T-cell Acute Lymphoblastic Leukemia Cases Research Articles

Abstract A40: CD44 expression in T-cell acute lymphoblastic leukemia and acute myeloid leukemia associated with RAS mutations

Abstract CD44 is an adhesion glycoprotein which helps with the homing of hematopoietic precursor cells. In acute myeloid leukemia (AML), CD44 has been investigated as a stem cell marker, and expression of its variant proteins has been associated with poor prognosis. Only in murine T-cell acute lymphoblastic leukemia (T-ALL) models, CD44 expression was associated with tumor progression, organ infiltration, and influencing survival. In early T-cell precursor-ALL (ETP-ALL, a T-ALL subset) several similarities were observed with AML genomic aberrations. Taking the CD44 gene that is a target of the RAS pathway, which promotes its alternative splicing, throughout a positive feedback loop, we have investigated whether the cellular expression of CD44 in different maturational subtypes of pediatric T-ALL and AML would predict RAS mutations. We have tested if the cellular CD44 status would be associated with patient's clinical characteristics. Methods: A series of 193 T-ALL and 28 AML patients (≤ 21 years) was tested by multiparameter flow cytometry with a panel of monoclonal antibodies combined as CD4FITC/CD7PE/CD45PercPCy5.5/CD8Pe-Cy7/CD44APC (T-ALL), and CD117PE/ CD45PercPCy5.5/HLA-DR PE-Cy7/CD44APC (AML). CD44 expression was evaluated by median fluorescence intensity (MFI) in blast cells and the value of the MFI in the 75th percentile was used as a cutoff to discriminate between high or low expression of CD44. Sanger sequencing was used to detect mutation in codons 12 and 13 of N/KRAS genes, after DNA extraction, amplification through polymerase chain reaction and product purification. Fisher´s exact test or chi-square test was used to evaluate the distribution of categorical variables, whereas Mann-Whitney (two groups) or Kruskal Wallis (more than two groups) tests were used to evaluate the distribution of non-parametric continuous variables; t-test and one-way ANOVA were used for parametric variables; p values of < 0.05 were considered statistically significant. Results: Only two cases were negative for CD44 (<20% positive blasts). There was no association between high expression of CD44 and organomegaly in T-ALL while for chloroma in AML the evaluation was impaired due to small series. There was no association between the expression of CD44 and T-ALL subtypes. AML patients have a higher cellular expression of CD44 (MFI: 18890 [1019-44720]) than T-ALL (MFI: 1211 [68-8325]) (p<0,0001). The CD44 expression in ETP-ALL were lower than in AML (MFI: 1504 [855-3296], p<0,0001). The frequency of N/KRAS mutations in T-ALL cases was 11,7% (12/102), whereas in AML cases it was 16.7%. There was no significant difference in CD44 expression between cases with N/KRAS mutations (MFI: 1715 [365-8325]) and without mutation (MFI: 1179 [68-5544]) in T-ALL, whereas in AML, N/KRAS mutated cases had a lower CD44 expression (MFI: 10979 [7650-18810]) than the cases without mutation (MFI: 21720 [1019-44720]) (p=0,032). Conclusions: CD44 cellular status was not relevant for T-ALL tumoral profile and its expression was not associated with T-ALL subtype. CD44 is underexpressed in T-ALL and ETP-ALL when compared with AML. N/KRAS mutation does not seems be associated with different expression of CD44 in pediatric T-ALL whereas further investigation is required in AML subsets. Citation Format: Luisa V. C. Marques, Elda P. Noronha, Franciane G. Andrade, Eugenia T. G. Pina, Maria S. Pombo-de-Oliveira. CD44 expression in T-cell acute lymphoblastic leukemia and acute myeloid leukemia associated with RAS mutations [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A40.

Study of NOTCH1 and FBXW7 Mutations and Its Prognostic Significance in South Indian T-Cell Acute Lymphoblastic Leukemia.

NOTCH1/FBXW7 mutations trigger oncogenic NOTCH1 signaling and its downstream target genes play crucial roles in the molecular pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL). In the present study, NOTCH1 and FBXW7 mutations were studied in 25 primary T-ALL samples. All 34 exons of NOTCH1 and hotspot exons (exon 9 and exon 10) of FBXW7 were polymerase chain reaction amplified and sequenced for mutations. Our results showed that 13/25 (52%) were NOTCH1-mutated, of which 11 patients (44%) showed mutation in the hotspot exons. Four patients (16%) had mutations in non-hotspot exons of NOTCH1. Notably, 2 T-ALL patients (8%) harbored mutations in both hotspot and non-hotspot exons of NOTCH1, whereas 2 patients (8%) had mutations in the hotspot exons of FBXW7. In all, 7 mutations were identified which were not previously reported. The real-time polymerase chain reaction study in 15 patients revealed that increased expression of activated NOTCH1 was found in NOTCH1/FBXW7 hotspot exon-mutated cases. In addition, NOTCH1/FBXW7-mutated patients had showed upregulated HES1, c-MYC, NOTCH3 gene expression. When survival analysis was performed including samples (n=50) from our previous study, an early treatment response and better survival was observed in NOTCH1/FBXW7 hotspot-mutated patients. Our study suggests that NOTCH1/FBXW7 hotspot-mutated T-ALL cases had better response to ALL BFM-95 protocol.

Identification of fusion genes and characterization of transcriptome features in T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is a clonal malignancy of immature T cells. Recently, the next-generation sequencing approach has allowed systematic identification of molecular features in pediatric T-ALL. Here, by performing RNA-sequencing and other genomewide analysis, we investigated the genomic landscape in 61 adult and 69 pediatric T-ALL cases. Thirty-six distinct gene fusion transcripts were identified, with SET-NUP214 being highly related to adult cases. Among 18 previously unknown fusions, ZBTB16-ABL1, TRA-SALL2, and involvement of NKX2-1 were recurrent events. ZBTB16-ABL1 functioned as a leukemogenic driver and responded to the effect of tyrosine kinase inhibitors. Among 48 genes with mutation rates >3%, 6 were newly found in T-ALL. An aberrantly overexpressed short mRNA transcript of the SLC17A9 gene was revealed in most cases with overexpressed TAL1, which predicted a poor prognosis in the adult group. Up-regulation of HOXA, MEF2C, and LYL1 was often present in adult cases, while TAL1 overexpression was detected mainly in the pediatric group. Although most gene fusions were mutually exclusive, they coexisted with gene mutations. These genetic abnormalities were correlated with deregulated gene expression markers in three subgroups. This study may further enrich the current knowledge of T-ALL molecular pathogenesis.

