HOXA9 Protein Research Articles

Mutational analysis and prediction of the potential impact of missense mutations in the HOXA9 gene in B-cell acute lymphoblastic leukemia

Background: The HOXA9 gene is an essential gene during the developmental stages of the embryo, and its mutations can result in different phenotypes in both fetal and adult life. Additionally, this gene encodes a transcription factor that plays a crucial role in hematopoietic processes. Deregulation of these pathways has been reported in some leukemia cases. This in-silico analysis aims to evaluate the pathogenic effect of missense mutations in the HOXA9 gene by utilizing various bioinformatics tools.Methods: From dbSNP NCBI, 288 non-synonymous/missense mutations of the HOXA9 gene have been obtained. These missense mutations' functional impact was analyzed using various bioinformatics tools, including SIFT, Polyphen-2, PROVEAN, I-Mutant, PHD-SNP, and SNP&GO. Additionally, their structural impacts were investigated using Netsurf P-2.0, HOPE, ConSurf, and PyMOL. Furthermore, the analysis of protein hydrophobicity changes was examined using PEPTIDE 2.0 and ExPASy web tools.Results: Out of the 288 non-synonymous mutations, 45 mutations have been identified as functional genetic variants that affect the structure and stability of the HOXA9 protein. According to the analysis, 10 out of the 45 missense mutations were more likely to be involved in changing the characteristics of the protein. These changes include absolute and relative solvent accessibility (ASA, RSA), classification secondary structure, surface accessibility, noncovalent interactions, and protein conformation.Conclusion: Based on the results of this in-silico study, high-risk deleterious missense mutations have been predicted in the HOXA9 gene. These mutations may be potential candidates for future experimental investigations in various hematologic malignancy conditions.

HOXA9 Regulome and Pharmacological Interventions in Leukemia.

HOXA9, an important transcription factor (TF) in hematopoiesis, is aberrantly expressed in numerous cases of both acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) and is a strong indicator of poor prognosis in patients. HOXA9 is a proto-oncogene which is both sufficient and necessary for leukemia transformation. HOXA9 expression in leukemia correlates with patient survival outcomes and response to therapy. Chromosomal transformations (such as NUP98-HOXA9), mutations, epigenetic dysregulation (e.g., MLL- MENIN -LEDGF complex or DOT1L/KMT4), transcription factors (such as USF1/USF2), and noncoding RNA (such as HOTTIP and HOTAIR) regulate HOXA9 mRNA and protein during leukemia. HOXA9 regulates survival, self-renewal, and progenitor cell cycle through several of its downstream target TFs including LMO2, antiapoptotic BCL2, SOX4, and receptor tyrosine kinase FLT3 and STAT5. This dynamic and multilayered HOXA9 regulome provides new therapeutic opportunities, including inhibitors targeting DOT1L/KMT4, MENIN, NPM1, and ENL proteins. Recent findings also suggest that HOXA9 maintains leukemia by actively repressing myeloid differentiation genes. This chapter summarizes the recent advances understanding biochemical mechanisms underlying HOXA9-mediated leukemogenesis, the clinical significance of its abnormal expression, and pharmacological approaches to treat HOXA9-driven leukemia.

Targeting CDK9 in KMT2A-Rearranged Infant Leukemia: Evidence for Activity and Drug Synergy with Enitociclib

