Secondary chromosome changes in mantle cell lymphoma: cytogenetic and fluorescence in situ hybridization studies

Repression of TRIM13 by chromatin assembly factor CHAF1B is critical for AML development

Acute myeloid leukemia (AML) is an aggressive blood cancer that stems from the rapid expansion of immature leukemic blasts in the bone marrow. Mutations in epigenetic factors represent the largest category of genetic drivers of AML. The chromatin assembly factor CHAF1B is a master epigenetic regulator of transcription associated with self-renewal and the undifferentiated state of AML blasts. Upregulation of CHAF1B, as observed in almost all AML samples, promotes leukemic progression by repressing the transcription of differentiation factors and tumor suppressors. However, the specific factors regulated by CHAF1B and their contributions to leukemogenesis are unstudied. We analyzed RNA sequencing data from mouse MLL-AF9 leukemic cells and bone marrow aspirates, representing a diverse collection of pediatric AML samples and identified the E3 ubiquitin ligase TRIM13 as a target of CHAF1B-mediated transcriptional repression associated with leukemogenesis. We found that CHAF1B binds the promoter of TRIM13, resulting in its transcriptional repression. In turn, TRIM13 suppresses self-renewal of leukemic cells by promoting pernicious entry into the cell cycle through its nuclear localization and catalytic ubiquitination of cell cycle-promoting protein, CCNA1. Overexpression of TRIM13 initially prompted a proliferative burst in AML cells, which was followed by exhaustion, whereas loss of total TRIM13 or deletion of its catalytic domain enhanced leukemogenesis in AML cell lines and patient-derived xenografts. These data suggest that CHAF1B promotes leukemic development, in part, by repressing TRIM13 expression and that this relationship is necessary for leukemic progression.

Non-Nodal CD5-Negative Mantle Cell Lymphoma with Secondary TP53 Deletion

Mantle cell lymphoma is a non-Hodgkin lymphoproliferative neoplasm with several clinical and morphologic variants linked, primarily, through genetic derangement of the cyclin D1 locus. Aberrant phenotypes have been described, though prognostic data in such cohorts are limited due to a paucity of cases. We report a case of mantle cell lymphoma with non-nodal clinical presentation, aberrant loss of CD5 expression, and concomitant cytogenetic deletion of 17p. While non-nodal disease is often associated with an improved prognosis in mantle cell lymphoma, this 67-year-old patient experienced a more challenging clinical course with a poor initial response to chemotherapy. Therefore, this case may represent a type of non-nodal mantle cell lymphoma with a prognosis similar to that of classical cases due to the additional phenotypic and genetic alterations found in this patient.

Long non-coding RNAs in normal and malignant hematopoiesis

Long non-coding RNAs (lncRNAs) are defined as ncRNAs of more than 200 nt in length. They are involved in a large spectrum of biological processes, such as maintenance of genome integrity, genomic imprinting, cell differentiation, and development by means of mechanisms that remain to be fully elucidated. Besides their role in normal cellular physiology, accumulating evidence has linked lncRNA expression and functions to cancer development and progression. In this review, we summarize and discuss what is known about their expression and roles in hematopoiesis with a particular focus on their cell-type specificity, functional interactions, and involvement in the pathobiology of hematological malignancies.

Genomic profiling of mantle cell lymphoma

Genomic profiling of mantle cell lymphoma (MCL) cells has enabled a better understanding of the complex mechanisms underlying the pathogenesis of disease. Besides the t(11;14)(q13;q32) leading to cyclin D1 overexpression, MCL exhibits a characteristic pattern of DNA copy number aberrations that differs from those detected in other B-cell lymphomas. These genomic changes disrupt selected oncogenes and suppressor genes that are required for lymphoma development and progression, many of which are components of cell cycle, DNA damage response and repair, apoptosis, and cell-signaling pathways. Additionally, some of them may represent effective therapeutic targets. A number of genomic and molecular abnormalities have been correlated with the clinical outcome of patients with MCL and are considered prognostic factors. However, only a few genomic markers have been shown to predict the response to current or novel targeted therapies. One representative example is the high-level amplification of the BCL2 gene, which predicts a good response to pro-apoptotic BH3 mimetic drugs. In summary, genomic analyses have contributed to the substantial advances made in the comprehension of the pathogenesis of MCL, providing a solid basis for the identification of optimal therapeutic targets and for the design of new molecular therapies aiming to cure this fatal disease.

