Alternative involvement of two cytogenetically distinguishable breakpoints on chromosome 8 in Burkitt's lymphoma associated translocations

Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection

Structural variant detection by next-generation sequencing (NGS) methods have a higher molecular resolution than conventional cytogenetic techniques (Aypar et al., Eur J Haematol 102(1):87-96, 2019; Smadbeck et al., Blood Cancer J 9(12):103, 2019) and are particularly helpful in characterizing genomic rearrangements. Mate pair sequencing (MPseq) leverages a unique library preparation chemistry involving circularization of long DNA fragments, allowing for a unique application of paired-end sequencing of reads that are expected to map 2-5 kb apart in the genome. The unique orientation of the reads allows the user to estimate the location of breakpoints involved in a structural variant either within the sequenced reads or between the two reads. The precision of structural variant and copy number detection by this method allows for characterization of cryptic and complex rearrangements that may be otherwise undetectable by conventional cytogenetic methods (Singh et al., Leuk Lymphoma 60(5):1304-1307, 2019; Peterson et al., Blood Adv 3(8):1298-1302, 2019; Schultz et al., Leuk Lymphoma 61(4):975-978, 2020; Peterson et al., Mol Case Studies 5(2), 2019; Peterson et al., Mol Case Studies 5(3), 2019).

Novel FISH probes designed to detect IGK-MYC and IGL-MYC rearrangements in B-cell lineage malignancy identify a new breakpoint cluster region designated BVR2

Detection of translocations involving MYC at 8q24.1 in B-cell lineage malignancies (BCL) is important for diagnostic and prognostic purposes. However, routine detection of MYC translocations is often hampered by the wide variation in breakpoint location within the MYC region, particularly when a gene other than IGH, such as IGK or IGL, is involved. To address this issue, we developed and validated four fluorescence in situ hybridization (FISH) probes: two break apart probes to detect IGK and IGL translocations, and two dual-color, dual-fusion FISH (D-FISH) probes to detect IGK-MYC and IGL-MYC. MYC rearrangements (four IGK-MYC, 12 IGL-MYC and four unknown partner gene-MYC) were correctly identified in 20 of 20 archival BCL specimens known to have MYC rearrangements not involving IGH. Seven specimens, all of which lacked MYC rearrangements using a commercial IGH/MYC D-FISH probe, were found to have 8q24 breakpoints within a cluster region >350-645 kb 3' from MYC, provisionally designated as Burkitt variant rearrangement region 2 (BVR2). FISH is a useful ancillary tool in identifying MYC rearrangements. In light of the discovery of the distally located BVR2 breakpoint cluster region, it is important to use MYC FISH probes that cover a breakpoint region at least 1.0 Mb 3' of MYC.

Epstein-Barr virus and cancer

EBV was the first human virus to be directly implicated in carcinogenesis. It infects >90% of the world's population. Although most humans coexist with the virus without serious sequelae, a small proportion will develop tumors. Normal host populations can have vastly different susceptibility to EBV-related tumors as demonstrated by geographical and immunological variations in the prevalence of these cancers. EBV has been implicated in the pathogenesis of Burkitt's lymphoma, Hodgkin's disease, non-Hodgkin's lymphoma, nasopharyngeal carcinoma, and lymphomas, as well as leiomyosarcomas arising in immunocompromised individuals. The presence of this virus has also been associated with epithelial malignancies arising in the gastric region and the breast, although some of this work remains in dispute. EBV uses its viral proteins, the actions of which mimic several growth factors, transcription factors, and antiapoptotic factors, to usurp control of the cellular pathways that regulate diverse homeostatic cellular functions. Recent advances in antiviral therapeutics, application of monoclonal antibodies, and generation of EBV-specific CTLs are beginning to show promise in the treatment of EBV-related disorders.

Expression of EBV encoded nuclear small non-polyadenylated RNA (EBER) molecules in 32 cases of childhood Burkitt's lymphoma from Israel

We have analyzed paraffin sections from 32 children with histologically confirmed Burkitt's Lymphoma (BL) for the presence of EBV using in situ hybridization to detect expression of the EBV-encoded early RNAs (EBERs). EBV was present in the tumors of 11 patients (34%). Sixty nine percent of the children presented with abdominal disease, 19% had bone marrow infiltration and only one child had jaw involvement. There was no statistically significant difference between EBV positive and EBV negative children with regard to age, gender, origin, primary site at presentation, or clinical stage of disease. However, there was a trend for younger age in the children with EBV positive BL with a median age of 4, compared to 7 years in children with EBV negative BL. None of the 7 children of Ashkenazi Jewish origin had EBER positive disease. There was no difference in the treatment outcome between the EBV positive patients (estimated survival at 24 months of 82%) and EBV negative children (estimated survival rate of 71% (p=0.58)). In conclusion, although this is only a small series it seems that childhood BL in Israel has the clinical characteristics of sporadic, non-African type with 34% EBV association and a low incidence of jaw tumors. Our data suggest that Ashkenazi Jewish children with BL are less likely to have EBV positive tumors than other ethnic groups. However, more patients will need to be studied in order to assess the validity of this observation.