BRD4 Proteolysis Targeting Chimera (PROTAC) ARV-825 Targets Both NOTCH1-MYC Regulatory Circuit and Leukemia-Microenvironment in T-ALL

Background:Salvage options for patients with relapsed T cell acute lymphoblastic leukemia (T-ALL) are limited, with less than 25% of these patients achieving second remission 1, 2. 70% of T-ALL cases have activating mutations of the NOTCH1 pathway, which transcriptionally activates MYC by binding to its ‘superenhancer’ region 3, 4. Other deregulated oncogenic pathways in T-ALL include PI3K/Akt, the anti-apoptotic Bcl-2 family, and CDKN2A/2B cell cycle regulators 5, 6. The NOTCH1-MYC regulatory circuit is an attractive therapeutic target, but clinical development of gamma-secretase inhibitors (GSI) to target NOTCH1 has been limited by ‘on target’ toxicities. A better target may be BRD4, a critical component of superenhancer complexes that binds to acetylated histone (3 and 4) and drives NOTCH1 mediated MYC transcription7.ARV-825 is a hetero-bifunctional PROteolysis TArgeting Chimera (PROTAC) that has 3 components: a thienodiazepine-based BRD4 ligand, a linker arm, and a cereblon-binding ligand. ARV-825 recruits BRD4 to the E3 ubiquitin ligase cereblon and leads to efficient and sustained degradation of BRD4, resulting in down-regulation of MYC.Methods: We investigated the effectiveness of ARV-825 against T-ALL cell lines, including GSI-resistant lines. Since microenvironmental signals are critical for the survival of T-ALL, we specifically tested the impact of BRD4 degradation on CD44/CD44v, which integrates cell-extrinsic microenvironmental signals and is part of cysteine transporter that maintains low intra-cellular reactive oxygen species (ROS), necessary for T-ALL survival and the persistence of disease. We also examined the anti-leukemic effect of ARV-825 in a T-ALL patient-derived xenograft (PDX) mouse model of disseminated leukemia with a constitutively active NOTCH1 mutation.Results: The IC50s for all tested T-ALL cell lines at 72 hours were in the low nanomolar range (< 50 nM). ARV-825 leads to sustained degradation of BRD4 and down-regulation of its transcriptional targets MYC, Bcl-2 and Bcl-XL and inhibits cell proliferation and induces apoptosis in GSI-sensitive (HPB-ALL, KOPT1) and GSI-resistant (MOLT4, SUPT1) cell lines.Mass cytometry based proteomic analysis (CyTOF) and immunoblotting showed that ARV-825 down-regulated cell intrinsic oncogenic molecules: transcription factors Myc and NFkB, cell cycle regulator CDK6, activated PI3K/Akt, and anti-apoptotic Bcl2 family proteins. In addition ARV-825 down regulated two key molecules involved in leukemia-stroma interaction; CD44 (Fig. 1), and CD98, a component of amino acid transporters xCT, LAT1 and 2, both essential in regulation of oxidative stress. Quantitative PCR and immunoblotting analysis confirmed the transcriptional down regulation of total CD44 and CD44 variants 8-10 (2-fold change treated vs . untreated). As a functional correlate of down-regulation of CD98/CD44/CD44v, flow cytometry confirmed increased intracellular ROS generation (Fig. 2).Finally, in a PDX mouse model of human T-ALL, ARV-825 treatment resulted in lower leukemia burden (confirmed by flow cytometry for human CD45+ cells in bone marrow) and better survival compared to vehicle-treated control mice (p=0.002) (Fig.3).Reference:1. Marks DI, Rowntree C. Management of adults with T-cell lymphoblastic leukemia. Blood 2017; 129(9): 1134-1142.2. Litzow MR, Ferrando AA. How I treat T-cell acute lymphoblastic leukemia in adults. Blood 2015; 126(7): 833-41.3. Sanchez-Martin M, Ferrando A. The NOTCH1-MYC highway toward T-cell acute lymphoblastic leukemia. Blood 2017; 129(9): 1124-1133.4. Demarest RM, Ratti F, Capobianco AJ. It's T-ALL about Notch. Oncogene 2008; 27(38): 5082-91.5. Girardi T, Vicente C, Cools J, De Keersmaecker K. The genetics and molecular biology of T-ALL. Blood 2017; 129(9): 1113-1123.6. Joshi I, Minter LM, Telfer J, Demarest RM, Capobianco AJ, Aster JC et al. Notch signaling mediates G1/S cell-cycle progression in T cells via cyclin D3 and its dependent kinases. Blood 2009; 113(8): 1689-98.7. Loven J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 2013; 153(2): 320-34. [Display omitted] DisclosuresQian:4Arvinas, LLC. New Haven, CT: Employment. Raina:4Arvinas, LLC. New Haven, CT: Employment. McKay:6 ImmunoGen, Inc.Waltham, MA: Employment. Kantarjian:Novartis: Research Funding; Amgen: Research Funding; Delta-Fly Pharma: Research Funding; Bristol-Meyers Squibb: Research Funding; Pfizer: Research Funding; ARIAD: Research Funding. Andreeff:Daiichi Sankyo: Consultancy.

WT1 loss attenuates the TP53-induced DNA damage response in T-cell acute lymphoblastic leukemia.

