TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia

Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy resulting from overproduction of immature T-cells in the thymus and is typified by widespread alterations in DNA methylation. As survival rates for relapsed T-ALL remain dismal (10 to 25%), development of targeted therapies to prevent relapse is key to improving prognosis. Whereas mutations in the DNA demethylating enzyme TET2 are frequent in adult T-cell malignancies, TET2 mutations in T-ALL are rare. Here, we analyzed RNA-sequencing data of 321 primary T-ALLs, 20 T-ALL cell lines, and 25 normal human tissues, revealing that TET2 is transcriptionally repressed or silenced in 71% and 17% of T-ALL, respectively. Furthermore, we show that TET2 silencing is often associated with hypermethylation of the TET2 promoter in primary T-ALL. Importantly, treatment with the DNA demethylating agent, 5-azacytidine (5-aza), was significantly more toxic to TET2-silenced T-ALL cells and resulted in stable re-expression of the TET2 gene. Additionally, 5-aza led to up-regulation of methylated genes and human endogenous retroviruses (HERVs), which was further enhanced by the addition of physiological levels of vitamin C, a potent enhancer of TET activity. Together, our results clearly identify 5-aza as a potential targeted therapy for TET2-silenced T-ALL.

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Cyclin D2 Dysregulation by Chromosomal Translocations to TCR Loci in T-Cell Acute Lymphoblastic Leukemia (T-ALL).

Blood ◽

10.1182/blood.v108.11.2073.2073 ◽

2006 ◽

Vol 108 (11) ◽

pp. 2073-2073

Author(s):

Emmanuelle Clappier ◽

Wendy Cuccuini ◽

Jean-Michel Cayuela ◽

Danielle Vecchione ◽

Andre Baruchel ◽

...

Keyword(s):

Cell Differentiation ◽

Acute Lymphoblastic Leukemia ◽

T Cell ◽

Lymphoblastic Leukemia ◽

T Cell Differentiation ◽

Chromosomal Translocations ◽

Genomic Rearrangements ◽

Cyclin D2 ◽

Cell Acute Lymphoblastic Leukemia ◽

Normal Human

Abstract D-type cyclins are key regulators of progression through G1 phase of the cell cycle. Strong expression of at least one of the three D cyclins is common in human cancers. However, while the cyclin D1 and D3 genes (CCND1 and CCND3) are recurrently involved in genomic rearrangements, especially in mantle-cell lymphoma and multiple myeloma, no clear involvement of the cyclin D2 gene (CCND2) has been reported to date in human malignancies. In T-cell acute lymphoblastic leukemia (T-ALL), the T-cell receptor genes TCRA/D and TCRB are frequently involved in chromosomal rearrangements. In order to identify new genomic rearrangements and oncogenes in human T-ALL, we performed an interphasic FISH screening of T-ALL cases using TCR flanking probes. Using this approach, we identified two new chromosomal translocations: t(7;12)(q34;p13) and t(12;14)(p13;q11), involving the TCRB and TCRA/D loci, respectively. Molecular analysis of the breakpoint sequences demonstrated the involvement of the CCND2 locus at 12p13. Expression analysis using RQ-PCR and immunoblotting demonstrated dramatic cyclin D2 overexpression in the translocated cases (n=3) compared to other T-ALLs (total, n=86), whereas other genes located near the translocation breakpoints were not deregulated on microarray analysis. To further evaluate expression in T-ALL with respect to normal T-cell differentiation, we analyzed CCND2 expression in purified subpopulations from normal human thymus. CCND2 levels were downregulated through progression from the early stages of normal human T-cell differentiation and transition to beta-selection. In the most immature T-ALLs, a moderate CCND2 expression was observed, consistent with their differentiation stage, while low expression was found in other T-ALL. By contrast, the massive and sustained expression in the CCND2-rearranged T-ALL cases strongly suggested an oncogenic role due to the TCR translocation. T-ALL oncogenesis is a multi-step process; we here found that the TCR-CCND2 translocations were associated with other oncogene expression (TAL1, HOXA, or TLX3/HOX11L2), NOTCH1 activating mutations, and/or CDKN2A/p16/ARF deletion, showing that cyclin D2 dysregulation could contribute to multi-event oncogenesis in various T-ALL groups. In conclusion, this report is the first clear evidence of a direct involvement of cyclin D2 in human cancer due to recurrent somatic genetic alterations. This reinforces the view that the strong expression of cyclin D2 which is detected in various types of cancer can contribute to oncogenesis, and points to cyclin D2 as a potential target for therapy in these tumors.

