Polysomy of chromosome 12 in 60 patients with non-Hodgkin's lymphoma assessed by fluorescence in situ hybridization: differences between follicular and diffuse large cell lymphoma

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

Combining RNA sequencing, ribosome profiling, and mass spectrometry, we elucidate the contribution of non-canonical translation to the proteome and major histocompatibility complex (MHC) class I immunopeptidome. Remarkably, of 14,498 proteins identified in three human B cell lymphomas, 2,503 are non-canonical proteins. Of these, 28% are novel isoforms and 72% are cryptic proteins encoded by ostensibly non-coding regions (60%) or frameshifted canonical genes (12%). Cryptic proteins are translated as efficiently as canonical proteins, have more predicted disordered residues and lower stability, and critically generate MHC-I peptides 5-fold more efficiently per translation event. Translating 5' "untranslated" regions hinders downstream translation of genes involved in transcription, translation, and antiviral responses. Novel protein isoforms show strong enrichment for signaling pathways deregulated in cancer. Only a small fraction of cryptic proteins detected in the proteome contribute to the MHC-I immunopeptidome, demonstrating the high preferential access of cryptic defective ribosomal products to the class I pathway.

DNA Copy Number Changes in Diffuse Large B Cell Lymphomas

Copy number aberrations (CNV/CNA) represent a major contribution to the somatic mutation landscapes in cancers, and their identification can lead to the discovery of oncogenetic targets as well as improved disease (sub-) classification. Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma in Western Countries and up to 40% of the affected individuals still succumb to the disease. DLBCL is an heterogenous group of disorders, and we call DLBCL today is not necessarily the same disease of a few years ago. This review focuses on types and frequencies of regional DNA CNVs in DLBCL, not otherwise specified, and in two particular conditions, the transformation from indolent lymphomas and the DLBCL in individuals with immunodeficiency.

Non-Hodgkin lymphoma with t(14;18): clonal evolution patterns and cytogenetic–pathologic–clinical correlations

PURPOSE

The pattern and frequency of secondary chromosome abnormalities in t(14;18)-carrying non-Hodgkin lymphomas (NHL) were evaluated for differences in relation to histologic NHL subtype and patients' outcome.

METHODS

One hundred and forty-nine NHL patients with t(14;18) and complete cytogenetic, morphologic, and clinical information were selected.

RESULTS

One hundred and twelve cases were follicular lymphoma (FL) and 37 were diffuse large B-cell lymphoma (DLBCL). One hundred and forty cases showed secondary aberrations (94%, median = 6.0). The most frequent were losses from chromosome arms 1p and 6q and +7 (26%). Loss from 1q, +7, and +12 were more frequent in DLBCL than in FL. Loss from 1p, Xp, and -16 were more frequent in FL grade 3 than in FL grades 1 and 2. Patients with <6.0 secondary cytogenetic aberrations had better prognosis than did those with a higher number of aberrations. Trisomy 21 was associated with shorter patient survival. FLIPI score, the number of secondary chromosomal aberrations, and +21 were all of independent prognostic value in Cox multivariate analysis. FL grade 1-3a patients that had received chemotherapy, showed a higher frequency of i(6p) and loss from 6q.

CONCLUSION

Secondary chromosomal aberrations showed some correlation with the morphologic subgroups of t(14;18)-NHL. Trisomy 21 and the presence of >6.0 secondary cytogenetic aberrations both correlated with shorter overall survival.

Characteristic chromosomal imbalances in primary central nervous system lymphomas of the diffuse large B-cell type

We performed a genome wide screening for genomic alterations on a series of 19 sporadic primary central nervous system lymphomas (PCNSL) of the diffuse large B-cell type by comparative genomic hybridization (CGH). The tumors were additionally analyzed for amplification and rearrangement of the BCL2 gene at 18q21 as well as for mutation of the recently cloned BCL10 gene at 1p22. Eighteen tumors showed genomic imbalances on CGH analysis. On average, 2.1 losses and 4.7 gains were detected per tumor. The chromosome arm most frequently affected by losses of genomic material was 6q (47%) with a commonly deleted region mapping to 6q21-q22. The most frequent gains involved chromosome arms 12q (63%), 18q and 22q (37% each), as well as 1q, 9q, 11q, 12p, 16p and 17q (26% each). High-level amplifications were mapped to 9p23-p24 (1 tumor) and to 18q21-q23 (2 tumors). However, PCR-based analysis, Southern blot analysis and high-resolution matrix-CGH of the BCL2 gene revealed neither evidence for amplification nor for genetic rearrangement. Mutational analysis of BCL10 in 16 PCNSL identified four distinct sequence polymorphisms but no mutation. Taken together, our data do not support a role of BCL2 rearrangement/amplification and BCL10 mutation in PCNSL but indicate a number of novel chromosomal regions that likely carry yet unknown tumor suppressor genes or proto-oncogenes involved in the pathogenesis of these tumors.