Loss-of-function mutations and deletions in Wilms tumor 1 (WT1) gene are present in approximately 10% of T-cell acute lymphoblastic leukemia. Clinically, WT1 mutations are enriched in relapsed series and are associated to inferior relapse-free survival in thymic T-cell acute lymphoblastic leukemia cases. Here we demonstrate that WT1 plays a critical role in the response to DNA damage in T-cell leukemia. WT1 loss conferred resistance to DNA damaging agents and attenuated the transcriptional activation of important apoptotic regulators downstream of TP53 in TP53-competent MOLT4 T-leukemia cells but not in TP53-mutant T-cell acute lymphoblastic leukemia cell lines. Notably, WT1 loss positively affected the expression of the X-linked inhibitor of apoptosis protein, XIAP, and genetic or chemical inhibition with embelin (a XIAP inhibitor) significantly restored sensitivity to γ-radiation in both T-cell acute lymphoblastic leukemia cell lines and patient-derived xenografts. These results reveal an important role for the WT1 tumor suppressor gene in the response to DNA damage, and support the view that anti-XIAP targeted therapies could have a role in the treatment of WT1-mutant T-cell leukemia.

Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia.

The outcome of treatment-refractory and/or relapsed pediatric T cell acute lymphoblastic leukemia (T-ALL) is extremely poor, and the genetic basis for this is not well understood. Here we report comprehensive profiling of 121 cases of pediatric T-ALL using transcriptome and/or targeted capture sequencing, through which we identified new recurrent gene fusions involving SPI1 (STMN1-SPI1 and TCF7-SPI1). Cases positive for fusions involving SPI1 (encoding PU.1), accounting for 3.9% (7/181) of the examined pediatric T-ALL cases, showed a double-negative (DN; CD4-CD8-) or CD8+ single-positive (SP) phenotype and had uniformly poor overall survival. These cases represent a subset of pediatric T-ALL distinguishable from the known T-ALL subsets in terms of expression of genes involved in T cell precommitment, establishment of T cell identity, and post-β-selection maturation and with respect to mutational profile. PU.1 fusion proteins retained transcriptional activity and, when constitutively expressed in mouse stem/progenitor cells, induced cell proliferation and resulted in a maturation block. Our findings highlight a unique role of SPI1 fusions in high-risk pediatric T-ALL.

Philadelphia (Ph) Chromosome (BCR-ABL1 fusion) As a Recurrent Genetic Abnormality Among Therapy-Related Acute Leukemia

Philadelphia (Ph) chromosome [t(9;22)] was reported as a rare recurrent balanced translocation among therapy-related acute leukemia (N=10, 2%) [Gene Chromosomes Cancer. 2002]. Here, we conducted a retrospective analysis of therapy-related acute leukemia with Ph chromosome (Ph+ t-AL) to better understand this entity. We included cases diagnosed at our institution between 2000 and 2016, excluding patients with CML in blastic phase. We defined Ph+ t-AL as acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML) harboring Ph chromosome that developed after prior exposure to cytotoxic therapy (chemotherapy, radiation or both).Of the 330 patients with Ph+ AL, 28 cases (8.4%) met our definition of Ph+ t-AL, including 25 (89%) B-cell ALL, 1 case of T-cell ALL, and 2 cases of AML. The median age at diagnosis was 56 years (range: 29-79), and 64% (N=18) of them were female. Breast cancer was the most common prior malignancy [N=8, 29%], followed by lymphoma [N=6, 21%] and sarcoma [N=4, 14%]. Prior cytotoxic therapy consisted of chemotherapy (32%), radiotherapy (29%) and chemoradiation (39%). Among 20 patients who had prior chemotherapy, 70% had received alkylating agents (i.e., cyclophosphamide, temozolomide), 70% had received topoisomerase II inhibitors (i.e., etoposide, anthracycline), 40% had received antimetabolites, (i.e., methotrexate) and 50% both alkylators and topoisomeraseII inhibitor. The median interval between prior malignancy and Ph+ t-AL diagnosis was 6.8 years (range: 2.5-19.6) and was not different according to prior cytotoxic therapy modality [chemotherapy/radiotherapy vs. either chemotherapy or radiotherapy alone (P = 0.66)]. The median white blood cells count at presentation was 20 x103/µL (range: 1.4-230). Myelodysplastic syndrome preceded one case of AML. Among 22 patients with available standard cytogenetics, 7 (32%) had Ph chromosome as the sole abnormality, while 15 (68%) had an additional cytogenetic abnormality (ACA). Complex (≥ 3 abnormalities) or monosomal karyotypes were observed respectively in 12 and 9 cases. Chromosome 7 abnormality was observed in 6 (27%) cases, including 5 of them with monosomy 7. In 18 patients (ALL = 17; AML = 1) with available molecular study for BCR/ABL1, all were positive for p190 fusion transcript, including 3 patients who carried both p210 and p190 (ALL =2; AML =1). The median time from prior diagnosis to AL onset was not different according to cytogenetics (isolated Ph chromosome vs. complex/monosomy karyotype) (P> 0.99). However, prior exposure to topoisomeraseII inhibitor was more common among patients with isolated Ph chromosome compared to patients with complex/monosomy karyotype (86% vs. 33%, P= 0.02).Tyrosine-kinase inhibitor (TKI) was administered as part of initial induction regimen to all patients except 4 (N= 24, 86%), who received TKI only upon leukemia relapse/progression. Of the 28 patients, 25 (89%) achieved complete remission (CR) with induction, and 17 (61%) patients subsequently underwent alloHCT; of them, 13 (76%) were in CR1. The 2-year overall survival and event-free survival were respectively 48% and 36% for all patients, and 63% and 41% for those who underwent alloHCT, respectively. The 2-year cumulative incidence rates of relapse and non-relapse mortality for transplanted patients were 19% and 25%, respectively.In conclusion, Ph+ chromosome is a recurrent therapy-related chromosomal aberration presenting most often as a B-cell ALL phenotype, and only rarely as T-cell ALL or AML. Ph+ t-AL is associated with high incidence of ACA, including complex and monosomal karyotype as well as chromosome 7 abnormalities, similar to therapy-related myeloid neoplasms. Similar to de novo Ph+ ALL, a high response rate to TKI-based regimen was observed among Ph+ t-AL. Given its therapeutic implication, presence of Ph chromosome should be excluded in all cases of t-AL. DisclosuresSong:Seattle Genetics: Consultancy. Ali:Incyte Corporation: Research Funding. Salhotra:Alexion: Consultancy. Snyder:Ariad: Consultancy; Novartis: Consultancy. Stein:Amgen: Consultancy, Research Funding, Speakers Bureau; Seattle Genetics: Research Funding; Stemline Therapeutics: Consultancy, Research Funding; Argios: Research Funding; Celgene: Research Funding. Forman:Mustang Therpapeutics: Other: Construct licensed by City of Hope.

