Analysis of chromosome 6q deletion in EBV-associated NK cell leukaemia/lymphoma

MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB

BACKGROUND

Deletions of 6q15-16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has a crucial role in innate immune signaling and was observed to be functionally and prognostically relevant in different cancer entities. Therefore, we correlated the presence of MAP3K7 deletions with clinical parameters in a cohort of 327 pediatric T-ALL patients and investigated the function of MAP3K7 in the T-ALL cell lines CCRF-CEM, Jurkat and MOLT-4.

METHODS

MAP3K7 deletions were detected by multiplex ligation-dependent probe amplification (MLPA). T-ALL cell lines were transduced with adeno-associated virus (AAV) vectors expressing anti-MAP3K7 shRNA or a non-silencing shRNA together with a GFP reporter. Transduction efficiency was measured by flow cytometry and depletion efficiency by RT-PCR and Western blots. Induction of apoptosis was measured by flow cytometry after staining with PE-conjugated Annexin V. In order to assess the contribution of NF-κB signaling to the effects of MAP3K7 depletion, cells were treated with TNF-α and cell lysates analyzed for components of the NF-κB pathway by Western blotting and for expression of the NF-κB target genes BCL2, CMYC, FAS, PTEN and TNF-α by RT-PCR.

RESULTS

MAP3K7 is deleted in approximately 10% and point-mutated in approximately 1% of children with T-ALL. In 32 of 33 leukemias the deletion of MAP3K7 also included the adjacent CASP8AP2 gene. MAP3K7 deletions were associated with the occurrence of SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and outcome. Depletion of MAP3K7 expression in T-ALL cell lines by shRNAs slowed down proliferation and induced apoptosis, but neither changed protein levels of components of NF-κB signaling nor NF-κB target gene expression after stimulation with TNF-α.

CONCLUSIONS

This study revealed that the recurrent deletion of MAP3K7/CASP8AP2 is associated with SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and risk of relapse. Homozygous deletions of MAP3K7 were not observed, and efficient depletion of MAP3K7 interfered with viability of T-ALL cells, indicating that a residual expression of MAP3K7 is indispensable for T-lymphoblasts.

Receptor-type tyrosine-protein phosphatase κ directly targets STAT3 activation for tumor suppression in nasal NK/T-cell lymphoma

Nasal-type natural killer/T-cell lymphoma (NKTCL) is an aggressive disease characterized by frequent deletions on 6q, and constitutive activation of signal transducer and activator of transcription 3 (STAT3). Phosphorylation at Tyr705 activates STAT3, inducing dimerization, nuclear translocation, and DNA binding. In this study, we investigated whether receptor-type tyrosine-protein phosphatase κ (PTPRK), the only protein tyrosine phosphatase at 6q that contains a STAT3-specifying motif, negatively regulates STAT3 activation in NKTCL. PTPRK was highly expressed in normal NK cells but was underexpressed in 4 of 5 (80%) NKTCL cell lines and 15 of 27 (55.6%) primary tumors. Significantly, PTPRK protein expression was inversely correlated with nuclear phospho-STAT3(Tyr705) expression in NKTCL cell lines (P = .025) and tumors (P = .040). PTPRK restoration decreased nuclear phospho-STAT3(Tyr705) levels, whereas knockdown of PTPRK increased such levels in NKTCL cells. Phosphatase substrate-trapping mutant assays demonstrated the binding of PTPRK to STAT3, and phosphatase assays showed that PTPRK directly dephosphorylated phospho-STAT3(Tyr705). Restoration of PTPRK inhibited tumor cell growth and reduced the migration and invasion ability of NKTCL cells. Monoallelic deletion and promoter hypermethylation caused underexpression of PTPRK messenger RNA in NKTCL, and methylation of the PTPRK promoter significantly correlated with inferior overall survival (P = .049) in NKTCL patients treated with the steroid-dexamethasone, methotrexate, ifosfamide, l-asparaginase, and etoposide regimen. Altogether, our findings show that PTPRK underexpression leads to STAT3 activation and contributes to NKTCL pathogenesis.

