Molecular diagnosis of Burkitt's lymphoma

Bayesian modelling of shared gene function

MOTIVATION

Biological assays are often carried out on tissues that contain many cell lineages and active pathways. Microarray data produced using such material therefore reflect superimpositions of biological processes. Analysing such data for shared gene function by means of well-matched assays may help to provide a better focus on specific cell types and processes. The identification of genes that behave similarly in different biological systems also has the potential to reveal new insights into preserved biological mechanisms.

RESULTS

In this article, we propose a hierarchical Bayesian model allowing integrated analysis of several microarray data sets for shared gene function. Each gene is associated with an indicator variable that selects whether binary class labels are predicted from expression values or by a classifier which is common to all genes. Each indicator selects the component models for all involved data sets simultaneously. A quantitative measure of shared gene function is obtained by inferring a probability measure over these indicators. Through experiments on synthetic data, we illustrate potential advantages of this Bayesian approach over a standard method. A shared analysis of matched microarray experiments covering (a) a cycle of mouse mammary gland development and (b) the process of in vitro endothelial cell apoptosis is proposed as a biological gold standard. Several useful sanity checks are introduced during data analysis, and we confirm the prior biological belief that shared apoptosis events occur in both systems. We conclude that a Bayesian analysis for shared gene function has the potential to reveal new biological insights, unobtainable by other means.

AVAILABILITY

An online supplement and MatLab code are available at http://www.sykacek.net/research.html#mcabf

Potency analysis of cellular therapies: the emerging role of molecular assays

Potency testing is an important part of the evaluation of cellular therapy products. Potency assays are quantitative measures of a product-specific biological activity that is linked to a relevant biological property and, ideally, a product's in vivo mechanism of action. Both in vivo and in vitro assays can be used for potency testing. Since there is often a limited period of time between the completion of production and the release from the laboratory for administration to the patient, in vitro assays such are flow cytometry, ELISA, and cytotoxicity are typically used. Better potency assays are needed to assess the complex and multiple functions of cellular therapy products, some of which are not well understood. Gene expression profiling using microarray technology has been widely and effectively used to assess changes of cells in response to stimuli and to classify cancers. Preliminary studies have shown that the expression of noncoding microRNA which play an important role in cellular development, differentiation, metabolism and signal transduction can distinguish different types of stem cells and leukocytes. Both gene and microRNA expression profiling have the potential to be important tools for testing the potency of cellular therapies. Potency testing, the complexities associated with potency testing of cellular therapies, and the potential role of gene and microRNA expression microarrays in potency testing of cellular therapies is discussed.

Deconstructing common variable immunodeficiency by genetic analysis

Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency. Patients have recurrent bacterial infections and an increased risk of developing autoimmune diseases, lung damage, and selected cancers. Since 2003, four genes have been shown to be mutated in CVID patients: ICOS, TNFRSF13B (encoding TACI), TNFRSF13C (encoding BAFF-R) and CD19. Heterozygous mutations in TNFRSF13B are also associated with CVID, whereas the other three genes are purely recessive. Recent genetic linkage studies have also identified possible loci for dominant CVID genes on chromosomes 4q, 5p and 16q. These findings markedly improved the genetic diagnosis of CVID and point towards new strategies for future genetic studies. In addition, some CVID genes might be relevant to more common diseases such as asthma and stroke.

Predicting the outcome in non-Hodgkin lymphoma with molecular markers

The World Health Organization classification divides non-Hodgkin lymphomas into B-cell, T-cell and natural killer-cell lymphomas. They are heterogeneous in epidemiology, histopathology and outcome. Clinical prognostic indices rely only on patient factors and staging. Molecular prognostic markers reflect the intrinsic lymphoma biology, measure tumour load and may provide novel therapeutic targets. Lymphomagenesis involves mutations, deletions or dysregulations of genes critical in the control of cell cycle and apoptosis, which are in turn prognostically important. Genome-wide gene expression profiling, either by allowing lymphomas to be classified according to different stages of lymphoid maturation, or by defining specific gene expression signatures, is also of prognostic significance. In lymphomas where viral infections of the neoplastic cells occur, quantification of viral copies is a surrogate marker for tumour load and hence prognosis. Molecular markers together with patient and clinicopathological features will provide more accurate prognostic models for risk stratification, in order to improve treatment outcome.