Case report: blastic Mantle Cell Leukemia

The patient, who was being followed up for Mantle Cell Lymphoma, was diagnosed with Mast Cell Leukemia 2 years after receiving R-CHOP treatment. The results of flow cytometry, which was performed upon determining leucocytosis and detecting blasts in the peripheral smear following the patient's presentation due to his poor general condition, was consistent with Mantle Cell Leukemia. This case is being presented since there are a very limited number of previously published cases on this topic.

The basis and rational use of molecular genetic testing in mature B-cell lymphomas

An increasing number of neoplasms are associated with variably specific genetic abnormalities. This is best exemplified by hematological malignancies, in which there is a growing list of entities that are defined by their genetic lesion(s); this is not (yet) the case in mature B-cell lymphomas. However, enhanced insights into the pathogenesis of this large and diverse group of lymphomas have emerged with the ongoing unraveling of a plethora of fascinating genetic abnormalities. The purpose of this review is to synthesize well-recognized data and nascent discoveries in our understanding of the genetic basis of a spectrum of mature B-cell lymphomas, and how this may be applied to contemporary clinical practice. Despite the explosion of new and exciting knowledge in this arena, with the potential for enhanced diagnostic and prognostic strategies, it is essential to remain cognizant of the limitations (and complexity) of genetic investigations, so that assays can be developed and used both judiciously and rationally.

DLEU2, frequently deleted in malignancy, functions as a critical host gene of the cell cycle inhibitory microRNAs miR-15a and miR-16-1

The microRNAs miR-15a and miR-16-1 are downregulated in multiple tumor types and are frequently deleted in chronic lymphocytic leukemia (CLL), myeloma and mantle cell lymphoma. Despite their abundance in most cells the transcriptional regulation of miR-15a/16-1 remains unclear. Here we demonstrate that the putative tumor suppressor DLEU2 acts as a host gene of these microRNAs. Mature miR-15a/miR-16-1 are produced in a Drosha-dependent process from DLEU2 and binding of the Myc oncoprotein to two alterative DLEU2 promoters represses both the host gene transcript and levels of mature miR-15a/miR-16-1. In line with a functional role for DLEU2 in the expression of the microRNAs, the miR-15a/miR-16-1 locus is retained in four CLL cases that delete both promoters of this gene and expression analysis indicates that this leads to functional loss of mature miR-15a/16-1. We additionally show that DLEU2 negatively regulates the G1 Cyclins E1 and D1 through miR-15a/miR-16-1 and provide evidence that these oncoproteins are subject to miR-15a/miR-16-1-mediated repression under normal conditions. We also demonstrate that DLEU2 overexpression blocks cellular proliferation and inhibits the colony-forming ability of tumor cell lines in a miR-15a/miR-16-1-dependent way. Together the data illuminate how inactivation of DLEU2 promotes cell proliferation and tumor progression through functional loss of miR-15a/miR-16-1.

Characterization of genetic changes in MCL by interphase FISH on tissue sections

Mantle cell lymphoma is a clinically heterogeneous disease, where further elucidation of pathogenetic mechanisms and better prognostic information is required. We evaluated genetic aberrations by interphase FISH on tissue sections or cytological material in 38 samples from 30 MCL patients, including 5 cases with cyclin D1 3'UTR low, which previously has been associated to unfavourable prognosis. The findings have been related to proliferation and clinical outcome. All but one of MCL showed t(11:14) translocation and in 22/30 samples taken at diagnosis or first relapse, one or several cytogenetic changes were detected; 11 deletions of ATM, 13 p53 deletions, 8 numerical c-myc-aberrations and 6 delp16. All but one MCL with low cyclin D1 3'UTR had additional cytogenetic changes, however no particular genetic change was strictly associated with this MCL variant. One fourth of MCL had none of the investigated additional aberrations and these tumours were in general less proliferative and some of these patients had a very long survival.