Introduction: Translocations of the lysine methyltransferase 2A (KMT2A) gene on 11q23 are seen in most infant leukemias. The outcomes in cases with KMT2A rearrangements (KMT2Ar) are significantly worse due to higher disease relapse rates and the emergence of chemo-resistance. Studies have shown that P-TEFb (CDK9/Cyclin T1) is an important component of the KMT2Ar complex and drives the transcriptional elongation step, subsequently contributing to the development of leukemia (Mueller, Dorothee et al.,2009). Based on this rationale, we investigated the potential of the selective P-TEFb/CDK9 inhibitor enitociclib in infant leukemia. Enitociclib potently inhibits MYC and MCL-1 in various tumor models (Sher, Steven et al.,2023). In addition, menin has been shown to be an important protein in the activation of target genes by KMT2Ar fusions, and menin inhibitors are considered promising therapeutic agents against infant leukemias, with at least four menin inhibitors currently in clinical development. We show preclinical data to support the activity of enitociclib with respect to cellular cytotoxicity, apoptosis induction and drug synergy in infant leukemia cells. Methods: A panel of pediatric leukemia cell lines representing high-risk and treatment resistant KMT2Ar cells were used. Leukemia cells with wild-type KMT2A as well as normal CD34+ cells and PBMCs from healthy donors were used as controls. Leukemic cells were treated with enitociclib (0.5µM - 0.03µM) and cell viability was measured using alamar blue assay. Apoptotic cell death following enitociclib treatment was measured by Annexin V/Propidium Iodide flow cytometry. Target modulation analyses were carried out by western blotting. Bone marrow (BM) stroma and leukemia co-culture experiments were performed to identify the effect of enitociclib on BM-derived growth support provided to leukemic cells. Drug combination assays were carried out with the menin inhibitor MI-463 and combination indices were calculated using the Chao-Talalay method. Rat xenograft models bearing infant leukemia cells were used to study the efficacy and tolerability of enitociclib therapy. Results: Data from in vitro cytotoxicity assays showed high sensitivity of KMT2Ar infant leukemia cells to enitociclib with IC 50 values of 30nM for KMT2Ar cells and 406nM for KMT2A-WT cells. Annexin V/PI staining showed a dose-dependent increase in cells in the late apoptotic stage for KMT2Ar cells after treatment. Target validation assays in KMT2Ar cells showed inhibition of transcriptional elongation by decreased serine phosphorylation by approximately 75% of RNA POL II CTD starting as early as 6 hours after treatment with 0.1µM enitociclib. Additionally, in KMT2Ar cells, an 80%-85% reduction in the amount of MCL-1 and MYC protein levels was observed after treatment with 0.1µM enitociclib for 6 hours. Furthermore, our data show that enitociclib may help to overcome the BM derived stromal mediated survival advantage in KMT2Ar leukemic cells. Enitociclib also potentiated the anti-leukemic effect of chemotherapies for childhood leukemia with the most effective combination observed with doxorubicin (0.01µM IC 50 for doxorubicin alone, 0.002µM IC 50 when combined with enitociclib) and prednisolone (25µM IC 50 for prednisolone only, 0.01µM IC 50 in combination). Drug combination assays showed effective synergy between enitociclib and the KMT2A-menin inhibitor MI-463 in KMT2Ar infant leukemia cells with a combination index of less than 1. As a detectable biomarker of activity, HOXA9 protein levels were found to be robustly diminished with 60% decrease after 24-hour treatment with the drug combination. In vivo, enitociclib given once weekly for 3 weeks led to complete remission in 10 out of 12 rats bearing KMT2Ar xenografts. Discussion: Our data demonstrate the ability of enitociclib to induce effective cellular cytotoxicity in high-risk KMT2Ar leukemia cells. We further show that enitociclib potentiated the anti-leukemic effect of chemotherapies that constitute the backbone of childhood leukemia protocols. Importantly, we show synergy with menin inhibition that is currently in consideration to be included in new generation clinical trials, suggesting the effective use of this novel combination in future treatment protocols. We provide the first in vitro and animal data supporting enitociclib in future treatment approaches for infants with KMT2Ar leukemia.

A Live Cell Protein Complementation Assay for ORFeome-Wide Probing of Human HOX Interactomes

Biological pathways rely on the formation of intricate protein interaction networks called interactomes. Getting a comprehensive map of interactomes implies the development of tools that allow one to capture transient and low-affinity protein-protein interactions (PPIs) in live conditions. Here we presented an experimental strategy: the Cell-PCA (cell-based protein complementation assay), which was based on bimolecular fluorescence complementation (BiFC) for ORFeome-wide screening of proteins that interact with different bait proteins in the same live cell context, by combining high-throughput sequencing method. The specificity and sensitivity of the Cell-PCA was established by using a wild-type and a single-amino-acid-mutated HOXA9 protein, and the approach was subsequently applied to seven additional human HOX proteins. These proof-of-concept experiments revealed novel molecular properties of HOX interactomes and led to the identification of a novel cofactor of HOXB13 that promoted its proliferative activity in a cancer cell context. Taken together, our work demonstrated that the Cell-PCA was pertinent for revealing and, importantly, comparing the interactomes of different or highly related bait proteins in the same cell context.