Proposed classification of lymphoid neoplasms for epidemiologic research from the Pathology Working Group of the International Lymphoma Epidemiology Consortium (InterLymph)

Recent evidence suggests that there is etiologic heterogeneity among the various subtypes of lymphoid neoplasms. However, epidemiologic analyses by disease subtype have proven challenging due to the numerous clinical and pathologic schemes used to classify lymphomas and lymphoid leukemias over the last several decades. On behalf of the International Lymphoma Epidemiology Consortium (InterLymph) Pathology Working Group, we present a proposed nested classification of lymphoid neoplasms to facilitate the analysis of lymphoid neoplasm subtypes in epidemiologic research. The proposed classification is based on the World Health Organization classification of lymphoid neoplasms and the International Classification of Diseases-Oncology, Third Edition (ICD-O-3). We also provide a translation into the proposed classification from previous classifications, including the Working Formulation, Revised European-American Lymphoma (REAL) classification, and ICD-O-2. We recommend that epidemiologic studies include analyses by lymphoma subtype to the most detailed extent allowable by sample size. The standardization of groupings for epidemiologic research of lymphoma subtypes is essential for comparing subtype-specific reports in the literature, harmonizing cases within a single study diagnosed using different systems, as well as combining data from multiple studies for the purpose of pooled analysis or meta-analysis, and will probably prove to be critical for elucidating etiologies of the various lymphoid neoplasms.

Nodal aggressive B-cell lymphomas: a diagnostic approach

The diffuse aggressive B-cell lymphomas, as recognised in the 2001 WHO classification, represent a clinically and biologically heterogeneous group of neoplasms that require very different therapeutic approaches and have very different outcomes. They should be diagnosed using a multiparameter approach that emphasises morphological and immunophenotypic studies, and in at least some cases, relies on cytogenetic and/or genotypic studies. Incorporation of clinical data may be important as well. There is also current interest in going beyond the basic diagnosis and providing pathological prognostic information when possible. Whereas the diagnosis of some cases will be relatively easy, the differential diagnosis in others is very difficult, with some cases in a grey zone between two different well defined categories.

Aberrant immunoglobulin class switch recombination and switch translocations in activated B cell-like diffuse large B cell lymphoma

To elucidate the mechanisms underlying chromosomal translocations in diffuse large B cell lymphoma (DLBCL), we investigated the nature and extent of immunoglobulin class switch recombination (CSR) in these tumors. We used Southern blotting to detect legitimate and illegitimate CSR events in tumor samples of the activated B cell-like (ABC), germinal center B cell-like (GCB), and primary mediastinal B cell lymphoma (PMBL) subgroups of DLBCL. The frequency of legitimate CSR was lower in ABC DLBCL than in GCB DLBCL and PMBL. In contrast, ABC DLBCL had a higher frequency of internal deletions within the switch mu (Smu) region compared with GCB DLBCL and PMBL. ABC DLBCLs also had frequent deletions within Sgamma and other illegitimate switch recombinations. Sequence analysis revealed ongoing Smu deletions within ABC DLBCL tumor clones, which were accompanied by ongoing duplications and activation-induced cytidine deaminase-dependent somatic mutations. Unexpectedly, short fragments derived from multiple chromosomes were interspersed within Smu in one case. These findings suggest that ABC DLBCLs have abnormalities in the regulation of CSR that could predispose to chromosomal translocations. Accordingly, aberrant switch recombination was responsible for translocations in ABC DLBCLs involving BCL6, MYC, and a novel translocation partner, SPIB.