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T-cell acute lymphoblastic leukemia

Hematology ◽

10.1182/asheducation-2016.1.580 ◽

2016 ◽

Vol 2016 (1) ◽

pp. 580-588 ◽

Cited By ~ 40

Author(s):

Elizabeth A. Raetz ◽

David T. Teachey

Keyword(s):

Acute Lymphoblastic Leukemia ◽

T Cell ◽

De Novo ◽

Residual Disease ◽

Lymphoblastic Leukemia ◽

Survival Rates ◽

Disease Response ◽

Cell Acute Lymphoblastic Leukemia ◽

Relapsed Disease ◽

Modern Genomic

Abstract T-cell acute lymphoblastic leukemia (T-ALL) is biologically distinct from its B lymphoblastic (B-ALL) counterpart and shows different kinetic patterns of disease response. Although very similar regimens are used to treat T-ALL and B-ALL, distinctions in response to different elements of therapy have been observed. Similar to B-ALL, the key prognostic determinant in T-ALL is minimal residual disease (MRD) response. Unlike B-ALL, other factors including age, white blood cell count at diagnosis, and genetics of the ALL blasts are not independently prognostic when MRD response is included. Recent insights into T-ALL biology, using modern genomic techniques, have identified a number of recurrent lesions that can be grouped into several targetable pathways, including Notch, Jak/Stat, PI3K/Akt/mTOR, and MAPK. With contemporary chemotherapy, outcomes for de novo T-ALL have steadily improved and now approach those observed in B-ALL, with approximately 85% 5-year event-free survival. Unfortunately, salvage has remained poor, with less than 25% event-free and overall survival rates for relapsed disease. Thus, current efforts are focused on preventing relapse by augmenting therapy for high-risk patients, sparing toxicity in favorable subsets and developing new approaches for the treatment of recurrent disease.

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Facts and Challenges in Immunotherapy for T-Cell Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences ◽

10.3390/ijms21207685 ◽

2020 ◽

Vol 21 (20) ◽

pp. 7685

Author(s):

Fátima Bayón-Calderón ◽

María L. Toribio ◽

Sara González-García

Keyword(s):

Acute Lymphoblastic Leukemia ◽

T Cell ◽

Malignant Disease ◽

Lymphoblastic Leukemia ◽

Antigen Receptors ◽

Challenges And Opportunities ◽

Life Threatening ◽

Cell Acute Lymphoblastic Leukemia ◽

T Cell Immunodeficiency ◽

T Cell Malignancies

T-cell acute lymphoblastic leukemia (T-ALL), a T-cell malignant disease that mainly affects children, is still a medical challenge, especially for refractory patients for whom therapeutic options are scarce. Recent advances in immunotherapy for B-cell malignancies based on increasingly efficacious monoclonal antibodies (mAbs) and chimeric antigen receptors (CARs) have been encouraging for non-responding or relapsing patients suffering from other aggressive cancers like T-ALL. However, secondary life-threatening T-cell immunodeficiency due to shared expression of targeted antigens by healthy and malignant T cells is a main drawback of mAb—or CAR-based immunotherapies for T-ALL and other T-cell malignancies. This review provides a comprehensive update on the different immunotherapeutic strategies that are being currently applied to T-ALL. We highlight recent progress on the identification of new potential targets showing promising preclinical results and discuss current challenges and opportunities for developing novel safe and efficacious immunotherapies for T-ALL.

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Chromosomal Rearrangements Affecting ABL1 in T-Cell Acute Lymphoblastic Leukemia.