Dual IKZF2 and CK1α Degrader Targets Acute Myeloid Leukemia Cells

Acute myeloid leukemia (AML) is an aggressive hematologic disease for which several epigenetic regulators have been identified as therapeutic targets. We previously found that a transcription factor and Ikaros family member, IKZF2 (HELIOS) is required for myeloid leukemic stem cell activity (Park et al. Cell Stem Cell 2019). Additionally, IKZF2 enhances self-renewal by increasing HOXA9 gene expression and in parallel blocks myeloid differentiation by reducing C/EBP expression. Thus, our studies suggested that targeting IKZF2 could be a new therapeutic strategy in AML. Immunomodulatory drugs (IMiDs; lenalidomide and others) have been used clinically to specifically target and degrade other Ikaros family members. However, these have been unable to target IKZF2. Utilizing a structure-guided approach, we developed a small molecule with low nanomolar degrader activity against IKZF2 (DEG-35). DEG-35 treatment in different AML cell lines induce apoptosis and differentiation with IC50 values of 5 ±0.4 nM in MOLM-13 cells to 27± 2.5 uM in NB4 cells. To understand if DEG35 has activity against other substrates, we performed global quantitative proteomics and found casein kinase 1 alpha (CK1α), a serine/threonine kinase previously identified to be critical for myeloid leukemogenesis and a known IMiD substrate, to be the most depleted protein (Jaras et al. JEM). Also, we performed a PRISM (Profiling Relative Inhibition Simultaneously in Mixtures) screen assay which utilizes 770 barcoded cell lines from 20 lineages and identified multiple correlations with the p53 pathway. Previous studies found that CK1α suppresses the activity of p53 phosphorylation or binding MDM proteins. To further probe the mechanism behind DEG35 activity, we performed RNA sequencing at 24hrs in MOLM-13 cells. Gene set enrichment analysis (GSEA) using the rank list of differentially expressed genes from the MOLM-13 cells treated with DMSO and DEG-35 revealed enrichment for genes upregulated in CK1α KO keratinocytes and p53 targets. Additionally, we found enrichment for the MLL-AF9 IKZF2 KO LSC gene sets, myeloid differentiation, loss of MEIS1-HOXA9 and MYC targets. Immunoblotting validated the reduction of MYC and HOXA9 protein in DEG-35 treated MOLM-13 cells. To determine the contribution of CK1α and IKZF2 to the cellular phenotypes in MOLM13 cells, we developed CK1α and IKZF2 nondegradable mutants. CK1α, G40N was able to significantly reduce the cell killing activity of DEG-35 by 94% compared to vector cells (**p<0.01). Moreover, p53 deletion was also able to block DEG-35 induced apoptosis by 98% and differentiation by 88% compared to control. Additionally, expression of IKZF2 H141Q rescued DEG-35 mediated differentiation by 55% (***p<0.001), but not apoptosis. Thus, we demonstrate that the degradation of IKZF2 and CK1α by DEG-35 blocks cell growth and induces myeloid differentiation in human AML cell lines through CK1α-p53- and IKZF2-dependent pathways. To further probe the efficacy and therapeutic index of targeting both IKZF2 and CK1α. We found that AML cells were more sensitive to DEG-35 compared to normal bone marrow cells (murine MLL-AF9 Crbn I1391V cells has 10 fold and AML PDX cells have 2-5 fold higher sensitivity to normal mouse or human bone marrow cells).Treatment of DEG-35 at 50 mg/kg in AML PDX-transplanted mice led to significant prolonged survival compared to vehicle treated mice (median survival of DMSO mice: 45 days vs DEG-35 mice: 61 days; ***p< 0.001) and reduced disease burden. To improve pharmacological properties, we developed analog DEG-77, which has 10-fold increased solubility than DEG-35 in DMSO. DEG77 exhibited better in vivo efficacy in the MLL-AF9 Crbn I1391V model (Increase in median survival by DEG-35: 2 days *p<0.05 vs DEG-77: 31 days ****p<0.0001). Importantly, the increase of median survival of 30 days (****p<0.0001) was also observed in the secondarily transplanted DEG-77 mice compared to DMSO mice, suggesting that DEG-35 can reduce LSC activity. In summary, we report the development of nanomolar monofunctional cereblon-dependent degraders of IKZF2 and casein kinase 1 alpha (CK1α). DEG-35 or the analog DEG-77 delays leukemia progression in murine and human AML mice models. Thus, we provide a novel strategy for multi-targeted degradation of IKZF2/CK1α to enhance efficacy against AML that may be expanded to additional targets and indications.

Systematically Interrogating Downstream Regulation Mechanisms of HOXA9 in MLL-r Leukemia Via Functional Noncoding CRISPR Screens

HOXA9 overexpression is observed in 50-70% of human acute myeloid leukemia (AML) and a subset of acute lymphoblastic leukemia (ALL) and positively correlates with poor patient outcomes. Leukemia subtypes with hallmark overexpression of HOXA9 include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. Frequent genetic translation of NUP98-HOXA9 retained the DNA binding domain of HOXA9, suggesting the transcription factor function is essential for leukemia initiation and maintenance. Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. However, HOXA9 protein itself is a poor therapeutic target as it lacks targetable binding domains. Therefore, understanding HOXA9's functional downstream targets will 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 established a HOXA9-miniAID expressing MLL-r B-ALL cell line to execute acute HOXA9 degradation in the same isogenic cell line background upon auxin treatment. Compared with conventional loss-of-function strategies, our AID cellular model allows the investigation of immediate downstream targets controlled by HOXA9. We have therefore identified about 1,800 reproducible peaks bound by HOXA9 at a genome-wide scale. About 80% of HOXA9 binding peaks were co-bound by HOXA9's binding partner MEIS1, and motif enrichment confirmed that more than 75% of peaks contained a typical HOXA9 consensus motif. Interestingly, >80% binding peaks are located in non-promoter cis-regulator elements. Given the essential role of HOXA9 in regulating MLL-r leukemia cell survival and differentiation, we reasoned that targeting specific HOXA9-bound peaks will affect downstream gene expression leading to a similar survival crisis seen in HOXA9 knockout cells. Based on this rationale, combinatorial CRISPR screens were performed in three biological replicates on the MLL-r SEM cell line stably expressing Cas9 and base editor (ABE8.0), followed by time-course dropout selection on days 7, 14, and 21. Integrative CRISPR screen analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Functional validation by targeting these six noncoding segments with Cas9, dCas9-KRAB in additional MLL-r leukemia cell lines MOLM13, MV4,11 confirmed the survival essential of these HOXA9-bound regions. No cellular phenotype was observed in non-MLL-r leukemia cell lines, including NALM6, JURKAT, or OCI-AML2. Transplanting SEM cells targeted with sgHOXA9-in-FLT3 into NSG mice, significant growth retardation was monitored by flow analysis of peripheral blood. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of these HOXA9-bound noncoding segments, including FLT3, XBP1, JUN, BAHCC1, and CCDC200. Chromatin conformation characterization by Capture-C further confirmed the long-range interaction between HOXA9 bound enhancers and corresponding gene promoters in MLL-r SEM cells. In summary, using state-of-art research tools and newly established cell models, we have conducted a systematic functional screen and mechanism study of an undocumented downstream transcriptional network of HOXA9 in MLL-r leukemia cells. 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 alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Targeting SAMHD1 Promotes Anti-Tumor Immunity in Acute Myeloid Leukemia

