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  • 1
    In: Blood, American Society of Hematology, Vol. 120, No. 21 ( 2012-11-16), p. 2388-2388
    Abstract: Abstract 2388 Acute myeloid leukemia (AML) is characterized by genomic abnormalities that impair differentiation and promote proliferation. There are known karyotypic alterations and somatic mutations associated with relapse risk, but are rarely predictive of response to induction chemotherapy. miRNAs are epigenetic regulators of cell cycle progression and proliferation and their altered expression can play roles in malignancy and cancer cell behavior. Aberrant expression of miRNAs has been implicated in AML pathogenesis and unique expression profiles have been established in specific subsets. Altered miR-181a and miR-155 expression was reported to correlate with specific cytogenetic and molecular characteristics and with clinical outcome. We inquired whether expression of miR-155 and miR-181a correlates with disease characteristics and clinical response in childhood AML. We evaluated diagnostic specimens from 175 AML patients with normal karyotype (NK) treated on COG AML trial AAML0531 for expression of the miRNAs by quantitative TaqMan MicroRNA Assays normalized against normal marrow. There was a 4 log-fold variation in miR-181a, and a 3 log-fold variation in miR-155 expression levels. Patients were divided into 4 quartiles (Q1-Q4) with Q1 consisting of patients with the lowest, and Q4 with the highest expression levels of the specific miRNA. We then correlated disease characteristics and clinical response across quartiles. There was no association of miR-181a or miR-155 expression with age, gender or race. For miR-155, patients in Q4 had a higher diagnostic WBC% than those in Q1-Q3 (60.4 vs. 23.3, p=0.003). Diagnostic bone marrow blast% for Q4 vs. Q1-Q3 was 83% vs. 65% (p=0.004). There was no correlation between miR-181a expression, for either diagnostic WBC (p=0.117) or bone marrow blast % (p=0.237). High miR-155 expression was accompanied by increased prevalence of FLT3-ITD mutations. 78% of patients in Q4 were FLT3-ITD+ vs. 27% in Q1-Q3 (p 〈 0.001). miR-155 expression was not associated with mutations in CEBPA (p=0.76), NPM1 (p=0.98) or WT1 (p=0.57) genes. With the high prevalence of FLT3-ITD, elevated miR-155 expression was associated with high-risk disease, where 50% in Q4 had high-risk disease vs. 12% in the Q1-Q3 (p 〈 0.001). High miR-155 expression was inversely associated with low-risk disease.18% in Q4 had low-risk disease vs. 40% in Q1-Q3 (p=0.009). miR-155 expression was correlated with response to induction chemotherapy. Of patients in Q4, 58% achieved a morphologic complete remission (CR) vs. 81% in Q1-Q3 (p=0.003). As FLT3-ITD is highly prevalent in Q4, we inquired if miR-155 expression correlated with response to induction therapy in FLT3-ITD- patients. FLT3-ITD- patients in Q4 had a 44% CR rate vs. 86% in Q1-Q3 (p=0.008), suggesting that in addition to its association with FLT3-ITD, miR-155 expression may independently provide data on potential response to chemotherapy. Evaluation of miR-181a expression demonstrated that prevalence of CEBPA mutations increased with increasing miR-181a expression and 40% of patients in Q4 were CEBPA+ vs. 7% in Q1-Q3 (p 〈 0.001). There was no association between miR-181a expression and FLT3-ITD (p=0.727), NPM1 (p=0.466) or WT1 (p=0.701) mutations. High miR-181a expression was highly associated with low-risk disease, with 57% in Q4 categorized as low risk vs. 27% in Q1-Q3 (p 〈 0.001). miR-181a expression was not associated with response to induction chemotherapy (CR 80% in Q4 vs. 74% in Q1-Q3, p=0.43). Remission induction rate was re-evaluated after exclusion of CEBPA+ patients. Expression levels had no effect on CR rate (p=0.62). However, of patients in Q4, 71% had evidence of minimal residual disease (MRD) vs. 36% in Q1-Q3 (p=0.003). The correlation of miR-181a expression and MRD remained significant even after exclusion of FLT3-ITD, NPM1 and CEBPA mutations (MRD of 86% vs. 31%, p=0.01). We demonstrate significant association of miR-155 and miR-181a expression with specific disease characteristics and clinically significant mutations in pediatric AML. We also show that elevated expression is highly predictive of induction failure, providing potential biomarkers for identifying patients at high risk of poor response prior to therapy. miRNA expression could provide clinically significant information for use in therapeutic allocation. Validation of this finding in a larger cohort of pediatric and adult patients is underway. Disclosures: Loken: Hematologics, Inc: Employment, Equity Ownership. Pardo:Hematologics Inc: Employment.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2012
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  • 2
    In: Blood, American Society of Hematology, Vol. 138, No. Supplement 1 ( 2021-11-05), p. 802-802
