Monoallelic Deletion Research Articles

Monoallelic Deletion of NFKBIA in Glioblastoma: When Less Is More

Bredel etal. (2010) recently identified a subset of glioblastomas that harbor monoallelic loss of NFKBIA, which negatively affects patient prognosis. This finding raises new questions as to the role of IκBα and NF-κB in glioblastoma, the relationship between EGFR and NF-κB signaling, and potential therapeutic targets.

Cellular angiofibroma: analysis of 25 cases emphasizing its relationship to spindle cell lipoma and mammary-type myofibroblastoma

Cellular angiofibroma represents a rare benign mesenchymal tumor, occurring mainly in the superficial soft tissue of the genital region. The involvement of 13q14 in some cases confirmed the morphological suggested link with spindle cell lipoma and mammary-type myofibroblastoma. We analyzed the clinicopathological and immunohistochemical features of 25 cases, and performed in a number of cases additional molecular studies. There were 17 female and 8 male patients (age ranged from 27 to 83 years); females tended to be younger. A marked predilection for the vulva (n=13) was observed, and neoplasms in males were predominantly located in the inguinal region (n=4), and one case each in the scrotum, perianal, the knee, and the upper eyelid. The tumors arose most commonly in the superficial soft tissue and were well circumscribed in all but two cases. The tumor size ranged from 1 to 9 cm. All lesions were composed of spindle-shaped cells associated with numerous small- to medium-sized blood vessels; however, a broad morphological variation with foci of lipogenic differentiation in nine cases and sarcomatous transformation in one case was found. By immunohistochemistry, 11 out of 22 cases expressed CD34. A focal reaction for α-smooth muscle actin was observed in 9 out of 22 cases, and two cases each stained weak and focally positive for epithelial membrane antigen and CD99. In all seven cases tested, a monoallelic deletion of RB1 was detected by FISH analysis. Follow-up, available in 14 patients, showed neither local recurrence nor metastasis. In conclusion, we affirm the link between cellular angiofibroma, spindle cell lipoma, and mammary-type myofibroblastoma, showing a spectrum of one entity with morphological variations dependent on anatomic location.

Gene dosage effects in chronic lymphocytic leukemia

To understand the influence of chromosomal alterations on gene expression in a genome-wide view, chromosomal imbalances detected by single nucleotide polymorphism (SNP) chips were compared with global gene expression in 16 cases of chronic lymphocytic leukemia (CLL). A strong concordance between chromosomal gain or loss and increased or reduced expression of genes in the affected regions was found, respectively. Regions of uniparental disomy (UPD) were rare and had usually no consistent influence on gene expression, but in one instance, a large UPD was associated with a downregulation of most genes in the affected chromosome. The frequently deleted miRNAs, MIRN15A and MIRN16-1, did not show a reduced expression in cases with monoallelic deletions. The BCL2 protein, considered to be downregulated by these miRNAs, was upregulated not only in CLL with biallelic deletion of MIRN15A and MIRN16-1, but also in cases with monoallelic deletion. This suggests a complex regulation of BCL2 levels in CLL cells. Taken together, in CLL, a global gene dosage effect exists for chromosomal gains and deletions and in some instances for UPDs. We did not confirm a consistent correlation between MIRN15A and MIRN16-1 expression levels and BCL2 protein levels, indicating a complex regulation of BCL2 expression.

Integrative Genomics Analyses Reveal Molecularly Distinct Subgroups of B-Cell Chronic Lymphocytic Leukemia Patients with 13q14 Deletion

Chromosome 13q14 deletion occurs in a substantial number of chronic lymphocytic leukemia (CLL) patients and it is believed to play a pathogenetic role. The exact mechanisms involved in this lesion have not yet been fully elucidated because of its heterogeneity and the imprecise knowledge of the implicated genes. This study was addressed to further contribute to the molecular definition of this lesion in CLL. We applied single-nucleotide polymorphism (SNP)-array technology and gene expression profiling data to investigate the 13q14 deletion occurring in a panel of 100 untreated, early-stage (Binet A) patients representative of the major genetics, molecular, and biological features of the disease. Concordantly with FISH analysis, SNP arrays identified 44 patients with del(13)(q14) including 11 cases with a biallelic deletion. The shorter monoallelic deletion was 635-kb long. The loss of the miR-15a/16-1 cluster occurred in all del(13)(q14) cases except in 2 patients with a monoallelic deletion, who retained both copies. MiR-15a/16 expression was significantly downregulated only in patients with the biallelic loss of the miRNA cluster compared to 13q normal cases. Finally, the natural grouping of SNP profiles by nonnegative matrix factorization algorithm showed that patients could be classified into 2 separate clusters, mainly characterized by short/biallelic versus wide/monoallelic 13q14 deletions. Supervised analyses of expression data showed that specific transcriptional profiles are correlated with these 2 genomic subgroups. Overall, our data highlight the presence of 2 distinct molecular types of 13q14 deletions, which may be of clinical relevance in CLL.

The BCL11B Tumor Suppressor Is Mutated In Human T-Cell Acute Lymphoblastic Leukemia

