Cytogenetics of lymphomas

Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer

B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.

Disruption of chromosomal locus 1p36 differentially modulates TAp73 and ΔNp73 expression in follicular lymphoma

The TP73 gene is located at the chromosome 1p36 locus that is commonly disrupted or deleted in follicular lymphoma (FL) with poor prognosis. Therefore, we analyzed the expression of the pro-apoptotic TAp73 and anti-apoptotic ΔNp73 isoforms in cases of FL with normal or abnormal 1p36. We observed a significant increase in ΔNp73 expression and ΔNp73:TAp73 ratio, lower expression of cleaved caspase-3 and a higher frequency of Ki-67 and proliferating cell nuclear antigen (PCNA) positive cells in cases of FL with abnormal 1p36. A negative correlation between the ΔNp73:TAp73 ratio and cleaved caspase-3 expression, and a positive correlation between ΔNp73 expression and Ki-67 or PCNA, were observed. The expression of TAp73 and its pro-apoptotic transcriptional targets BIM. PUMA and NOXA were significantly lower in FL compared to reactive follicular hyperplasia. Together, our data demonstrate that 1p36 disruption is associated with increased ΔNp73 expression, decreased apoptosis and increased proliferation in FL.

BCL2, BCL6, IGH, TP53, and MYC protein expression and gene rearrangements as prognostic markers in diffuse large B-cell lymphoma: a study of 44 Turkish patients

The purpose of this study was to determine the frequency of BCL2, BCL6, IGH, TP53, and MYC protein expression and rearrangements of the respective genes in diffuse large B-cell lymphoma (DLBCL) patients and to assess their prognostic values. Samples from 44 patients with DLBCL were evaluated using fluorescence in situ hybridization and immunohistochemical analyses. BCL6 was the most rearranged gene (63.6%), followed by MYC (31.8%), TP53 (22.7%), and BCL2 (18.2%). Multiple rearrangements were detected in 40.9% of the cases. BCL6 was the most expressed protein (78.6%), followed by TP53 (69.04%), BCL2 (59.5%) and MYC (14.3%). Expression of multiple proteins was detected in 67.4% of the cases. BCL2 (P = .003) expression had a significant negative influence on overall survival,whereas BCL6 (P = .014) expression had a significant positive influence. Our results with a different pattern of gene rearrangements and associated protein overexpression indicate the molecular genetic complexity of DLBCLs, which reflects the morphologic, biologic, and clinical heterogeneity of these lymphomas.

Lessons we learn from hematopathology consultation in Taiwan

The appropriate management of hematology patients depends first on correct diagnoses. Expert review is important in reaching accurate diagnoses. To improve diagnostic accuracy, the Taiwan Society of Pathology and the Taiwan Division of the International Academy of Pathology has been conducting an expert consultation program for general pathologists since 2001. As per this program, we have received a total of 395 cases (406 samples) for review. We found that meaningful diagnostic discrepancies occurred frequently in hematopathology reviews. Ambiguous or nondiagnostic original reports were the major causative factor for the major discrepancy cases, which demonstrates that diagnostic uncertainty is a big problem for referring pathologists. However, the World Health Organization lymphoma classification may be poorly reproducible in countries where extensive use of an ancillary technique is not used by general pathologists. This review is intended to report the misdiagnoses most commonly seen in the hematopathology practice in Taiwan. Awareness of the easily misinterpreted entities helps to achieve the right diagnosis and improve patient care.

Clinical significance of cytogenetic aberrations in bone marrow of patients with diffuse large B-cell lymphoma: prognostic significance and relevance to histologic involvement

Background

Although knowledge of the genetics of diffuse large B-cell lymphoma (DLBCL) has been increasing, little is known about the characteristics and prognostic significance of cytogenetic abnormalities and the clinical utility of cytogenetic studies performed on bone marrow (BM) specimens. To investigate the significance of isolated cytogenetic aberrations in the absence of histologic BM involvement, we assessed the implication of cytogenetic staging and prognostic stratification by a retrospective multicenter analysis of newly diagnosed DLBCL patients.

Methods

We analyzed cytogenetic and clinical data from 1585 DLBCL patients whose BM aspirates had been subjected to conventional karyotyping for staging. If available, interphase fluorescence in situ hybridization (FISH) data were also collected from patients.

