ALBERT

Description: Background Glucocorticoids (GCs) such as prednisolone and dexamethasone are critical components of multi-agent chemotherapy regimens used in the treatment of acute lymphoblastic leukemia (ALL). Children with ALL are stratified into risk groups based on diagnostic features (i.e. age and cytogenetics) and therapy response. It has been established that the initial response to prednisolone is a major prognostic factor. Moreover, at relapse, de novo or acquired resistance to GCs is common and represents an important determinant in treatment failure. Recent studies performed by us and others have identified IKZF1 gene deletions and mutations as an independent prognostic factor that predicts prognosis and treatment outcome of children with B cell precursor ALL (BCP-ALL). These monoallelic IKZF1 gene deletions either affect the whole gene or may result in expression of dominant-negative IKZF1 isoforms due to intragenic deletions. However, it has not been established whether loss of IKZF1 function directly impacts the response to glucocorticoids. Results We examined whether haplodeficiency for Ikzf1 gene expression in mouse lymphocytes affects glucocorticoid-induced apoptosis. Splenocytes from Ikzf1+/- knockout mice were activated with lipopolysaccharide (LPS) and treated with increasing concentrations of either prednisolone or dexamethasone for 48 hours. B-lymphocytes haplodeficient for IKZF1 showed a significantly enhanced survival after treatment with GCs compared to wild type cells, as measured in an MTS assay and by AnnexinV staining. In case of prednisolone, the inhibitory concentration (IC50) was about ∼200-fold higher in the Ikzf1+/- splenocytes as compared to the wild-type cells. Gene expression analysis revealed that Ikzf1+/- splenocytes displayed lower overall expression levels as well as diminished transcriptional activation of several glucocorticoid receptor (GR)-induced target genes (i.e. Sgk1, Irs2, Zfp36L2). Furthermore, in luciferase reporter assays we established that IKZF1 overexpression enhances GR-mediated transcriptional activation in response to prednisolone. Finally, lentivirus-mediated IKZF1-shRNA expression in Nalm6 cell line, which reduces endogenous IKZF1 protein levels to around 50%, inhibits prednisolone and dexamethasone-induced apoptosis, demonstrating that also in human leukemia cells reduced IKZF1 expression levels protect against GC-induced cell death. In conclusion, our data provide evidence that loss of IKZF1 function mediates resistance to glucocorticoid-induced apoptosis, which may contribute to the poor outcome of IKZF1-deleted BCP-ALL. Disclosures: No relevant conflicts of interest to declare.

Description: Background Treatment outcome in acute lymphoblastic leukemia (ALL) has improved over the past 30 years, with overall survival rates of ∼45% in adults and ∼85% in children. Gross cytogenetic abnormalities, including numerical changes and chromosomal translocations, are of considerable prognostic value in both pediatric and adult ALL. In addition, we and others have recently identified novel molecular markers associated with a poor outcome in ALL, including deletions of the lymphoid transcription factor IKZF1. In order to identify downstream signaling events associated with these genetic alterations, we performed an integrated analysis of genomic abnormalities, including copy number alterations, sequence mutations and chromosomal translocations, with alterations in protein expression and modification. Methods A cohort of 91 precursor B-ALL cases treated at M.D. Anderson Cancer Center in Houston, USA, including 82 newly diagnosed cases and 5 diagnosis-relapse pairs was used for this study. The cohort consisted of 6 children (age 1-6), 30 young adults (age 15-39) and 45 adults (age〉39), and 20 patients carried a BCR-ABL1 chromosomal translocation. Copy number alterations in eight genes frequently deleted in ALL (IKZF1, PAX5, EBF1, RB1, CRLF2, CDKN2A/2B, BTG1, and ETV6) were determined by multiplex ligation-dependent probe amplification analysis. IKZF1 deletions were associated with relapse (Pearson's chi-square test, p=0.009), and the presence of BCR-ABL1 translocation (p=0.032). Protein expression and modification levels were determined by probing Reverse Phase Protein Arrays (RPPA) containing protein lysates of all above samples with 128 rigorously validated antibodies including 34 phospho-specific antibodies. Hierarchical clustering analysis was used to determine which (phospho)proteins are differently expressed in genetic subsets of ALL. The significance of correlations was determined using two-sample t-test, with correction for multiple testing (Beta-Uniform Mixture model). Results We identified clustering of cases with a BCR-ABL1 chromosomal translocation (p=0.01; false discovery rate (FDR)=0.1), IKZF1-deletions (p=0.01, FDR=0.072), RB1-deletions (p=0.03, FDR=0.43) and EBF1 deletions (p=0.05, FDR=0.63). As expected RB1 deletion positive cases were characterized by decreased levels of (phospho)-RB1 and increased levels of cyclin E, illustrating the