TAL1 Super Enhancer Aberration and Stil-TAL1 Fusion in Pediatric T Cell Acute Lymphoblastic Leukemia

Abstract Background Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic cancer accounting for 10 to 15% of newly diagnosed pediatric ALL cases, and is associated with a poor treatment outcome compared with B-cell ALL especially in relapsed cases despite recent improvement with an intensive treatment. TAL1 deletion on chromosome 1p33 which is also known as STIL-TAL1, is found in 20-25% of cases with T-ALL, which results in overexpression of TAL1 under the control of the promoter of STIL located next to TAL1. Recently, TAL1 super enhancer aberration (TAL1-SE) was reported, which introduce binding motifs for the MYB transcription factor in a noncoding region. This somatic mutation results in aberrant expression of TAL1 without STIL-TAL1. Clinical features of TAL1-SE and its difference with STIL-TAL1 cases have been poorly studied, and this could be a new instrument of treatment stratification in T-ALL. Methods Targeted capture sequencing for coding regions of 151 genes using a custom-made bait including the TAL1-SE region was performed in 132 Japanese T-ALL cases under 15 years old to detect somatic mutations. For the further analysis, whole transcriptome sequencing (WTS) was performed in 88 cases. Screening for STIL-TAL1 fusion by reverse transcription PCR was also performed in additional 44 cases. All cases of TAL1-SE and STIL-TAL1 were validated by Sanger sequencing. Our pipelines,"Genomon 2" algorithm, were used for detection of somatic mutations and fusions. Most samples of DNA and RNA were offered from Tokyo Children's Cancer Study Group (TCCSG), and available clinical data were mainly based on the TCCSG clinical study treated with BFM-based ALL treatment protocol. Results TAL1-SE and STIL-TAL1 were found mutually exclusive in 6 (4.5%) and 24 cases (18.1%), respectively. All patients with TAL1-SE were under 10 years old. TAL1-SE cases showed a favorable 3-year overall survival (3y-OS) compared with STIL-TAL1 cases which were reported to show a good prognosis (83.3% vs 85.9% respectively, p = 0.71). However, 3-year disease free survival (3y-DFS) was 22.2% and 72.3% respectively (p = 0.04), indicating higher relapse rate in TAL1-SE cases, and they were probably rescued by second line treatment. Patients with STIL-TAL1 showed significantly poorer prednisolone response (over 1,000 /µl of blast at day 8, p &lt; 0.05), though they showed favorable 3y-OS, which might be resulted from frequent high WBC counts at diagnosis (&gt; 100×106/l, 59%). Comparison of TAL1 expression using read counts of WTS revealed significantly higher TAL1 expression in TAL1-SE cases than STIL-TAL1 cases (p &lt; 0.05). To reveal the difference of gene expression profile between STIL-TAL1 and TAL1-SE, unsupervised consensus clustering of gene expression data in 24 cases performed WTS (6 cases of TAL1-SE and 18 cases of STIL-TAL1) divided into 2 clusters. All cases with TAL1-SE were grouped into the same cluster with 10 STIL-TAL1 cases (Cluster 1). The other 8 STIL-TAL1 cases were classified as Cluster 2. A genetic landscape of these 24 cases showed more frequent NOTCH1 and/or FBXW7 mutations in Cluster 1 (87.5% vs 37.5%, p = 0.02), whereas mutations in genes encoding transcription factor such as RUNX1 and BCL11B were found only in Cluster 1 (n = 1, n = 3, respectively). There was a tendency of better 3y-OS and 3y-DFS in Cluster 2 (73.9% vs 100%, p = 0.14, 55.6% vs 85.7%, p = 0.15, respectively). Conclusion TAL1-SE and STIL-TAL1 showed a relatively good prognosis, though high relapse rate in TAL1-SE and a poor prednisolone response in STIL-TAL1 were observed. STIL-TAL1 cases were biologically divided into 2 groups based on the expression profile (with TAL1-SE and STIL-TAL1 only), and these 2 groups showed different clinical and genetic features such as 3y-OS or frequency of NOTCH1/FBXW7 mutations. Our findings illustrate the clinicopathological differences between STIL-TAL1 and TAL1-SE cases, and thus, it might be helpful for development a new therapeutic strategy for these patients with TAL1 overexpression T-ALL. Disclosures Kataoka: Boehringer Ingelheim: Honoraria; Kyowa Hakko Kirin: Honoraria; Yakult: Honoraria. Ogawa:Takeda Pharmaceuticals: Consultancy, Research Funding; Kan research institute: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding.

Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with variable prognosis. It represents 15% of diagnosed pediatric ALL cases and has a threefold higher incidence among males. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined. Using an integrative approach combining genomic and transcriptomic data, we molecularly characterized 30 pediatric T-ALLs and identified common recurrent T-ALL targets such as FBXW7, JAK1, JAK3, PHF6, KDM6A and NOTCH1 as well as novel candidate T-ALL driver mutations including the p.R35L missense mutation in splicesome factor U2AF1 found in 3 patients and loss of function mutations in the X-linked tumor suppressor genes MED12 (frameshit mutation p.V167fs, splice site mutation g.chrX:70339329T>C, missense mutation p.R1989H) and USP9X (nonsense mutation p.Q117*). In vitro functional studies further supported the putative role of these novel T-ALL genes in driving transformation. U2AF1 p.R35L was shown to induce aberrant splicing of downstream target genes, and shRNA knockdown of MED12 and USP9X was shown to confer resistance to apoptosis following T-ALL relevant chemotherapy drug treatment in Jurkat leukemia cells. Interestingly, nearly 60% of novel candidate driver events were identified among immature T-ALL cases, highlighting the underlying genomic complexity of pediatric T-ALL, and the need for larger integrative studies to decipher the mechanisms that contribute to its various subtypes and provide opportunities to refine patient stratification and treatment.

MiR-146b negatively regulates migration and delays progression of T-cell acute lymphoblastic leukemia.

Previous results indicated that miR-146b-5p is downregulated by TAL1, a transcription factor critical for early hematopoiesis that is frequently overexpressed in T-cell acute lymphoblastic leukemia (T-ALL) where it has an oncogenic role. Here, we confirmed that miR-146b-5p expression is lower in TAL1-positive patient samples than in other T-ALL cases. Furthermore, leukemia T-cells display decreased levels of miR-146b-5p as compared to normal T-cells, thymocytes and other hematopoietic progenitors. MiR-146b-5p silencing enhances the in vitro migration and invasion of T-ALL cells, associated with increased levels of filamentous actin and chemokinesis. In vivo, miR-146b overexpression in a TAL1-positive cell line extends mouse survival in a xenotransplant model of human T-ALL. In contrast, knockdown of miR-146b-5p results in leukemia acceleration and decreased mouse overall survival, paralleled by faster tumor infiltration of the central nervous system. Our results suggest that miR-146b-5p is a functionally relevant microRNA gene in the context of T-ALL, whose negative regulation by TAL1 and possibly other oncogenes contributes to disease progression by modulating leukemia cell motility and disease aggressiveness.

Abstract 1180: The TCA cycle transferase DLST is critical for MYC-mediated leukemogenesis

Abstract The proto-oncogene MYC has been implicated in the pathogenesis of many human cancers, including hematological and solid malignancies1. In the majority of T-ALL cases, MYC is aberrantly expressed downstream of activated NOTCH1 mutations. Despite the pivotal role of MYC in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) and many other cancers, the mechanisms underlying MYC-mediated tumorigenesis remain inadequately understood2. Here we utilized a well-characterized zebrafish model of Myc-induced T-ALL for genetic studies to identify novel genes contributing to disease onset. We found that heterozygous inactivation of a tricarboxylic acid (TCA) cycle enzyme, dihydrolipoamide S-succinyltransferase (Dlst), significantly delayed tumor onset. Concordant with our zebrafish results, RNAi knockdown of DLST led to decreased cell viability and induction of apoptosis in human T-ALL cell lines. DLST is the E2 transferase of the -ketoglutarate dehydrogenase complex (KGDHC), which converts -ketoglutarate (-KG) to succinyl-CoA in the TCA cycle3. Polar metabolomics profiling revealed that the TCA cycle was disrupted by DLST knockdown in human T-ALL cells, as demonstrated by an accumulation of -KG and its precursor glutamine, as well as a loss of succinyl-CoA. Addition of succinate, the downstream TCA cycle intermediate, to human T-ALL cells was sufficient to rescue defects in cell viability caused by DLST inactivation. Taken together, our studies identify DLST as an important mediator of MYC-driven leukemogenesis and provide compelling evidence for the metabolic dependence of T-ALL cells on the TCA cycle. 1. Nesbit CE, Tersak JM, Prochownik EV. MYC oncogenes and human neoplastic disease. Oncogene 1999 May 13; 18(19): 3004-3016. 2. Sharma VM, Calvo JA, Draheim KM, Cunningham LA, Hermance N, Beverly L, et al. Notch1 contributes to mouse T-cell leukemia by directly inducing the expression of c-myc. Molecular and cellular biology 2006 Nov; 26(21): 8022-8031. 3. Sheu KF, Blass JP. The alpha-ketoglutarate dehydrogenase complex. Ann N Y Acad Sci 1999; 893: 61-78. Citation Format: Nicole Anderson, Dun Li, H.L. Peng, Marc Mansour, Fabrice Laroche, Evisa Gjini, Daniel Helman, Itrat Harrold, Le Meng, Takaomi Sanda, Adam Amsterdam, Donna Neuberg, Travis Denton, Anurag Singh, A Thomas Look, Hui Feng. The TCA cycle transferase DLST is critical for MYC-mediated leukemogenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1180.

Persistent donor derived Vδ4 T cell clones may improve survival for recurrent T cell acute lymphoblastic leukemia after HSCT and DLI.

The outcome for T-cell acute lymphoblastic leukemia (T-ALL) in relapse after hematopoietic stem cell transplantation (HSCT) is quite poor, while, both donor lymphocytes infusion (DLI) and adoptively infusion of γδ T cells in leukemia patients after HSCT have demonstrated good results in prolonging survival time of patients. Here, we reported a T-ALL case who experienced three relapses and received HSCT and DLI with an overall survival (OS) time lasting for more than seven years. Based on our previous identification of a leukemic and reactive clone in this patient, continual γδ T cell repertoire monitoring affirmed that the same Vδ5 leukemic clone existed in most samples from the patient, particularly including a sample taken at the time of the third T-ALL relapse, while it could not be detected in the donor sample. In addition, an identical Vδ4 monoclonal T cell that proliferated in the recipient for several years was confirmed to come from the donor graft, and its expression level significantly increased in third leukemia recurrence. These results indicate that clonally expanded Vδ4 T cells may represent a reconstituted γδ T cell repertoire after HSCT, which also hints to a relatively better outcome for this case. Based on this case study, we recommend DLI should be as a treatment strategy for patients who achieve CR or relapse from HSCT. Moreover, dynamically monitoring the TCR repertoire in patients who receive HSCT will benefit in supervising of malignant clone evolution and residue, identifying T cell clones mediate anti-infection, GvHD or GvL.