Blood ◽

10.1182/blood.v104.11.2894.2894 ◽

2004 ◽

Vol 104 (11) ◽

pp. 2894-2894

Author(s):

Jan Cools ◽

Carlos Graux ◽

Marc Boogaerts ◽

Peter Vandenberghe ◽

Iwona Wlodarska ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

T Cell ◽

Cell Biology ◽

Lymphoblastic Leukemia ◽

Functional Characterization ◽

Recurrent Event ◽

Exon 2 ◽

Male Age ◽

Cell Acute Lymphoblastic Leukemia ◽

T Cell Malignancies

Abstract T-cell Acute Lymphoblastic Leukemia (T-ALL) is a heterogeneous entity with several biologically distinct subtypes that differ in clinical outcome. Cytogenetics in T-ALL shows recurrent involvement of TCR a/d (14q11) and TCR b (7q34) rearrangements. The Philadelphia translocation, encoding the BCR-ABL1 (BCR-ABL) fusion gene, is typically found in chronic myeloid leukemia (CML) and precursor B-cell acute lymphoblastic leukemia (B-ALL), but is exceptionally rare in T-ALL. To study the potential involvement of ABL1 gene rearrangements in T-cell malignancies, we screened 90 T-ALL cases by fluorescence in situ hybridization (FISH), using BCR and ABL1 probes. No BCR-ABL1 rearrangements were detected, but 5 patients showed amplification of ABL1 and are described in a separate abstract and 2 patients showed a chromosomal rearrangement affecting ABL1. The first patient (male, age 16, 455x109 WBC/L, 99% blasts, cortical T immunophenotype) showed a cryptic t(9;14)(q34;q32). This was demonstrated in 7/12 metaphases and 60% of nuclei using FISH with the 5′/3′-ABL1 probes RACE-PCR detected a fusion between EML1 at 14q32 and ABL1 at 9q34. The fusion transcript joins exon 1–18 of EML1 to exon 2 of ABL1 and generates an ORF of 4926 nt. The functional characterization of the fusion protein is ongoing. The second patient (male, age 16, 25x109 WBC/L, 35% blasts, mature T-cell immunophenotype) showed a 47, XY, +10[5], idem, inv(9)(p21q34)[2}]/46, XY[9] karyotype. One third of the metaphases are tetraploid with the same distribution of abnormalities. The split signals obtained with the 5′-/3′ABL1 probes in the inv(9) subclone point to an ABL1 rearrangement that is being characterized at the present. These result suggest that ABL1 rearrangements are a rare but recurrent event in T-cell malignancies and support a role of ABL1 in T-cell biology. The therapeutic potential of ABL1 inhibitors for treating this group of T-ALL needs to be explored.

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Targeted sequencing to identify genetic alterations and prognostic markers in pediatric T-cell acute lymphoblastic leukemia

Scientific Reports ◽

10.1038/s41598-020-80613-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ya-Hsuan Chang ◽

Chih-Hsiang Yu ◽

Shiann-Tarng Jou ◽

Chien-Yu Lin ◽

Kai-Hsin Lin ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

T Cell ◽

Signaling Pathway ◽

Prognostic Markers ◽

Lymphoblastic Leukemia ◽

Survival Rates ◽

Genetic Alterations ◽

Targeted Sequencing ◽

Single Nucleotide Variants ◽

Cell Acute Lymphoblastic Leukemia

AbstractT-cell acute lymphoblastic leukemia (T-ALL) is caused by the accumulation of multiple genetic alterations. To determine the frequency of common genetic mutations and possible prognostic markers in childhood T-ALL, we performed targeted sequencing of 67 genes across 64 cases treated according to Taiwan Pediatric Oncology Group protocols between January 2002 and December 2015. Together, 302 variants were identified in 60 genes including 233 single nucleotide variants and 69 indels. Sixty-four samples had a median number of six genetic lesions each (range 1–17). Thirteen genes had mutation frequencies > 10%, and 5 were > 20%, with the highest being NOTCH1 (70.31%). Protocadherins FAT1 (32.81%) and FAT3 (17.19%), and the ubiquitin ligase component FBXW7 (28.13%) had higher mutation frequencies than previously reported. Other mutation frequencies (PHF6, DNM2, DNMT3A, CNOT3, and WT1) were within previously reported ranges. Three epigenetic-related genes (KMT2D, DNMT3A, and EZH2) were mutated in our cohort. JAK-STAT signaling pathway genes had mutation frequencies of 3–13% and were observed in 23 cases (35.94%). Changes to genes in the ErbB signaling pathway were detected in 20 cases (31.25%). Patients with NOTCH1/FBXW7 mutations and RAS/PTEN germline exhibited better 5-year overall survival rates.