AbstractAbstract 4177The BCL11B transcription factor, previously identified as a central player in normal α/β T-cell development, has recently been found to play critical roles in the maintenance of T-cell identity, with biallelic Bcl11b inactivation in T-cell precursors severely impairing their continued development into the T-cell lineage. Previous work has demonstrated that Bcl11b haploinsufficiency accelerates the onset of thymic lymphomas in p53-mutant mice, as well as T-lymphoid blast crisis in a mouse model of chronic myeloid leukemia induced by BCR-ABL. Furthermore, we have recently identified recurrent monoallelic Bcl11b deletions in 91% of T-cell acute lymphoblastic leukemias (T-ALL) arising in Atm-deficient mice, further supporting a role for Bcl11b haploinsufficiency in T-cell leukemogenesis. In order to determine whether BCL11B inactivation plays a role in the molecular pathogenesis of human T-ALL, we analyzed BCL11B status in primary T-ALL patient samples by array CGH and sequencing analysis. Monoallelic BCL11B deletions were identified in 6% of cases (n = 3 of 47) analyzed by array CGH, including one microdeletion within the BCL11B locus, one small deletion involving BCL11B and 6 additional genes, and one large 26 Mbp deletion of the distal arm of chromosome 14. BCL11B sequencing revealed heterozygous missense mutations in an additional 9% (n = 4 of 43) of primary T-ALL patient samples and in 19% (n = 3 of 16) of T-ALL cell lines. Structural homology modeling revealed that many of the mutations identified, including 3 of the 4 in the primary patient samples, disrupted key amino acids within BCL11B zinc finger domains that are involved in DNA recognition or structural stabilization required for zinc finger domain-mediated transcriptional activity. Analysis of TCRγ rearrangement status and gene expression data revealed that most cases with BCL11B inactivation were characterized by biallelic TCRγ rearrangements together with an early thymocyte precursor (ETP) gene expression signature, indicating developmental arrest at a prethymocyte stage of T-cell development, which we and others have shown confers an increased risk of treatment failure (Coustan-Smith et al. Lancet Oncol 2009; Gutierrez et al. J Clin Oncol 2010). Given that BCL11B expression during normal T-cell development increases markedly at the prethymocyte stage, our findings suggest that BCL11B inactivation may be directly responsible for developmental arrest at a prethymocyte stage during thymocyte transformation. Our findings provide compelling evidence that BCL11B is a tumor suppressor in a subset of human T-ALLs with a high risk of treatment failure. Disclosures:No relevant conflicts of interest to declare.

Longitudinal Genomic Analyses In Chronic Lymphocytic Leukemia (CLL) Patients Reveal Clonal Relationship and Genomic Evolution In Disease Progression and After Therapy

Longitudinal Genomic Analyses In Chronic Lymphocytic Leukemia (CLL) Patients Reveal Clonal Relationship and Genomic Evolution In Disease Progression and After Therapy

Acute Lymphoblastic Leukemia-Associated PAX5 Mutations Induce Aberrant B Cell Development

AbstractAbstract 10Over 60% of pediatric B progenitor acute lymphoblastic leukemia (ALL) cases contain somatic mutations in genes regulating B cell development, with PAX5 being the most common target of mutation (>32% of cases). The transcription factor PAX5 is required for commitment and maintenance of the B lymphoid lineage. A variety of PAX5 mutations has been identified including, mono-allelic deletions, sequence mutations, internal deletions, frame-shift mutations and translocations. We have previously shown that these PAX5 mutations result in reduced transcriptional activity either as a result of haploinsufficiency or the generation of altered PAX5 isoforms with reduced DNA-binding and/or transcriptional activity. However, the direct effect of the mutations on normal B cell development remains unknown. To address this question, we assessed the ability of a series of PAX5 mutations to rescue normal B cell development in Pax5-/- bone marrow (BM) cells using a murine in vitro culture system.Whole BM or transduced cells were grown in IL-7 producing stromal-supported cultures for two weeks and then assessed for their extent of B cell differentiation using flow cytometry. Under these in vitro conditions, both Pax5+/+ and Pax5+/− BM cells differentiated to a Hardy fraction D pre-B cell stage of differentiation (CD43−/B220+/CD19+/BP1+), with only a slight decrease in the level of expression of BP1 detected in the Pax5+/− cells. By contrast, Pax5-/- cells failed to undergo significant differentiation under these in vitro growth conditions and were arrested at an early pro-B stage of development (CD43+/−/B220+/CD19−/BP1−). To assess the biological activity of the identified PAX5 mutants, we then transduced lineage-depleted BM cells from Pax5+/+, Pax5+/− and Pax5-/- mice with MSCV-based retroviral vectors expressing either wild type (WT) or mutant PAX5 followed by in vitro culture. Three classes of PAX5 mutations were assessed: DNA binding domain mutations (P80R, P34Q, and V26G), an internal deletion mutation (Δe6-8), and translocation-induced PAX5 chimeric genes (PAX5-ETV6, PAX5-FOXP1 and PAX5-ZNF521). As expected, expression of WTPAX5 resulted in full rescue of Pax5-/- cells and induced no significant effects on the ability of Pax5+/+ and +/− cells to differentiate. By contrast, PAX5 DNA-binding domain mutants resulted in only partial rescue of Pax5-/- cells, with P80R inducing B220+/CD19−/BP1−, P34Q producing B220+/CD19+ cells with weak BP1 expression, and V26G yielding CD19+/BP1+ cells with minimally reduced levels of BP1. Similarly, expression of Δe6-8 resulted in partial rescue with the expansion of B220+/CD19+/−/BP1− cells. In stark contrast, expression of the translocation encoded PAX5 fusion proteins failed to induce any evidence of rescue. Moreover, these fusion proteins induced only minimal perturbations in the ability of Pax5+/+ and +/− cells to differentiate, suggesting that these fusion proteins were weak competitive inhibitors of normal Pax5 transcriptional activity under intra-cellular conditions. To further characterize the effects of these PAX5 mutations on B cell differentiation, we next analyzed the gene expression patterns of the resultant cell populations using the Mouse Genome 430 2.0 Arrays (Affymetrix) and compared the profiles to those obtained from purified Hardy fractions from normal murine BM. The expression signatures of the Pax5-/- cells were identical to those for normal Hardy fraction A and shifted to the signature of Hardy fraction C following rescue with WTPAX5. Transduction of Pax5-/- cells with either V26G or P34Q resulted in a near complete rescue with expression signatures similar to those obtained for Hardy fractions B/C. By contrast, transduction with P80R or Δe6-8 yielded a more incomplete rescue with expression profiles that were between Hardy fractions A and B. Interestingly, a number of genes within the B cell receptor signaling pathway were altered in cells rescued by P80R and Δe6-8, including the down regulation of CD19, Btk and Blnk. In summary, our data demonstrate that leukemia-associated PAX5 mutations have a graded effect on the transcriptional network that controls normal B cell development and differentiation. Defining the differential target gene specificity of the various PAX5 mutants should provide valuable insights into the molecular mechanisms through which these genetic lesions contribute to leukemogenesis. Disclosures:No relevant conflicts of interest to declare.

