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Material and Methods, Figure legends

Phenotypic, transcriptomic and genetic validation of PDX models

List of the SNVs identified through RNA-sequencing

Differentially expressed genes in the human B-ALL cohort

Characteristics of the B-ALL cohort

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Purpose:Children with Down syndrome (constitutive trisomy 21) that develop acute lymphoblastic leukemia (DS-ALL) have a 3-fold increased likelihood of treatment-related mortality coupled with a higher cumulative incidence of relapse, compared with other children with B-cell acute lymphoblastic leukemia (B-ALL). This highlights the lack of suitable treatment for Down syndrome children with B-ALL.Experimental Design:To facilitate the translation of new therapeutic agents into clinical trials, we built the first preclinical cohort of patient-derived xenograft (PDX) models of DS-ALL, comprehensively characterized at the genetic and transcriptomic levels, and have proven its suitability for preclinical studies by assessing the efficacy of drug combination between the MEK inhibitor trametinib and conventional chemotherapy agents.Results:Whole-exome and RNA-sequencing experiments revealed a high incidence of somatic alterations leading to RAS/MAPK pathway activation in our cohort of DS-ALL, as well as in other pediatric B-ALL presenting somatic gain of the chromosome 21 (B-ALL+21). In murine and human B-cell precursors, activated KRASG12D functionally cooperates with trisomy 21 to deregulate transcriptional networks that promote increased proliferation and self renewal, as well as B-cell differentiation blockade. Moreover, we revealed that inhibition of RAS/MAPK pathway activation using the MEK1/2 inhibitor trametinib decreased leukemia burden in several PDX models of B-ALL+21, and enhanced survival of DS-ALL PDX in combination with conventional chemotherapy agents such as vincristine.Conclusions:Altogether, using novel and suitable PDX models, this study indicates that RAS/MAPK pathway inhibition represents a promising strategy to improve the outcome of Down syndrome children with B-cell precursor leukemia.

List of the SNVs identified through whole exome sequencing

List of fusion transcripts identified through RNA-sequencing

List of datasets enriched in murine B cell precursors (GSEA analyses)

Previous studies have established that UV irradiation results in epidermal growth factor receptor (EGFR) activation in keratinocytes. However, the signaling pathways and cellular effects related to this process remain incompletely elucidated. Herein, we describe for the first time that UVA-mediated EGFR activation results in β-catenin tyrosine phosphorylation at the Y654 residue responsible for the dissociation of E-cadherin/α-catenin/β-catenin complexes. Moreover, UVA induces an EGFR-dependent, but Wnt-independent, β-catenin relocalization from the membrane to the nucleus followed by its association with T-cell factor 4 (TCF4). This newly formed β-catenin/TCF4 complex binds to a specific site on matrix metalloproteinase 1 (MMP1) promoter and governs MMP1 gene and protein expression, as well as cell migration in collagen and gelatin. Altogether, these results suggest that UVA stimulates keratinocyte invasiveness through two coordinated EGFR-dependent processes: loss of cell-to-cell contact due to β-catenin/E-cadherin/α-catenin dissociation and increased cell migration through extracellular matrix component degradation due to β-catenin/TCF4–dependent MMP1 regulation. These events may represent an important step in epidermis repair following UVA injury and their abnormal regulation could contribute to photoaging and photocarcinogenesis. [Cancer Res 2009;69(8):3291–9]

The effects of cell adhesion on leukemia cell proliferation remain poorly documented and somehow controversial. In this work, we investigated the effect of adhesion to fibronectin on the proliferation of acute myeloid leukemia (AML) cell lines (U937 and KG1a) and CD34+ normal or leukemic primary cells. We observed an increased rate of proliferation of AML cells when adhered to fibronectin, concomitant with accelerated S-phase entry and accumulation of CDC25A. Conversely, normal CD34+ cell proliferation was decreased by adhesion to fibronectin with a concomitant drop in CDC25A expression. Importantly, we showed that both small interfering RNA (siRNA)–mediated CDC25A down-regulation and a recently developed CDC25 pharmacologic inhibitor impaired this adhesion-dependent proliferation, establishing a functional link between CDC25A accumulation and adhesion-dependent proliferation in leukemic cells. CDC25A accumulation was found only slightly dependent on transcriptional regulation and essentially due to modifications of the proteasomal degradation of the protein as shown using proteasome inhibitors and reverse transcription-PCR. Interestingly, CDC25A regulation was Chk1 dependent in these cells as suggested by siRNA-mediated down-regulation of this protein. Finally, we identified activation of the phosphatidylinositol 3-kinase/Akt pathway as an adhesion-dependent regulation mechanism of CDC25A protein expression. Altogether, our data show that in leukemic cells adhesion to fibronectin increases CDC25A expression through proteasome- and Chk1-dependent mechanisms, resulting in enhanced proliferation. They also suggest that these adhesion-dependent proliferation properties of hematopoietic cells may be modified during leukemogenesis. (Cancer Res 2006; 66(14): 7128-35)