State of the art in natural killer cell malignancies

The recently updated World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues, published in 2008, has made great advances in revising the disorders previously included in the pool of natural killer (NK) cell tumors. Although NK cell neoplasms represent a relatively rare group of diseases, accounting for <5% of all lymphoid neoplasms, they include very distinctive conditions both clinically and pathologically. This family of diseases includes the most indolent clinical forms, such as the provisional new entry of chronic lymphoproliferative disorder of NK cells (CLPD-NK) in the WHO classification, as well as one of the most fatal diseases recognized in medical oncology, aggressive NK cell leukemia (ANKL), which is characterized by a prognosis of weeks, or even days. In addition, some disorders previously identified as blastic NK cell lymphoma within the NK cell system have been more properly defined and included in the blastic plasmacytoid dentritic cell neoplasms, although rare cases of bona fide immature NK lymphoid tumors (now classified as NK cell lymphoblastic leukemia/lymphoma) have been reported in the literature. This paper focuses on recent concepts and progress in morphology, pathogenesis, clinicopathological features, treatment approaches, and outcomes of NK cell malignancies.

Deletion Mapping of the Long Arm of Chromosome 6 in Peripheral T and NK Cell Lymphomas

Deletion of chromosome 6q has frequently been observed in natural killer (NK) cell lymphomas. The aim of this study, is to localize the commonly affected region in chromosome 6q and to compare the frequency of loss of heterozygosity (LOH) between the peripheral T and NK cell lymphomas. Eight cases of peripheral T cell lymphomas, not otherwise characterized (PTCL-NOC), and 5 cases of nasal-type NK/T cell lymphomas were enrolled for the study. Twelve polymorphic markers covering the regions from 6q13 to 6q24, according to the Entrez Database (National Center for Biotechnology Information, NIH, Bethesta, MD), were used for LOH analysis. Results showed LOH at least one locus on chromosome 6q was observed in all cases. Of the informative cases, the overall frequency of LOH for each marker ranged from 8.3 to 58.3%. NK/T cell lymphomas showed a higher frequency of LOH compared to the PTCL (47.44 +/- 12.39 vs. 30.89 +/- 11.97%). The average frequency of LOH was 31.93 +/- 16.04% in stages I + II of the disease, whereas the average was 45.78 +/- 4.15% in stages III + IV. The most frequently involved regions were at markers D6S434 (5 of 8 informative cases, 62.5%) on chromosome 6q16.3 in the PTCL, D6S302 (4 of 5 cases, 80%) on chromosome 6q21 and D6S287 on 6q22.3 (4 of 5 cases, 80%) in the NK/T cell lymphoma. In conclusion, LOH of chromosome 6q is more common in nasal-type NK/T cell lymphoma than PTCL. The difference between the commonly lost region of chromosome 6q in NK/T cell lymphoma and that in PTCL suggests that different tumor suppressor genes are involved in the genetic evolution pathway of these two diseases.

Distribution and Prognosis of WHO Lymphoma Subtypes in Taiwan Reveals a Low Incidence of Germinal-Center Derived Tumors

To assess the distribution of lymphomas in Taiwan according to the WHO (World Health Organization) classification, 175 recently diagnosed cases of malignant lymphomas were studied and the clinicopathologic data were analyzed. B-cell lymphomas accounted for 57.1% of cases, T-cell lymphomas 38.9%, and Hodgkin's lymphoma 4%. Extranodal lymphomas predominated (55.4%). The most common subtype of B-cell lymphoma was diffuse large B-cell lymphoma (33.1%). All tumor types believed to be derived from germinal center (GC) B-cells including follicular lymphoma (4.6%), Burkitt lymphoma (1.7%), Hodgkin lymphoma (4.0%), and GC-like diffuse large B-cell lymphoma (as defined by combined expression of bc1-6 and CD10) were rather uncommon as compared to frequencies seen in series from Western countries. The common T-cell lymphomas included nasal and extranasal NK/T cell lymphoma (7.4%), mycosis fungoides (7.4%), and unspecified peripheral T-cell lymphoma (6.9%). Adult T-cell leukemia/lymphoma was very uncommon and accounts for only 0.6%. The proportional increase in T-cell lymphomas that were unrelated to type I human T-cell lymphotropic virus (HTLV-1) may be linked to differential Epstein-Barr virus (EBV) oncogenesis. The survival data revealed that mantle cell lymphoma, NK/T-cell lymphoma, unspecified peripheral T-cell lymphoma, and subcutaneous panniculitis-like T-cell lymphoma had an aggressive course. Our results confirm the utility of the WHO classification scheme for prognostic stratification and further highlight the distinctive distribution pattern of malignant lymphoma in Taiwan including the higher relative incidence of T cell lymphomas and the rarity of germinal center-derived B-cell tumors.