Incidence of Cytogenetic Abnormalities In Newly Diagnosed Binet Stage A CLL and Relationship with Prognostic Biomarkers and with Stereotyped B Cell Receptors: Updated Results on 344 Patients Included In the Prospective O-CLL1 GISL Study.

AbstractAbstract 4613 Background:Biologic risk factors such as immunoglobulin variable heavy chain (IgVH) gene mutation status and CD38 and ZAP-70 expression levels, along with genomic aberrations, have been integrated in clinical prognostic evaluation of CLL. Additionaly, CLL subsets expressing a certain stereotyped B-cell receptors have also been indicated to share biological and clinical features. Aims:We investigated, by FISH, the incidence of the major cytogenetic alterations (+12 and 13q14, 17p13, 11q23 deletions), their clinical implication and their relationship with prognostic biomarkers in 344 out of 384 Binet A CLLs enrolled in the prospective multicenter O-CLL1 GISL trial. Stereotypy subsets identification have been performed in 324 patients. Methods:Molecular markers characterization and FISH protocols were previously reported (Cutrona et al. Haematologica, 2008; Fabris et al. Genes Chromosomes Cancer, 2008), while stereotyped subsets were defined according to Stamatopoulos et al (Blood, 2007) and Murray et al (Blood, 2008). Results:At least one abnormality was found in 225/344 (65.4%) cases. The most frequent abnormality was del(13q14), detected in 173 CLLs (50.3%) followed by +12 (44/344;12.8%) (one case harboring 17p13 deletion), del(17p13) (9/344, 2.6%) and del(11q23) (18/344, 5.2%). 13q14 deletion was found as a sole abnormality in 155 (45%) patients; in the remaining cases, it was combined with +12 (3 pts) and 17p13 (4 pts) or 11q23 deletions (11 pts). The 13q deletion was found as a monoallelic deletion in 139/173 (80.3%); the presence of a biallelic deletion (> 20% of interphase nuclei) was found in the remaining 34 cases. No acquisition of new cytogenetic aberrations was evidenced among the 13 CLLs developing progressive disease (range, 6 to 32 months; median, 20 months); in only one case, the proportion of nuclei with 17p13 and 13q14 deletions increased from the time of diagnosis (from 33% to 92%). Biomarkers data were available in all of the patients. CD38 percentages (mean value ± sem) were 7.9±1.3, 15.1±1.9, 51.7±5.5, 22.0±7.8,40.8±13.2, 39.8±7.3 for del(13q14), normal karyotype, +12, del(11q23), del(17p13) and multiple alterations, respectively (p<0.0001). The percentages of IgVH mutations significantly correlated with cytogenetic alterations; namely, 5.7±0.2 for cases with del(13q14), 4.7±0.4 for normal karyotype, 2.3±0.5 for +12, 0.05±0.05 for del(11q23), 2.0±1.1 for del(17p13) and 1.0±0.4 for multiple alterations (p<0.0001). Similarly, a significant correlation was found for ZAP-70 expression: namely 32.9±1.6 for cases with del(13q14), 38.5±2.1 for normal karyotype, 46.4±3.6 for +12, 67.0±8.3 for del(11q22), 41.0±12.8 for del(17p13) and 50.7±5.4 multiple alterations (p<0.0001). Cytogenetic abnormalities were clustered in 3 risk groups [i.e. low del(13q14) and normal; intermediate (+12); and high risk 17p13 and 11q23 deletions] and correlated with a scoring system in which patients were stratified in 4 different groups according to the absence or presence of 1, 2 or 3 biomarkers (Morabito et al., Br. J. Haematol., 2009). Notably, 166/175 cases scoring 0, gathered in the low FISH group, whereas 21/26 high FISH risk cases clustered in scoring 2–3 (p<0.0001). A significantly higher risk of starting treatment was found in high vs. intermediate (p=0.024) and low FISH risk (p=0.001) CLLs. Finally, stereotyped IgVH sequences were found in 108/324 (33%). Unfavorable stereotyped subsets (#1, #2, #3, #7 and #9) were significantly more frequent in CLLs with poor-prognostic aberrations (p=0.0203; RR=3.589). Conclusions:Our data indicate that cytogenetic lesions predicting unfavorable prognosis show a relatively low incidence in newly diagnosed Binet stage A CLLs and are significantly associated with negative prognostic biomarkers predictive of disease progression. Our prospective study also confirms the prognostic value of risk FISH categories in predicting the time to the first treatment and revealed a higher rate of unfavorable stereotyped IgVH subsets in patients carrying poor-prognostic genomic aberrations. Finally, preliminary evidence in a limited number of cases indicates that the acquisition of new genetic abnormalities seem to be an infrequent event during disease progression. Disclosures:No relevant conflicts of interest to declare.

A20 Gene Deregulation In Waldenstrom's Macroglobulinemia.

