The DNA polymerase δ complex (PolD), comprising catalytic subunit POLD1 and accessory subunits POLD2, POLD3, and POLD4, is essential for DNA synthesis and is central to genome integrity. We ...identified, by whole exome sequencing, a homozygous missense mutation (c.1118A > C; p.K373T) in
POLD3
in a patient with Omenn syndrome. The patient exhibited severely decreased numbers of naïve T cells associated with a restricted T-cell receptor repertoire and a defect in the early stages of TCR recombination. The patient received hematopoietic stem cell transplantation at age 6 months. He manifested progressive neurological regression and ultimately died at age 4 years. We performed molecular and functional analysis of the mutant POLD3 and assessed cell cycle progression as well as replication-associated DNA damage. Patient fibroblasts showed a marked defect in S-phase entry and an enhanced number of double-stranded DNA break-associated foci despite normal expression levels of PolD components. The cell cycle defect was rescued by transduction with WT POLD3. This study validates autosomal recessive POLD3 deficiency as a novel cause of profound T-cell deficiency and Omenn syndrome.
Maladie résiduelle phénotypique dans les LAM Touzart, Aurore
Option/bio : le journal de l'analyse médicale et de la biologie clinique,
03/2011, Volume:
22, Issue:
451
Journal Article
The SET-NUP214 (TAF1/CAN) fusion gene is a rare genetic event in T-cell acute lymphoblastic leukemia (T-ALL). Eleven (6%) of 196 T-ALL patients enrolled in the French Group for Research on Adult ...Acute Lymphoblastic Leukemia (GRAALL) 2003 and 2005 trials harbored a SET-NUP214 transcript. SET-NUP214–positive patients were predominantly (10 91% of 11) T-cell receptor (TCR)–negative and strikingly associated with TCRγδ lineage T-ALLs, as defined by expression of TCRγδ, TCRδ and/or TCRγ rearrangements but no complete TCRβ variable diversity joining rearrangement in surface CD3/TCR-negative cases. When compared with SET-NUP214–negative patients, SET-NUP214–positive patients showed a significantly higher rate of corticosteroid resistance (91% vs 44%; P = .003) and chemotherapy resistance (100% vs 44%; P = .0001). All SET-NUP214–positive patients but one achieved complete remission, and 9 were allografted. Despite the poor early-treatment sensitivity, the outcome of SET-NUP214–positive patients was similar to that of SET-NUP214-negative patients.
•SET-NUP214 is a recurrent (6%) γδ lineage-specific fusion transcript in adult T-ALL.•SET-NUP214 is strongly associated with corticosteroid and chemotherapy resistance but does not negatively influence clinical outcome.
T-cell acute lymphoblastic leukaemias (T-ALL) are aggressive malignant proliferations characterized by high relapse rates and great genetic heterogeneity. TAL1 is amongst the most frequently ...deregulated oncogenes. Yet, over half of the TAL1(+) cases lack TAL1 lesions, suggesting unrecognized (epi)genetic deregulation mechanisms. Here we show that TAL1 is normally silenced in the T-cell lineage, and that the polycomb H3K27me3-repressive mark is focally diminished in TAL1(+) T-ALLs. Sequencing reveals that >20% of monoallelic TAL1(+) patients without previously known alterations display microinsertions or RAG1/2-mediated episomal reintegration in a single site 5' to TAL1. Using 'allelic-ChIP' and CrispR assays, we demonstrate that such insertions induce a selective switch from H3K27me3 to H3K27ac at the inserted but not the germline allele. We also show that, despite a considerable mechanistic diversity, the mode of oncogenic TAL1 activation, rather than expression levels, impact on clinical outcome. Altogether, these studies establish site-specific epigenetic desilencing as a mechanism of oncogenic activation.