Results

Histologic BM involvement were found in 259/1585 (16.3%) patients and chromosomal abnormalities were detected in 192 (12.1%) patients (54 patients with single abnormalities and 138 patients with 2 or more abnormalities). Isolated cytogenetic aberrations (2 or more abnormalities) without histologic involvement were found in 21 patients (1.3%). Two or more cytogenetic abnormalities were associated with inferior overall survival (OS) compared with a normal karyotype or single abnormality in both patients with histologic BM involvement (5-year OS, 16.5% vs. 52.7%; P < 0.001) and those without BM involvement (31.8% vs. 66.5%; P < 0.001). This result demonstrated that BM cytogenetic results have a significant prognostic impact that is independent of BM histology. The following abnormalities were most frequently observed: rearrangements involving 14q32, 19q13, 19p13, 1p, 3q27, and 8q24; del(6q); dup(1q); and trisomy 18. In univariate analysis, several specific abnormalities including abnormalities at 16q22-q24, 6p21-p25, 12q22-q24, and -17 were associated with poor prognosis. Multivariate analyses performed for patients who had either chromosomal abnormalities or histologic BM involvement, revealed IPI high risk, ≥ 2 cytogenetic abnormalities, and several specific chromosomal abnormalities, including abnormalities at 19p13, 12q22-q24, 8q24, and 19q13 were significantly associated with a worse prognosis.

Conclusions

We suggest that isolated cytogenetic aberrations can be regarded as BM involvement and cytogenetic evaluation of BM improves staging accuracy along with prognostic information for DLBCL patients.

Hematopathologic discrepancies between referral and review diagnoses: a gap between general pathologists and hematopathologists

Abstract The World Health Organization (WHO) lymphoma classification has been widely adopted by hematopathologists. However, its practical application by general pathologists is largely unknown. Using a hematopathology consultation program in Taiwan, we reviewed 406 cases. Diagnostic discrepancies were scored based upon whether the divergence would alter disease management according to National Comprehensive Cancer Network guidelines. Major discrepancies accounted for 55% (222/406), minor discrepancies for 5% (20/406) and agreement for 40% (164/406) cases. The more common groups in major discrepancies were non-diagnostic/ambiguous referral reports (116/222, 52%), tumor type revisions (52/222, 23%) and changes from malignant to benign lesions (32/222, 14%). In a total of 259 cases of lymphoma, the concordance rates were 41% (77/187) and 33% (24/72) for B-cell and T/natural killer (NK)-cell lymphomas, respectively. It appears that the WHO approach has made lymphoma classification rather poorly reproducible at least in countries where extensive use of an ancillary technique is not employed by general pathologists.

Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines

Molecular characterization of tumour cell lines is increasingly regarded as a prerequisite for defining their validity as models of in vivo neoplasia. We present the first comprehensive catalogue of genomic and transcriptional characteristics of five widely used canine lymphoid tumour cell lines. High-resolution microarray-based comparative genomic hybridization defined their unique profiles of genomic DNA copy number imbalance. Multicolour fluorescence in situ hybridization identified aberrant gains of MYC, KIT and FLT3 and deletions of PTEN and CDKN2 in individual cell lines, and also revealed examples of extensive structural chromosome reorganization. Gene expression profiling and RT-PCR analyses defined the relationship between genomic imbalance and transcriptional dysregulation in each cell line, clarifying their relevance as models of discrete functional pathways with biological and therapeutic significance. In combination, these data provide an extensive resource of molecular data for directing the appropriate use of these cell lines as tools for studying canine lymphoid neoplasia.

Refining tumor-associated aneuploidy through 'genomic recoding' of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas

Identification of the genomic regions most intimately associated with non-Hodgkin lymphoma (NHL) pathogenesis is confounded by the genetic heterogeneity of human populations. We hypothesize that the restricted genetic variation of purebred dogs, combined with the contrasting architecture of the human and canine karyotypes, will increase the penetrance of fundamental NHL-associated chromosomal aberrations in both species. We surveyed non-random aneuploidy in 150 canine NHL cases, revealing limited genomic instability compared to their human counterparts and no evidence for CDKN2A/B deletion in canine B-cell NHL. 'Genomic recoding' of canine NHL data into a 'virtual human' chromosome format showed remarkably few regions of copy number aberration (CNA) shared between both species, restricted to regions of dog chromosomes 13 and 31, and human chromosomes 8 and 21. Our data suggest that gene discovery in NHL may be enhanced through comparative studies exploiting the less complex association between CNAs and tumor pathogenesis in canine patients.