Downregulation of Bfl-1 protein expression sensitizes malignant B cells to apoptosis

Elevated expression of the antiapoptotic protein Bfl-1 (A1) was previously reported in several cancer cell lines. Recently, molecular profiling of large B-cell lymphoma identified Bfl-1 as a gene signature in 'OxPhos' diffuse large B-cell lymphoma subtype and in primary mediastinal large B-cell lymphoma, suggesting that in addition to Bcl-2, Bcl-xL and Mcl-1, Bfl-1 may be a relevant target in the design of new strategies for cancer therapy. Using short hairpin RNA strategy, we show here that Bfl-1 silencing in one lymphoblastoid B-cell line and in two diffuse large B-cell lymphoma cell lines potently induces their apoptosis and sensitizes those cell lines to anti-CD20 (Rituximab)-mediated cell death as well as to apoptosis induced by chemotherapeutic molecules such as doxorubicin, vincristine, cisplatin and fludarabine. These results demonstrate for the first time that Bfl-1 is an essential protein for survival of malignant B cells and suggest Bfl-1 may represent a potential target for future drug development against B cell lymphoma.

Gastrointestinal lymphoproliferative disorders

Malignant lymphomas can be first detected in some patients in endoscopic biopsies of the gastrointestinal (GI) tract. However, their recognition and accurate classification often pose problems for the pathologist for several reasons. First, the small sampling size limits pattern recognition and the number of ancillary studies which can be performed. Second, the immune system of the GI tract is capable of intense hyperplastic responses which may mimic lymphoma. Third, in a fashion similar to cutaneous lesions, those in the alimentary tract may be visualized and biopsied at a very early phase in their development when differentiation into neoplasia may be incomplete. Some forms of immune response actually pass through a poorly defined transition into lymphoma. Examples of such 'dysplasia' of the gut immune system include Helicobacter gastritis, coeliac disease and multicentric lymphoid hyperplasia associated with underlying immunodeficiency. With ever increasing endoscopic scrutiny of the gut by gastroenterologists, it is not surprising that the frequency of these indeterminate cases seems to be growing. In combination with careful clinical correlation and conventional microscopic analysis, selective immunohistochemical studies currently constitute the most powerful ancillary method in the pathologist's effort to recognize and classify GI lymphomas accurately.

Mapping of MYC breakpoints in 8q24 rearrangements involving non-immunoglobulin partners in B-cell lymphomas

Chromosomal translocations joining the immunoglobulin (IG) and MYC genes have been extensively reported in Burkitt's and non-Burkitt's lymphomas but data concerning MYC rearrangements with non-IG partners are scarce. In this study, 8q24 breakpoints from 17 B-cell lymphomas involving non-IG loci were mapped by fluorescence in situ hybridization (FISH). In seven cases the breakpoint was inside a small region encompassing MYC: in one t(7;8)(p12;q24) and two t(3;8)(q27;q24), it was telomeric to MYC whereas in four cases, one t(2;8)(p15;q24) and three t(8;9)(q24;p13) it was located in a 85 kb region encompassing MYC. In these seven cases, partner regions identified by FISH contained genes known to be involved in lymphomagenesis, namely BCL6, BCL11A, PAX5 and IKAROS. Breakpoints were cloned in two t(8;9)(q24;p13), 2.5 and 7 kb downstream from MYC and several hundred kb 5' to PAX5 on chromosome 9, joining MYC to ZCCHC7 and to ZBTB5 exon 2, two genes encoding zinc-finger proteins. In these seven cases, MYC expression measured by quantitative reverse transcription-polymerase chain reaction (RT-PCR) was significantly higher when compared to that of patients without 8q24 rearrangement (P=0.006). These results suggest that these rearrangements are the consequence of a non-random process targeting MYC together with non-IG genes involved in lymphocyte differentiation and lymphoma progression.