validity of our approach. EBF1-deleted cases showed relatively high levels of SHIP1, SSBP2 and phospho-STAT5, and lower levels of FAK and LYN. The protein signatures of BCR-ABL1-positive cases and IKZF1-deletion positive cases largely overlapped, and were characterized by elevated levels of (phospho)PKCα, SMAD1, phospho-STAT3, and phospho-STAT5 and lower levels of LYN and cyclinD3 (Figure 1). In total 70% of the BCR-ABL1-positive cases carried an IKZF1 deletion and several BCR-ABL1-negative cases with similar RPPA signature could be identified, all of which were IKZF1-deletion positive. These cases may represent the “BCR-ABL1-like” cases that were previously identified using gene expression signatures (Mullighan et al. 2009, NEJM 360:470-480; Den Boer et al. 2009, Lancet Oncol. 10:125-134), and could reflect activation of cAbl or other cellular tyrosine kinases. Together, we conclude that integrated analysis of genetic and proteomic aberrations identified protein signatures downstream of recurrent mutational events in ALL, a strategy that promises to facilitate the discovery of novel therapeutic targets in ALL and may aid in the identification of (high risk) patients that would benefit from tyrosine kinase inhibition. Disclosures: No relevant conflicts of interest to declare.

Description: We and others have shown that the B cell Translocation Gene 1 (BTG1) locus is affected by genomic deletions in 9% of pediatric acute lymphoblastic leukemia (ALL) patients. The fact that multiple subclones carrying distinct deletions can be present in individual patients suggests that interfering with normal BTG1 function provides a selective growth advantage to leukemic cells. However, it remains unclear how loss of BTG1 promotes clonal outgrowth. We detected an up to 15-fold increases of BTG1 expression when lymphoid cells were exposed to various challenge conditions, including nutrient limitation and ER stress induction. To test for a functional role for BTG1 in the cellular response to stress, we cultured BTG1 knockout cells in medium without glucose or amino acid (Figure 1) and found that BTG1 knockout cells show a 20-30% improved survival rate as compared to wildtype cells.Figure 1BTG1 knockout cells are resistant to Asparaginase treatment.Figure 1. BTG1 knockout cells are resistant to Asparaginase treatment. As Activating Transcription Factor 4 (ATF4) is a master regulator of cellular stress signaling, we hypothesized that the improved survival after BTG1 loss is regulated via ATF4. By immunoprecipitation experiments, we showed that BTG1 complexes with ATF4. In addition, co-expression of BTG1 attenuates ATF4 transcriptional activity on target gene promoters and suppresses both recombinant and endogenous ATF4 function in these promoter reporter assays (Figure 2).Figure 2BTG1 attenuates ATF4 transcriptional activity.Figure 2. BTG1 attenuates ATF4 transcriptional activity. Although BTG1 possesses no catalytic activity, it functions as a transcriptional co-regulator that acts by recruiting Protein Arginine Methyl Transferase 1 (PRMT1) to transcription factor complexes. By in vitro methylation assays with purified proteins we showed that ATF4 is directly methylated by PRMT1 on a single arginine residue. In addition we found that the PRMT1 interacting domain in BTG1, while dispensable for the BTG1-ATF4 interaction, is essential for the BTG1 mediated suppression of ATF4 function. In search for additional evidence for the functional interaction between BTG1 and ATF4 we performed global expression analysis on murine cells expressing the B cell marker B220. This revealed a significant deregulation of ATF4 target genes in BTG1 knockout cells when compared to wildtype cells. Together, our data indicate that BTG1 suppresses activation of ATF4 in response to cellular stress. Loss of BTG1 function, as it occurs during leukemia development, enhances ATF4 activity, thereby promoting cell survival under cellular stress conditions such as nutrient deprivation or ER stress. Leukemic cells carrying BTG1 deletions may thus benefit from this increased resistance to cellular stress, not only during leukemia development but also during treatment. Hence, targeting the ATF4 stress response pathway may prevent relapse of therapy-resistant leukemic clones. Cells were treated with 2 IU/L Asparaginase for 24 hours. After treatment, cell viability was measured using an MTT assay. The average of 4 independent experiments is plotted with error bars representing the standard error of the mean. A luciferase reporter gene controlled by the ATF4 responsive ASNS promoter region was transfected into HEK293 cells. Asparaginase treatment induces endogenous ATF4 expression, which results in an increase in luciferase signal (Mock transfected cells). Co-expression of BTG1 represses both endogenous ATF4 activity as well as ectopically expressed ATF4 activity as detected by a decrease in luciferase signal. The average of 2 independent experiments is plotted with error bars representing the standard deviation. Disclosures: No relevant conflicts of interest to declare.