Telomerase catalytic subunit (hTERT) has been shown to play a critical role not only in telomere homeostasis but also in cellular survival, DNA repair, and genetic stability. In a previous study, we described that tumor necrosis factor-×α (TNF×α) induced in the leukemic KG1 cells a senescence state characterized by decreased hTERT activity followed by prolonged growth arrest, increased× β-galactosidase activity, telomere shortening, and major chromosomal instability. Interestingly, granulocyte-macrophage colony-stimulating factor (GM-CSF) abrogated all these events. In the present study, we show for the first time that TNF×α acts by inhibiting the hTERT gene in both normal CD34×+ cells and fresh leukemic cells. Using KG1 cells as a representative cellular model, we show that TNF×α induced sphingomyelin hydrolysis, ceramide production, and c-Jun N-terminal kinase (JNK) activation, all of which are critical components of TNF×α signaling, resulting in hTERT gene inhibition. Moreover, we provide evidence that the protective effect of GM-CSF is related to its capacity to interfere with both ceramide generation and ceramide signaling. Negative regulation of the hTERT gene may represent one mechanism by which TNF×α interferes with normal hemopoiesis.

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Global transcriptional technologies have revolutionised the study of lymphoid cell populations, but human γδ T lymphocytes specific for phosphoantigens remain far less deeply characterised by these methods despite the great therapeutic potential of these cells. Here we analyse the transcriptome of circulating TCRVγ(+) γδ T cells isolated from healthy individuals, and their relation with those from other lymphoid cell subsets. We report that the gene signature of phosphoantigen-specific TCRVγ(+) γδ T cells is a hybrid of those from αβ T and NK cells, with more 'NK-cell' genes than αβ T cells have and more 'T-cell' genes than NK cells. The expression profile of TCRVγ(+) γδ T cells stimulated with phosphoantigen recapitulates their immediate physiological functions: Th1 cytokine, chemokine and cytotoxic activities reflect their high mitotic activity at later time points and do not indicate antigen-presenting functions. Finally, such hallmarks make the transcriptome of γδ T cells, whether resting or clonally expanding, clearly distinctive from that of NK/T or peripheral T-cell lymphomas of the γδ subtype.

Adult and child B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) differ in terms of incidence and prognosis. These disparities are mainly due to the molecular abnormalities associated with these two clinical entities. A genome-wide analysis using oligo SNP arrays recently demonstrated that PAX5 (paired-box domain 5) is the main target of somatic mutations in childhood BCP-ALL being altered in 38.9% of the cases. We report here the most extensive analysis of alterations of PAX5 coding sequence in 117 adult BCP-ALL patients in the unique clinical protocol GRAALL-2003/GRAAPH-2003. Our study demonstrates that PAX5 is mutated in 34% of adult BCP-ALL, mutations being partial or complete deletion, partial or complete amplification, point mutation or fusion gene. PAX5 alterations are heterogeneous consisting in complete loss in 17%, focal deletions in 10%, point mutations in 7% and translocations in 1% of the cases. PAX5 complete loss and PAX5 point mutations differ. PAX5 complete loss seems to be a secondary event and is significantly associated with BCR-ABL1 or TCF3-PBX1 fusion genes and a lower white blood cell count.