Large B cell lymphoma presenting initially in bone marrow, liver and spleen: an aggressive entity associated frequently with haemophagocytic syndrome

AIMS

To describe diffuse large B cell lymphoma (DLBCL) presenting initially in bone marrow, liver and spleen (BLS-type) without lymphadenopathy.

METHODS AND RESULTS

The clinicopathological and cytogenetic features of 11 such cases (eight men, three women; mean age: 62.7 years are described). Usually presenting with fever and haemophagocytic syndrome suggesting infection and complicating timely diagnosis, bone marrow examination showed patchy and interstitial infiltration of large tumour cells without sinusoidal involvement. All cases had a high Ki-67 index (≥90%), commonly a non-germinal centre/activated B cell immunophenotype and were negative for Epstein-Barr virus and human herpesvirus 6 and 8. The more frequent cytogenetic changes involved chromosomal loci 14q32 and 9p24, as well as del(3)(q21), add(7)(p22), t(3;6), del(8)(p22), +18 and add(19)(p13). Clinical behaviour was very aggressive, with a 2-year survival rate of 18% (45% of patients died within 3 weeks). High-dose chemotherapy with haematopoietic stem cell transplantation prolonged survival in one patient.

CONCLUSIONS

Although it shares with intravascular LBCL a subtle presentation and an aggressive clinical course, this primary BLS large cell lymphoma variant is distinguished by lacking an intravascular component and having different cytogenetic findings.

The role of fluorescence in situ hybridization and polymerase chain reaction in the diagnosis and classification of lymphoproliferative disorders on fine-needle aspiration

BACKGROUND

Fine-needle aspiration (FNA) has been used in the evaluation of lymphadenopathy for a long time and is highly reliable in the identification of metastatic malignancies. However, the role of FNA in the assessment of new lymphoproliferative disorders continues to be a subject of debate. The objective of the current study was to evaluate the role of molecular cytogenetic studies in FNA diagnoses of lymphoproliferative disorders.

METHODS

A retrospective, computer-based search for lymph node FNAs from 2006 to 2007 was performed. Cases with either fluorescence in situ hybridization (FISH) and/or polymerase chain reaction (PCR) studies were subjected to further analysis.

RESULTS

In total, 243 lymph node FNAs were performed during the period, including 104 that were positive/suspicious for metastatic malignancies, 16 that were positive/suspicious for lymphomas, 15 that demonstrated atypical lymphoid proliferation, 73 that were reactive, 14 that were deemed granulomas, and 21 that were determined to be nondiagnostic. Molecular analysis included combined FISH/PCR in 4 cases, FISH only in 7 cases, and PCR only in 4 cases. By using multiplex PCR, 6 cases with atypical/negative flow cytometry results were diagnosed as 4 B-cell lymphomas, 1 T-cell lymphoma, and 1 reactive lymph node; and 4 cases that had atypical T cells determined by flow cytometry were diagnosed as reactive. One CD10-negative follicular lymphoma and 2 cases with suspicious flow cytometry results were positive for t(14;18)(q32;q21) by FISH. Forty-five cases had follow-up histology with 3 false-negative findings and no false-positive results.

CONCLUSIONS

In this study, multiplex PCR studies for immunoglobulin heavy-chain or T-cell receptor gene rearrangements were useful for demonstrating clonality, and FISH studies were able to detect translocations or gene rearrangements that allowed for the subclassification of B-cell non-Hodgkin lymphomas.

A case-control study of tobacco use and other non-occupational risk factors for lymphoma subtypes defined by t(14; 18) translocations and bcl-2 expression

OBJECTIVE

We re-evaluated reported associations between tobacco use and other factors and non-Hodgkin lymphoma (NHL) t(14; 18)-subtypes based on fluorescence in situ hybridization (FISH) assays believed to be more sensitive than polymerase chain reaction (PCR), previously used for detecting t(14; 18).

METHODS

Commercial FISH assays and bcl-2 immunostaining were performed on paraffin sections to determine t(14; 18) and bcl-2 case-subtypes. Polytomous logistic regression models estimated associations between NHL case-subtypes (versus 1,245 population-based controls) and tobacco use as well as other factors.