The overall outcome of AML, which is characterized by HOXA9 overexpression (>50% cases), remains unfavorable. Success of allogeneic hematopoietic stem cell transplantation and immunotherapy highlights that T cell activation is critical for AML eradication. Notably, suppression of T cell immunity is common in the AML BM microenvironment, thus there is a pressing need to define underlying mechanisms. Recent studies reveal that the dNTP and Ara-CTP (active form of cytarabine) hydrolase SAMHD1, whose loss-of-function mutation is seen in inflammatory encephalopathy named Aicardi-Goutières syndrome, limits type-1 Interferon (IFN-I) and T cell responses by suppressing cGAS/STING signaling. Interestingly, our analysis of GEO datasets showed elevated SAMHD1 levels in specimens from AML patients relative to healthy donors, correlated with HOXA9 expression (A) and decreased T cell function. We thus asked whether SAMHD1 levels are associated with a particular cytogenetic change or mutation upstream of HOXA9 dysregulation. Accordingly, analysis of GSE data demonstrated that AML cases with MLL rearrangement (MLL-r, t[11q23]) or NPM1 mutation (NPM1c) exhibited elevated SAMHD1 levels relative to those without either alteration (B, C). Notably, HOXA9 knockdown (KD) decreased SAMHD1 protein levels in Molm13 (MLL-r+) and OCI-AML3 (NPM1c+) cells. ChIP-Q-PCR analysis of cord blood CD34+ cells engineered with Flag-tagged HoxA9 showed significant enrichment of HoxA9 protein at the predicted SAMHD1 promoter region relative to a control site. That region also showed significant enrichment of H3K27Ac (an active transcription mark) in HoxA9-overexpressing relative to control cells. We next assessed SAMHD1 loss-of-function in MLL-AF9 (MA9) knock-in mice, first by transducing leukemia cells from MA9+ BM with a doxycycline (DOX)-inducible control or shSAMHD1 and then transplanting them into either WT immunocompetent or immunodeficient (Rag2-/-) recipients to induce leukemia. Following DOX treatment, Rag2-/- mice bearing SAMHD1-KD or control transplants exhibited comparable survival. However, WT recipients bearing SAMHD1-KD AML survived significantly longer than controls (D, E). Moreover, SAMHD1-KD-mediated leukemia ablation was reproduced in HOXA9-Meis1 transduction/transplantation AML. Furthermore, depletion of T cells, but not B cells, blocked survival advantages seen in SAMHD1-KD-transplanted animals. To determine if IFN-I responses underlie these effects, we implanted SAMHD1-KD MA9 cells into WT or Ifnar1-/- recipients and observed significant abolition of SAMHD1-KD anti-AML effects. Moreover, SAMHD1-KD induced cGAS activation, as evidenced by elevated levels of the immune transmitter cGAMP in BM fluid from SAMHD1-KD relative to control MA9 mice. Accordingly, we observed upregulation of multiple interferon-stimulated genes (ISGs) such as ISG15 and CXCL10 downstream of cGAS/STING after SAMHD1-KD, effects blocked by cGAS deletion. To determine if immune activation requires SAMHD1 catalysis, we knocked out endogenous SAMHD1 in THP1 cells, which we then engineered cells to express doxycycline-inducible SAMHD1 variants including WT (SAMWT), catalytically-dead mutant SAMHD1 (SAMMT) or empty vector (MOCK). Comparison of ISGs expression in each group indicated that, relative to MOCK, SAMWT but not SAMMT downregulated ISGs, suggesting that blocking SAMHD1 catalysis promotes innate immunity. To identify SAMHD1 inhibitors, we conducted a structure-based virtual screen of 8,000,000 compounds (Molport). We then assessed the top 500 candidates using cell-based phenotypic screening based on cytarabine sensitization, namely, the inhibitor should sensitize SAMWT but not SAMMT cells to Ara-C toxicity (F). We then selected the 20 best candidates to evaluate for inhibition of SAMHD1 catalysis and chose Samin27 as the most potent lead compound. Importantly, we confirmed direct Samin27 interaction with SAMHD1 protein by nuclear magnetic resonance (NMR) (G). Samin27 treatment of SAMHD1-proficient human and mouse AML lines significantly upregulated ISGs expression. These results suggest that SAMHD1 plays an oncogenic role in AML by suppressing innate immunity. Further analysis is required to determine whether our compound can ablate AML in vivo when combined with currently available immune checkpoint inhibitors. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

MiR-652 Inhibits the Proliferation, Migration, and Invasion of Osteosarcoma Cells by Targeting HOXA9 and Regulating the PI3K/Akt Signaling Pathway.