    Abstract: Hematopoietic stem cells (HSC) are defined by the expression of the CD34 antigen on the cell surface whereby CD34+/CD38- repopulating cells have been the hallmark. This combination of antigens defining normal HSC has also been used to define leukemic stem cells (LSC). Although there is recognition of variability of CD34 expression in AML and lack of CD34 expression in a subset of AMLs (e.g., NPM1c), accurate and functional consequence of CD34 expression in AML has not yet been fully defined. We examined CD34 transcript (RNA seq) and protein expression (flow cytometry) as well as methylation status in a cohort of 2185 adult and pediatric AML cases. We demonstrate that CD34 is silenced in a significant proportion of AML through epigenetic mechanism and correlate CD34 expression with disease characteristics, fusions, mutations, and clinical outcome. Ribodepleted RNA seq data from 1048 pediatric AML (Children's Oncology Group, AAML1031), 390 adult AML (TCGA and BeatAML), 68 bone marrow, and 16 CD34+ PBMC from healthy donors were interrogated for CD34 expression. CD34 negative cohort ( & lt;1 TPM) were compared to the highest CD34 expressors (above median; 25-840 TPM). This evaluation demonstrated that 25% of pediatric patients had striking paucity of CD34 expression, suggesting silencing of the transcription process. Similar CD34 silencing was seen in 12% of adult AML (Fig. 1A). A correlation of CD34 expression with fusion and SNV subtypes revealed striking lack of CD34 expression in patients with KMT2A (54%), NUP98-KDM5A (81%), KAT6A-CREBBP (83%) fusions and NPM1 mutation (62%; Fig. 1B). The paucity of CD34 expression in KMT2A-r cohort was also seen in adults with a frequency of 61% CD34-Neg in KMT2A-r. Outcome evaluation of all patients based on CD34 expression failed to demonstrate differences in EFS or OS. However, significant variability in CD34 expression within KMT2A-r cases prompted further analysis. KMT2A-r patients with and without CD34 expression had an OS of 40% and 60%, respectively (p=0.0013, Fig. 1C). Despite the recent allocation of some KMT2A-r to high risk status based on fusion partners, the majority of KMT2A-r patients remain standard risk (SR). We examined the clinical outcome for SR KMT2A-r patients (which represents 71% of KMT2A-r). Using the same cutoffs, CD34-Neg group showed dramatically better outcomes, with 5 yr estimates of 42% vs. 24%, EFS and 67% vs. 38%, OS (p=0.0019, p & lt;0.0001, Fig. 1D). The observation by transcriptome was validated by multi-dimensional flow cytometry (MDF) conducted at Hematologics, Inc. CD34 expression data by MDF was available from 1613 patients enrolled on COG AAML0531 and AAML1031. CD34 expression & lt;1200 molecules were considered negative. Of the 1613 patients with MDF, 867 patients had RNA sequencing data available. Correlation of CD34 transcript to MFI by MDF demonstrated 95% concordance. Using CD34 cutoffs by MDF, KMT2A-r patients with and without CD34 expression had an EFS of 22% vs. 37%, (p=0.0195) and an OS of 30% vs 61%, (p & lt;0.0002, Fig. 1E). Importantly, SR KMT2A-r also demonstrated that those with CD34 expression had an OS of 36% whereas CD34-Neg patients had an OS of 64% (p & lt;0.0001), substantiating the transcriptome data. Analyzed separately, the KMT2A-r cases in COG AAML0531 and AAML1031 demonstrated similar outcome differences for these individual SR cohorts. Given CD34 silencing in such a large cohort of patients, we inquired the underlying mechanism of such significant silencing. We evaluated the corresponding methylation data (Illumina EPIC array) to determine whether CD34 expression may be modulated through epigenetic mechanisms. Correlation of CD34 transcript expression with CD34 promotor methylation status demonstrated significant hypermethylation of the CD34 promotor sites (Fig. 1F). The CD34 antigen plays an important role as a marker of HSCs and LSCs, however, at least 25% of patients lack expression. CD34-Neg is markedly correlated with KMT2A-r AML and specifically enriched in fusion partners which lack risk stratifying features. CD34-Neg also exhibit significantly improved OS and EFS over CD34-expressors. These outcome observations may have dramatic and immediate implications in the clinical management of the SR KMT2A cohort. Flow based CD34 quantification may be an immediate tool used to identify KMT2A-r patients with CD34 expression; these patients may benefit from intensive or targeted therapies. Figure 1 Figure 1. Disclosures Eidenschink Brodersen: Hematologics, Inc.: Current Employment, Other: Equity Ownership. Pardo: Hematologics, Inc.: Current Employment. Loken: Hematologics, Inc.: Current Employment, Other: current equity holder in a privately owned company.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2021
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  • 3
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 3772-3772