The prognostic implications of DNMT3A genotype in T-ALL are incompletely understood. We performed comprehensive genetic and clinicobiological analyses of T-ALL patients with DNMT3A mutations treated ...during the GRAALL-2003 and -2005 studies. Eighteen of 198 cases (9.1%) had DNMT3A alterations. Two patients also had DNMT3A mutations in non-leukemic cell DNA, providing the first potential evidence of age-related clonal hematopoiesis in T-ALL. DNMT3A mutation was associated with older age (median 43.9 years v 29.4 years, p < 0.001), immature T-receptor genotype (53.3% v 24.4%, p = 0.016) and lower remission rates (72.2% mutated v 94.4% non-mutated, p = 0.006). DNMT3A alterations were significantly associated with worse clinical outcome, with higher cumulative incidence of relapse (CIR, HR 2.33, 95% CI 1.05-5.16, p = 0.037) and markedly poorer event-free survival (EFS, HR 3.22, 95% CI 1.81-5.72, p < 0.001) and overall survival (OS, HR 2.91, 95% CI 1.56-5.43, p = 0.001). Adjusting for age as a covariate, or restricting the analysis to patients over 40 years, who account for almost 90% of DNMT3A-mutated cases, did not modify these observations. In multivariate analysis using the risk factors that were used to stratify treatment during the GRAALL studies, DNMT3A mutation was significantly associated with shorter EFS (HR 2.33, 95% CI 1.06 - 4.04, p = 0.02). Altogether, these results identify DNMT3A genotype as a predictor of aggressive T-ALL biology. The GRAALL-2003 and -2005 studies were registered at www.clinicaltrials.gov as #NCT00222027 and #NCT00327678, respectively.
T-cell acute lymphoblastic leukemia (T-ALL) and T-cell acute lymphoblastic lymphoma (T-LBL) are aggressive immature T-cell malignancies that are often characterized by improper T-cell receptor (TCR) ...recombinations leading to aberrant activation of proto-oncogenes. Current multi-agent combination chemotherapy treatment provides an overall survival rate of ~80% in children and 50% in adults. However, the prognosis of patients with relapsed and refractory T-ALL/T-LBL remains extremely poor and the development of more effective and specific antileukemic drugs is critical. Therefore, we aim to identify new oncogenes, define their mechanism of action and establish strategies to develop targeted, highly specific antileukemic drugs.
Here, we used Targeted Locus Amplification (TLA, de Vree et al., Nat Biotechnol., 2014) to identify a novel TCRβ driven t(6;7)(p21;q34) translocation in a human T-LBL patient resulting in aberrant activation of the PIM1 proto-oncogene. PIM1 is a constitutively active serine/threonine kinase involved in cell cycle progression, apoptosis, transcription and drug resistance and is overexpressed in a variety of human cancers. Its expression is controlled by the JAK/STAT signaling pathway. Further characterization of this PIM1 rearranged patient sample revealed cooperative genetic alterations that target known T-ALL/T-LBL onco- and tumor suppressor genes, including NOTCH1, IKZF1, EP300 and CDKN2A.
Comparing PIM1 expression between normal T-cell subsets, T-ALL and T-LBL patient samples using qPCR revealed subsets in both T-LBL and T-ALL patients with high PIM1 levels. This PIM1 expression can be both monoallelicaly (due to translocation) or biallelicaly (due to upstream mutations in f.e. the JAK/STAT pathway). Using publically available gene expression datasets, we show that oncogenic PIM1 activation is largely restricted to immature, TLX1, TLX3, NKX2-1 or HOXA positive T-ALL and T-LBL patients, and is mostly not present in TAL1 or LMO2 rearranged tumors. This pattern of PIM1 activation is in line with the preferential occurrence of JAK-STAT pathway alterations in these genetic subtypes of human T-ALL/T-LBL.
To study the oncogenic properties of PIM1 in the context of malignant T-cell transformation, we did RNA sequencing and phosphoproteomics on the T-ALL/T-LBL tumor line HSB-2 (cell line with the highest PIM1 expression) and on ex vivo treated leukemic cells harvested from the spleen of T-LBL engrafted NSG mice after PIM1 inhibition with TP-3654 (Foulks et al., Neoplasia, 2014). These data revealed that PIM1 inhibition has broad effects on transcription and phosphorylation substrates involved in cell cycle, translation and apoptosis. For example, we showed that the oncogenic properties of PIM1 are, at least in part, mediated by phosphorylation of GSK3β and subsequent stabilization of anti-apoptotic MCL1.
Next, we evaluated the therapeutic potential of PIM1 inhibition. Daily TP-3654 treatment for 4 weeks of T-LBL engrafted NSG mice resulted in strong anti-leukemic effects. In vitro combination treatment with TP-3654 and glucocorticoids showed strong synergism, while the combination with other chemotherapeutics such as asparaginase and vincristine did not. Moreover, the combination of TP-3654 and the glucocorticoid dexamethasone in vivo almost completely cured the leukemic mice (<1% hCD45 positive blasts in the peripheral blood).
All together, our study identifies PIM1 as a putative oncogene in T-ALL and T-LBL and suggests that inhibition of this serine/threonine kinase could serve as a novel therapeutic strategy in these aggressive T-cell neoplasms.
No relevant conflicts of interest to declare.
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