Immune regulation in Epstein-Barr virus-associated diseases

Epstein-Barr virus (EBV) is a member of the human herpesvirus family and, like many other herpesviruses, maintains a lifelong latent association with B lymphocytes and a permissive association with stratified epithelium in the oropharynx. Clinical manifestations of primary EBV infection range from acute infectious mononucleosis to an asymptomatic persistent infection. EBV is also associated with a number of malignancies in humans. This review discusses features of the biology of the virus, both in cell culture systems and in the natural host, before turning to the role of the immune system in controlling EBV infection in healthy individuals and in individuals with EBV-associated diseases. Cytotoxic T cells that recognize virally determined epitopes on infected cells make up the major effector arm and control the persistent infection. In contrast, the options for immune control of EBV-associated malignancies are more restricted. Not only is antigen expression restricted to a single nuclear antigen, EBNA1, but also these tumor cells are unable to process EBV latent antigens, presumably because of a transcriptional defect in antigen-processing genes (such as TAP1 and TAP2). The likelihood of producing a vaccine capable of controlling the acute viral infection and EBV-associated malignancies is also discussed.

Epstein-Barr virus as an agent of haematological disease

Epstein-Barr virus (EBV) encodes genes that permit its persistence in human B lymphocytes and genes that ensure its replication in epithelial cells. Immune restraints on the virus are usually so effective that most EBV infections are limited to a minute fraction of B lymphocytes and of epithelial cells. As a result, most EBV infections are never symptomatic. Occasionally, the virus causes disease, often with the cooperation of the immune system or other less characterized cofactors. Infectious mononucleosis, a generally self-limited lymphoproliferative illness common in adolescents and young adults, is due to primary EBV infection and to the brisk cellular immune response it elicits. Lymphoproliferative disorders of EBV-infected B cells arise almost exclusively when cellular immunity is grossly compromised. EBV-positive Burkitt's lymphoma contain a translocated and deregulated c-myc oncogene and EBV-positive non-Hodgkin's lymphomas are characterized by the presence of Reed-Sternberg's and Hodgkin's cells, features that have not been directly linked to EBV. Many recent observations, however, including evidence that virus infection precedes malignant transformation and is often associated with a characteristic pattern of viral gene expression, provide continued interest in the relationship between the virus and these haematological malignancies.

Breakpoints of Burkitt's lymphoma t(8;22) translocations map within a distance of 300 kb downstream of MYC

The variant translocation t(8;22) in Burkitt's lymphoma (BL) cells joins band q24 of chromosome 8 distal to the proto-oncogene MYC to the immunoglobulin lambda locus. The distribution of breakpoints on chromosome 8 of 11 cell lines with t(8;22) has been investigated by in situ fluorescence hybridization and pulsed-field gel electrophoresis. We show that these chromosomal breakpoints generally fall within a region of about 300 kb 3' of MYC and that at least 8 out of 11 affect the previously characterized transcriptional unit PVT1. Comparable results were obtained in earlier experiments analyzing the variant t(2;8). Recently, in a series of BL cells carrying t(8;14), breakpoints upstream of MYC have been described at a similar distance. Therefore, our results suggest that deregulation of MYC by the immunoglobulin loci can occur at a distance of up to about 350 kbp of MYC.

Gene mapping in cancer

Observation of genetic alterations that appear consistently in specific types and stages of cancer provides a strong impetus to cancer geneticists to focus their investigations on the exploration of such volatile regions of the human genome. Introduction of powerful molecular cytogenetic and molecular genetic methods in recent years permits more detailed analysis, which will help researchers in their efforts to determine if such areas of the human genome have a functional role in the initiation and progressive development of leukemias and solid tumors. This discussion will focus on several provocative molecular cytogenetic tools that are currently available to localize potential cancer-associated genes and on how these methods are being used in conjunction with the current modes of analysis, including cytogenetics and somatic cell genetics. In addition, we will explore how these methods will help to isolate and dissect recently discovered cancer-associated genes within the human genome. All of these methods used in combination with each other will provide essential DNA markers for future diagnostic and prognostic evaluation of cancer.