Description: Background The chromosomal translocation BCR-ABL1 is frequently present in adult B cell precursor acute lymphoblastic leukemia (BCP-ALL) in about 30% of the patients, while in pediatric BCP-ALL it occurs only in 3% of the patients. However, in both cases the disease is characterized by the almost obligatory presence of IKZF1 gene deletions and mutations, arguing that loss of IKZF1 function is required for oncogenic transformation by p190BCR-ABL1. The IKZF1 gene encodes a transcription factor that belongs to the Ikaros family of zinc-finger proteins, which mainly acts as a transcriptional repressor protein through the recruitment of both HDAC-dependent and HDAC-independent co-repressor molecules. However, in some cases IKZF1 has also been shown to transcriptional activate specific target genes through association with the SWI/SNF chromatin remodeling complexes. We hypothesized that IKZF1-mediated transcription in a direct or indirect manner is modulated by BCR-ABL1 signaling. Therefore, we performed cell biological assays and proteomic studies to investigate the effect of p190BCR-ABL1 expression on IKZF1 protein function. Results Using a luciferase reporter assay employing the human BAX- promoter, we established that IKZF1-induced transcriptional repression was alleviated by p190BCR-ABL1 expression. This effect could be reversed by Imatinib treatment, suggesting that BCR-ABL1 signaling interferes with the normal function of IKZF1. Next, we assessed the effect of p190BCR-ABL1 on doxycycline-induced expression of IKZF1 using the murine lymphoid Tet-on Ba/F3 (TonB) cell line. Gene expression analysis showed that several target genes that are repressed by IKZF1 in TonB cells, such as p16Ink4a, Cnot6, Dscc1 and Tspan5, are transcriptionally induced by co-expression of p190BCR-ABL1. In order to understand how p190BCR-ABL1 signaling affects IKZF1 protein function, mass spectrometry was performed on FLAG-affinity purified IKZF1 from transiently transfected HEK293 cells in the absence or presence of p190BCR-ABL1. These analyses revealed that p190BCR-ABL1 expression induces phosphorylation of IKZF1 on specific serine, threonine and tyrosine residues as well lysine acetylation. Transient transfection of lysine acetyltransferase PCAF (KAT2B) confirmed that IKZF1 is modified by lysine acetylation. Western blot analysis using phospho-specific antibodies showed that IKZF1 is subject to tyrosine phosphorylation by p190BCR-ABL1, both in HEK293 cells and TonB cells. Using an in vitro kinase assay, we demonstrated that IKZF1 can be directly phosphorylated by active recombinant ABL kinase. Conclusion Our studies show that p190BCR-ABL1 signaling induces a multitude of different post-translational modifications on IKZF1, which could modify its properties as transcriptional regulator. We propose that modulation of IKZF1 tumor suppressor function by p190BCR-ABL1 signaling is the driving force for IKZF1 gene deletions in BCP-ALL patients harboring a BCR-ABL1 translocation. Disclosures: No relevant conflicts of interest to declare.