Cytogenetic abnormalities additional to t(11;14) correlate with clinical features in leukaemic presentation of mantle cell lymphoma, and may influence prognosis: a study of 60 cases by FISH

Mantle cell lymphoma (MCL), characterised by t(11;14)(q13;q32), has a poor prognosis. Many cases have additional cytogenetic abnormalities, and often have a complex karyotype. Fluorescence in situ hybridisation (FISH) was used to study 60 cases with leukaemic presentation of MCL, to determine the frequency, clinical correlations and prognostic impact of a panel of molecular cytogenetic abnormalities: 17p13 (TP53 locus), 13q14, 12 p11.1-q11 (centromere), 6q21 and 11q23. CD38 expression, of prognostic value in chronic lymphocytic leukaemia (CLL), was also studied, and correlations with clinical and cytogenetic abnormalities sought. Eighty per cent of cases had at least one abnormality in addition to t(11;14). Deletions at 17p13 (TP53) and 13q14 were most frequent and involved the majority of the leukaemic clone. Cases with TP53 deletion were more likely to have splenomegaly and marked leucocytosis (>30 x 10(9)/l), and less likely to have lymphadenopathy than those without deletion. Deletions at 11q23 and 6q21 were associated with extranodal disease. 13q14 and 11q23 deletions showed a trend towards worse prognosis by univariate analysis. In multivariate analysis, deletions at 13q14 and 6q21 were independent predictors of poor outcome. Deletion at 17p13 did not show prognostic impact in this series. CD38, positive in two-thirds of cases, was associated with male gender and nodal disease but not with any cytogenetic abnormality, or with survival.

The RBCC gene RFP2 (Leu5) encodes a novel transmembrane E3 ubiquitin ligase involved in ERAD

RFP2, a gene frequently lost in various malignancies, encodes a protein with RING finger, B-box, and coiled-coil domains that belongs to the RBCC/TRIM family of proteins. Here we demonstrate that Rfp2 is an unstable protein with auto-polyubiquitination activity in vivo and in vitro, implying that Rfp2 acts as a RING E3 ubiquitin ligase. Consequently, Rfp2 ubiquitin ligase activity is dependent on an intact RING domain, as RING deficient mutants fail to drive polyubiquitination in vitro and are stabilized in vivo. Immunopurification and tandem mass spectrometry enabled the identification of several putative Rfp2 interacting proteins localized to the endoplasmic reticulum (ER), including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). Importantly, we also show that Rfp2 regulates the degradation of the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein), establishing Rfp2 as a novel E3 ligase involved in ERAD. Finally, we show that Rfp2 contains a C-terminal transmembrane domain indispensable for its localization to the ER and that Rfp2 colocalizes with several ER-resident proteins as analyzed by high-resolution immunostaining. In summary, these data are all consistent with a function for Rfp2 as an ERAD E3 ubiquitin ligase.

Heterogeneous Abnormalities of CCND1 and RB1 in Primary Cutaneous T-Cell Lymphomas Suggesting Impaired Cell Cycle Control in Disease Pathogenesis