RESULTS

Adjusting for age, state, and proxy status, t(14; 18)-negative NHL was associated with any tobacco use (vs. no tobacco use, OR = 1.9, 95% CI = 1.0-3.5), including current smoking (vs. no cigarette use, OR = 1.9, 95% CI = 1.1-3.2). Tobacco exposures were not clearly associated with t(14; 18)-positive NHL or bcl-2 case-subtypes. Hair-dye use and family history of a hemolymphatic cancer were associated with t(14; 18)-negative NHL, but the number of exposed cases was small.

CONCLUSIONS

The association between t(14; 18)-negative NHL and cigarette smoking was unexpected given previous evidence of associations between smoking and follicular lymphoma (which is largely t(14; 18)-positive). Future studies characterizing additional molecular characteristics of t(14; 18)-negative NHL may help determine whether the association with smoking may have been causal versus an artifact of chance or bias.

TERC telomerase subunit gene copy number in different disease stages of non-hodgkin lymphoma and in hepatitis C

ABSTRACT Focal amplification of specific regions of the genome creates high copy number and expression of oncogenes in tumors. By applying fluorescence in situ hybridization (FISH) to leukocytes of hepatitis C (HCV) patients and non-Hodgkin lymphoma (NHL) patients, we estimated gene dosage of the TERC gene at 3q26.3. Higher TERC copy numbers were found in NHL at diagnosis compared to HCV patient groups. Higher TERC copy numbers were also observed in NHL patient at diagnosis and relapse compared to patients in remission. We believe that the TERC gene amplification is involved in the process of genetic instability leading to tumor genesis such as in NHL.

Telomere aggregates in non-Hodgkin lymphoma patients at different disease stages

Telomeres of tumor nuclei tend to form aggregates (TA). The same phenomenon was also observed in premalignant states. The aim of this study was to estimate TA formation in leukocytes of patients with non-Hodgkin lymphoma (NHL) at different disease stages (diagnosis, treatment, relapse, and remission). The peptide nucleic acid Telomere Kit was used to evaluate TA formation, using two-dimensional fluorescence microscopy. A higher rate of TA was found in all the NHL stages (including remission) than in the control group. Significantly higher TA formation was also observed in the relapse group, compared to the diagnosis group. It may be possible that patients with higher TA numbers are prone to relapse. From our previous results involving replication pattern, random aneuploidy rate, and (recently) TA formation, it can be concluded that the patients in remission are at higher risk of developing relapse than the normal population throughout their life span. The genetic instability parameters remain in the cells of these patients, who must continue to be monitored throughout their life.

Primary cardiac lymphoma: molecular cytogenetic characterization of a rare entity

BACKGROUND

The majority of cardiac atrial neoplasms represent benign myxomas. Rarely, malignant cardiac neoplasms are encountered and can include primary cardiac neoplasms, as well as secondary tumors involving the heart. As many cardiac neoplasms lack pathognomonic clinical features, histopathologic diagnosis is crucial for classification and appropriate treatment of these neoplasms. Molecular investigation is critical to begin to catalogue genomic changes that correlate with these malignancies.

METHODS

A 60-year-old man presented with superior vena cava syndrome, and computed tomographic scan revealed an infiltrative mass of the right atrium that nearly filled the atrial chamber and partially occluded superior vena cava flow. Urgent surgical resection revealed a soft mass with the appearance of "fish flesh." Histologic, immunochistochemical, cytogenetic, and detailed molecular investigations were carried out.

RESULTS

Histologic examination revealed complete replacement of the atrial wall by diffuse sheets of pleomorphic lymphoid cells with occasional smaller plasmacytoid cells. The predominant lymphoid population was immunoreactive for CD45, CD20, CD79a, BCL-2, BCL-6, Ki-67, CD10, p53, and light chain restricted for IgM lambda. A diagnosis of primary cardiac diffuse large B-cell lymphoma with plasmacytoid differentiation was established and was supported by cytogenetic studies demonstrating the presence of a t(14;18)(q32;q21) translocation in addition to other chromosomal abnormalities. Fluorescence in situ hybridization revealed no evidence of a C-MYC translocation.

CONCLUSION

In this single case, comparative genomic hybridization analysis using both bacterial artificial chromosome and oligonucleotide arrays correlated well with cytogenetic findings and allows for the cataloguing of more subtle genomic events.