    Abstract: E-selectin (E-sel) is a cell adhesion glycoprotein that is expressed on endothelial cells and has been implicated in therapeutic resistance. In most myeloid leukemias, leukemic blasts express E-sel ligands (EsL), which contain the glycan epitope of the carbohydrate sialyl Lex (sLex). This expression increases the likelihood of adhesion to vascular endothelial cells and facilitates sequestration in the bone marrow vascular niche, leading to cell adhesion-mediated drug resistance and poor clinical outcome. E-sel antagonists like uproleselan, interrupts leukemic cell homing to the vascular niche, increases susceptibility to cytotoxic and targeted therapies and can be potent adjuncts to therapeutics. Recent data demonstrated a correlation between leukemic cell surface levels of EsL and response to uproleselan, linking EsL expression to response. We questioned whether transcriptome profiling of EsL-forming glycosylation genes can be used to identify elevated EsL expression in patients with acute myeloid leukemia (AML), and subsequently which patients might best respond to uproleselan. RNA-seq data from patients treated in COG AAML1031 (N = 1,074) was available for evaluation. We examined transcriptome expression of 24 genes that code for enzymes involved in glycosylation of EsL. All analyses were performed in R. Cox proportional hazards models were generated using the survival package. Multidimensional flow cytometry (MDF) was used to detect cell surface EsL expression by two techniques: direct binding of an E-sel/hIg, PE labeled chimera, and the anti-sLex antibody HECA-452. Seven of the 24 genes examined had minimal expression (mean 〈 1 TPM) and were excluded from further analysis. The remaining 17 were variably expressed (Fig. 1A). To assess association of expression with outcome, univariate Cox models for overall survival (OS) were generated, using gene expression as a continuous coefficient (N = 1,061). Of the 17 genes, 7 were significantly associated with increased risk (p 〈 0.05, Fig. 1B). ST3GAL4 and FUT7 were targeted for further evaluation, as they directly synthesize sLex (Fig. 1C), and were significantly associated with adverse outcome (HR = 1.013, p 〈 0.0001, and HR = 1.023, p 〈 0.0001, respectively). Patients highly expressing FUT7 (highest quartile of expression) had significantly worse outcome than low expressors (lowest 3 quartiles of expression), with a 5-year OS of 50.3% vs. 68.3% (p 〈 0.0001, Fig. 1D). Similarly, those with high ST3GAL4 expression had a 5-year OS of 51.3%, compared to 68.1% for low expressors (p 〈 0.0001, Fig. 1D). A subset of patients highly expressed both genes (ST3GAL4 and FUT7 high; SFhigh, N = 132). Compared to patients that did not highly express either gene (SFlow), these individuals had particularly adverse survival (45.8% OS vs 71.0% OS, p 〈 0.0001). Patients with one of two high expressing genes (SFinter) had a 5-year OS of 55.5%, illustrating what may be a compounding unfavorable impact conferred on survival (Fig. 1E). Further investigation of clinical characteristics within these 3 groups revealed that 71.5% of infants 〈 1 year were SFlow, with only 4.66% in SFhigh. In addition, CBF-AML was greatly underrepresented in SFhigh, with 97% of both t(8;21) and inv(16) patients in SFlow, and 0% in SFhigh. To verify surface protein expression of the two genes, leukemic specimens from SFhigh patients (N = 10) and SFlow patients (N = 10) underwent cell surface expression evaluation of glycosylated EsL using two MDF assays. SFlow patients had low or undetectable levels of cell surface EsL by both assays, whereas SFhigh patients had significantly higher expression of EsL (p 〈 0.001, Fig. 1F). This suggests a strong correlation between transcriptome measurements of EsL glycosylation genes and cell surface glycosylation levels of EsL. In summary, we have shown that multiple genes involved in the glycan synthesis of EsLs are highly expressed in pediatric AML. Two of these genes, ST3GAL4 and FUT7, are associated with poor outcome. Additionally, high expression of these genes is detectable at the transcript level and associated with cell surface EsL expression. These genes provide novel targets for overcoming drug resistance induced by the tumor microenvironment, and lend support for the use of EsL glycosylation genes as predictive biomarkers. These data also confirm the importance of E-sel in disease progression in AML and its potential as a therapeutic target. Figure 1 Disclosures Pardo: Hematologics, Inc: Employment. Eidenschink Brodersen:Hematologics, Inc: Employment. Magnani:GlycoMimetics Inc: Employment, Equity Ownership. Fogler:GlycoMimetics Inc: Employment, Equity Ownership. Loken:Hematologics, Inc: Employment, Equity Ownership.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
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  • 4
    In: Blood, American Society of Hematology, Vol. 128, No. 22 ( 2016-12-02), p. 2873-2873