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Natural killer (NK)-cell malignancies are among the most aggressive lymphoid neoplasms with very poor prognosis. We performed array comparative genomic hybridization analysis on a number of NK cell lines and primary tumors to gain better understanding of the pathogenesis and tumor biology of these malignancies. We also obtained transcriptional profiles of genes residing in these regions and compared them with normal and activated NK cells. Only 30-50% of the genes residing in the gained or deleted regions showed corresponding increased or decreased expression. However, many of the upregulated genes in regions of gain are functionally important for the proliferation and growth of the neoplastic population. Genes downregulated in regions of loss included many transcription factors or repressors, tumor suppressors or negative regulators of the cell cycle. The minimal common region of deletion in 6q21 included three known genes (PRDM1, ATG5 and AIM1) showing generally low expression. Mutations resulting in truncated PRDM1 and changes in conserved amino-acid sequences of AIM1 were detected. Highly methylated CpG islands 5' of PRDM1 and AIM1 correlated with low expression of the transcripts. Reversal of methylation by Decitabine induced expression of PRDM1 and cell death. In conclusion, we have shown a general tumor-promoting effect of genetic alterations and have identified PRDM1 as the most likely target gene in del6q21. ATG5, an essential gene for autophagy and AIM1, a gene implicated in melanoma, may also participate in the functional abnormalities.

Progress in understanding and managing natural killer-cell malignancies

The World Health Organization classification of haematolymphoid tumours recognizes three categories of natural killer (NK)-cell neoplasms: blastic NK-cell lymphoma, aggressive NK-cell leukaemia, and extranodal NK/T-cell lymphoma, nasal-type. Recent studies indicate that CD4+CD56+ blastic NK-cell lymphoma is of plasmacytoid dendritic cell origin, and true tumours of precursor NK-cell origin may be present mainly in the CD4-CD56+ subset. Myeloid/NK-cell precursor acute leukaemia may also develop from precursor NK cells. However, because the developmental pathway of normal NK cells is not well understood, tumours of precursor NK-cell origin are not clearly identified. Among mature NK-cell tumours, extranodal NK/T-cell lymphoma is relatively common in Asia and Latin America. In localized disease, chemoradiotherapy seems to be promising, and in advanced disease, new combination chemotherapies are under active investigation. Aggressive NK-cell leukaemia is rare and has a poor prognosis. Because NK-cell neoplasms are rare and difficult to manage, rigorous studies are required for their understanding and management.

Extranodal NK/T-cell lymphoma, nasal type

Extranodal NK/T-cell lymphoma, nasal type (ENKTCL), previously known as lethal midline granuloma is a distinct clinico-pathological entity associated with Epstein-Barr virus that typically causes destruction of the midface, palatal and orbital walls. In addition, ENKTCL can involve the skin, soft tissue, testes, gastrointestinal and upper respiratory tract. ENKTCL neoplastic cells express some T-cell associated antigens, most commonly CD2 and cytoplasmic CD3epsilon and, in favour of an NK-cell origin, CD56. Early stage disease may respond to radiotherapy alone, however late stage disease does not respond well to any available therapies. Overall, patients with ENKTCL have a cumulative probability of survival at 5 years ranging from 37.9% to 45.3%.