AbstractAbstract 3628 Background.Waldenstrom's macroglobulinemia (WM) is a rare lymphoproliferative disorder characterized by bone marrow (BM) infiltration of lymphoplasmacytic cells and monoclonal IgM gammopathy. The deletion 6q is the most frequent cytogenetic aberration in WM and it has been suspected that this region harbours a tumour suppressor gene of pathogenic significance for WM. Comparative genomic hybridization (CGH) array delineated several minimal deleted regions (MDR) on 6q and pointed out key regulator genes of the NFKB pathway involved in these deletions, including A20 gene. The zinc finger protein A20 has been characterized as dual inhibitor of NFKB activation and was recently described as a tumor suppressor gene in lymphoma. However, the mechanisms of A20 deregulation are not fully understood in WM. We aimed to study the mechanisms of A20 deregulation in WM using gene expression profiling (GEP) and single nucleotide polymorphism (SNP) based arrays, a powerful high resolution method allowing both the detection of loss of heterozygosity (LOH) and copy number alteration (CNA) analysis in the same experiment. Methods.We have studied BM samples from 42 patients (pts) with WM (31 males, mean age: 67 years). Conventional karyotype study was analyzed following stimulation with IL2 and DSP30 of BM cells. FISH analysis was performed to detect deletion 6q21 (MYB probe). DNA and RNA were extracted following BM CD19 B cell negative selection. Quantification of copy number of A20 gene was performed using real time PCR, RNAse P gene was used as reference gene. Genome-Wide Human SNP Array 6.0 (Affymetrix chips) was used to detect both LOH and CNA in 31 pts. Paired samples (B cells/normal T lymphocytes) were used as an intra-individual reference to distinguish germline polymorphisms from somatic abnormalities in 29 patients. Size, position and location of genes were referenced using UCSC HG18 assembly, LOH and CNA were identified using genotyping console 3.02 software (Affymetrix) and Partek genomic suite. Gene expression profiling (GEP) was performed in 11 pts using Affymetrix U133A arrays. Gene-expression intensity values were log transformed, normalized and analyzed using GeneSpring GX software. Results.SNP array identified deletion 6q in 9/31 (29%) patients, confirmed by FISH analysis. All cases were monoallelic deletion. In 90% of cases, deletion 6q was associated with others genetic abnormalities. In one case, we observed a loss of 6q combined with a gain of 6p. Deletion 6q was associated with gain of chromosome 4 in 2 cases, and with deletion of 13q in 3 cases. The MDR was located on chromosome 6q21-6q25. This MDR contained several candidate genes included always deletion of A20 gene, located on 6q23, and was confirmed by real time DNA PCR quantification in all cases. Overall, the frequency of A20 gene deletion in our entire WM cohort (N=42 pts) was 29.2% (12/42), determined by real time DNA PCR of the copy number of A20 gene.In patient without deletion 6q, we looked at potential deregulated mechanisms of A20 by LOH with no CNA, e.g. UPD (uniparental disomy). We have not seen any UPD targeting the A20 gene.We then looked at A20 gene expression by GEP, and found no significant variation of A20 gene expression related to A20 monoallelic deletion as compared to pts with two copies, reflecting probably the existence of other mechanisms of A20 gene deregulation. This result was consistent with the absence of clear difference in genome-wide expression profiling in pts with 6q deletion and those without the deletion. As A20 is a key player in the negative feedback loop regulation of NFKB, we also looked at the gene expression of a set of genes involved in NFKB pathway. The presence or absence of A20 deletion did not influence the gene expression profiling of this NFKB pathway gene set. Conclusion.We described a high frequency of deletion of A20 gene. In most cases, deletion of A20 was associated with other genetic abnormalities. A20 deletion was not associated with a significant signature by GEP. Additional studies are needed to understand the cellular consequences of A20 deletions in the pathogenesis of WM. Disclosures:Leleu:Celgene: Consultancy, Research Funding; Janssen Cilag: Consultancy, Research Funding; Leo Pharma: Consultancy; Amgen: Consultancy; Chugai: Research Funding; Roche: Consultancy, Research Funding; Novartis: Consultancy, Research Funding.

TNFAIP3 (A20) Genetic Alterations In EBV Associated AIDS Related Lymphomas

AbstractAbstract 802 Introduction:AIDS related lymphomas (ARL) are a heterogeneous group of lymphoproliferative disorders that are frequently associated with Epstein Barr virus (EBV) infection. EBV expresses latent viral oncoproteins that constitutively activate the transcription factor NF-κB, a potent inducer of genes involved in B cell survival and proliferation (Keller SA et al, Blood 2006). Lymphomas that are not associated with EBV can also display increased NF-κB activity and recent reports have described mutations in regulators of NF-κB in subsets of B cell lymphomas. One of the frequently mutated regulatory genes is TNFAIP3, which encodes A20, an ubiquitin modifying enzyme involved in the termination of NF-κB signaling. Mutations resulting in the inactivation of A20 have been found in a significant proportion of marginal zone lymphoma (Novak U et al, Blood 2009), classical Hodgkin lymphoma, primary mediastinal B cell lymphoma (Schmitz R et al, J Exp Med 2009), and diffuse large B cell lymphoma (Compagno M et al, Nature 2009). In ARL the incidence of alterations in A20 and the relationship with EBV infection has not been described. Materials and Methods:We evaluated archival formalin fixed paraffin embedded tissue samples of ARL for genetic alterations in A20. Tissue was collected through an international collaboration between Weill Cornell Medical College in New York, USA and Siena University in Siena, Italy. A tissue microarray with 46 cases of ARL was prepared and characterization of lymphoma subtype and EBV viral status were determined by immunohistochemistry and in situ hybridization for Epstein-Barr encoded RNA. Fluorescent in situ hybridization (FISH) was used to evaluate for genomic deletions in A20, and translocations of cMYC, BCL-2 and BCL-6. Direct sequencing of the coding region and splice sites of A20 was performed to evaluate for additional genetic alterations. Immunohistochemistry was used to evaluate for the presence of A20 protein. Results:Fluorescent in situ hybridization revealed A20 monoallelic or biallelic deletion in 6 of 25 cases (24%). A20 point mutations were found in 3 of 23 cases (13%). Nonsense mutations coding for a premature stop codon in exon 2 were seen in 2 cases. The third case was found to have a missense mutation in exon 7 resulting in an amino acid change. Two of the 3 cases with an A20 point mutation had A20 deletion in the complementary allele indicating biallelic alteration of the A20 gene. Immunohistochemistry for A20 was performed and is reported for the first time in this abstract. Absence of A20 protein was demonstrated in 4 of 33 samples (12%). Included among the cases negative for A20 on immunohistochemistry is the single case with biallelic A20 deletion demonstrated by FISH. In total 10 of 39 (26%) cases with adequate sample for evaluation were determined to have inactivation of A20 by FISH, sequencing, immunohistochemistry, or a combination. A20 inactivation was seen among all histologic subtypes of ARL including Burkitt lymphoma (n=2), diffuse large B cell lymphoma of the germinal center B cell (n=2) and non-germinal center B cell (n=2), plasmablastic lymphoma (n=3) and B cell lymphoma, unclassifiable, intermediate between BL and diffuse large B cell lymphoma (n=1). Interestingly, the incidence of EBV infection was higher in cases with A20 inactivation than in those with intact A20. EBV was present in 6/10 cases with A20 alteration (60%) vs. 8/29 cases with intact A20 (28%). The EBV latent viral protein LMP-1, which activates NF-κB, was not expressed in cases with A20 alteration. Conclusions:This is the first report to demonstrate A20 inactivation in EBV-associated lymphoma. A20 molecular analysis has been previously reported in Hodgkin Lymphoma (HL) where A20 inactivation and EBV infection were found to be almost mutually exclusive (Schmitz R et al, J Exp Med 2009). The EBV gene expression pattern differs in HL and ARL. In HL EBV expresses the viral oncoprotein LMP-1, which leads to constitutive activation of NF-κB. In ARL viral gene expression is more heterogeneous and in this cohort of ARL, LMP-1 was not expressed in any of the cases with EBV infection and A20 loss. Our data indicate that A20 may represent a tumor suppressor gene in a significant subset of ARL and that A20 inactivation may be associated with positive EBV status. In EBV related lymphoma inactivation of A20 may be an alternative mechanism of NF-κB upregulation in the absence of LMP-1. Disclosures:No relevant conflicts of interest to declare.