Objective The aim of this study was to investigate the abnormal expression of miR-652 in osteosarcoma and its related mechanism. Materials and Methods Reverse transcription-polymerase chain reaction (RT-PCR) was used to detect the expression of miR-652 and HOXA9 in osteosarcoma tissues and normal tissues. A bioinformatics method was used to predict target genes of miR-652, and then luciferase reporter genes and western blot tests were used to verify expression of target genes. The miR-652 overexpression models were established by transfecting miR-652 mimics into osteosarcoma U-2OS cells, and HOXA9 overexpression models were simultaneously established by transfecting pcDNA3.1-HOXA9 into osteosarcoma U-2OS cells. Cell proliferation ability was detected by the CCK-8 assay, cell migration ability was detected by the scratch test, and cell invasion ability was detected by the Transwell invasion assay. Western blot tests were used to verify the expression of HOXA9, p-PI3K, p-AKT, MMP2 and MMP9. Results miR-652 and HOXA9 showed low expression and overexpression, respectively, in osteosarcoma tissues. Proliferation, invasion, and migration abilities of osteosarcoma cells and the level of protein expression of p-PI3K, p-Akt, MMP2, and MMP9 were significantly decreased with enhanced miR-652 expression (P < 0.01), while overexpression of HOXA9 reversed this situation. The results of dual-luciferase reporter gene showed that expression and activity of HOXA9 were downregulated accordingly, and the level of HOXA9 protein was decreased with enhancing miR-652 expression (P < 0.01). Conclusion miR-652 may negatively regulate HOXA9 expression and inhibit the proliferation, migration, and invasion abilities of osteosarcoma cells through the PI3K/Akt signaling pathway.

Molecular regulators of HOXA9 in acute myeloid leukemia.

Dysregulation of the oncogenic transcription factor HOXA9 is a prominent feature for most aggressive acute myeloid leukemia cases and a strong indicator of poor prognosis in patients. Leukemia subtypes with hallmark overexpression of HOXA9 include those carrying MLL gene rearrangements, NPM1c mutations, and other genetic alternations. A growing body of evidence indicates that HOXA9 dysregulation is both sufficient and necessary for leukemic transformation. The HOXA9 mRNA and protein regulation includes multilayered controls by transcription factors (such as CDX2/4 and USF2/1), epigenetic factors (such as MLL-menin-LEDGF, DOT1L, ENL, HBO1, NPM1c-XPO1, and polycomb proteins), microRNAs (such as miR-126 and miR-196b), long noncoding RNAs (such as HOTTIP), three-dimensional chromatin interactions, and post-translational protein modifications. Recently, insights into the dynamic regulation of HOXA9 have led to an advanced understanding of the HOXA9 regulome and provided new cancer therapeutic opportunities, including developing inhibitors targeting DOT1L, menin, and ENL proteins. This review summarizes recent advances in understanding the molecular mechanisms controlling HOXA9 regulation and the pharmacological approaches that target HOXA9 regulators to treat HOXA9-driven acute myeloid leukemia.

PS1006 INHIBITORS OF HOXA9 LEUKEMOGENIC TRANSCRIPTION FACTOR ARE EFFICIENT ON HUMAN AML CELL MODELS BUT NOT ON NORMAL HUMAN BONE MARROW CD34+ HEMATOPOIETIC CELLS

Background:The HOXA9 protein is a transcription factor associated with normal hematopoiesis and which expression on hematopoietic stem cells and progenitor cells decreases in the course of blood cell differentiation. The expression of HOXA9 is however maintained at high level in several subtypes of acute myeloid leukemia (AML) such as mll‐rearranged leukemias, NPM1‐mutated AMLs and AML presenting MYST3‐CREBP, NUP98‐NSD1 or RUNX/EVI1 translocations. The over‐expression of HOXA9 in these AML subtypes is associated with the maintenance of cell proliferation and the blockade of cell differentiation. It is well known that HOXA9 exerts its leukemic potential through DNA interaction and, therefore, we selected direct inhibitors of HOXA9/DNA interaction to block its activity and evaluate them on a murine leukemia cell model (Depauw et al., 2019).Aims:In order to go further, we aim at evaluating them on human AML cell models expressing or not HOXA9 and on normal human CD34+ hematopoietic cells to address any potential effect of our inhibitors on normal hematopoiesis.Methods:The expression level of HOXA9 was quantified by qRT‐PCR on a series of human AML cell lines. The sensitivity of those cell lines regarding two selected inhibitors was seen addressed using global cell survival analysis using MTS reaction. Methylcellulose clonogenic assays were performed on a series of human AML cell lines and on normal human bone marrow CD34+ hematopoietic cells. Knock‐down of HOXA9 expression was performed as a control using lentiviral delivery of HOXA9‐specific or control shRNAs.Results:A strong correlation between HOXA9 expression and the sensitivity to two of our inhibitors was evidenced in a series of 14 human AML cell lines with linear determination coefficients of R of ∼0.75 and ∼0.8.Clonogenic assays evidenced a decrease in the number and size of the colony forming units of treated related to untreated AML cell models. The relevance of HOXA9 expression in the clonogenicity is addressed by use of lentivirally transduced shHOXA9 in some of the AML cell models. By contrast, no difference were observed on either the number, the size and the differentiation subtypes of the colonies obtained from treated versus untreated normal human CD34+ hematopoietic cells.Summary/Conclusion:In conclusion, we selected inhibitors of HOXA9/DNA interaction that alter cell proliferation and clonogenic activity in a series of HOXA9‐positive AML cell models but that do not affect the progenitor cell number from normal bone marrow CD34+ cells.