Cytogenetics of lymphomas

Cytogenetic analysis is now a routine part of the diagnosis and management of a significant number of lymphoid malignancies. Whilst conventional cytogenetics remains the most comprehensive method for assessing chromosome abnormalities, the technical difficulties associated with conventional cytogenetics in most lymphomas has resulted in increased use of fluorescence in situ hybridisation (FISH) to identify specific abnormalities that are useful in either the diagnosis or management of these disorders. The finding of one of the Burkitt's translocations is of major importance in the diagnosis of Burkitt's and Burkitt's-like lymphomas, whereas the t(14;18), although seen in most follicular lymphomas (FL), is not usually required to make a diagnosis. Thus, whilst cytogenetics may be of interest in FL, it is not an essential part of the diagnostic work-up. Conventional cytogenetics may be useful for identifying markers of resistance to Helicobacter pylori therapy in MALT lymphomas. In disorders such as Hodgkin lymphoma, hairy cell leukaemia and lymphoplasmacytoid lymphoma, although many cytogenetic abnormalities have been observed, no consistent or specific abnormalities have been identified and so, at this point in our knowledge of the genetics of these disorders, cytogenetics cannot be considered a useful test for either diagnosis or prognosis. In contrast, the diagnosis of mantle cell lymphoma is now dependent upon the identification of the 11;14 translocation that results in cyclin D1 up-regulation. It is widely acknowledged that FISH is the most consistently useful test to identify the juxtaposition of the CCND1 and IGH genes in mantle cell lymphoma and is regarded as the 'gold standard'. FISH also has a role in identifying genetic abnormalities of prognostic significance in chronic lymphocytic leukaemia. Given the wealth of genetic and cytogenetic abnormalities that are continuing to be found in chronic lymphoid malignancies, it will be some time before the optimal use of both conventional cytogenetics and FISH is established in the diagnosis and management of lymphomas.

KSHV-Positive Solid Lymphomas Represent an Extra-Cavitary Variant of Primary Effusion Lymphoma

Primary effusion lymphoma (PEL) is a unique form of non-Hodgkin lymphoma (NHL) associated with Kaposi sarcoma-associated herpesvirus (KSHV; HHV-8) that displays a distinct constellation of clinical, morphologic, immunologic, and molecular characteristics. Rare KSHV-containing immunoblastic lymphomas occurring in solid tissues have been described. Whether they represent part of the spectrum of PEL has not been determined. The morphologic, immunophenotypic, and molecular features of KSHV-positive solid lymphomas occurring in 8 HIV+/AIDS patients were systematically investigated and compared with those of 29 similarly analyzed PELs. The 8 KSHV-positive solid lymphomas were virtually indistinguishable from the 29 PELs based on morphology (immunoblastic/anaplastic), immunophenotype (CD45 positive; T cell antigen negative; CD30, EMA, CD138 positive; CD10, CD15, BCL6 negative) and genotype (100% immunoglobulin genes rearranged; no identifiable abnormalities in C-MYC, BCL6, BCL1, BCL2; and uniformly EBV positive). The only identifiable phenotypic difference was that the KSHV-positive solid lymphomas appeared to express B cell-associated antigens (25%) and immunoglobulin (25%) slightly more often than the PELs (<5% and 15%, respectively; P = 0.11 and P = 0.08, respectively). The clinical presentation and course of the patients who develop KSHV-positive solid lymphomas were also similar, except for the lack of an effusion and somewhat better survival (median 11 months vs. 3 months). However, the 3 KSHV-positive solid lymphoma patients alive without disease 11, 25, and 44 months following initial presentation were recently diagnosed patients and, unlike the other patients with KSHV-positive solid lymphomas, received anti-retroviral therapy. These findings strongly suggest that these decidedly rare KSHV-positive solid lymphomas belong to the spectrum of PEL. Therefore, we propose that the KSHV-positive solid lymphomas be designated extra-cavitary PELs.

Cytogenetic evolution of follicular lymphoma

Follicular lymphoma (FL) is closely associated with the chromosomal translocation t(14;18)(q32;q21), which results in an overexpression of the anti-apoptotic bcl-2 gene product leading to a survival advantage of B-lymphocytes. However, in animal models, this genomic aberration is not sufficient for the initiation of the malignant phenotype. Additional genomic rearrangements are required for disease progression. In this review, the most important additional aberrations and possible candidate genes in the respective genomic regions are discussed. In addition, relevant data regarding their role in disease progression as well as the association with clinical presentation and clinical course are presented.