Dissecting the Genetic Basis of Marginal Zone Lymphoma Reveals a Predilection for NF-Kb Activation by Clonal MZL Located at Extranodal Sites

AbstractAbstract 4160We propose that the pathophysiology of marginal zone B-cell lymphomas (MZL) could allow for their classification into lymphoid organs located in MZL and extra-nodal MZL of MALT type; the former category encompassing splenic MZL (SMZL) and nodal MZL (NMZL). The rarity of these lymphomas and difficulty in distinguishing them from other low-grade B-cell lymphoma such as lymphoplasmacytic lymphomas hampers further understanding of disease biology. In an attempt to better characterize the genetic basis of these entities and compare acquired genetic changes based on this categorization we performed array-based comparative genomic hybridization (using the 244A array, Agilent) in a cohort of MZL cases. In total we analyzed 101 MZL, including 46 MALT (including 8 cases with t(11;18)(q21;q21)), 35 SMZL and 20 NMZL. Overall, 90.1% cases have copy-number abnormalities (CNA). Genomic complexity was greatest in MALT without t(11;18)(q21;q21)(4 CNA), followed NMZL (3.5 CNA), SMZL (3 CNA) and MALT with t(11;18)(q21;21)(1 CNA). Seventeen minimal deleted regions (MDRs) and 9 minimal amplified regions (MARs) were defined based on the presence in at least one entity with a frequency of 10% or higher. Gains of chromosomes 3, 12 and 18 were found in all entities. Deletion of 6q was the most common abnormality in MALT (21.1%) and, to less extent, SMZL and NMZL. Biallelic and focal monoallelic deletions on 6q23.3-q24.1 identified TNFAIP3 as the sole gene inside the common MDR between entities. Deletion of chromosome 13 was observed in all entities, but NMZL and MALT were characterized by whole chromosome deletions, whereas focal deletions on 13q14.3 (MIR16-1/MIR15A) were identified in SMZL. A subset of abnormalities was shared for more than one entity: deletions 9p21.3 (CDKN2A) and 11q21-q22 (ATM) were found in NMZL and SMZL but not in MALT; deletion 7q32.1-q33 was the most common CNA in of SMZL but was also found in MALT; gain of 6p was found in MALT and NMZL but not in SMZL. Other CNA were only found in one entity such as deletion of 17p13.3-p12 (TP53) in SMZL, deletion of 15q25.3-q26.2 in NMZL. In addition to 17% of cases with the t(11;18)(q21;q21), extra copies of MALT1, focal amplifications of REL and/or monoallelic/biallelic deletions of TNFAIP3 were identified in an additional 46% of MALT lymphomas. These CNA were identified alone or in combination, but all of them were mutually exclusive with the t(11;18)(q21;21), thus totalizing 63% of MALT lymphomas with abnormalities affecting regulator genes from the NF-kB signaling pathway. Moreover, depending on the anatomic site of the MALT lymphoma, the prevalence of CNA affecting the NF-kB pathways varies from 50% in lacrimal glands to 75% in salivary glands. Abnormalities affecting regulator genes of the NF-kB signaling pathways were identified in a significantly lower frequency in NMZL (30%) and SMZL (31%) entities, suggesting its differential role in the pathogenesis of different entities. Using this high-resolution approach we show that while many abnormalities are shared unique patterns of genomic gains and losses characterize subgroups of MZL. Extranodal MZL seems to have a higher propensity of constitutive genetic upregulation of NF-kB pathways. Furthermore, this study remarks the importance of this pathway also in the subgroup of MALT lymphomas without translocations affecting the pathway. Disclosures:Fonseca:Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.

HoxA cluster is haploinsufficient for activity of hematopoietic stem and progenitor cells

Functional compensation between homeodomain proteins has hindered the ability to unravel their role in hematopoiesis using single gene knockouts. Because HoxB genes are dispensable for hematopoiesis, and most HoxA genes are expressed an order of magnitude higher than other cluster genes in hematopoietic stem cell (HSC)-enriched populations, we hypothesize that maintenance of HoxA cluster expression is important for adult hematopoiesis and that global decrease of HoxA gene expression levels affects steady-state hematopoiesis. Expression levels of HoxA cluster genes have been determined in primitive hematopoietic populations derived from adult mice using quantitative reverse transcriptase polymerase chain reaction. Furthermore, the functional effect of single allelic deletion of the entire HoxA cluster on hematopoietic cells was analyzed by competitive repopulation assays using HoxA(+/-) mice. We show that the HoxA cluster is predominantly expressed in long-term HSCs and that expression declines with progression to short-term HSCs and early progenitors in a quantifiable manner. Monoallelic deletion of the HoxA cluster caused a general increase in primitive hematopoietic cell populations, but a decrease in side populations. In addition exhaustion of B-cell progenitors with age was observed, resulting in less mature B cells. Moreover, bone marrow of HoxA(+/-) mice had a significant larger population of Mac1/Gr1 neutrophils, which might be caused by accelerated maturation of myeloid progenitors. Transplantation assays demonstrated that HoxA(+/-) HSCs were less competitive in long-term repopulation of myeloablated recipients, which appeared intrinsic to HSCs. These results show for the first time that maintenance of adult HSCs and progenitors is particularly sensitive to HoxA gene levels, suggesting a specific role for the HoxA cluster in primary regulation of definitive hematopoiesis.