Receptor or nonreceptor tyrosine kinases (TKs) are known to play an important role in leukemogenesis. Here we studied the level of protein tyrosine phosphorylations in a series of fresh AML samples and evaluated the effect of TK inhibitors. Compared with normal hematopoietic progenitors, a high level of tyrosine phosphorylation was detected in most acute myeloid leukemia (AML) samples. The Src family kinases (SFKs) appeared constitutively activated in most cases, including in the CD34+CD38−CD123+ compartment as revealed by the level of phosphorylated tyrosine 416. Lyn was the major SFK family member expressed in an active form in AML cells where it was abnormally distributed throughout the plasma membrane and the cytosol as opposed to normal hematopoietic progenitors. The SFK inhibitor, PP2, strongly reduced the global level of tyrosine phosphorylations, inhibited cell proliferation, and induced apoptosis in patient samples without affecting normal granulomonocytic colony forming units. Moreover, silencing Lyn expression by small interfering RNA in primary AML cells strongly inhibited proliferation. Interestingly, a link between Lyn and the mTOR pathway was observed as PP2 and a Lyn knockdown both affected the phosphorylation of mTOR targets without inhibiting Akt phosphorylation. Lyn should be considered as a novel pharmacologic target for AML therapy.

Chronic myeloid leukemia (CML) is the paradigm of malignancy treated by targeted therapies by the use of tyrosine kinase inhibitors (TKI), essentially Imatinib, Dasatinib and Nilotinib. Despite their major efficiency, especially as first line therapies, resistance to these drugs develop partly due to genetic instability inherent to CML. BCR-ABL-kinase mutations remain the first cause of resistance, which appears to be due to clonal selection of cells bearing a given mutation under TKI therapies. Amongst these mutations, the “gatekeeper” T315I mutant is a major concern as it confers resistance to all three TKI clinically used and patients with this mutation have a poor prognosis. The inaccessibility of the TKI to the ABL kinase pocket might not be the only “mechanistic” cause of resistance and it has been suggested that T315I-mutated BCR-ABL (Skaggs BJ et al, 2006) could induce a specific phosphoproteome signature. To evaluate this possibility, we decided to determine if a specific gene expression profiling can be associated with T315I-mutated BCR-ABL, as compared to native BCR-ABL. The human hematopoietic cell line UT7 was transfected with retroviral vectors encoding for native BCR-ABL (UT7.11) or BCR-ABL with the T315I mutation (UT7.T315I). The cell lines were characterized by their cell growth, Western blotting and sequencing. UT7.11 cells were sensitive to Imatinib, Dasatinib and Nilotinib as well as to Ponatinib whereas UT7-T315I cells were resistant to all three TKI except for Ponatinib. Affymetrix microarrays were performed in triplicate on each of three groups (UT7, UT7.11, UT7.T315I). The datas were normalized using the dchip software. Bioinformatics analyzes were performed with R software (packages FactoMineR, limma, PAMR) Mev in TM4 software, enrichment analysis with the GSEA software (Broad institute). The principal component analysis (PCA) showed that the overall RNA expression of UT7.T315I was different from that of UT7.11 (native BCR-ABL) and parental UT7. On factorial map, UT7.11 was found more distant from parental UT7 than UT7.T315I. The contrast analysis of the linear model by the algorithm limma between the 3 groups, showed a strong differential signature of UT7.11 as compared to parental UT7 and UT7.T315I (respectively 4792 and 4813 genes). Only 800 genes were found to be differentially expressed between UT7.T315I and parental UT7. In hierarchical clustering, the total signature obtained in limma confirmed a closed profile between parental UT7 and UT7.T315I. Among the results of the limma model, we identified a 286 specific genes signature for UT7.T315I (both different from parental UT7 and UT7.11 and also not regulated between UT7.11 and UT7). This specific list of UT7.T315I was validated with the T315I group sample segregation by different multivariate methods: PCA, hierarchical clustering and non-negative matrix factorization. Among this T315I-specific gene list limma, 34 ZNF family genes were found (11.88%). Predicting class algorithm based on shunkren centroid (PAMR) separated the three group samples with low classification error and a global list of 368 genes: only 75 genes predicted UT7.T315I group and from this list 13 were in the ZNF gene family (13.33%). By the method of gene set enrichment analysis (GSEA), we explored the top 100 ranked genes as upregulated in UT7.T315I by comparing the two other sample groups. This gene set showed a high representation of ZNF family genes (25%). The design of a gene set with ZNF family genes selected showed a positive enrichment of ZNF (NES = +1.35, p-value Disclosures: Turhan: Bristol Myers Squibb, Novartis: Consultancy, Honoraria.