Diagnosis and Treatment of Childhood Non-Hodgkin Lymphoma

Major advances have been made in the treatment of childhood non-Hodgkin lymphoma (NHL). The recognition that different NHL subtypes require different treatment strategies was fundamental to developing successful therapy regimens. Currently established therapy groups are lymphoblastic lymphoma (LBL) of precursor B- or T-cell type, mature B-cell neoplasms (B-NHL), and anaplastic large cell lymphoma (ALCL). Accurate diagnostic classification is crucial for allocating patients to appropriate treatment groups. Therapy protocols designed to treat children with acute lymphoblastic leukemia (ALL) have proven highly efficacious for treating children with LBL and are associated with event-free survival (EFS) rates up to 80%. For children with B-NHL, a strategy of rapidly repeated short, dose-intense courses proved more efficacious, with EFS rates up to 90%. In patients with ALCL, comparable results are achieved with either strategy, although this group has the highest relapse rate. The price of these efficacious treatments is considerable toxicity. On the other hand, the chance to survive after relapse is still dismal due to the almost complete lack of established salvage regimen. Thus, refinement of the balance between treatment burden and individual patient risk for failure is a major future task. A variety of new treatment options, some already established for treating adult NHL, await evaluation in childhood NHL.

EBV-associated diseases in the AIDS patient

EBV-associated malignancies remain a considerable problem in HIV-infected individuals, even in the era of HAART. Although EBV is a common factor, each disease has a unique pathogenesis. Study of these diseases reveals the viral proteins expressed in the malignancies that might contribute to the development of the disease as well as the molecular basis for pathogenesis. It is likely that this knowledge will contribute to the development of novel therapeutics that will result in more favorable outcomes in the future.

Microarray expression technology in clinical research of non-Hodgkin lymphoma

Nowadays, in genomocentric era accelerated research of the human genome coupled with advances is enabling the comprehensive molecular profiling of human tissue. Particularly, DNA microarrays are powerful tools for obtaining global view of human non-Hodgkin lymphomas gene expression. Complex information from lymphomas "expression profiling" studies can, in turn, be used to create molecular markers that have diagnostic or prognostic implications. The gene "expression profiling" is not of routine clinical oncology practice, but is used in genomic classification of clinically relevant subgroups of non-Hodgkin lymphoma. The genomics biomarkers have been incorporated into current prognostic models which are based on IPI, R-IPI, and FLIPI. Molecular or pharmacogenomic profiling can be used as new therapeutic targets for patients who are refractory to current therapy. We discus the utility of DNA microarray-based lymphoma profiling in clinical oncology research, and identify future of research in lymphoma evolving fields.

Burkitt lymphoma: revisiting the pathogenesis of a virus-associated malignancy

Burkitt lymphoma (BL), a tumor occurring in endemic, sporadic and AIDS-associated forms, is the classic example of a human malignancy whose pathogenesis involves a specific cellular genetic change, namely, a chromosomal translocation deregulating expression of the c-myc oncogene, complemented in many cases by the action of an oncogenic virus, the Epstein-Barr virus (EBV). Here we review recent work in two complementary areas of research: (1) on cellular genetic changes that occur in addition to the c-myc translocation in BL, in particular the capacity of p53/ ARF pathway breakage or of c-myc mutation to decouple the pro-proliferative effects of c-myc deregulation from its pro-apoptotic effects; and (2) on a postulated role for EBV in BL pathogenesis, through adopting restricted forms of virus latent gene expression that remain compatible with the c-myc-driven growth program but offer the tumor additional protection from apoptosis. We stress the many fundamental questions that remain to be resolved and, in that regard, highlight the general lessons that might be learned through understanding how two other infectious agents, malaria and HIV, dramatically enhance BL incidence.