Effect of phosphoinositide-phospholipase c beta1 monoallelic deletion in low-risk MDS patients treated with darbepoetin.

6609 Background: Myelodysplastic syndromes (MDS) are a heterogeneous group of hematologic diseases with a variable risk of evolution into acute myeloid leukemia, moreover recent results proved that phosphoinositide- phospholipase (PI-PLC) C beta1 monoallelic deletion is associated with a higher risk of AML evolution. We examined the treatment outcome of low-risk MDS pts with beta1 monoallelic deletion treated with EPO. Methods: Before treatment, by FISH analysis we assessed the presence of PI-PLCbeta1monoallelic deletion in thirty low-risk MDS pts (16 male 14 female median age 65 years) who received EPO (darbepoetin 40,000 every 2 weeks). Results: The PI-PLCbeta1 mono-allelic deletion was found in 9/30 low risk MDS pts; four of them showed a rapid evolution into AML, whilst the remaining five pts did not respond to EPO treatment. Conclusions: The PI-PLCbeta1 mono-allelic deletion is associated with a worse clinical outcome even in low-risk MDS patients who apparently have a good response profile for EPO (recent diagnosis, absence of transfusion dependence, EPO levels < 500). No significant financial relationships to disclose.

Somatic alterations in the melanoma genome: A high‐resolution array‐based comparative genomic hybridization study

We performed DNA microarray-based comparative genomic hybridization to identify somatic alterations specific to melanoma genome in 60 human cell lines from metastasized melanoma and from 44 corresponding peripheral blood mononuclear cells. Our data showed gross but nonrandom somatic changes specific to the tumor genome. Although the CDKN2A (78%) and PTEN (70%) loci were the major targets of mono-allelic and bi-allelic deletions, amplifications affected loci with BRAF (53%) and NRAS (12%) as well as EGFR (52%), MITF (40%), NOTCH2 (35%), CCND1 (18%), MDM2 (18%), CCNE1 (10%), and CDK4 (8%). The amplified loci carried additional genes, many of which could potentially play a role in melanoma. Distinct patterns of copy number changes showed that alterations in CDKN2A tended to be more clustered in cell lines with mutations in the BRAF and NRAS genes; the PTEN locus was targeted mainly in conjunction with BRAF mutations. Amplification of CCND1, CDK4, and other loci was significantly increased in cell lines without BRAF-NRAS mutations and so was the loss of chromosome arms 13q and 16q. Our data suggest involvement of distinct genetic pathways that are driven either through oncogenic BRAF and NRAS mutations complemented by aberrations in the CDKN2A and PTEN genes or involve amplification of oncogenic genomic loci and loss of 13q and 16q. It also emerges that each tumor besides being affected by major and most common somatic genetic alterations also acquires additional genetic alterations that could be crucial in determining response to small molecular inhibitors that are being currently pursued.

Abstract 2143: High-Resolution Molecular Karyotyping of Chronic Myeloid Leukemia Patients in Blast Crisis by 6.0 SNP-Arrays Identifies Focal Copy Number Alterations Affecting the Whole Sequence or Specific Exons of Oncogenes and Tumor Suppressor Genes

Abstract Despite the striking efficacy of targeted therapy for chronic myeloid leukemia (CML), a proportion of patients (pts) still experience progression from the initial chronic phase to an acute phase (blast crisis; BC) characterized by high disease aggressiveness and poor prognosis. BC is known to be associated with accumulation of additional genetic alterations, but these alterations have so far been only partially characterized. We used Human 6.0 SNP Arrays (Affymetrix) to perform high-resolution molecular karyotyping of 29 DNA samples from BC (myeloid, n=17 lymphoid, n=11) CML pts. The 6.0 SNP Array technology relies on 1.8 million markers evenly spaced across the genome, with a median inter-marker distance &amp;lt;700 bp. We decided to exploit this unprecedented resolution aiming our analysis to the identification of very small CNAs that may have been missed by previous studies using less sensitive assays. Gains/losses mapping to known regions of copy number variation (CNV) were excluded. Our approach revealed a number of focal gains or losses ranging from 4 to 47Kb, affecting a single gene or, more frequently, only part of a gene. Amplifications were as frequent as monoallelic deletions and involved the promoter region and/or one or more exons. In some cases, a complex pattern of amplification of some exons and monoallelic deletion of others was recognized within the same gene. Alterations involved the following genes: AKT3; CDC73; RB1; JAK2; JAK1;K ERG; ETS1; SMAD; PIK3CA; EPHA3; RUNX1T1; ETV1; AKT2; MDM4; KALRN; FHIT; K-RAS; PTEN; FAF1; SKAP2; PTCH1; GAS2; FGFR2; SOS1; NRG1; MET; PBX4; ETV5; N-RAS, HGF, TEC; PAK2; H-RAS. The precise anatomy of alterations involving each gene will be presented. Deeper characterization of these alterations at the DNA and RNA levels by polymerase chain reaction and sequencing is now ongoing; results will be presented. All the genes identified in our screening were transcription factors, adaptor proteins, receptor and non-receptor kinases involved in cell proliferation and apoptosis - with a known role as oncogenes or tumor suppressors or oncogene/tumor suppressor interactors. Although these results confirm a high degree of heterogeneity in the alterations detectable in BC CML pts, members of the RAS pathway were the most frequently altered genes. Deeper characterization by polymerase chain reaction and sequencing is ongoing and will be presented. In conclusion, the power of 6.0 SNP Array technology allowed us to detect previously unidentified alterations targeting whole or part of key oncogenes or tumor suppressors whose deregulation may play a role in determining the aggressive phenotype of BC CML and which may represent potential therapeutic targets. Supported by European LeukemiaNet, AIL, AIRC, PRIN, Fondazione del Monte di Bologna e Ravenna. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2143.