Genome-wide array-based comparative genomic hybridization of natural killer cell lymphoma/leukemia: different genomic alteration patterns of aggressive NK-cell leukemia and extranodal Nk/T-cell lymphoma, nasal type

Natural killer (NK) cell lymphomas/leukemias are highly aggressive lymphoid malignancies, but little is known about their genomic alterations, and thus there is an urgent need for identification and analysis of NK cell lymphomas/leukemias. Recently, we developed our own array-based comparative genomic hybridization (array CGH) with an average resolution of 1.3 Mb. We performed an array CGH analysis for 27 NK-cell lymphoma/leukemia cases that were classified into two disease groups based on the World Health Organization Classification (10 aggressive NK-cell leukemia cases and 17 extranodal NK/T-cell [NK/T] lymphomas, nasal type). We identified the differences in the genomic alteration patterns of the two groups. The recurrent regions characteristic of the aggressive NK-cell leukemia group compared with those of the extranodal NK/T lymphoma, nasal-type group, were gain of 1q and loss of 7p15.1-p22.3 and 17p13.1. In particular, gain of 1q23.1-24.2 (P = 0.041) and 1q31.3-q44 (P = 0.003-0.047), and loss of 7p15.1-p22.3 (P = 0.012-0.041) and 17p13.1 (P = 0.012) occurred significantly more frequently in the former than in the latter group. Recurrent regions characteristic of the extranodal NK/T lymphoma, nasal-type group, compared with those of the other group were gain of 2q, and loss of 6q16.1-q27, 11q22.3-q23.3, 5p14.1-p14.3, 5q34-q35.3, 1p36.23-p36.33, 2p16.1-p16.3, 4q12, and 4q31.3-q32.1. Our results can be expected to provide further insights into the genetic basis of lymphomagenesis and the clinicopathologic features of NK-cell lymphomas/leukemias.

Polymorphism in the manganese superoxide dismutase (MnSOD) gene and risk of breast cancer in young women

PURPOSE

Manganese superoxide dismutase (MnSOD) is one of the major enzymes implicated in the cellular defence against reactive oxygen species. Low expression of MnSOD has been observed in different cancer tissues and several reports have shown that overexpression of MnSOD inhibits growth in various human cancer cells. These observations suggest that MnSOD is involved in carcinogenesis. A polymorphism (Ala-9Val) in the mitochondrial targeting sequence (MTS) of the MnSOD gene has been proposed to affect protein localization and thereby influence cellular defence against superoxide radicals.

METHODS

In the present case-control study, including 118 early onset breast cancer patients (<or=36 years) and 174 age-matched controls, the MTS polymorphism and loss of heterozygosity (LOH) in the locus of MnSOD were analysed.

RESULTS

We found that individuals with MnSOD(Val/Val) and MnSOD(Val/Ala) genotypes showed an increased risk of breast cancer (OR, 2.7; 95% CI, 2.2-5.5, p=0.01, OR, 3.0; 95%CI, 1.4-6.5, p=0.002). Moreover, 45% of the informative cases expressed allelic loss at the chromosomal locus of the MnSOD gene. No correlation was found between LOH and the genotype.

CONCLUSION

The present study suggests that MnSOD may be implicated in breast carcinogenesis in young women.

Development of a dual-color fluorescence in situ hybridization probe set on chromosome 6q to improve cytogenetic diagnosis of lymphoid malignancies

Deletions in the long arm of chromosome 6 are one of the most commonly observed chromosome aberrations in lymphoid malignancies and have been identified as an adverse prognostic factor in subsets of leukemia and lymphoma. Although large deletions can readily be detected with conventional banding methods, subtle rearrangements represent a major diagnostic challenge. To identify and follow up 6q abnormalities that are difficult to detect with conventional banding analysis, we have developed a dual-color fluorescence in situ hybridization probe set on 6q21 and 6q27. We have also demonstrated its potential for clinical applications. While applying this new probe set to clinical cytogenetic studies, we identified a unique t(6;14) translocation in a patient with acute lymphoid leukemia. Because the translocation breakpoint on chromosome 6 is located within a common deletion region in patients with lymphoid malignancies, the determination of this translocation breakpoint will facilitate the identification of a candidate tumor suppressor gene in 6q.

Putative gene loci associated with carcinogenesis and metastasis of endocervical adenocarcinomas of uterus determined by conventional and array-based CGH

OBJECTIVES

This study aimed to estimate the gene loci associated with carcinogenesis of endocervical adenocarcinoma of uterus (EA) and metastasis. Study design Sixteen patients with EA were studied; 6 had nodal metastasis. DNA was extracted from EAs, and subjected to both conventional comparative genomic hybridization (CGH) and array-based CGH. Copy number abnormalities were compared between cases with and without nodal metastasis.