Diagnosis and Treatment of Childhood Non-Hodgkin Lymphoma

Major advances have been made in the treatment of childhood non-Hodgkin lymphoma (NHL). The recognition that different NHL subtypes require different treatment strategies was fundamental to developing successful therapy regimens. Currently established therapy groups are lymphoblastic lymphoma (LBL) of precursor B- or T-cell type, mature B-cell neoplasms (B-NHL), and anaplastic large cell lymphoma (ALCL). Accurate diagnostic classification is crucial for allocating patients to appropriate treatment groups. Therapy protocols designed to treat children with acute lymphoblastic leukemia (ALL) have proven highly efficacious for treating children with LBL and are associated with event-free survival (EFS) rates up to 80%. For children with B-NHL, a strategy of rapidly repeated short, dose-intense courses proved more efficacious, with EFS rates up to 90%. In patients with ALCL, comparable results are achieved with either strategy, although this group has the highest relapse rate. The price of these efficacious treatments is considerable toxicity. On the other hand, the chance to survive after relapse is still dismal due to the almost complete lack of established salvage regimen. Thus, refinement of the balance between treatment burden and individual patient risk for failure is a major future task. A variety of new treatment options, some already established for treating adult NHL, await evaluation in childhood NHL.

Should Adolescents with NHL Be Treated as Old Children or Young Adults?

The SEER (Surveillance, Epidemiology, and End Results) data for the years 1975–1998 show that children with non-Hodgkin lymphoma (NHL) have a better treatment outcome than do adults. Many factors may contribute to this age-related difference. Some factors are related to the patient (e.g., drug distribution and clearance, performance status, compliance, sex) whereas others pertain to tumor histology and biology. The spectrum of NHL subtypes is well known to differ in children and adults. From ages 5 through 14 years, Burkitt lymphoma is the predominant histologic subtype, whereas diffuse large B-cell lymphoma is most common in the 15- to 29-year age range. Because different treatment strategies are often used in children and adults with NHL, the choice of therapy for adolescents and young adults (ages 15 through 29 years) is challenging and somewhat controversial. It is reasonable to consider pediatric strategies for some adolescents and very young adults with NHL, and pediatric strategies are currently used to treat adults with certain subtypes of NHL (Burkitt lymphoma, lymphoblastic lymphoma). However, the use of pediatric strategies in adults does not guarantee a comparable outcome, as illustrated by trials for adult lymphoblastic lymphoma. There is clearly a need for further biologic study of NHL in children, adolescents, and young adults. Age-related differences in tumor biology have been demonstrated in anaplastic large-cell lymphoma (ALCL) and diffuse large B-cell lymphoma (DLBCL). Additional biologic data will not only improve prognosis and treatment stratification but, more important, will lead to the identification of specific molecular targets for therapy.

Blood genomic profiling: novel diagnostic and therapeutic strategies for stroke?

Findings from gene expression profiling studies are leading to new diagnostic and therapeutic strategies that can be applied in medical practice, especially in the field of oncology. Promising results of gene expression profiling of the peripheral blood in patients with ischaemic stroke have been obtained in recent pilot studies, demonstrating a partially reproducible gene signature of acute cerebral ischaemia. However, questions remain. Given that blood is at least in part a surrogate tissue for ischaemic stroke, the specificity of these signatures needs to be evaluated. Furthermore, it needs to be determined whether standardization of this methodology is required and whether clinical signatures can be identified that are improvements over the tools currently used in clinical practice. Clinically useful signatures would include those of haemorrhagic as well as ischaemic stroke, reclassification of stroke type and prognosis, and vascular disease risk. If these conditions are met, then it should be possible to develop cost-effective and rapid assays.

Linking oncogenic pathways with therapeutic opportunities

The accumulation of multiple mutations and alterations in the cancer genome underlies the complexity of cancer phenotypes. A consequence of these alterations is the deregulation of various cell-signalling pathways that control cell function. Molecular-profiling studies, particularly DNA microarray analyses, have the potential to describe this complexity. These studies also provide an opportunity to link pathway deregulation with potential therapeutic strategies. This approach, when coupled with other methods for identifying pathway activation, provides an opportunity to both match individual patients with the most appropriate therapeutic strategy and identify potential options for combination therapy.