We have recently demonstrated that the mTOR/4E-BP1/p70S6K pathway is constitutively activated in AML cells but not in their normal counterpart. Rapamycin inhibits AML cell proliferation in 60% of cases and induces transient blood and marrow blast clearance in refractory AML patients (Blood2005; 105:2527–34). However, exact mechanisms of activation of this pathway in AML are poorly understood. Since receptor or non-receptor tyrosine kinases (TK) play a crucial role in leukemogenesis and may activate downstream effectors such as mTOR/4E-BP1/p70S6K, we have studied the basal profile of protein tyrosine phosphorylations in a series of fresh samples and the effect of several TK inhibitors on mTOR targets in order to identify upstream regulators of this pathway. PP2 (Src Familly Kinases, SFK inhibitor), herbimycin A (pan TK) but not SU6656 (pp60 c-src), AG1296 (c-Kit, PDGFR, FLT3) and AG490 (JAK2) inhibited the phosphorylation of p70S6K and 4E-BP1 in KG1 cell line. PP2 consistently inhibited the phosphorylation of mTOR targets in 30 fresh AML samples. Using immunostaining with anti-phosphotyrosine antibody, we detected a high level of tyrosine phosphorylations in all AML samples (in contrast to normal CD34+cells) and consistently found a signal at 55–60 kD which may correspond to SFK. Moreover, PP2 dramatically reduced the global level of tyrosine phosphorylations suggesting that SFK play a role on TKs activation cascade and could act upstream mTOR. Lyn, Hck and Fgr were expressed in 100%,78% and 67% of cases while Lck and Fyn were weakly or not expressed in AML cells. All samples showed phosphorylation on Y416 residue demonstrating the constitutive activation of SFK. We also used flow cytometry to detect SFK phosphorylation in the more immature compartment of the leukemic clone. In 4/5 cases, the CD34+CD38−CD123+ cell sub population displayed a high level of phosphorylation on Y416 that was inhibited by PP2. In KG1, PP2 inhibited cell growth in a time and dose dependent manner. This effect was mainly due to a cell cycle arrest in G1 and to a lesser extent, apoptosis induction. In clonogenic assays, PP2 inhibited the capacity of fresh AML cells to generate AML-CFU and induced apoptosis in short term culture (n=6). Because the two Lyn kinase isoforms were expressed in all cases and corresponded to the two bands detected by p-SrcY416 antibody, we thought to determine if this this kinase was the major component of SFK in AML. Lyn was highly phosphorylated on Y416 after immunoprecipitation. Specific down regulation by si-RNA to Lyn induced a significant decrease of p70S6K and 4E-BP1 phosphorylation and inhibited cell proliferation in KG1 and U937. Using confocal microscopy, Lyn was mainly localized all over the plasma membrane and colocalized with anti-p-SrcY416 whereas its distribution in normal CD34+ cells was restricted to several distinct points across the membrane. These data demonstrate that SFK and particularly Lyn kinase, are aberrantly deregulated in AML cells, control cell proliferation at least in part through mTOR pathway and represent a new target for the treatment of this disease.

Tumor necrosis factor alpha (TNFα) is a multifunctional cytokine, which is overproduced in a series of hematological diseases, including acute myeloblastic leukemia (AML) and myelodysplasia (MDS). Apoptotic cell killing has been the most frequently documented cellular effect of TNFα in AML cells. Much little is known about TNFα effect in AML cells, which display an intrinsic defect in their apoptotic machinery. In this study, we describe that prolonged exposure to TNFα, but not Fas, resulted in senescence in the immature CD34+ CD38− KG1 cell line. Indeed, TNFα-treated KG1 cells displayed growth arrest, increased senescence-associated β-galactosidase activity, telomere shortening and additional chromosomal abberations. In these cells, as well as in fresh AML cells, treatment with TNFα resulted in decreased hTERT gene trancription and hTERT activity. Moreover, we found that ceramide production and JNK activation were critical signaling components in TNFα-induced hTERT gene inhibition. GM-CSF stimulation inhibited ceramide production, JNK activation, hTERT inhibition, and senescence markers induction. To conclude, our study suggests that, at least in some AML cells, TNFα is a regulator of hTERT with important functional consequences in terms of growth capacity and genetic stability. Moreover, the pro-senescent effect of TNFα is efficiently counter-regulated by stimulatory cytokines such as GM-CSF.