    Abstract: In efforts to discover genes uniquely expressed in childhood AML, we performed transcriptomesequencing (RNA-Seq) in pediatric AML and contrasted the expression signature to that in normal marrow hematopoiesis. This effort led to the discovery of over 200 genes that lack expression in normal hematopoietic cells, but are variably expressed in pediatric AML cells. Mesothelin(MSLN) was discovered to be one of the most highly expressed genes in a subset of childhood AML cases (p 〈 10-15).Mesothelin is a cell-surface protein that is expressed onmesothelial cells ofserosal lining. MSLN is over-expressed on a variety of solid tumors, including lung, pancreatic, and ovarian cancers, and is associated with increased malignant transformation, cellular proliferation, and tumor aggressiveness. Given its cell surface expression, MSLN has emerged as an attractive target for immunotherapeutic interventions in solid tumors in adults. In this study, RNA obtained from diagnostic bone marrow specimens from childhood AML (N=434) and normal marrow (N=20) was subjected to wholetranscriptomesequencing and MSLN expression was quantified and normalized and reported as reads perkilobaseof exon per million reads mapped (RPKM). Similar data was obtained from adult TCGA AML database. Quantitative RT-PCR (qRT-PCR) and multidimensional flowcytometry(MDF) was used for confirmation of the transcript and cell surface protein expression. TARGET AML methylation data was used for correlation with transcript expression. Of the 434 specimens analyzed, MSLN mRNA expression was variably expressed (RPKM range 0-618.8), with expression detected in 119 patients (27%). Confirmatory studies by qRT-PCR on specimens with and without MSLN expression (N=137) showed correlation between RNA-Seqand PCR data. Cell surface MSLN expression was assessed by MDF using a PE-conjugated MSLN antibody (PE-mesoAb) and verified expression of MSLN protein on the leukemic cell surface in every case with MSLN transcript expression (Figure 1A). Evaluation of CD34+/CD38- hematopoietic progenitor cells by PE-mesoAbdemonstrated lack of MSLN expression by MDF. Evaluation of matched diagnostic and relapse specimens from MSLN-expressing patients (n=27) confirmed that MSLN expression was largely stable (R2=0.87), thus substantiating its expression in the major AML clone. Comparison of MSLN expression in pediatric vs. adult AML demonstrated a higher prevalence in pediatric AML (TARGET: 27% vs. TCGA: 11%)(Figure 1B). Evaluation of the clinical and biologic features in MSLN expressing (MSLN+) and non-MSLN expressing (MSLN-) pediatric patients revealed that MSLN expression was rarely observed in patients with normal karyotype (p 〈 0.001) or with the most common somatic mutations of FLT3/ITD, NPM1, CEBPA (p 〈 0.001 in all cases). However, MSLN expression was significantly higher in patients with inv(16), t(8;21) and MLL translocations (p 〈 0.001, p 〈 0.001, and p=0.02 respectively; Figure 1C). Given that a majority of patients with core binding factor (CBF) AML were MSLN+, we evaluated the clinical implications of MSLN expression in this favorable risk cohort. Among CBF patients, MLSN+ patients (n=95) had a relapse risk of 51% vs. 32% in the MSLN- (n=62) cohort (p=0.03; Figure 1D), with a corresponding disease free survival of 46% vs. 64% respectively (p=0.03). We further inquired about the mechanism by which MSLN expression might be regulated. Whole genome sequencing data failed to identify any genomic alterations in MSLN that could result in high expression. Therefore, we interrogated the possibility of epigenetic regulation of MSLN expression. Integration of the expression and methylation profiling cases with matching RNA-Seqand methylation data (N=246) demonstrated thathypomethylationof the MSLN promoter significantly correlated with high MSLN expression, implicating epigenetic regulation in the expression of MSLN in AML. Mesothelin, a therapeutic target in solid tumors, is highly expressed in biologically distinct subsets of childhood AML. High expression on leukemic blasts and lack of expression in normal hematopoiesis makes this antigen an ideal target for therapeutic intervention in AML. As a cell surface protein, this antigen avails itself for immune targeting by antibody drug conjugates, CAR-T cells, and T cell receptor mediated targeting. Figure 1 Mesothelin expression in childhood AML. Figure 1. Mesothelin expression in childhood AML. Disclosures Loken: Hematologics: Employment, Equity Ownership. Pardo:Hematologics, Inc: Employment.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
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  • 5
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 63-63
    Abstract: Asparaginase is an important drug for the treatment of acute lymphoblastic leukemia (ALL); however, hypersensitivity reactions to asparaginase can lead to suboptimal asparaginase exposure and to a higher risk of disease recurrence. Factors influencing the frequency of asparaginase hypersensitivity include asparaginase formulation, the schedule of asparaginase administration, and concurrent chemotherapy. In addition, using a candidate gene approach, our group previously identified a genetic association between HLA-DRB1*07:01 and asparaginase hypersensitivity in patients of European ancestry.