T-cell acute lymphoblastic leukemia with co-expression of CD56, CD34, CD117 and CD33: A case with poor prognosis.

T-cell acute lymphoblastic leukemia (ALL) is an aggressive hematological malignancy, accounting for ~25% of all adult cases of ALL. We herein report a case of T-cell ALL exhibiting aberrant CD34, CD56, CD33 and CD117 expression in addition to T-cell markers, which did not respond to induction treatment. A 55-year-old woman was admitted to our hospital with a sore throat unresponsive to medication for 1 month. The laboratory examination revealed pancytopenia and the peripheral blood smear examination revealed blast cells. On flow cytometric analysis, the blast cells were found to be positive for cytoplasmic CD3, CD2, CD5, CD7, CD34, CD56, CD33 and CD117, and negative for myeloperoxidase, CD13, CD11b, CD15, CD19, CD79a, CD22 and CD10. The patient was diagnosed with T-cell ALL according to the 2008 World Health Organisation classification. The patient did not respond to Hyper-cyclophosphamide, vincristine, adriamycin and dexamethasone (CVAD) course A treatment and succumbed to the disease during Hyper-CVAD course B treatment. To the best of our knowledge, this is the first report of aberrant co-expression of the natural killer cell marker CD56, myeloid cell markers CD117 and CD33 and stem cell marker CD34 in a patient with T-cell ALL. This appears to be associated with an unfavorable outcome, despite the use of intensive chemotherapy.

Clinical Characteristics and Treatment Efficacy of Children with SIL/TAL1 Positive T-Cell Acute Lymphoblastic Leukemia

To investigate the clinical features, treatment and prognosis of children with SIL-TAL1 fusion gene positive T-cell acute lymphoblastic leukemia (T-ALL). The data of 101 children with T-ALL were collected from April 2005 to November 2012 in Beijing Children's Hospital. The common clinical features, early treatment response, minimal residual disease (MRD), event-free survival (EFS) and relapse-free survival (RFS) were compared between children with SIL-TAL1 positive and negative T-ALL. The treatment efficacy in children with SIL-TAL1 positive T-ALL was compared between BCH-2003 and CCLG-2008 protocol. Out of 101 cases, 22 cases (21.9%) of T-ALL carried SIL-TAL1 fusion gene. The distribution of sex, age, response to prednisone and central nervous system (CNS) involvement were no significant different at diagnosis between SIL-TAL1 positive and negetive patients. However, the WBC count in SIL-TAL1 positive cases were significantly higher than that of SIL-TAL1 negative cases at diagnosis (P<0.05). Additionally, MRD levels were not significantly different between children with SIL-TAL1 positive or negative T-ALL at 3 time points including: after the remission induction therapy, before delayed intensive therapy II and before maintenance therapy. However, the number of cases with high MRD levels before consolidation therapy were more in SIL-TAL1 positive group than that in SIL-TAL1 negative group (P<0.05). The cases with high MRD levels before delayed intensive therapy I was more in SIL-TAL1 negative group than that in the SIL-TAL1 positive group (P>0.05). Besides, there were no significant differences in 5-year EFS and RFS between the two groups. The risk of 22 children with SIL-TAL1 positive acute T-ALL was again stratified according to the typing stemdard in CCLG-2008 protocol, as a result, the risk in BCH-2003 group (10 cases) was significantly higher than that in BCH-2008 group (12 cases) (P<0.05), but no significant difference was found in common clinical features, early treatment response, MRD levels and treatment efficacy. Although WBC level was significantly higher in SIL-TAL1 positive group than that in SIL-TAL1 negative group, the treatment efficacy in SIL-TAL1 positive group was similar to SIL-TAL1 negative group. Meanwhile, the children with SIL-TAL1+ T-ALL may respond poorly to early intensive therapy, the BCH-2003 protocol may be more suitable for the patients with this subtype of leukemia.

MicroRNAs regulate TAL1 expression in T-cell acute lymphoblastic leukemia.

The transcription factor TAL1 is a proto-oncogene whose aberrant expression in committed T-cell precursors is associated with the development of T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms leading to aberrant activation of TAL1 in T-ALL patients who lack chromosomal rearrangements involving the TAL1 locus remain largely unknown. We hypothesized that TAL1 levels decrease during normal T-cell development at least in part due to miRNA-dependent silencing, in which case TAL1 over-expression in some T-ALL cases could be the consequence of deregulated miRNA expression. By performing computational prediction of miRNAs that bind to the human TAL1 mRNA we compiled a list of miRNAs that are candidates to regulate TAL1. Using a luciferase reporter system and mutagenesis assays we confirmed the miRNA-TAL1 mRNA interactions and selected candidate miRNAs: miR-101, miR-520d-5p, miR-140-5p, miR-448 and miR-485-5p. Over-expression of these microRNAs in different T-ALL cell lines consistently resulted in the down-regulation of TAL1 protein. In accordance, inhibition of miR-101 and miR-520d-5p promoted TAL1 protein expression. Importantly, we found that miR-101, miR-140-5p, miR-448 and miR-485-5p were down-regulated in T-ALL patient specimens and T-ALL cell lines. Our results show for the first time the existence of epigenetic regulation of TAL1 by specific miRNAs which may contribute, at least in part, to the ectopic expression of TAL1 in some T-ALL cases.