Upregulation of cyclin D1/B-cell leukemia/lymphoma 1 (CCND1/BCL1) is present in most mantle cell lymphomas with the t(11;14)(q13;q32) translocation. However, little is known about the abnormalities of CCND1 and its regulator RB1 in primary cutaneous T-cell lymphomas (CTCL). We analyzed CCND and RB status in CTCL using fluorescent in situ hybridization (FISH), immunohistochemistry (IHC), and Affymetrix expression microarray. FISH revealed loss of CCND1/BCL1 in five of nine Sézary syndrome (SS) cases but gain in two cases, and RB1 loss in four of seven SS cases. IHC showed absent CCND1/BCL1 expression in 18 of 30 SS, 10 of 23 mycosis fungoides (MF), and three of 10 primary cutaneous CD30+ anaplastic large-cell lymphoma (C-ALCL). Increased CCND1/BCL1 expression was seen in nine MF, seven C-ALCL, and six SS cases. Absent RB1 expression was detected in 8 of 12 MF and 7 of 9 SS cases, and raised RB1 expression in 7 of 8 C-ALCL. Affymetrix revealed increased gene expression of CCND2 in four of eight CTCL cases, CCND3 in three cases, and CDKN2C in two cases with a normal expression of CCND1 and RB1. These findings suggest heterogeneous abnormalities of CCND and RB in CTCL, in which dysregulated CCND and RB1 may lead to impaired cell cycle control.

Genome-wide array-based CGH for mantle cell lymphoma: identification of homozygous deletions of the proapoptotic gene BIM

Mantle cell lymphoma (MCL) is characterized by 11q13 chromosomal translocation and CCND1 overexpression, but additional genomic changes are also important for lymphomagenesis. To identify the genomic aberrations of MCL at higher resolutions, we analysed 29 patient samples and seven cell lines using array-based comparative genomic hybridization (array CGH) consisting of 2348 artificial chromosome clones, which cover the whole genome at a 1.3 mega base resolution. The incidence of identified genomic aberrations was generally higher than that determined with chromosomal CGH. The most frequent imbalances detected by array CGH were gains of chromosomes 3q26 (48%), 7p21 (34%), 6p25 (24%), 8q24 (24%), 10p12 (21%) and 17q23 (17%), and losses of chromosomes 2p11 (83%), 11q22 (59%), 13q21 (55%), 1p21-p22 (52%), 13q34 (52%), 9q22 (45%), 17p13 (45%), 9p21 (41%), 9p24 (41%), 6q23-q24 (38%), 1p36 (31%), 8p23 (34%), 10p14 (31%), 19p13 (28%), 5q21 (21%), 22q12 (21%), 1q42 (17%) and 2q13 (17%). Our analyses also detected several novel recurrent regions of loss located at 1p36, 1q42.2-q43, 2p11.2, 2q13, 17p13.3 and 19p13.2-p13.3, as well as recurrent regions of homozygous loss such as 2p11 (Ig(kappa)), 2q13 and 9p21.3-p24.1 (INK4a/ARF). Of the latter, we investigated the 2q13 loss, which led to identification of homozygous deletions of the proapoptotic gene BIM. The high-resolution array CGH technology allowed for the precise identification of genomic aberrations and identification of BIM as a novel candidate tumor suppressor gene in MCL.

DLEU2 encodes an antisense RNA for the putative bicistronic RFP2/LEU5 gene in humans and mouse

Our group previously identified two novel genes, RFP2/LEU5 and DLEU2, within a 13q14.3 genomic region of loss seen in various malignancies. However, no specific inactivating mutations were found in these or other genes in the vicinity of the deletion, suggesting that a nonclassical tumor-suppressor mechanism may be involved. Here, we present data showing that the DLEU2 gene encodes a putative noncoding antisense RNA, with one exon directly overlapping the first exon of the RFP2/LEU5 gene in the opposite orientation. In addition, the RFP2/LEU5 transcript can be alternatively spliced to produce either several monocistronic transcripts or a putative bicistronic transcript encoding two separate open-reading frames, adding to the complexity of the locus. The finding that these gene structures are conserved in the mouse, including the putative bicistronic RFP2/LEU5 transcript as well as the antisense relationship with DLEU2, further underlines the significance of this unusual organization and suggests a biological function for DLEU2 in the regulation of RFP2/LEU5.