[PMID 24970932] The objective of our current study was to use a genome-wide approach to identify additional genetic loci associated with hypersensitivity and to assess the relative importance of HLA-DRB1 as a genetic risk factor. Asparaginase hypersensitivity was assessed in children with ALL enrolled on SJCRH protocols Total XIIIA (n = 154), Total XV (n = 498) and Total XVI (n = 271) or Children’s Oncology Group (COG) protocols POG 9906 (n = 222) and AALL0232 (n = 2,163). Patients enrolled on protocols Total XIIIA, Total XV and POG 9906 received native E. coli asparaginase during treatment, whereas patients on Total XVI and AALL0232 received PEGylated E. coli asparaginase. Hypersensitivities were graded according to the NCI common toxicity criteria, and reactions of grade 2 and above were considered cases. Germline DNA was genotyped using the Affymetrix 500K, Affymetrix 6.0, or the Illumina Exome Beadchip array. Univariate analysis of risk factors associated with asparaginase hypersensitivity using the combined cohort of patients (n = 3,308) identified a significant positive association with treatment arm (P 〈 2.2x10-16; highest risk in patients enrolled on Total XV), native E coli asparaginase formulation (P 〈 2.2x10-16), age 〈 10 years (P = 3.3x10-4), male gender (P = 0.06), and racial ancestry (P = 2.1x10-4; highest risk among African ancestry). In multivariate analysis, treatment arm (P 〈 2.2x10-16), gender (P = 0.04), racial ancestry (P = 0.07), and ALL lineage (P = 0.003) remained significant risk factors. A multivariate logistic regression model adjusted for treatment arm, racial ancestry, gender, age, and ALL lineage was used to identify genomic variants associated with asparaginase hypersensitivity in the combined patient cohort. The minor allele of an intronic polymorphism in NFATC2 (rs6021191) was associated with hypersensitivity at the genome-wide significance threshold (P = 2.6x10-8, OR = 3.17). The minor allele frequency (MAF) for the NFATC2 high-risk variant was highest in non-European ancestries (MAF European = 0.001, MAF African = 0.142, MAF Hispanic = 0.043, MAF Asian = 0.151, MAF Other = 0.034). Using RNA-seq data available from the ALL tumor samples of 65 SJCRH patients, we found that patients carrying the variant had higher expression of NFATC2 compared to non-carriers (P = 1.0x10-3). NFATC2 is known to play a critical role in inducing T-cell gene transcription during immune responses. The strongest association detected using SNPs from the Illumina Exome array was found in HLA-DRB1 (rs17885382, P = 4.0x10-6, OR = 1.65), and the SNP is in near complete linkage disequilibrium with the HLA-DRB1*07:01 allele, which we previously found associated with asparaginase hypersensitivity. A gene-level analysis was performed using SNP-set Kernel Association Test (SKAT), and the gene with the strongest association with hypersensitivity was PPT2, located in the HLA class III region on chromosome 6 (P = 3.70x10-6). To determine potential biological pathways differentially represented by the genes identified by our analysis, we used Ingenuity Pathway Analysis on the top 1% of genes associated with hypersensitivity as identified by our single SNP (68 genes) and gene level analysis (18 genes). We found an enrichment of genes (8 out of 21 genes, P = 2.6x10-5) within the top network involved in humoral immunity, suggesting that other genes regulating immune responses may also contribute to the risk of developing asparaginase hypersensitivity. In conclusion, the top inherited genetic loci (NFATC2, HLA-DRB1*0701, PPT2) associated with asparaginase hypersensitivity are directly involved in human immune response, and pathway analysis suggests that inherited variations in other genes involved in humoral immunity likely play a role in the development of asparaginase hypersensitivity. Disclosures Evans: St. Jude: In accordance with institutional policy (St. Jude), I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Patents & Royalties. Relling:St. Jude: In accordance with institutional policy (St. Jude), I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Patents & Royalties.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 6
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 2709-2709
    Abstract: The bone marrow (BM) microenvironment is increasingly recognized as an important contributor to acute myeloid leukemia (AML) pathogenesis. However, despite growing interest in characterizing different components and cellular architecture of the BM niche and their biological significance in leukemogenesis, the proteomic constitution of the BM extracellular compartment that distinguishes a leukemic niche from its normal counterpart has not yet been fully described. We therefore performed a quantitative, large-scale proteomic analysis of 1,305 human proteins of the non-cellular compartment of BM (plasma) samples from ten relapsed or refractory AML patients and from ten age- and sex-matched healthy donors (HDs) using an aptamer-based, highly multiplexed, affinity proteomics platform (SOMAscan). This screen identified a total of 168 differentially abundant proteins, of which 91 were significantly more and 77 proteins significantly less abundant in leukemic BM compared