Abstract 323: Early detection of cytogenetic switch from monoallelic to biallelic 13q14 deletion using BCL-2 index in CLL

Abstract Monoallelic deletion of 13q14.3 is the most common cytogenetic abnormality in chronic lymphocytic leukemia (CLL). The recently described mir15a/16-1 mutation can result in increased BCL-2 expression reflecting 13q14 status. We present a case of CLL with a transient bimodal BCL-2 subclone. The patient is a 60 years old female, Rai stage IV, with a ten-year history of CLL. Prognostic markers included: mutated IgVH, Zap70, CD38 and CD49d negative, with 75 % monoallelic 13q14 deletion at the time of diagnosis. At year ten, seven-color flow cytometric evaluation was performed twice within a three month interval showed three subpopulations. BCL-2 mean fluorescence intensity (MFI), and BCL-2 index were estimated on each population. Based on forward scatter (FS) vs. side scatter (SS), and BCL-2 MFI, these cells were sorted. Interphase FISH was performed on sorted cells using D13S319 spectrum orange/LSI 13q34 spectrum green probe to define 13q14x1, 13q14x2, and diploid cells. A lymphoid population was identified by CD45 vs. SS gating. Using FS vs. SS 90.6% were small lymphoid cells (SL1) and 6.4 % were large lymphoid cell (LL1). The overall small lymphocyte population showed 1% diploid cell, 78% 13q14x1, 21% 13q14x2, with BCL-2 index 1.9. The CD19+CD5+ (SL1) population could be further sub-divided into two distinct malignant BCL-2 subclone. Each subclone had a different BCL-2 index, and different percentage of (13q14x1, 13q14x2). The first subclone (42.8%) brightly expressed BCL-2 (SL1B), and showed 59% 13x14x1, and 41% 13q14x2 with a BCL2 index of 3.1. The second subclone (57.2%) dimly expressed BCL-2 (SL1D), and showed 89% 13q14x1, 10.5 % 13q14x2, and 0.5 % diploid cell with a BCL2 index of 1.1. Both subclone were : kappa+, CD5+, CD19+,CD20+,CD27+,CD23+,CD45+, and they were negative for CD38, CD49d,and ZAP-70 . The 6.4 %(LL1) population showed 2% diploid cell, 59% 13q14x1, 39% 13q14x2, with BCL-2 index 3.5.A second sample three month later showed one uni-modal homogenous BCL-2 population within the small lymphoid cells (SL2), and a decreased in the percentage of large lymphoid cell population (LL2). Both SL2, and LL2 showed increased in the BCL-2 index compared to the first sample. SL2 (93.5 %) showed 0.5 % diploid cell, 61.5% 13q14x1, 38 % 13q14x2, with BCL-2 index 2.2, and LL2 (2.9 %) showed 1.5% diploid cell, 52.5% 13q14x1, 46% 13q14x2, and BCL-2 index 4.5. This case demonstrates that there may be a relationship between the levels of BCL-2 MFI in the CLL lymphocyte, and the relative proportions of leukemia cells having either 13q14x1, or 3q14x2. Our study is the first to explore the importance of identification of subclones within a patient harboring different BCL-2 MFI at any given time. This denotes a difference in 13q14 status, and might signal the start of a new phase of the disease. This type of analysis enabled us to time the occurrence of events if we have the BCL-2 index base line for the clone at the time of initial diagnosis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 323.

Abstract 331: A comprehensive high-resolution genomic analysis of primary central nervous system lymphomas (PCNSL) shows a highly complex karyotype characterized by abnormalities affecting multiple genes involved in critical pathways associated with lymphocyte maturation and survival

Abstract Introduction. PCNSL is an aggressive primary brain tumor characterized by a perivascular accumulation of malignant cells that have lymphoid characteristics. As there is significantly less information regarding the molecular pathogenesis of PCNSL in comparison with systemic lymphomas the aim of this study was to perform a comprehensive high-resolution genomic analysis in a cohort of PCNSL cases to better characterize the disease at chromosomal and gene level. Material and Methods. Specimens from 7 EBV- and HIV-negative and presumed immunocompetent PCNSL patients with sufficient frozen tissue for DNA extraction were studied. Copy-number abnormalities were analyzed by array CGH using SurePrint G3 (1 million probes) microarray (Agilent). B-cell differentiation status was characterized by immunostains for CD10, MUM-1, and CD138. Results. PCNSL cases were characterized by highly complex genomes with a median of 23 copy-number abnormalities per patient (range 16-49). Twenty-four chromosomal regions were affected in recurrent deletions and 19 in copy-number gains. Gain of 12q12-q24.33 and losses of 9p21.3 and 6q were the most common abnormalities, found in five of the seven patients. There was not a deleted region on 6q unique to all cases, with 6q14.1-q14.3, 6q16.3-q22.2 and 6q25.3-q26 losses being found in 4 out of 5 cases with 6q deletions. Two regions of interest were biallelically deleted. CDKN2A was the sole gene included in all cases with 9p21.3, being biallelically deleted in two out of 5 cases. TOX and CD58, genes associated with the development and activation of T cells, were also biallelically affected. Focal monoallelic deletions affecting negative regulators of the NFkB signaling pathway (MAP4K1, TANK, TAX1BP1, TRIB3), cell cycle (RB1) and immune-cell regulation (SIRPB1, CBLB, NFATC2) were also identified. Overall, a total of 22 genes were included in homozygous deletions in at least one case. Several chromosomal breakpoints were identified inside genes that encode transcription factors previously identified as being part of fusion protein in other hematological malignancies (FOXP1, ETV6 and NCOA2). Conclusion. This pilot study showed evidence for a highly complex genome, mainly characterized by abnormalities affecting a plethora of genes involved in lymphocyte development, activation and NF-kB signaling pathways regulation. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 331.