A Novel Combination Therapy for Paediatric T Cell Acute Lymphoblastic Leukaemia

T cell acute lymphoblastic leukaemia (T-ALL) is a rare form of leukaemia that accounts for approximately 15% of paediatric ALL cases. Unfortunately, approximately 20% of patients do not achieve long term remission as a result of failure of therapy to eradicate the disease. T-ALL is a highly heterogeneous disease that displays a spectrum of immunophenotypes, chromosomal aberrations and gene expression profiles. This heterogeneity has prompted research into more targeted therapies, with the aim of overcoming drug resistance often found with standard chemotherapeutic regimens. Here, we build upon use of the drug Parthenolide (PTL), which has shown promise in treatment of T-ALL and other leukaemias such as BCP-ALL and AML, in combination with ABT-263, a BCL-2 family antagonising agent. Bone marrow samples from 10 T-ALL cases, taken at diagnosis, were treated with PTL in vitro for 24 hours then viability was assessed using the annexin V / PI flow cytometric assay. Variable cytotoxic effects were observed in samples treated with PTL (1-10µM), with half maximal inhibitory concentrations ranging from 2.6-10 µM. At the highest dose tested, the proportion of surviving cells ranged from 5.79-56% (median 35.33%). BM from 5 of these samples was used for whole genome microarray (WGA) analysis. We compared gene expression in bulk ALL and in specific subpopulations, known to have leukaemia initiating capacity in vivo; CD34+/CD7+, CD34+/CD7-, CD34-/CD7+ and CD34-/CD7- cells. WGA data demonstrated that CD34+/CD7- was the only subpopulation to express significantly lower levels (5.38 fold) of the pro-apoptotic gene Bcl-2L11 (BIM) compared to the unsorted bulk T-ALL cells, p=0.006. Interestingly, we have previously shown that CD34+/CD7- cells from a few patients were resistant to PTL treatment in vivo compared to unsorted cells. To validate these results, mRNA and relative protein quantification was performed by qPCR and western blotting in bulk material from 8 of the 10 samples, 3 of which had been analysed by microarray for BIM expression. We found that the gene and protein expression levels of BIM were negatively correlated with PTL resistance in vitro, p≤0.0001 and p=0.049 respectively. This suggests that reduced BIM expression is related to PTL resistance. We next evaluated the effects of combining PTL and ABT-263 on T-ALL cells in vitro. ABT-263 is a BH3 protein mimetic, like BIM it promotes apoptosis by blocking the inhibitory effects that BCL-2 anti-apoptotic proteins have on pro-apoptotic proteins. The effects of combining the drugs were assessed in 7 of the original 10 samples. Unsorted ALL cells were incubated with PTL and ABT-263 for 24 hours, before viability was analysed by flow cytometry and drug synergy was calculated via the Chou Talalay method. This drug combination showed enhanced cytotoxicity to T-ALL cells compared to PTL (p=0.0282) or ABT-263 (p=0.0358) alone. Moreover, the highest combined dose tested (2.5µM PTL with 0.25µM ABT-263) killed 86.1±9% cells cf 71.8±18% with ABT-263 alone and only 21.7±11% with PTL alone. The combination also showed synergism with a combination index value below 1 in all doses tested. Previous findings in our laboratory have shown that in vivo PTL treatment eliminated childhood leukaemia in NOD/LtSz-scid IL-2Rγc null (NSG) mice, in most cases tested. It may be possible to further enhance this toxicity using ABT-263 alone or in combination with PTL. NSG mice were inoculated with unsorted T-ALL cells and leukaemia was allowed to establish until levels in peripheral blood (PB) exceeded 0.1%. NSG mice were subsequently treated orally for 21 days with 100mg/kg of ABT-263 or placebo and leukaemia burden was monitored weekly in PB aspirates. Twenty-eight days following commencement of treatment, leukaemia burden in the placebo treated group was 80.73±2.94% and the animals were electively culled. In contrast, disease burden was significantly lower in the treated animals at this stage (35.2±2.1%, p=0.004). ABT-263 treatment has significantly improved survival of all xenografts to date, (P<0.014). In summary, we have shown that PTL resistance is related to the expression of BIM. By combining PTL with ABT-263, which mimics the pro-apoptotic action of BIM, the drugs work synergistically to enhance T-ALL cytotoxicity in vitro. Ongoing in vivo studies will assess the full potential of this combination therapy for paediatric T-ALL. DisclosuresNo relevant conflicts of interest to declare.

Calcineurin/CXCR4 in T-ALL.