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RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia

Blood ◽

10.1182/blood-2017-03-775536 ◽

2017 ◽

Vol 130 (15) ◽

pp. 1722-1733 ◽

Cited By ~ 20

Author(s):

AHyun Choi ◽

Anuradha Illendula ◽

John A. Pulikkan ◽

Justine E. Roderick ◽

Jessica Tesell ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

T Cell ◽

Lymphoblastic Leukemia ◽

Hematopoietic Cells ◽

Enhancer Activity ◽

Key Points ◽

Cell Acute Lymphoblastic Leukemia ◽

Normal Human

Key Points RUNX1 maintains Myb and Myc enhancer activity and is required for leukemogenesis in vivo. RUNX1 inhibition impairs the growth of primary T-ALL patient cells without an effect on normal human hematopoietic cells.

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Intravenous Forodesine (BCX-1777), a Novel Purine Nucleoside Phosphorylase (PNP) Inhibitor, Demonstrates Clinical Activity in Phase I/II Studies in Patients with B-Cell Acute Lymphoblastic Leukemia.

Blood ◽

10.1182/blood.v104.11.2743.2743 ◽

2004 ◽

Vol 104 (11) ◽

pp. 2743-2743 ◽

Cited By ~ 7

Author(s):

Richard R. Furman ◽

Varsha V. Gandhi ◽

J. Claude Bennett ◽

Shanta Bantia ◽

J. Michael Kilpatrick

Keyword(s):

Bone Marrow ◽

Acute Lymphoblastic Leukemia ◽

T Cell ◽

Phase I ◽

B Cell ◽

Lymphoblastic Leukemia ◽

Clinical Activity ◽

Cell Acute Lymphoblastic Leukemia ◽

Pre Treatment ◽

T Cell Malignancies

Abstract Forodesine is a potent, specific transition-state analog inhibitor of PNP with clinical activity in T-cell malignancies. Pharmacodynamic studies support that this anti-leukemic effect is mediated through the accumulation of plasma 2′-deoxyguanosine (dGuo) and intracellular Dgtp. In vitro studies indicated that B-cell acute lymphoblastic leukemia (B-ALL) cells can also accumulate Dgtp. These preclinical data led to a phase I/II multicenter dose-escalation study to evaluate forodesine in pts with various hematologic malignancies. 15 pts were treated with forodesine, including 6 with B-ALL. Forodesine was given via a 30-min IV infusion followed 24 hrs later by doses every 12 hrs for a total of 9 doses. A second course could be repeated after a 2-week break. Doses were escalated by 50% to pts grouped in cohorts of 3 (starting dose: 40 mg/m2). There was a rapid rise in plasma dGuo and a maximum PNP inhibition was achieved at 40 mg/m2 (Fig 1). 7/15 treated pts (2 T-cell malignancies and 5 B-ALL), including 5/6 treated B-ALL pts, demonstrated a hematologic benefit, defined as a decrease in tumor burden. 3 of the responding B-ALL pts were further treated with 6 courses of forodesine on a compassionate use protocol. One pt treated at 135 mg/m2 demonstrated a complete response with a decrease in bone marrow blast cells from 22% to 5% at the end of therapy. The other 2 pts, treated with 90 mg/m2 and 135 mg/m2 forodesine respectively, showed dramatic improvement in their CBC despite the persistence of bone marrow blasts. The dramatic fall in WBC count was accompanied in each pt by a rise in plasma dGuo (Cmax: 1.9–7.1 μM) and intracellular Dgtp (380–800 pmoles/107 cells vs 25–40 pmoles/107 cells pre-treatment), The response of the pt treated with 90 mg/m2 forodesine is shown in Fig 2. The absolute neutrophil count (ANC) improved from ~0 at pre-treatment to 1800 cells/mm3 at Day 18. To-date forodesine has been safe and well-tolerated at all dose levels tested with no dose-limiting toxicities. Clinical activity has been seen in T- and B-ALL. It is interesting to note the restoration of normal hematopoiesis, indicating the specificity of forodesine for leukemic cell populations and supporting that forodesine represents an important breakthrough in the development of less toxic ALL therapy. This encouraging clinical activity has led to the initiation of a phase II trial in pts with B-ALL. Additional clinical and pharmacodynamic results will be presented.

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