Nuclear Inositide Signalling: Role of PI‐PLCbeta1 in MDS and AML

The nuclear signaling evoked by phosphoinositide‐ specific‐phospholipase C (PI‐PLC)beta1 targets specific regions of Cyclin D3 as well CD24 promoter, hinting at a role in haematopoiesis, given that both Cyclin D3 and CD24 are involved in the very early steps of this process. PI‐PLCbeta1 could also play a role in the progression of Myelodysplastic Syndromes (MDS) into Acute Myeloid Leukemia (AML) since the mono‐allelic deletion of PI‐PLC beta1 is responsible in MDS patients for a higher risk of evolution to AML. Given that a single patient treated with azacitidine, a DNA methyltransferase inhibitor, displayed a direct correlation between PI‐PLCbeta1 gene expression and drug responsiveness, we hypothesized that PI‐PLCbeta1 could be a target for demethylating therapy. By quantifying the degree of PI‐PLCbeta1 methylation and gene expression in MDS patients at baseline and during azacitidine administration we found an increase of PI‐PLCbeta1 mRNA in responder patients and a reduction of promoter methylation. The molecular response correlated to and anticipated the clinical one, suggesting that PI‐PLCbeta1 gene reactivation predicts azacitidine responsiveness. Our results demonstrate for the first time that PI‐PLCbeta1 promoter is hypermethylated in high‐risk MDS patients and that the amount of PI‐PLCbeta1 mRNA predicts the clinical response to azacitidine.

Genetic and epigenetic silencing of the beclin 1 gene in sporadic breast tumors.

BackgroundBeclin 1, an important autophagy-related protein in human cells, is involved in cell death and cell survival. Beclin 1 mapped to human chromosome 17q21. It is widely expressed in normal mammary epithelial cells. Although down-regulated expression with mono-allelic deletions of beclin 1 gene was frequently observed in breast tumors, whether there was other regulatory mechanism of beclin 1 was to be investigated. We studied the expression of beclin 1 and explored the possible regulatory mechanisms on its expression in breast tumors.Methods20 pairs of tumors and adjacent normal tissues from patients with sporadic breast invasive ductal cancer (IDCs) were collected. The mRNA expression of beclin 1 was detected by real-time quantitative RT-PCR. Loss of heterozygosity (LOH) was determined by real-time quantitative PCR and microsatellite methods. The protein expression of beclin 1, p53, BRCA1 and BRCA2 was assessed by immunohistochemistry. CpG islands in 5' genomic region of beclin 1 gene were identified using MethylPrimer Program. Sodium bisulfite sequencing was used in examining the methylation status of each CpG island.ResultsDecreased beclin 1 mRNA expression was detected in 70% of the breast tumors, and the protein levels were co-related to the mRNA levels. Expression of beclin 1 mRNA was demonstrated to be much higher in the BRCA1 positive tumors than that in the BRCA1 negative ones. Loss of heterozygosity was detected in more than 45% of the breast tumors, and a dense cluster of CpG islands was found from the 5' end to the intron 2 of the beclin 1 gene. Methylation analysis showed that the promoter and the intron 2 of beclin 1 were aberrantly methylated in the tumors with decreased expression.ConclusionsThese data indicated that LOH and aberrant DNA methylation might be the possible reasons of the decreased expression of beclin 1 in the breast tumors. The findings here shed some new light on the regulatory mechanisms of beclin 1 in breast cancer.

Comprehensive Analysis of PTEN Allelic Status Confirms Gross Genomic Rearrangement as the Main Mechanism of PTEN Inactivation in Sporadic Breast Carcinomas.

Abstract BackgroundThe PTEN tumour suppressor gene is frequently inactivated in a wide range of cancers and encodes a nonredundant phosphatase which antagonizes the PI3K signalling pathway. Previous IHC analysis and genomic characterization (through BAC CGH array) of a series of 135 sporadic breast carcinomas identified some tumours with decreased or absent PTEN levels and/or loss at 10q23.3, including the PTEN locus. Comprehensive molecular genetic analysis of PTEN, in addition to PI3KCA and TP53 point mutation screening were performed on this large homogenous series of breast carcinomas, giving a molecular portrait of key players of sporadic breast carcinogenesis.Materials and methodsA series of 135 sporadic invasive ductal carcinomas resected between 1989 and 1992 at Institut Bergonie underwent PTEN molecular genetic screening through QMPSF to detect gross genomic rearrangements and the recently developed Enhanced Mismatch Mutation Analysis (EMMA) to detect point mutations and to confirm gross genomic rearrangements. Tumours with a suspected PTEN large deletion identified using these techniques, along with any additional tumours previously shown to have decreased or absent PTEN levels and/or loss at 10q23.3, were analyzed using Agilent 4x44K high density oligo CGH arrays. The TP53 status of all tumours was assessed through IHC and direct sequencing. In addition, molecular analysis of the recurrent point mutations of PI3KCA, the catalytic subunit of the PI3 kinase, was performed.ResultsGross PTEN gene rearrangements were detected in 48 tumours through QMPSF ; 19 biallelic large deletions, 21 monoallelic large deletions and 8 large duplications. Variant EMMA profiles indicating a PTEN point mutation have been identified in approximately 15% of tumours which are confirmed by direct sequencing. High density oligo CGH array performed on 54 tumours demonstrates 7 monoallelic large deletions and 9 biallelic large deletions to date (analysis to be completed). A total of 39 tumours were shown to have mutant TP53 on IHC and/or a TP53 mutation, which interestingly only includes 8/19 tumours with a biallelic PTEN large deletion. Finally, an overall assessment of the above gene status, including results of the PI3KCA point mutation screen will be presented.ConclusionThis study shows that the predominant mechanism of PTEN inactivation in sporadic breast carcinomas is through gross genomic rearrangements rather than deleterious point mutations, and that this is not restricted to BRCA1-mutated tumours. Furthermore, previous reports have suggested that biallelic inactivation of PTEN in tumours with wild-type TP53 would result in cell death and therefore not be advantageous for tumour growth. In this series, we did not observe a correlation between biallelic inactivation of PTEN and TP53 mutation status (p=0.31, chi-squared test). Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3151.