Genetic characterization of HHV-8/KSHV-positive primary effusion lymphoma reveals frequent mutations of BCL6: implications for disease pathogenesis and histogenesis

Human herpesvirus-8/Kaposi sarcoma-associated herpesvirus-positive primary effusion lymphoma (PEL) is a recently identified B-cell non-Hodgkin lymphoma category characterized by liquid growth in the serous body cavities. Apart from viral infection, no genetic alteration is known to be associated with PEL and no recurrent cytogenetic abnormality has been identified in these lymphomas. Yet the consistent monoclonality of PEL indicates that the disease is not solely a virus-driven proliferation. Here we report that PEL is associated with a high frequency of mutations of BCL6 5' noncoding regions, and we identify karyotypic abnormalities that may be recurrently involved in these lymphomas. Mutations of BCL-6 5' noncoding regions occurred in 8/13 PEL. Mutations occurred in the absence of BCL6 gross rearrangements were often multiple in the same patient (7/8 mutated cases), and occurred in both HIV-positive and HIV-negative individuals. Since BCL6 mutations are regarded as a genetic marker of B-cell transition through the germinal center (GC), these data are consistent with histogenetic derivation of PEL from GC or post-GC B-cells. Cytogenetic and FISH analysis of seven PEL cell lines showed frequent occurrence of complete or partial trisomy 12 (7/7 cases), trisomy 7 (4/7 cases), and abnormalities of bands Iq21-25 (5/7 cases).

Cytogenetic changes in the progression of lymphoma

The study of chromosomal changes related to tumor progression in NHL is complicated by the various histologic classification systems and the lack of large serial studies comparing abnormalities at different disease stages. The T-cell lymphomas frequently involve rearrangements of the T-cell receptors and tumor progression is marked by a change from single cell aberrations and polyclonality in low grade disease to monoclonal formation, complex clones, polyploidy, and abnormalities of 1p, 6q, 7, and 13 in high grade T-NHL. In B-cell NHL, specific translocations and oncogene rearrangements are associated with specific NHL subtypes de novo; many of these translocations involve immunoglobulin genes, such as t(14;18) in follicular lymphoma, t(11;14) in MCL, t(3;14) in DLLC, and t(8;14) in Burkitt's lymphoma. Tumor progression is associated with secondary abnormalities which are generally not confined to a particular NHL subtype. Some abnormalities, such as those involving chromosomes 1, 6, and 17, >4-6 clonal markers/cell, and rearrangements of c-MYC and TP53, have prognostic significance while others, such as trisomies 7, 12, 18, and X, are associated with tumor progression but their influence on overall survival is uncertain.

Trisomy 12 is seen within a specific subtype of B-cell chronic lymphoproliferative disease affecting the peripheral blood/bone marrow and co-segregates with elevated expression of CD11a

In order to delineate the specific morphological and immunophenotypic features of B-cell lymphoproliferative disorders associated with trisomy 12, 172 sequential unselected cases of CD19+CD5+ B-cell disorders, primarily affecting the peripheral blood and bone marrow, were studied. Trisomy 12 was found in 24 cases (13.9%), with all cases morphologically classified as either CLL-PL or CLL-mixed by FAB criteria. Trisomy 12 was not found in any cases of typical CLL. Trisomy 12 cases demonstrated a significant higher expression of CD11a (P<0.0001) and CD20 (P<0.0006) when compared to cases with the equivalent morphology and immunophenotype, but without the chromosomal abnormality. Trisomy 12 cases also demonstrated a higher frequency of FMC7, CD38 expression and moderate to strong surface immunoglobulin staining. However, no correlation was detected between the percentages of trisomy 12 cells and cells expressing CD11a, CD38, FMC7 or sIg mean fluorescent intensity. Cells from trisomy 12 positive cases were sorted according to their CD11a expression using fluorescent activated cell sorting. There was a significant increase in the percentage of trisomy 12 cells within the CD11a+ sorted fraction compared to the unsorted population (P < 0.05), implying that trisomy 12 is associated with increased expression of CD11a. With the highly specific morphological and immunophenotypic features demonstrated by trisomy 12 cases in this study, it is highly likely that these cases constitute a specific group of B-cell lymphoproliferative disorders.

