HOXA9 is required for survival in human MLL rearranged acute leukemias
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE13714 | GEO | 2009/01/01
SECONDARY ACCESSION(S): PRJNA110389
REPOSITORIES: GEO
Similar Datasets
Project description:Leukemias that harbor translocations involving the mixed lineage leukemia gene (MLL) possess unique biological characteristics and often have an unfavorable prognosis. Gene expression analyses demonstrate a distinct profile for MLL-rearranged leukemias with consistent high-level expression of select Homeobox genes including HOXA9. Here, we investigated the effects of HOXA9 suppression in MLL-rearranged and MLL-germline leukemias utilizing RNAi. Gene expression profiling after HOXA9 suppression demonstrated co-downregulation of a program highly expressed in human MLL-AML (this study) and murine MLL-leukemia (Krivtsov et al. 2006) stem cells including HOXA10, MEIS1, PBX3 and MEF2C. Our data indicates an important role for HOXA9 in human MLL-rearranged leukemias, and suggests targeting HOXA9 or downstream programs may be a novel therapeutic option. Experiment Overall Design: RNA was purified from t(9;11) MOLM-14 AML cells 44h after transduction in triplicates with 2 of the two most effective HOXA9shRNA constructs (3 x 1F3-HOXA9shRNA; 3 x 2A5-HOXA9shRNA) or GFP-controlshRNA (6x).
2009-01-26 | E-GEOD-13714 | biostudies-arrayexpress
Project description:Aberrant HOXA9 expression is a hallmark of most aggressive acute leukemias, including a vast majority of human acute myeloid leukemia (AML) and subtypes of acute lymphoblastic leukemia (ALL). HOXA9 overexpression not only predicts poor patient diagnosis and outcome, but also plays critical roles in leukemia transformation and maintenance. Besides in few clinical cases as a translocation partner, HOXA9 gene generally shows lower frequencies of somatic mutations and is rarely amplified, indicating that transcriptional and epigenetic regulatory mechanisms might be predominantly utilized. However, our current understanding on the upstream regulation of HOXA9 in acute leukemia is still very limited, hindering development of effective methods to treat leukemia driven by aberrant HOXA9 expression. To mitigate these challenges, we have established the first HOXA9 endogenous reporter in an MLL-rearranged leukemia cell line to faithfully dictate HOXA9 expression by mCherry. By utilizing the reporter cell line and CRISPR/Cas9 genome editing tools, we have exploited comprehensive loss-of-function screenings to systematically discover novel transcription factors controlling HOXA9 expression. USF2 was discovered as a novel regulator of HOXA9 that directly binds to HOXA9’s promoter. USF2 depletion significantly down-regulated HOXA9 expression. Notably, in patients with MLL-rearranged B-ALL, transcriptional expression of USF2 and that of HOXA9 were positively correlated. In contrast, chromatin looping factor CTCF was dispensable for controlling HOXA9 expression in MLL-rearranged SEM cells. Collectively, these studies have functionally interrogated the regulome of HOXA9 and advance our understanding of the molecular regulation network in HOXA9-driven leukemia.
2020-10-30 | GSE140664 | GEO
Project description:To investigate whether co-expression of PBX3/MEIS1 can mimic that of MLL-AF9, HOXA9/MEIS1 or HOXA9/PBX3 in inducing leukemogenesis, we conducted in vivo mouse bone marrow transplantation (BMT) assays. Briefly, normal mouse bone marrow (BM) progenitor (i.e., lineage negative; Lin-) cells collected from B6.SJL (CD45.1) donor mice (CD45.1) were retrovirally co-transduced with MSCVneo-MLL-AF9+MSCV-PIG (MLL-AF9), MSCVneo-HOXA9+MSCV-PIG (HOXA9), MSCVneo-HOXA9+MSCV-PIG-MEIS1 (HOXA9+MEIS1), MSCVneo-HOXA9+MSCV-PIG-PBX3 (HOXA9+PBX3), MSCV-PIG-PBX3+MSCVneo-MEIS1 (PBX3+MEIS1), MSCVneo+MSCV-PIG-PBX3 (PBX3) , MSCVneo+MSCV-PIG-MEIS1 (MEIS1), or MSCVneo+MSCV-PIG (normal control; NC). Retrovirally transduced cells then were cultured with cytokines as well as puromycin and G418. Seven days later, the donor cells were transplanted into lethally irradiated (960 rads) 8- to 10-week-old C57BL/6 (CD45.2) recipient mice. The transplanted mice were watched for leukemogenesis. Then, gene expression profiling was conducted with bone marrow samples collected from leukemia groups and control group.
2016-03-03 | GSE68643 | GEO
Project description:TET1, the founding member of the TET family of enzymes (TET1/2/3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), was first identified as a partner gene in MLL-rearranged leukemia, but its definitive pathological role in leukemia is unclear. The down-regulation of all three TET genes and loss-of-function mutations of TET2 have been frequently observed in various cancers, and it was thought that they all play tumor-suppressor roles in tumorigenesis. Here we show that TET1 is likely a direct target of MLL and significantly up-regulated in MLL-rearranged leukemia, associated with an increased level of 5hmC. Our further in vitro and in vivo studies demonstrate that Tet1 plays an indispensable oncogenic role in MLL-rearranged leukemia, through cooperating with MLL fusion proteins in regulating their co-targets including the Hoxa/Meis1/Pbx3/Flt3 genes. Our data delineate a MLL-fusion/Tet1/Hoxa/Meis1/Pbx3/Flt3 signaling axis in MLL-rearranged leukemia, and highlight TET1 as a potential therapeutic target in treating this presently therapy-resistant disease. We report genome-wide 5hmC enrichment profiles and RNA-Seq gene expression in MLL-AF9 transformed and control mouse bone marrow mononuclear cells. These 5hmC profiles are derived from selctive chemical labeling and enrichment of 5hmC containing genomic DNA fragments, while the RNA-Seq expression profiles are generated from polyA enriched RNA
2015-12-14 | E-GEOD-42990 | biostudies-arrayexpress
Project description:TET1, the founding member of the TET family of enzymes (TET1/2/3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), was first identified as a partner gene in MLL-rearranged leukemia, but its definitive pathological role in leukemia is unclear. The down-regulation of all three TET genes and loss-of-function mutations of TET2 have been frequently observed in various cancers, and it was thought that they all play tumor-suppressor roles in tumorigenesis. Here we show that TET1 is likely a direct target of MLL and significantly up-regulated in MLL-rearranged leukemia, associated with an increased level of 5hmC. Our further in vitro and in vivo studies demonstrate that Tet1 plays an indispensable oncogenic role in MLL-rearranged leukemia, through cooperating with MLL fusion proteins in regulating their co-targets including the Hoxa/Meis1/Pbx3/Flt3 genes. Our data delineate a MLL-fusion/Tet1/Hoxa/Meis1/Pbx3/Flt3 signaling axis in MLL-rearranged leukemia, and highlight TET1 as a potential therapeutic target in treating this presently therapy-resistant disease.
2015-12-14 | GSE42990 | GEO
Project description:Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.
2023-10-10 | GSE215926 | GEO
Project description:Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.
2023-10-10 | GSE216017 | GEO
Project description:Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.
2023-10-10 | GSE216010 | GEO
Project description:Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.
2023-10-10 | GSE215927 | GEO
Project description:Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.
2023-10-10 | GSE216031 | GEO