A new human plasma cell line, Karpas 620, with translocations involving chromosomes 1, 11 and 14

We report here the establishment of a new cell line, Karpas 620 (K620), from the peripheral blood of an elderly woman with an IgG-kappa plasma cell leukaemia (PCL). The line has the same hypotetraploid karyotype as the fresh cells from the patient. The cultured cells have the ultrastructural appearance of plasma cells with abundant rough endoplasmic reticulum (RER) and secrete kappa light chain. They are positive for surface antigens HLA DR, and WR17 (CD 37) and negative for CD1, CD3, CD4 and CD8. Using high resolution (HR) cytogenetic analysis it has been possible to identify all the marker chromosomes including several rearrangements commonly seen in malignancies of B cell lineage. These are a 14q+ marker with a typical 'Burkitt' morphology der(14)(pter----q32.3::8q24.1----qter) but with no reciprocal 8q-, and three translocations involving chromosome 11 at q13 with partners other than chromosome 14, namely 1q32.1, 8q24.22 and 13q14.3. An earlier report of molecular studies on the DNA of K620 has shown a rearrangement near the region on 11q13 designated BCL-1 (Rabbitts et al. 1988). This is the first report of a rearrangement in the region of 11q13 in a cell line originating from a case of plasma cell leukaemia.

t(2;8) variant translocation in Burkitt's lymphoma: mapping of chromosomal breakpoints by in situ hybridization

In 6 different Burkitt lymphoma cell lines with t(2;8) variant translocations (J1, LY66, LY91, BL21, BL64, JBL2) the breakpoints on chromosome 8q+ were mapped in relation to each other and to c-myc by in situ hybridization. The probes used were derived from chromosome 8q24 and comprised a c-myc probe, a probe located 48 kb downstream of c-myc, 3 probes adjacent to the chromosomal breakpoints of BL64, LY91 and JBL2, respectively, and 2 probes located in the 5' and 3' part of the thyroglobulin gene. The breakpoints of LY91 and JBL2 lie less than 200 kb and greater than 200 kb downstream of c-myc, whereas the distance to c-myc of the BL64 breakpoint and of the thyroglobulin probes is unknown. By recording the hybridization signals specific for these probes on chromosomes 2p- and 8q+ of each cell line it was possible to establish the order of breakpoints on band 8q24 relative to the c-myc and thyroglobulin genes as follows: centromere--c-myc--J1--BL64--BL21--LY91--JBL2--+ ++LY66--thyroglobulin--telomere. This information is essential for further mapping of this important chromosomal region.

Human chromosome 8

The role of human chromosome 8 in genetic disease together with the current status of the genetic linkage map for this chromosome is reviewed. Both hereditary genetic disease attributed to mutant alleles at gene loci on chromosome 8 and neoplastic disease owing to somatic mutation, particularly chromosomal translocations, are discussed.

Population analysis of karyotypic heterogeneity of the Raji Burkitt lymphoma cell line. Analysis of 100 karyotypes

A constant lymphoblastoid line Raji (Burkitt lymphoma) has been used as a model for population cytogenetic studies. In analyzing 100 G-banded metaphase plates, four karyotypically distinct clones of cells with 48 chromosomes have been recognized, forming a modal class. In tracing the origin of marker chromosomes (in all 15), the presence of material specific for Burkitt chromosome markers 14q+ and 8q- has been shown. The application of the method of karyotype reconstruction has shown a uniformity in the overall chromosome material of all four groups of cells despite a different set of normal and marker chromosomes. The presence of 40% of cells with unique structural rearrangements (USR) demonstrated, to a significant extent, the structural instability of chromosomes in Raji cells. The nonrandom nature of distribution of "hot spots" along the chromosomes in the process of formation of both markers and USR has been shown. A preferential involvement of chromosomes #6, #7, and #8, as well as of separate regions 1p32, 6q15, 11q13, and 21p13 has been recorded. This report discusses aspects of karyotypic heterogeneity of cell populations in vitro and structural instability of regions of chromosomes #1 and #11, that coincide with the localization of the oncogene L-MYC or sequence BLYM-1 and the oncogene BCL-1.

Complex translocation t(8;12;14) in a cell line derived from a child with nonendemic Burkitt-type acute lymphoblastic leukemia

A cell line is described with a typical Burkitt lymphoma (BL) marker 14q+ due to the classical reciprocal translocation between chromosome #8 and #14 with breakpoints at 8q24.1 and 14q32.3. In addition, an interstitial piece from the long arm of 12(q24.1-q24.3) is inserted at the site of the exchange on chromosome #8, proximal to 14q32.3.

Human chromosome 22

The acrocentric chromosome 22, one of the shortest human chromosomes, carries about 52 000 kb of DNA. The short arm is made up essentially of heterochromatin and, as in other acrocentric chromosomes, it contains ribosomal RNA genes. Ten identified genes have been assigned to the long arm, of which four have already been cloned and documented (the cluster of lambda immunoglobulin genes, myoglobin, the proto-oncogene c-sis, bcr). In addition, about 10 anonymous DNA segments have been cloned from chromosome 22 specific DNA libraries. About a dozen diseases, including at least four different malignancies, are related to an inherited or acquired pathology of chromosome 22. They have been characterised at the phenotypic or chromosome level or both. In chronic myelogenous leukaemia, with the Ph1 chromosome, and Burkitt's lymphoma, with the t(8;22) variant translocation, the molecular pathology is being studied at the DNA level, bridging for the first time the gap between cytogenetics and molecular genetics.