The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors

HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, leading to a global dispensability of the HX motif for trimeric complex formation in the large majority of HOX proteins. In addition, it was shown that the anterior HOXB3 and central HOXA7 and HOXC8 proteins could use different alternative TALE interaction motifs, with or without the HX motif, depending on the DNA-binding site and cell context. Here we dissected the molecular interaction properties of the human posterior HOXA9 protein with its TALE cofactors, PBX1 and MEIS1. Analysis was performed on different DNA-binding sites in vitro and by doing Bimolecular Fluorescence Complementation (BiFC) in different cell lines. Notably, we observed that the HOXA9-TALE interaction relies consistently on the redundant activity of the HX motif and two paralog-specific residues of the HOXA9 HD. Together with previous work, our results show that HOX proteins interact with their generic TALE cofactors through various modalities, ranging from unique and context-independent to versatile and context-dependent TALE binding interfaces.

PARP inhibitors: a treatment option for AML?

A new study provides a rationale for the use of poly (ADP-ribose) polymerase (PARP) inhibitors to trigger irreparable DNA damage as a therapeutic approach in acute myeloid leukemia (AML). It also provides support for combining PARP inhibitors with agents that reduce HOXA9 protein levels.

Determination of biological processes regulated by HOXA9 in cells derived from Cervical, Uterine and its influence on the immune response.

Determination of biological processes regulated by HOXA9 in cells derived from Cervical, Uterine and its influence on the immune response.

A Twist1-MLL-WDR5-HOTTIP Complex Regulates HOXA9 Chromatin to Facilitate Metastasis of Prostate Cancer

The Twist1 transcription factor induces a transcriptional program resulting in cellular phenotypic changes, the epithelial-mesenchymal transition (EMT), during cancer progression. Twist1 is overexpressed in prostate cancer (PCa) specimens correlating with metastatic disease. We have demonstrated previously that Twist1 activates transcription of HOXA9 which contributes to the induction of a Twist1-dependent metastatic phenotype in PCa. Twist1 is canonically known as a transcription factor, but recent data suggest an epigenetic role for Twist1 in gene regulation. During embryogenesis, the histone methyltransferase complex, MLL-WDR5 and the lncRNA HOTTIP, regulate the expression of the HOXA cluster of genes by H3K4 chromatin methylation. Interestingly, PCa whole exome sequencing has shown frequent mutations in MLL2. Taken together, we hypothesized that Twist1 cooperates with the MLL-WDR5-HOTTIP (MWH) complex to drive expression of HOXA9 mediating PCa metastasis. Isogenic PCa cell lines using parental Myc-CaP and PC3 cells were created. Stable overexpression and knockdown (KD) experiments were performed with retroviral vectors. Transient KD with siRNA used commercial liposomal transfection reagents. Molecular biology procedures such as co-immunoprecipitation (IP), RNA IP (RIP), qPCR, Western and chromatin-IP (ChIP) were performed as stated below. We also used in vitro assays that mimic the various stages of cancer progression to metastasis as below. The MSKCC cBioPortal was used to perform PCa expression analysis. Twist1 could interact with components of the MWH complex as shown by Twist1 co-IP of WDR5 and RIP of HOTTIP. Twist1 overexpression also upregulated expression of the lncRNA HOTTIP in PCa cells. Functionally, WDR5 KD reduced cellular migration and invasion in Twist1 overexpressing cells. Similarly, KD against the lncRNA component HOTTIP also reduced Twist1-induced migration. Importantly, WDR5 or HOTTIP knockdown could abrogate Twist1-induced HOXA9 expression as shown by reduced HOXA9 message and protein levels. ChIP analysis of the HOXA9 promoter revealed that Twist1-overexpressing PCa cells had increased H3K4me3 levels specific for MWH activity. Last, TWIST1and genes encoding MWH complex components were co-overexpressed in PCa samples. Twist1 plays key roles during development and is a master transcriptional regulator of the EMT that promotes cancer metastasis. We demonstrated three important findings in Twist1-overexpressing PCa: (1) Twist1 forms a complex with the MWH methyltransferase complex; (2) the MWH complex activates HOXA9 expression by H3K4me3 chromatin modification of HOXA9 promoter region; and (3) the MWH complex is required for full Twist1-induced pro-metastatic behaviors.

