF9 case analysed for external comparison, the fusion was only identified in CD19+ blast/B cell populations, not in any HSPC population. Unexpectedly, we were also able to identify the presence of the MLL-AF4 fusion in apparently normally differentiated CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells from the peripheral blood/bone marrow of 4/5 cases examined. This finding was further supported by single cell analysis of LS01PALL which identified the fusion in 2/22 CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells analysed. Furthermore, the matched AML sample (LS01RAML) also contained MLL-AF4 positive mature T lymphoid cells. These data imply that MLL-AF4 does not impose a complete block on normal haematopoietic differentiation, and raise the question of what additional factors contribute to leukaemic lineage determination in the setting of the MLL-AF4 translocation. To examine the functional capacity of MLL-AF4 transformed precursor cells we generated a patient-derived xenograft model using NOD-scid/IL2Rγ-/- (NSG) mice. Serial xenotransplantation identified an MLL-AF4 positive clone persisting within the human CD34+CD38-CD45RA-CD90+ compartment across four generations of mice, confirming self-renewal of this population. Together these data identify an early multipotent progenitor or HSC as the putative cell of origin for MLL-AF4 ALL. Furthermore, they demonstrate that MLL-AF4, uniquely amongst MLL fusion genes, imposes a profound lymphoid bias on the developing leukemia but without completely abolishing broader, non-malignant, haematopoietic differentiation.
2020-04-21 | GSE132396 | GEO
Project description:MLL-AF4 is a hallmark genomic aberration which arises prenatally in high-risk infant acute lymphoblastic leukemia (ALL). In human embryonic stem cells (hESCs), MLL-AF4 skewed hemato-endothelial specification but was not sufficient for transformation. Additional cooperating genetic insults seem required for MLL-AF4-mediated leukemogenesis. FLT3 is highly expressed in MLL-AF4+ ALL through activating mutations (FLT3-TKD or FLT3-ITD) or increased transcriptional expression, being therefore considered a potential cooperating event in MLL-AF4+ ALL. Here, we explored the developmental impact of FLT3 activation on its own or in cooperation with MLL-AF4 in the hematopoietic fate of hESCs. FLT3 activation did not impact specification of CD45-CD31+ hemogenic precursors but significantly enhanced the formation of CD45+CD34+ and CD45+ blood cells and blood progenitors with clonogenic potential. Importantly, FLT3 activation through FLT3 mutations or FLT3-WT overexpression completely abrogated hematopoietic differentiation from MLL-AF4-expressing hESCs, indicating that FLT3 activation cooperates with MLL-AF4 to inhibit human embryonic hematopoiesis. Cell cycle/apoptosis analyses suggest that FLT3 activation directly impacts hESC specification rather than selective proliferation/survival of hESC-emerging hematopoietic derivatives. Transcriptional profiling supported the limited impact of FLT3 activation on hESC specification towards CD45-hemogenic precursors and the enhanced hematopoiesis upon FLT3 activation, and inhibited hematopoiesis upon MLL-AF4 expression in FLT3-activated hESCs which was associated to large transcriptional changes and regulation of master early hematopoietic genes. Also, although FLT3 activation and MLL-AF4 cooperate to inhibit embryonic hematopoiesis the underlying molecular/genetic mechanisms differ depending on how FLT3 activation is achieved. Finally, FLT3 activation did not cooperate with MLL-AF4 to immortalize/transform hESC-derived hematopoietic cells. 18 samples were analyzed. CD45- hemogenic precursors EV, 2 biological rep CD45- hemogenic precursors FLT3-TKD, 2 biological rep CD45- hemogenic precursors FLT3-WT, 2 biological rep CD45- hemogenic precursors FLT3-TKD/MLLAF4, 2 biological rep CD45- hemogenic precursors FLT3-WT/MLLAF4, 2 biological rep CD45+ blood cells EV, 1 biological rep CD45+ blood cells FLT3-TKD, 2 biological rep CD45+ blood cells FLT3-WT, 2 biological rep CD45+ blood cells FLT3-TKD/MLLAF4, 2 biological rep CD45+ blood cells FLT3-WT/MLLAF4, 1 biological rep
2013-06-04 | E-GEOD-40103 | biostudies-arrayexpress
Project description:MACE sequencing of MLL-AF4 KD and control PDX cells out of an inducible knockdown in vivo experiment showed a specific change in the gene expression profile to leukemic patient without MLL rearrangement pointing out the specificity of the shRNA system.
2021-08-15 | GSE181973 | GEO
Project description:MLL-AF4 is a hallmark genomic aberration which arises prenatally in high-risk infant acute lymphoblastic leukemia (ALL). In human embryonic stem cells (hESCs), MLL-AF4 skewed hemato-endothelial specification but was not sufficient for transformation. Additional cooperating genetic insults seem required for MLL-AF4-mediated leukemogenesis. FLT3 is highly expressed in MLL-AF4+ ALL through activating mutations (FLT3-TKD or FLT3-ITD) or increased transcriptional expression, being therefore considered a potential cooperating event in MLL-AF4+ ALL. Here, we explored the developmental impact of FLT3 activation on its own or in cooperation with MLL-AF4 in the hematopoietic fate of hESCs. FLT3 activation did not impact specification of CD45-CD31+ hemogenic precursors but significantly enhanced the formation of CD45+CD34+ and CD45+ blood cells and blood progenitors with clonogenic potential. Importantly, FLT3 activation through FLT3 mutations or FLT3-WT overexpression completely abrogated hematopoietic differentiation from MLL-AF4-expressing hESCs, indicating that FLT3 activation cooperates with MLL-AF4 to inhibit human embryonic hematopoiesis. Cell cycle/apoptosis analyses suggest that FLT3 activation directly impacts hESC specification rather than selective proliferation/survival of hESC-emerging hematopoietic derivatives. Transcriptional profiling supported the limited impact of FLT3 activation on hESC specification towards CD45-hemogenic precursors and the enhanced hematopoiesis upon FLT3 activation, and inhibited hematopoiesis upon MLL-AF4 expression in FLT3-activated hESCs which was associated to large transcriptional changes and regulation of master early hematopoietic genes. Also, although FLT3 activation and MLL-AF4 cooperate to inhibit embryonic hematopoiesis the underlying molecular/genetic mechanisms differ depending on how FLT3 activation is achieved. Finally, FLT3 activation did not cooperate with MLL-AF4 to immortalize/transform hESC-derived hematopoietic cells.
2013-06-04 | GSE40103 | GEO
Project description:MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs. We used microarray to estudy gene expression profile comparing ALL vs HSC, HPC and myeloid HPSC. We used highly FACS-purified (purity>98%) MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs. For each independent sample technical duplicates were always performed. Total RNA was extracted using TRIol reagent, and quantified on a Nanodrop spectrophotometer and Bioanalyzer. High-quality RNA was reverse transcribed and the obtained cDNA was used as a template to synthesize biotinylanted cDNA, then was fragmented and hybridized as duplicates/triplicates to HG-U133 plus2.0 GeneChips (Affymetrix) according to manufacturer's guideline.
2016-03-22 | E-GEOD-79450 | biostudies-arrayexpress