Description: Chronic myeloid leukemia (CML) is a rare malignancy in children and is mostly diagnosed in the chronic phase (CP). In adults, the five-year overall survival rate is 89% for patients on Imatinib and disease progression occurs in 1-3% per year (Druker 2006). Once a blast crisis (BC) has occurred, treatment options are limited with a median survival of only a few months (Cortes 2008). Therefore, early recognition of patients at risk for developing a BC is desirable. Besides the translocation t(9;22)(q34;q11), IKZF1, PAX5, and CDKN2A deletions have been reported in CML lymphoid blast crisis (LyBC) of both adult and pediatric patients (Mullighan 2008, Alpár 2012). The aim of this study was to investigate the presence of IKZF1 deletions and other copy number alterations (CNAs) by MLPA analysis in a large cohort of pediatric CML patients at time of diagnosis in order to determine whether CNAs commonly found in pediatric ALL might predict disease progression and / or treatment response. Between October 1991 and October 2012 a total of 86 children with newly diagnosed CML were included. The median follow up was 31 months. Among the 86 patients, 82 patients were diagnosed in CP, 2 patients in accelerated phase (AP), and 2 patients in LyBC. Six patients experienced progression to a BC respectively a myeloid blast crisis (MyBC) (N=2) and LyBC (N=4). At time of diagnosis, an IKZF1 deletion was detected in one patient diagnosed with CML-AP (Table A, patient no 58). IKZF1 and EBF1 deletions were detected in one patient diagnosed with CML-LyBC (Table A, patient no 22). No CNAs were detected in the 82 patients diagnosed with CML-CP. At time of disease progression, new CNAs were detected at time of the LyBC (Table A, patient no 62, 64, and 67). Due to the absence of material no CNAs could be detected in both patients experiencing a MyBC. In conclusion, we were able to detect CNAs in progressive CML disease (CML-AP and CML-LyBC) and not in the samples at the time of chronic phase in this large pediatric cohort of CML patients. Therefore, the investigated CNAs could not be used to predict disease progression at time of diagnosis. The CNAs detected in patients with progressive CML were similar to specific CNAs detected in pediatric B-cell precursor ALL, indicating a similar disease development (Kuiper 2010). Additionally, our results are in accordance with existing literature, suggesting that mechanisms of disease progression in pediatric and adult CML might be similar (Brazma, 2007). Disclosures: No relevant conflicts of interest to declare.

Description: Background Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and is characterized by the acquisition of recurrent genetic aberrations, which include chromosomal translocations, submicroscopic deletions and point mutations. The t(12;21) ETV6-RUNX1 translocation is present in about 25% of all pediatric B-cell precursor ALL (BCP-ALL) cases and represents an early genetic event, which can already be detected in utero. However, ETV6-RUNX1 expression is insufficient to induce leukemia and requires other cooperating genetic lesions for BCP-ALL to develop. Results Using extensive genomic profiling of pediatric BCP-ALL we and others have demonstrated that several recurrent gene deletions can be found in ETV6-RUNX1-positive leukemia. These include focal deletions affecting the B-cell translocation gene 1 (BTG1), which is a member of the BTG/Tob family of anti-proliferation genes. BTG1 deletions are present in 9% of all BCP-ALL cases, but appear to be specifically enriched (20%) in ETV6-RUNX1-positive leukemia. BTG1 protein displays no intrinsic enzymatic activity but may act by recruiting effector molecules like protein arginine methyltransferase 1 (PRMT1) to specific transcription factors, including RUNX1 and ATF4. To investigate whether loss of BTG1 function cooperates with ETV6-RUNX1 in leukemic transformation we developed an in vitro transformation assay. To this end, primitive fetal liver progenitors (FLPs) were purified as c-Kit+ Ter119- cells from fetal livers of embryonic day 13.5 (E13.5) of C57Bl6/J wild-type and Btg1-/- mice. After transduction with control pMSCV-IRES-GFP (pMIG) and pMIG-ETV6-RUNX1 retrovirus, cells were serially replated in methylcellulose or liquid culture in the presence of cytokines SCF, FLT3L and IL-7. We observed a proliferative growth advantage of ETV6-RUNX1 over control virus, and in BTG1-deficient FLPs as compared to wild-type FLPs. Notably, the proliferative advantage of BTG1-deficient FLPs was even further enhanced by co-expression of ETV6-RUNX1. By immunoprecipitation from FLPs, we could demonstrate that endogenous PRMT1 binds to ETV6-RUNX1, and this interaction is lost in BTG1-deficient FLPs, arguing that BTG1 is required for the interaction between PRMT1 and ETV6-RUNX1. In summary, our data indicate that loss of BTG1 function promotes leukemic transformation induced by oncogenic fusion protein ETV6-RUNX1, which implies that BTG1 gene deletions can act as a cooperating event in ETV6-RUNX1-driven leukemogenesis. Disclosures: No relevant conflicts of interest to declare.