Aberrations in chromosomes associated with lymphoma and therapy-related leukemia in benzene-exposed workers

Epidemiological studies show that benzene exposure is associated with an increased incidence of leukemia and perhaps lymphoma. Chromosomal rearrangements are common in these hematopoietic diseases. Translocation t(14;18), the long-arm deletion of chromosome 6 [del(6q)], and trisomy 12 are frequently observed in lymphoma patients. Rearrangements of the MLL gene located on chromosome 11q23, such as t(4;11) and t(6;11), are common in therapy-related leukemias resulting from treatment with topoisomerase II inhibiting drugs. To examine numerical and structural changes in these chromosomes (2, 4, 6, 11, 12, 14, and 18), fluorescence in situ hybridization (FISH) was employed on metaphase spreads from workers exposed to benzene (n = 43) and matched controls (n = 44) from Shanghai, China. Aneuploidy (both monosomy and trisomy) of all seven chromosomes was increased by benzene exposure. Benzene also induced del(6q) in a dose-dependent manner (P(trend) = 0.0002). Interestingly, translocations between chromosomes 14 and 18, t(14;18), known to be associated with follicular non-Hodgkin lymphoma, were increased in the highly exposed workers (P < 0.001). On the other hand, translocations between chromosome 11 and other partner chromosomes that are found in therapy-induced leukemias were not increased. These data add weight to the notion that benzene can induce t(14;18) and del(6q) found in lymphoma, but do not support the idea that benzene induces t(4;11) or t(6;11). However, they do not rule out the possibility that other rearrangements of the MLL gene at chromosome 11q23 may be induced by benzene.

Recommended curriculum for teaching hematopathology to subspecialty hematopathology fellows

The performance and interpretation of clinical hematology and hematopathology laboratory tests and diagnosis of benign or malignant hematolymphoid disorders present unique challenges to hematopathology fellow trainees. To assist hematopathology fellowship program directors in preparing trainees to meet these challenges, a task force of pathologists with expertise in hematopathology developed a suggested training curriculum that includes a comprehensive list of topics in the areas of analytic hematology, bone marrow pathology, lymph node pathology, splenic pathology, lymphoma diagnostics, cytogenetics, and molecular diagnostics. This report also includes recommendations for training experiences that will facilitate the transition of subspecialty residents to practicing consultants in hematopathology.

Molecular cytogenetic characterization of t(14;19)(q32;p13), a new recurrent translocation in B cell malignancies

Translocations involving an immunoglobulin (IG) locus are a recurring theme in B cell neoplasia. The rearrangements lead to the joining of an IG gene with a (proto)oncogene, whereby the latter comes under the influence of transcription-stimulating sequences in the constitutively active IG locus resulting in deregulation of the oncogene and neoplastic growth. We present here three cases of B cell neoplasia that showed a t(14;19)(q32;p13) by karyotypic analysis. Detailed molecular cytogenetic characterization of the breakpoints on chromosomes 14 and 19 in the two cases from which extra material was available, demonstrated the involvement of the immunoglobulin heavy-chain (IGH@)-variable region on chromosome 14 in both and, in one case, that the breakpoint was within the BRD4 gene on chromosome 19. Against the background of what one knows about IGH@ involvement in lymphatic malignancies, it is difficult to envisage a fusion gene with qualitatively altered protein product as the crucial pathogenetic outcome of the translocation. In spite of the fact that we found BRD4 split by the t(14;19)(q32;p13) in one of the two informative cases, we cannot be sure that this was the pathogenetically relevant target gene. Other pathogenetic possibilities could be deregulation of the neighboring NOTCH3 and/or ABHD9 genes, located distal to BRD4 in 19p13.

Diagnostic pathology of lymphoproliferative disorders

The last 20 years have seen a dramatic change in the way we classify, and therefore diagnose, lymphoma. Two decades ago, the International Working Formulation enabled diagnosis and management on the basis of H&E sections alone, with no mandatory requirement for immunophenotyping, molecular studies or any other ancillary investigations. The concept of categorisation by 'clinicopathological entities' defined by clinical features, morphology, immunophenotype and more recently, genotype, began with the Kiel, and Lukes and Collins classifications in the late 1970s, becoming fully expressed in the REAL and subsequently WHO classifications. The current, multidisciplinary approach to categorisation adds significantly to the task facing the anatomical pathologist, since it requires distribution of biopsy material to all the appropriate specialised laboratories, the gathering of a range of cross-disciplinary information, the correlation of all diagnostic findings, deduction of a definitive diagnosis and, finally, integration of all the above into a single multiparameter report. In this review, we summarise the contemporary approach to the biopsy, diagnosis and reporting of lymphoproliferative disorders.