with healthy marrow (FC ≥ 1.5, FDR ≤ 0.05). Comparative analysis of BM plasma and peripheral blood (PB) serum samples from the same AML patients and HDs revealed 65 similarly regulated proteins (37 up-regulated vs. 28 down-regulated) and 1 differently regulated protein between the two compartments. Out of the total 168 proteins, 102 proteins were specifically dysregulated only in the BM compartment. TruSeq Stranded Total RNA-sequencing (Illumina) was also performed using paired-end 75bp sequencing on a HiSeq 3000. RNA was isolated from PAXgene BM RNA tubes (Qiagen) collected in parallel with samples for proteomic analysis. Results of analysis of differentially expressed transcripts only partially overlapped with those candidates identified from our validated proteomic approach, indicating that sequencing of RNA derived from cellular sources of BM may be a suboptimal screening strategy to determine the true proteomic composition of the extracellular compartment of the AML marrow microenvironment. In addition to several previously reported proteins, our proteomics screen discovered numerous aberrantly expressed proteins in leukemic marrow whose role in AML pathogenesis is currently unknown. Using pathway analysis, we identified sets of proteins enriched for specific biological pathways including RAS, ephrin, PDGF, PI3K/AKT, MAPK, Notch, TLR, JAK-STAT, NFκB, Rap1, and Tie2 signaling pathways. A systems biology analysis approach revealed the highly connected network of cytokines and chemokines as the most striking AML-associated proteomic alteration in the BM. We identified IL-8 as a differentially expressed and key central molecule of this network in AML, consistent with recent reports. Importantly, we also identified significantly elevated levels of CKβ8 and CKβ8-1, alternatively spliced isoforms of the myelosuppressive chemokine CCL23 also known as myeloid progenitor inhibitory factor 1 (MPIF-1) or CKβ8, in both leukemic marrow and PB serum samples (Figure 1). Given the critical importance of cytopenias, often disproportional to the degree of leukemic marrow involvement, in the morbidity and mortality of patients with myelodysplastic syndrome (MDS) and AML, we subsequently confirmed this striking finding by performing orthogonal validation in a larger cohort of MDS and AML patients using an ELISA-based immunoassay. This novel finding suggests the possibility that CCL23 may play a role in suppression of normal hematopoiesis in MDS and AML. In support of this hypothesis, we demonstrated in vitro myelosuppressive effects of CCL23 isoforms on colony formation by human CD34+ hematopoietic stem and progenitor cells (HSPCs) in an in vitro colony forming unit assay, resulting in an approximately 2.5-fold decrease in CFU-GM and an evident decrease in CFU-GEMM counts. In summary, our broad and quantitative proteomic dataset of extracellular factors present in leukemic and normal aging bone marrow has already provided novel mechanistic insights into AML pathogenesis and should serve, together with paired RNA-sequencing information, as a useful public resource for the research community. Disclosures Lai: Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Jazz Pharma: Speakers Bureau; Astellas: Speakers Bureau; Daiichi-Sankyo: Membership on an entity's Board of Directors or advisory committees; Agios: Membership on an entity's Board of Directors or advisory committees. Hourigan:SELLAS Life Sciences Group AG: Research Funding; Merck, Sharpe & Dohme: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
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  • 7
    In: Blood, American Society of Hematology, Vol. 126, No. 1 ( 2015-07-02), p. 69-75
    Abstract: The rs6021191 variant in NFATC2 is associated with an increased risk of asparaginase hypersensitivity and is an expression quantitative trait locus associated with expression of NFATC2. Exome interrogation confirms the importance of the HLA-DRB1*07:01 allele in asparaginase hypersensitivity.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 8
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 3714-3714
    Abstract: Current regimens for remission induction therapy of pediatric acute lymphoblastic leukemia (ALL) include multiple potentially hepatotoxic drugs, including asparaginase. The objective of our genome-wide association study (GWAS) was to identify genetic loci associated with elevated alanine transaminase (ALT) levels immediately after remission induction in children with ALL. The patients included were enrolled on St. Jude Children's Research Hospital (SJCRH) protocols Total XV (n = 373) or Total XVI (n = 342); germline DNA was genotyped using the Affymetrix 500K, Affymetrix 6.0, or the Illumina Exome Beadchip arrays. In multivariate analysis, risk factors associated with higher ALT included older age, higher body mass index, European (versus African) ancestry, treatment with PEGylated E. coli asparaginase (versus native E. coli asparaginase), and receiving additional doses of asparaginase during induction due to high level of minimal residual disease at day 15-19 of induction. GWAS identified an association between I148M PNPLA3 rs738409 (C 〉 G) variant and post-induction ALT (Figure 1A; P = 7.9x10-9; median ALT of 34, 45, and 58 IU/L in CC, GC and GG genotypes, respectively), and the effect of the PNPLA3 variant was consistent for both protocols, both ALL risk groups, and among patients of European, African, and Hispanic ancestry. The PNPLA3 variant has previously been linked to elevated ALT and to the development of steatosis in adults;[PMID: 22001757; 18820647] in mice, this same variant led to a loss of catalytic function and to an increase of PNPLA3 accumulation in hepatic lipid droplets and to the development of steatosis.