Blastic mantle cell lymphoma developing concurrently in a patient with chronic myelogenous leukemia and a review of the literature

Non-Hodgkin's lymphoma (NHL) occurring as a synchronous malignancy with chronic myelogenous leukemia (CML) is rare. To our knowledge, this is the first case reported of a patient who developed mantle cell lymphoma (MCL) after therapy with imatinib mesylate for CML. After a 3-year history of CML, the patient developed a lymphocytosis associated with diarrhea, anorexia, and weight loss. Imaging studies revealed abdominal adenopathy and extensive lymphomatous infiltration of the liver, stomach, pancreas, and kidneys. Flow cytometric and cytogenetic studies were consistent with MCL. Fluorescence in situ hybridization (FISH) of the bone marrow revealed a genetically distinct lymphoid neoplasm rather than an extramedullary blast crisis of CML. The development of lung cancer, prostate cancer, CML and MCL in this patient suggests a genetic predisposition, although other factors, including environmental exposures and therapy with imatinib mesylate could have had a contributory or synergistic role in the development of MCL.

Characterization of a novel B-CLL candidate gene--DLEU7--located in the 13q14 tumor suppressor locus

Deletion of chromosome 13q14 is the most frequent genetic aberration in B-cell chronic lymphocytic leukemia (CLL), found in more than 50% of cases, indicating that this region contains a gene(s) involved in the development of CLL. However, the pathogenic gene in the critical 13q14 region has not yet been defined. Here, we have cloned and characterized a novel gene, DLEU7, located adjacent to the consensus deleted region, and overlapping the 3' end of DLEU1 tail to tail. Human DLEU7 encodes a putative 221 amino acid protein, with significant conservation in rodents. Mutational and expression analysis in primary CLL samples failed to demonstrate any specific mutations in DLEU7, but no DLEU7 expression could be detected in CLL cells. Methylation of a CpG island in the promoter region of DLEU7 was further analyzed as a possible mechanism for the absence of DLEU7 expression, and the promoter was found to be methylated in the majority of the CLL samples investigated.

A subset of t(11;14) lymphoma with mantle cell features displays mutated IgVH genes and includes patients with good prognosis, nonnodal disease

We analyzed lymphocyte morphology, histology, immunophenotype, immunoglobulin heavy chain (IgVH) gene mutations, and clinical course in 80 unselected patients presenting with circulating t(11;14) lymphocytes. Of the 80 patients, 43 had peripheral lymphadenopathy (nodal group), and histology confirmed mantle cell lymphoma (MCL) in all. There were 37 patients with no lymphadenopathy (nonnodal group); 13 of 37 had histology, all showing MCL. IgVH genes were unmutated in 28 (90%) of 31 nodal and 15 (44%) of 34 nonnodal cases (P =.0001); CD38 was positive in 32 (94%) of 34 nodal and 16 (48%) of 33 nonnodal cases (P <.001); 41 (95%) of 43 nodal patients required immediate treatment compared with 18 (49%) of 37 nonnodal patients who had indolent disease (P <.0001). Median survival (95% confidence interval) was 30 months (10-50) in the nodal group and 79 months (22-136) in the nonnodal group (P =.005). Mutation status did not statistically affect survival, but of 6 long-term survivors (> 90 months) all were nonnodal and 5 of 5 had mutated IgVH genes. Lymphocyte morphology was heterogeneous in both groups: typical MCL in 56 cases (34 nodal, 22 nonnodal), blastoid MCL in 8 cases (3 nodal, 5 nonnodal), and small-cell MCL in 16 cases (6 nodal, 10 nonnodal, P =.12). Matutes immunophenotyping score was 1 in 65 cases and 2 in 15 (8 nodal, 7 nonnodal). We find no evidence against a diagnosis of MCL in the nonnodal group and suggest that mutated IgVH genes may help identify patients with indolent disease.