Symplekin, a polyadenylation factor, prevents MOZ and MLL activity on HOXA9 in hematopoietic cells

MOZ and MLL encoding a histone acetyltransferase and a histone methyltransferase, respectively, are targets for recurrent chromosomal translocations found in acute myeloblastic or lymphoblastic leukemia. We have previously shown that MOZ and MLL cooperate to activate HOXA9 gene expression in hematopoietic stem/progenitors cells. To dissect the mechanism of action of this complex, we decided to identify new proteins interacting with MOZ. We found that the scaffold protein Symplekin that supports the assembly of polyadenylation machinery was identified by mass spectrometry. Symplekin interacts and co-localizes with both MOZ and MLL in immature hematopoietic cells. Its inhibition leads to a decrease of the HOXA9 protein level but not of Hoxa9 mRNA and to an over-recruitment of MOZ and MLL onto the HOXA9 promoter. Altogether, our results highlight the role of Symplekin in transcription repression involving a regulatory network between MOZ, MLL and Symplekin.

Low Expression of miR-196b Enhances the Expression of BCR-ABL1 and HOXA9 Oncogenes in Chronic Myeloid Leukemogenesis

MicroRNAs (miRNAs) can function as tumor suppressors or oncogene promoters during tumor development. In this study, low levels of expression of miR-196b were detected in patients with chronic myeloid leukemia. Bisulfite genomic sequencing PCR and methylation-specific PCR were used to examine the methylation status of the CpG islands in the miR-196b promoter in K562 cells, patients with leukemia and healthy individuals. The CpG islands showed more methylation in patients with chronic myeloid leukemia compared with healthy individuals (P<0.05), which indicated that low expression of miR-196b may be associated with an increase in the methylation of CpG islands. The dual-luciferase reporter assay system demonstrated that BCR-ABL1 and HOXA9 are the target genes of miR-196b, which was consistent with predictions from bioinformatics software analyses. Further examination of cell function indicated that miR-196b acts to reduce BCR-ABL1 and HOXA9 protein levels, decrease cell proliferation rate and retard the cell cycle. A low level of expression of miR-196b can cause up-regulation of BCR-ABL1 and HOXA9 expression, which leads to the development of chronic myeloid leukemia. MiR-196b may represent an effective target for chronic myeloid leukemia therapy.

Effects of RNA interference targeting HOXA9 on the proliferation and apoptosis of human acute monocytic leukemia U937 cells

Objective To investigate the effects of small interference RNA (siRNA) targeting HOXA9 on the proliferation and apoptosis of human acute monocytic leukemia U937 cell line.Methods Effective and specific siRNA oligo targeting HOXA9 was designed and compounded.It was transfected transiently into U937 cells by cationic liposome.The cells was divided into three groups:experimental group(siRNA targeting HOXA9 was transfected by liposome),negative control group (negative siRNA was transfected by liposome) and cell control group (add equal cells and medium).The expression of HOXA9 mRNA and protein were detected by reverse transcription PCR and Western blot.The cell proliferation was assessed by MTT.The apoptosis of each group were measured by Annexin V-FITC.Results Aftcr transfected by siRNA targeting HOXA9,the relative mRNA expression levels of HOXA9 in the experimental group,negative control group and cell control group were (22.980±0.548) ％,(82.371±1.517) ％ and (84.637±2.252) ％,respectively (P ＜ 0.05),and the relative protein expression levels were (50.377±2.773).％,(105.500±3.900) ％ and (111.392±3.905) ％,respectively (P ＜ 0.05).The inhibitory rates of cell proliferation and the apoptosis rates of the experimental group were significantly increased.The inhibitory rates of cell proliferation of 24 h,48 h and 72 h were (41.909±4.333) ％,(54.470±3.756) ％ and (65.835±1.024) ％,respectively,and the apoatosis rate was (26.800±2.081) ％.Compared with 2 controls,the experimental group differences had statistically significance (P ＜ 0.05).Conclusion siRNA targeting HOXA9 can effectively silence HOXA9 gene expression in U937 cell,suppress cell proliferation and induce cell apoptosis obviously,which providing experimental basis for clinical lenkemia therapy by targeting HOXA9 gene. Key words: Genes, Homeobox A9; Leukemia; RNA interference; U937 cells

The Role of HOXA9 in Human Laryngeal Squamous Cell Carcinoma

The present study was performed to investigate the expression of HOXA9 in human laryngeal squamous cell carcinoma and its possible roles in the progression. The levels of HOXA9 mRNA and protein were evaluated in human laryngeal squamous cell carcinoma. Hep-2 cells were transfected with h-HOXA9-siRNA. CCK-8 was used to analyze cell proliferation. Flow cytometry (FCM) was used to analyze cell cycle. The mobility of cells was tested by transwell migration assay. The expression of HOXA9 in laryngeal squamous cell carcinoma was significantly higher than normal mucosa tissues. In in vitro experiments, downregulation of HOXA9 strongly inhibited cell growth in Hep-2 by arresting cells in G1 phase (p < 0.05). Transwell migration assay showed that more HOXA9-negative cells migrated to the lower side of the membrane than positive ones (p < 0.01). HOXA9 acts as an oncogene in laryngeal squamous cell carcinoma. It could promote the proliferation and migration of Hep-2 cells.