[PMID: 24917523] Within patients of African ancestry, we identified a variant near PIGV rs12748152 (C 〉 T) associated with lower ALT levels at P = 1.7x10-8; median ALT of 28 and 6 IU/L in CC and TC genotypes, respectively (Figure 1B), consistent with lower ALT values observed in patients of African ancestry. The PIGV variant explained 7% of the variation in ALT for patients of African ancestry. The results of our study suggest that post-remission induction ALT levels may be related to treatment-related variables, such as increased asparaginase exposure, and to host genetic factors, at least some of which contribute to hepatic dysfunction in settings outside of ALL therapy. Figure 1. Alanine transaminase (ALT) levels by PNPLA3 or PIGV genotype Figure 1. Alanine transaminase (ALT) levels by PNPLA3 or PIGV genotype Disclosures Evans: Prometheus Labs: Patents & Royalties: Royalties from licensing TPMT genotyping.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 9
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 3768-3768
    Abstract: Infants with acute leukemia present special challenges, due in part to the unusual features of their disease. A clonal oncofusion protein is detectable in the vast majority of infants presenting with acute leukemia, whether myeloid (AML), lymphoblastic (ALL), or mixed-phenotype (MPAL). Many recurrent oncofusion proteins seen in this age group involve the KMT2A (formerly MLL, Mixed Lineage Leukemia) gene, located on chromosomal band 11q23, which is notorious for both lineage switching and poor clinical prognosis. Other fusions involve components of the nuclear pore complex (NUP98), chromatin modifiers (KAT6A), or lineage-associated pioneer factors (such as MYB and GLIS2). This diversity of oncofusion proteins has hampered efforts to develop targeted agents, and over half of infant cases eventually succumb to their disease. Previous work showed that infant ALL is distinct from childhood or adult ALL. Here we show that infant AML is similarly distinct from AML in other age groups, and this difference yields transformative opportunities to repurpose existing targeted and immune therapies. mRNA sequencing (RNAseq) analysis of over 1500 participants in Children's Oncology Group clinical trials revealed hundreds of infant-AML-specific transcripts, many associated with early B cell development. 18 of the affected genes form a canonical B-cell regulatory circuit, including the epigenetic regulators BRD4 and POU2AF1, and their onco-fetal targets LIN28B and IGF2BP3. These four genes also host hypo-methylated super-enhancers in most infant AML cases, but in few older patients. The MYC proto-oncogene is directly implicated in a regulatory loop involving microRNA let7a-2, which is expressed in a mutually exclusive manner with its target and regulator LIN28B (Fig 1A). By contrast, the WT1 gene, abundantly expressed in over 90% of AML cases from other age groups, is transcribed at low levels in most infant AML cases. Single-sample gene set enrichment analysis revealed that most cases of infant AML bear more similarity to infant B-cell ALL or MPAL than to AML in older children, adolescents, and adults (Fig 1B). Higher-order chromatin conformation further emphasizes these differences. The MYC proto-oncogene, a critical node in the gene regulatory network (Fig. 1A) observed across infant acute leukemia cases, is routinely amplified via trisomy 8 in this age group (and in fact all childhood leukemia). The IGF2BP3 gene, another critical node (Fig. 1A), is rarely deleted in infants (deletions of 7q tend to spare 7p15, and complex karyotype cases often retain two or more copies on derivative chromosomes). The immature humoral and adaptive immune system in infants complicates treatment in this age group, but also yields metabolic vulnerabilities which can be exploited to break the nearly ubiquitous positive feedback loop described herein. These age-specific differences suggest that alternative therapeutic targets and modalities are warranted not only in infant AML, but across infant acute leukemia more generally. The relatively small numbers of infant acute leukemia cases by lineage, along with common mechanisms that appear to sustain most cases of infant acute leukemia, and frequent clinical reports of lineage switching in infants regardless of morphology at presentation, all support this