Mantle cell lymphoma: improved diagnostics using a combined approach of immunohistochemistry and identification of t(11;14)(q13;q32) by polymerase chain reaction and fluorescence in situ hybridization

INTRODUCTION

Mantle cell lymphoma (MCL) is a clinicopathological entity characterized by an aggressive clinical course, morphological features, and overexpression of cyclin D1 due to juxtaposition of the bcl-1 locus (and CCND1 gene coding for the cyclin D1) to the IgH gene. This phenomenon is caused by t(11;14)(q13;q32). The morphological diagnosis of MCL may pose difficulties. Ancillary methods are available to support the diagnosis.

PATIENTS AND METHODS

We studied a group of 32 patients with MCL; 24 men and 8 women. The median age at the diagnosis was 64 years. We characterized the investigated group by histology, and to analyze the immunohistochemical (IHC) profile we used a panel of antibodies including anti-cyclin D1. Polymerase chain reaction (PCR) was used to detect the rearrangement of bcl-1/IgH in 26 cases (in 11 patients, the DNA was isolated from frozen tissues or from nucleated cells of bone-marrow aspirate or peripheral blood, in 15 patients we utilized paraffin-embedded material). Dual color fluorescence in situ hybridization (FISH) on interphase nuclei detecting the t(11;14)(q13;q32) was applied in all 32 cases.

RESULTS

Cyclin D1 IHC was positive in 29 of 30 cases tested (97%). In six, the result was weak and difficult to rely on to support the diagnosis. PCR revealed the fusion gene in 14 of the 26 cases (54%). The best yield was obtained from fresh and frozen samples (8 of 11 positive). Using FISH, we identified the translocation in all 32 patients, the findings being easily interpretable in 29 patients. In three cases, the intensity of red and green signals was weaker and difficult to read though the co-hybridized signals were identified. The classical pattern of the translocation was observed in 26 patients, while in 3 we found variant patterns suggesting a loss of the V segment of the IgH gene (2x) and a shift in the breakpoint region at chromosome 11 (1x).

CONCLUSION

The diagnosis of MCL should be supported by a complex laboratory approach. Interphase FISH seems a useful complementary method to morphology and IHC. It is applicable to various tissues and cells prepared as tissue imprints or histological sections.

CD5- mantle cell lymphoma

Mantle cell lymphoma (MCL) typically expresses B-cell antigens and CD5 and overexpresses bcl-1 protein. However, unusual cases of bcl-1+ and CD5-MCL have been observed, posing a practical challenge for correct diagnosis and management. We identified 25 cases (48 samples) of bcl-1+ and CD5- lymphoma. CD5 expression was assessed by flow cytometric analysis alone (1 case), immunohistochemical analysis alone (17 cases), or dual flow cytometric/immunohistochemical methods (7 cases). The morphologic features were consistent with MCL with centrocytic cytomorphology in 20 cases and blastic variant in 5 cases. The t(11;14) was confirmed in 8 of 11 cases by fluorescence in situ hybridization of paraffin-embedded tissue. Cytogenetic analysis revealed the t(11;14) within a complex karyotype in 2 additional cases. These data show that MCL may lack CD5 expression. Evaluation of bcl-1 expression by immunohistochemical analysis or molecular genetics may be indicated if MCL is suspected clinically or morphologically despite a lack of CD5 expression.

Properties of the mantle cell and mantle cell lymphoma

The major lymphoid inhabitant of the follicular mantle is the mantle cell, an immunologically naïve B cell. It is the putative cell of origin of mantle cell lymphoma (MCL), the cells of which have similar morphologic, immunophenotypic, and molecular characteristics to the normal B lymphocytes of the mantle zone. In the past year a number of advances have been made in the biology of the normal mantle cell, its interactions with the other constituents of the follicular and mantle zone microenvironments, and the development of neoplasia in this cell population. In addition, new developments in diagnostic molecular pathology have been used to more readily identify cases of MCL. The authors summarize these new advances in the understanding of the biology of the mantle cell and newer ancillary techniques in the diagnosis of lymphomas arising from this cell type.