Tumor genes and their proteins in cytologic and surgical specimens: relevance and detection systems

Oncogenesis is the consequence of a series of genetic alterations that allow unrestrained cellular growth, tissue invasion, and eventual metastases. Tumor-related genes can be classified into functional categories. Proto-oncogenes/oncogenes have a stimulatory role in cell growth, and the inactivation of cancer-suppressor genes/antioncogenes results in the loss of cell cycle regulation. More recently, three other groups of tumor-related genes have been recognized. They include the antiapoptosis genes which protect from programmed cell death, the antimetastasis genes, and multidrug resistance genes. Besides aiding in tumor diagnosis, the detection of such tumor-associated genes and their products allows the identification of individuals with an inherited predisposition to neoplastic growths, and the overexpression of many of these oncogene products has been shown to be a potential marker of tumor behavior and a predictor of treatment outcome and response. The ability to utilize DNA and RNA probes for nucleic acid hybridization and polymerase chain reaction procedures in cell and tissue preparations of solid tumors and lymphoid proliferations expands and complements the information provided by immunohistochemical techniques. These probes allow direct visualization and correlation of specific genes and their protein products with cytomorphologic features, and form a powerful addition to the armamentarium of the cytopathologist and surgical pathologist.

Chromosome X numerical abnormalities in patients with non-Hodgkin's lymphoma. A study of 59 patients using fluorescence in situ hybridization

Chromosome X numerical abnormalities are frequently observed in non-Hodgkin's lymphoma (NHL), with an incidence of 3% to 14% for chromosomal loss and 7% to 33% for chromosomal gain. Because sex chromosome numerical abnormalities are thought to be due to aging, little information is known about their relation to gender, therapy, and prognosis. Therefore, to determine the incidence and clinical relevance of this abnormality in NHL, we studied specimens from 59 NHL patients (31 men and 28 women) by fluorescence in situ hybridization (FISH) using a directly conjugated centromeric probe for chromosome X. The median age for the entire group was 52 years (range, 31-88 years). All specimens were obtained by fine-needle aspiration of diseased lymph nodes. Sex-matched lymphocytes from benign hyperplastic lymph nodes were used as controls. The overall incidence of chromosome X numerical abnormalities was 49.2%. Female patients had a higher overall incidence than males (76% vs. 24%; p < 0.001). The median percentage of cells involved in this abnormality in each specimen was 5.2%. There was no statistically significant difference in the incidence in previously treated than untreated patients (53.1% vs. 44.4%; p < 0.75) and in intermediate-grade NHL than low-grade NHL (61.1% vs. 50%; p < 0.75). There was a trend towards a higher incidence of chromosome X loss in older patients. While the difference in the incidence of chromosome X abnormalities observed between women and men may be due to the difference in the normal copy numbers of this chromosome in each sex group, this abnormality remained higher than any other autosomal chromosome abnormality in NHL previously evaluated by FISH. We conclude that, although FISH detected a high incidence of chromosome X numerical abnormalities and that females had a higher incidence than males, only a small percentage of the cells were involved, suggesting that this abnormality is most likely a secondary genetic defect that is not important in the pathogenesis of NHL.

High incidence of monosomy 18 in lymphoid malignancies that have bone marrow and peripheral blood involvement

We studied the incidence of numerical chromosome 18 abnormalities in 107 patients with lymphoid malignancies by fluorescence in situ hybridization (FISH) using a directly conjugated centromeric probe for chromosome 18. Samples were obtained by fine needle aspiration of diseased nodes, bone marrows or peripheral blood. Monosomy 18 was more common in chronic lymphocytic leukemia (43%), small lymphocytic lymphoma (28%), and follicular lymphomas (12.5%) than in diffuse lymphomas (5.3%; p < 0.01). Monosomy 18 was detected in 9.7-17.1% of the cells in non-Hodgkin's lymphoma (NHL) (background, 5.4%; 99% CI, 4.2%-6.6%) and in 8%-16.7% (median, 10%) of the cells in (CLL) (background, 3.4%; 99% CI, 2.5%-4.3%). All patients with monosomy 18 were found to have bone marrow involvement. Of all untreated patients who had disease involving the bone marrow, 32% were found to have monosomy 18. Trisomy 18 was detected in 3.6%-48.2% of the cells in NHL (background, 0.9%; 99% CI, 0.2%-1.6%) and was most common in diffuse large-cell lymphoma (34%) and follicular lymphomas (31%). None of the patients with small lymphocytic lymphoma or chronic lymphocytic leukemia had trisomy 18. There was no correlation between trisomy 18 and response to treatment or clinical presentation. In this study, monosomy 18 was observed frequently in patients with lymphoid malignancies that involve the bone marrow and peripheral blood. Our data suggest that important gene(s) located on chromosome 18 may be involved in homing of the malignant lymphocytes to the bone marrow and peripheral blood.