contention. Our results indicate that combination therapies coupling experimental ages (such as DFMO, which targets metabolic regulation of MYC, LIN28B, and let-7a via ornithine decarboxylase, and has shown substantial efficacy in MYCN-amplified neuroblastoma) with already approved agents such as BET inhibitors (which target BRD4) and blinatumomab (targeting CD19 as a canonical B-cell antigen) may be warranted. These immune-targeting combinations represent promising and potentially lineage-agnostic approach to improving outcomes for infants with acute leukemia, a group of patients for whom novel therapeutic strategies are desperately needed, and for whom less toxic, more effective, targeted combination therapies may spare a lifetime of late effects. Disclosures Pardo: Hematologics, Inc: Employment. Kaeding:Celgene: Employment. Loken:Hematologics, Inc: Employment, Equity Ownership. Farrar:Novartis: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
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  • 10
    Online Resource
    Online Resource
    American Society of Hematology ; 2014
    In:  Blood Vol. 124, No. 21 ( 2014-12-06), p. 2295-2295
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 2295-2295
    Abstract: In order to study interventions that influence the severity of symptoms and serum asparaginase activity following asparaginase-induced hypersensitivity reactions, we developed a murine model of asparaginase allergy that recapitulates key features of clinical hypersensitivity to native E. coli asparaginase. BALB/c mice received 10 μg ip doses of E. coli asparaginase formulated with aluminum hydroxide adjuvant on day 0 and 14 of treatment in order to sensitize mice to asparaginase. Asparaginase allergies were induced in sensitized mice by challenging with a 100 μg iv dose of E. coli asparaginase on day 24 of treatment. The severity of hypersensitivity was reflected by the decrease in rectal temperature following the asparaginase challenge. Pre-challenge plasma samples were collected for anti-asparaginase antibody levels before inducing asparaginase allergies, and post-challenge samples were collected at the end of the experiment for measuring anti-asparaginase antibody levels, asparaginase activity, and mouse mast cell protease 1 (mMCP-1) levels. Sensitized mice developed high levels of anti-asparaginase IgG antibodies (P = 1.1 x 10-7) and had immediate hypersensitivity reactions (P = 3.3 x 10-10) to asparaginase upon challenge compared to non-sensitized mice. Furthermore, sensitized mice had profoundly lower plasma asparaginase activity (P = 4.2 x 10-13) and elevated levels of mouse mast cell protease 1 (mMCP-1, P = 6.1 x 10-3) after the asparaginase challenge compared to non-sensitized mice. We investigated the influence of pretreatment with the H1 receptor antagonist triprolidine, the H2 receptor antagonist cimetidine, the PAF receptor antagonist CV-6209, or dexamethasone on the severity of asparaginase-induced allergies. Our studies showed that the combination of triprolidine and CV-6209 was best for mitigating asparaginase-induced hypersensitivity symptoms (i.e., temperature drop) compared to non-pretreated, sensitized mice (P = 1.2 x 10-5). However, pretreatment with oral dexamethasone (4 mg/L in drinking water starting 7 days before asparaginase sensitization) was the only agent capable of mitigating the severity of the hypersensitivity symptoms (P = 0.03) and also partially restoring asparaginase activity (P = 8.3 x 10-4) compared to sensitized mice. Dose adjustment strategies were investigated for rescuing asparaginase activity in sensitized mice without requiring pretreatment with dexamethasone, and a 5-fold greater dose of asparaginase was required to restore enzyme activity to a similar concentration as in non-sensitized mice. In the absence of pretreatment, we found that the severity of asparaginase-induced reactions increased in a dose-dependent manner and that mMCP-1 levels correlated to the severity of the reactions (R2 = 0.577, P = 3.0 x 10-16). Our results suggest a role of histamine and PAF in asparaginase-induced allergies and demonstrate possible strategies for mitigating the severity of asparaginase-induced reactions and maintaining targeted concentrations of asparaginase. Furthermore, our results indicate that mast cell-derived proteases released during allergic reactions to asparaginase may be a useful marker of hypersensitivity, as elevated levels of mMCP-1 were detected in all sensitized mice and correlated with the severity of the reaction. Disclosures Evans: St. Jude: In accordance with institutional policy (St. Jude), I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Patents & Royalties. Relling:St. Jude: In accordance with institutional policy (St. Jude), I and/or my spouse have in the past received a portion of the income St. Jude receives from licensing patent rights related to TPMT polymorphisms as clinical diagnostics. Patents & Royalties.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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