Association of β-catenin, Wnt1, Smad4, Hoxa9, and Bmi-1 with the prognosis of esophageal squamous cell carcinoma

In our previous study, Human Signal Transduction in Cancer Gene Array was used in 12 fresh tumor samples to detect the gene expression profiles in the esophageal squamous cell carcinoma (ESCC) tissues matched adjacent non-cancerous samples. Among genes up-regulated at least twofold, β-catenin, Wnt1, Smad4, Hoxa9, and Bmi-1 were found. So subsequently, the aim of this study was to investigate the prognosis and clinicopathologic roles of β-catenin, Wnt1, Smad4, Hoxa9, and Bmi-1 in ESCC tissue. The mRNA and protein expression levels of β-catenin, Wnt1, Smad4, Hoxa9, and Bmi-1 genes in 70 ESCC and adjacent non-cancerous paraffin-embedded samples were determined by Real-Time Quantitative PCR (RT-PCR) and immunohistochemical staining. The mRNA expression level of β-catenin, Wnt1, Smad4, Hoxa9, and Bmi-1 in ESCC was significantly higher than that in the adjacent non-cancerous tissues (0.0821 ± 0.0416 vs. 0.0185 ± 0.0201, P = 0.0000; 1.9934 ± 1.9888 vs. 0.8863 ± 0.665, P = 0.0184; 0.0298 ± 0.0215 vs. 0.0189 ± 0.0187, P = 0.0017; 2.098 ± 0.091 vs. 1.016 ± 0.078, P = 0.0000; 2.181 ± 2.158 vs. 0.931 ± 0.894, P = 0.0152; respectively), and the protein expression level of determined genes was also significantly higher than that in the adjacent non-cancerous tissues (0.2835 ± 0.0844 vs. 0.2352 ± 0.0670, P = 0.0003; 0.3830 ± 0.0947 vs. 0.2721 ± 0.1474, P = 0.0000; 0.2637 ± 0.0348 vs. 0.2042 ± 0.0180, P = 0.0000; 0.2058 ± 0.0316 vs. 0.1218 ± 0.0518, P = 0.0000; 0.2736 ± 0.0834 vs. 0.2251 ± 0.0571, P = 0.0001; respectively). Then, the overexpression of mRNA and protein levels of β-catenin, Wnt1 and Bmi-1 was aggressively associated with lymph node metastasis, advanced pathological stage, and prognosis of the patients with ESCC (P < 0.05). The up-expression of Hoxa9 mRNA and protein was also aggressively associated with lymph node metastasis and advanced pathological stage (P < 0.05); however, the overexpression of Hoxa9 protein was not associated with the prognosis (P > 0.05). Meanwhile, the hypo-expression of Smad4 mRNA was aggressively associated with advanced pathological stage and prognosis of the patients with ESCC (P < 0.05); however, the hypo-expression of Smad4 protein was neutral to the prognosis and lymph node metastasis (P > 0.05). β-catenin, Wnt1, Smad4, Hoxa9, and Bmi-1 protein expression analysis showed that the positive outcomes of the combined detection of Wnt1 and β-catenin expression or Wnt1, β-catenin and Bmi-1 expression were significantly worse than those of a single target protein expression (P < 0.05). Meantime, the prognosis of the combined positive expression of Wnt1, β-catenin, and Bmi-1 was poorer than that in the combined positive expression of Wnt1 and β-catenin (P < 0.05). The prognosis of ESCC patients with the overexpression of Wnt1/β-catenin and Bmi-1 was relatively poor, and the level of Wnt1/β-catenin and Bmi-1 was conversely correlated with advanced pathological stage and lymph node metastasis. The expression level of Smad4 and Hoxa9 mRNA was also associated with the prognosis of the patients with ESCC, pathological stage, and lymph node metastasis; however, they might not be the independent prognostic factor.

HOXA9 Modulates Its Oncogenic Partner Meis1 To Influence Normal Hematopoiesis

While investigating the mechanism of action of the HOXA9 protein, we serendipitously identified Meis1 as a HOXA9 regulatory target. Since HOXA9 and MEIS1 play key developmental roles, are cooperating DNA binding proteins and leukemic oncoproteins, and are important for normal hematopoiesis, the regulation of Meis1 by its partner protein is of interest. Loss of Hoxa9 caused downregulation of the Meis1 mRNA and protein, while forced HOXA9 expression upregulated Meis1. Hoxa9 and Meis1 expression was correlated in hematopoietic progenitors and acute leukemias. Meis1(+/-) Hoxa9(-/-) deficient mice, generated to test HOXA9 regulation of endogenous Meis1, were small and had reduced bone marrow Meis1 mRNA and significant defects in fluorescence-activated cell sorting-enumerated monocytes, mature and pre/pro-B cells, and functional B-cell progenitors. These data indicate that HOXA9 modulates Meis1 during normal murine hematopoiesis. Chromatin immunoprecipitation analysis did not reveal direct binding of HOXA9 to Meis1 promoter/enhancer regions. However, Creb1 and Pknox1, whose protein products have previously been reported to induce Meis1, were shown to be direct targets of HOXA9. Loss of Hoxa9 resulted in a decrease in Creb1 and Pknox1 mRNA, and forced expression of CREB1 in Hoxa9(-/-) bone marrow cells increased Meis1 mRNA almost as well as HOXA9, suggesting that CREB1 may mediate HOXA9 modulation of Meis1 expression.