The calcineurin/NFAT signaling pathway is implicated in a wide variety of biological processes, acting as a bridge pathway between calcium signals and gene expression. Although its role as an effector of immune responses figured prominently in early studies, it forms just one part of a larger picture. Indeed calcineurin has been shown to participate in the development and function of e.g. the immune, cardiovascular, nervous and musculoskeletal systems, and dysregulation of calcineurin/NFAT signaling contributes to pathologies affecting these tissues, in particular cancer [1]. Activation of the calcineurin/NFAT pathway was first observed in human lymphoma, as well as in mouse models of T cell acute lymphoblastic leukemia (T-ALL) and xenotransplanted human T-ALL [2]. In T-ALL, calcineurin activation is independent of preTCR/TCR signaling (the major calcineurin activator in normal T cell progenitors), but strongly depends upon micro-environmental signals. The fundamental, intrinsic role of calcineurin in T-ALL was demonstrated in several mouse models, in which conditional calcineurin genetic deletion was restricted to leukemic cells. Calcineurin was found essential to the physical and functional interactions that leukemic cells establish with supportive stromal cells, with its deletion resulting in impaired leukemia propagation, reduced cell survival, proliferation, migration and homing [3]. The therapeutic relevance of these findings was highlighted by preclinical studies showing strong anti-leukemic effects of calcineurin inhibitors (namely cyclosporin A or tacrolimus [FK506]) and long-term leukemia remission in a mouse T-ALL model when vincristine treatment was combined with calcineurin genetic inactivation [2, 3]. However, available calcineurin inhibitors appear suboptimal as potential therapeutic agents since they are associated with a number of toxic side effects [4], show clear off-target effects in T-ALL cells [3] and are expected to interfere with the anti-tumor immune response. A recently developed, alternative option is to identify and target molecular pathways acting downstream of calcineurin and critical to T-ALL maintenance [5]. Our global transcriptomic analysis identified a large number of calcineurin-dependent genes in T-ALL, involved in an array of biological function, including the de-repression of known tumor suppressive pathways (e.g. CDKN1A) [3]. Although of high biological interest, these deregulations are not easily accessible for targeted therapy. In contrast, genes/proteins implicated in the adhesion/migration to the bone marrow microenvironment are promising candidates (i) for a thorough understanding of the factors that contribute to microenvironment-mediated support of leukemia progression and (ii) for the design of niche-targeted therapies. Along these lines, we linked calcineurin-dependent regulation of the adhesive/migratory properties of T-ALL cells to a boost of CXCR4 surface expression and the subsequent ability of the leukemic cells to respond to CXCL12 [5]. Upregulation of CXCR4 cell surface expression was also demonstrated in diagnostic T-ALL cases and primary xenograft in NSG mice [5][6]. The mechanism by which calcineurin affects CXCR4 trafficking is partially explained by the Cn-dependent up-regulation of cortactin [5], an actin-binding protein implicated in the regulation of endosomal trafficking [7]. Because actin polymerization is required for CXCR4 and other chemokine receptors trafficking to recycling vesicles, inhibition of cortactin expression in calcineurin-deficient T-ALL cells likely results in impaired actin dynamics in this endosomal compartment. Further investigation of the intrinsic function of CXCR4 in murine and human T-ALL revealed an important role of CXCL12/CXCR4 signaling in both survival/proliferation and homing/migration of leukemic cells to the supportive bone marrow niche [5][6]. Intravital multiphoton imaging and genetic studies revealed a strong interaction between T-ALL cells and CXCL12-expressing niche(s), and an essential supportive function of CXCL12 produced by vascular endothelial cells [6]. Local CXCL12 production, in addition to induction of CXCR4-dependent signaling cues will result in activation of T-ALL cells specific integrins, further stabilizing adhesion to integrin ligands expressing niche(s) and induction of additional pro-survival signals. In this scenario, the nature of the niche cells expressing the integrin ligands requires further characterization. Strikingly, CXCR4 is also critical to leukemia initiating cell activity (LIC) in murine T-ALL and human xenografts [5][6], highlighting an unexpected, fundamental function of microenvironmental signals for T-ALL maintenance and progression. Many inhibitors of CXCL12 or CXCR4 have been developed and are tested in clinical studies in other pathological contexts, in particular other hematological malignancies [8]. However, only in T-ALL anti-CXCR4 monotherapy shows strong efficacy, suggesting a strong dependence of these tumor cells on CXCR4 signaling [6]. As relapse in T-ALL remains a challenging issue, these new data call for clinical trials to incorporate CXCR4 antagonists either as single agents following induction therapy, or as part of the first induction therapy regimen or later, during the consolidation phase. In conclusion, the calcineurin/NFAT pathway acts as a fundamental bridge between microenvironmental-derived signals and T-ALL cells, mediating a complex crosstalk that is so far only partially dissected, but that already lead to the identification of novel targets of therapeutic relevance to T-ALL treatment.

Targeted sequencing identifies associations between IL7R-JAK mutations and epigenetic modulators in T-cell acute lymphoblastic leukemia.

T-cell acute lymphoblastic leukemia is caused by the accumulation of multiple oncogenic lesions, including chromosomal rearrangements and mutations. To determine the frequency and co-occurrence of mutations in T-cell acute lymphoblastic leukemia, we performed targeted re-sequencing of 115 genes across 155 diagnostic samples (44 adult and 111 childhood cases). NOTCH1 and CDKN2A/B were mutated/deleted in more than half of the cases, while an additional 37 genes were mutated/deleted in 4% to 20% of cases. We found that IL7R-JAK pathway genes were mutated in 27.7% of cases, with JAK3 mutations being the most frequent event in this group. Copy number variations were also detected, including deletions of CREBBP or CTCF and duplication of MYB. FLT3 mutations were rare, but a novel extracellular mutation in FLT3 was detected and confirmed to be transforming. Furthermore, we identified complex patterns of pairwise associations, including a significant association between mutations in IL7R-JAK genes and epigenetic regulators (WT1, PRC2, PHF6). Our analyses showed that IL7R-JAK genetic lesions did not confer adverse prognosis in T-cell acute lymphoblastic leukemia cases enrolled in the UK ALL2003 trial. Overall, these results identify interconnections between the T-cell acute lymphoblastic leukemia genome and disease biology, and suggest a potential clinical application for JAK inhibitors in a significant proportion of patients with T-cell acute lymphoblastic leukemia.

High frequency of cryptic chromosomal rearrangements involving the LMO2 gene in T-cell acute lymphoblastic leukemia

High frequency of cryptic chromosomal rearrangements involving the LMO2 gene in T-cell acute lymphoblastic leukemia

T-cell acute lymphoid leukemia resembling Burkitt leukemia cell morphology: A case report.

Biphenotypic acute leukemia (BAL) is an uncommon type of cancer, which accounts for <5% of all adult ALs. Based upon a previously described scoring system, the European Group for the Immunological Classification of Leukemias (EGIL) proposed a set of diagnostic criteria for BAL. This scoring system is based upon the number and degree of specificity of several markers for myeloid or T/B-lymphoid blasts. The present study describes a case of T-cell acute lymphoblastic leukemia (T-ALL) with Burkitt-like cytology, which according to the French-American-British classification, corresponded to a diagnosis of Burkitt type L3 ALL. Flow cytometry analysis demonstrated that the blasts were positive for T-lymphoid markers, cytoplasmic cluster of differentiation (CD)3, CD7 and CD56, and myeloid markers, CD13, CD33 and CD15. At first, a diagnosis of BAL was suggested by the EGIL score, however, according to the 2008 World Health Organization criteria, a case of T-ALL with aberrant myeloid markers was established. The study also reviewed the literature and discussed the limitations of the EGIL scoring system in clinical decision making, to aid in the selection of an appropriate therapeutic regimen.