RESULTS

In all EAs, high frequencies of copy number losses were detected in genes LRP1B (on 2q21.2), DAB2 (5p13), and DCC (18q21.3), as well as regions 3p, 16q, and 22q, and copy number amplifications in genes NRAS (1p13.2), TOP2A (17q21-q22), NCOA3(AIB1) (20q12), and ARSA (22q tel). Nodal metastasis was associated with high frequencies of copy number loss in genes PGRMC2 and LAMA3 and amplification in CDK6 and NCOA3(AIB1).

CONCLUSION

This is the first report of gene copy number alterations spanning the whole genome in EA. These altered genes are speculated to be associated with EAs as a tumor suppressor and/or oncogene.

Allelotyping of gastrointestinal nasal-type NK/T-cell lymphoma

Nasal-type natural killer/T-cell lymphoma (NKL) is a rare but distinct malignancy that often involves the mid-facial region and the gastrointestinal tract. This study is the first genome-wide allelotyping analysis on this rare lymphoma. We applied 382 microsatellite markers covering loci which spanned 22 autosomes to screen for allelic imbalances (AI) in six intestinal NKL. The most common chromosomal regions of allelic imbalances were found in 11p, 9q and 13q. Novel spots of allelic losses spots found at 2p21, 2q37.22, 18p11.21 and 18q12.1. In spite of presence of a few recurrent loci of imbalances, the allelotyping results show that NKL is heterogeneous.

Allelic Imbalance Mapped to 6q14.1 Is Associated With Loss of Expression of 5-HT Receptor 1B in Non-Hodgkin Lymphomas

Previous studies on lymphomas suggested that the long arm of chromosome 6 harbors 1 or more tumor suppressor genes. This study analyzed the status of 25 microsatellite markers in 39 cases, including 9 nodal and 30 extranodal, of non-Hodgkin lymphomas. Thirty of the 39 cases (77%) showed abnormality in at least 1 of the markers. Of the 655 informative results, 135 (20%) were abnormal. These included 5 homozygous deletions, 91 allelic imbalances (AI), and 38 microsatellite instability. The 2 commonest regions of abnormality were mapped to 6q14.1 and 6q27. There was no significant difference in the frequency of these regional losses between nodal and extranodal lymphomas, B-or T-cell lineage, and association with Epstein-Barr virus. The first common deletion region at 6q14.1 is flanked by the HTR1B (5-hydroxytryptamine receptor 1B) gene proximally and a novel unknown gene. AI in the region was found associated with loss of expression HTR1B by RT-PCR. The deletion region at 6q27 was narrowed to approximately 3Mb and maximal at marker D6S386. This locus includes the recently identified SMOC2 (secreted modular calcium-binding protein 2), AF6, and DLL1 (human delta-like 1 protein) genes. RT-PCR analyses of AF6 and DLL1 expression showed poor correlation with the AI results.

Diagnosis and treatment of Epstein-Barr virus-associated natural killer cell lymphoproliferative disease

Epstein-Barr virus (EBV) exhibits tropism for both lymphocytes and epithelial cells and can induce both replicative (productive/lytic) and latent (persistent) infections that result in a variety of human diseases. With regard to lymphocytes, latent EBV infection is linked to development of heterogeneous lymphoproliferative disease (LPD), such as B-cell LPD and T-cell/natural killer cell (T/NK cell) LPD. Unlike B-cell LPD, LPD derived from T-cells and NK cells sometimes has overlapping clinical symptoms, as well as histologic and immunophenotypic features, because both types of cells are derived from a common precursor. However, determination of cell lineage is important in classification of lymphoid neoplasms, and combined modern techniques allows us to distinguish NK cell LPD from T-cell LPD in most instances. Because NK cell LPD seems to be heterogeneous in terms of clinical features, prognosis, and diagnosis and has a monoclonal or polyclonal (or oligoclonal) nature, this review attempts to clarify recent research and clinical findings and to establish diagnostic and therapeutic strategies.