Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain ...therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.
In this issue of
, Schaffer and colleagues uncover a novel epigenetic mechanism of resistance to the Bruton tyrosine kinase inhibitor ibrutinib in activated B-cell-like diffuse large B-cell lymphoma ...(ABC-DLBCL), whereby tumor cells rewire the B-cell receptor (BCR)-driven NF-κB signaling cascade through the small GTPase RAC2. This circuit can be efficiently targeted by RAC1/2 small-molecule inhibitors, suggesting a promising new therapeutic approach to overcome acquired ibrutinib resistance in ABC-DLBCL and possibly other B-cell malignancies relying on active BCR signaling.
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Abstract
Diffuse large B cell lymphoma (DLBCL), the most common form of human lymphoma, is a heterogeneous neoplasm comprising multiple genetic, phenotypic and clinical subtypes, approximately 50% of ...which are incurable. These tumors may arise de novo or from the transformation of more indolent lymphomas, as observed in 30-40% of follicular lymphoma (FL) cases. Over the past decade, the introduction of next-generation sequencing technologies combined with genome-wide copy number analysis has allowed to comprehensively define the genomic landscape of this disease, leading to the identification of multiple genes and signaling pathways that are dysregulated by genetic lesions and represent potential targets for diagnosis and therapy. In addition to perturbations in the transcriptional control of apoptosis, differentiation and DNA damage responses or NF-κB activation, these efforts revealed the frequent targeting of genes implicated in chromatin remodeling and immune recognition/surveillance.
In particular, one of the most commonly disrupted programs in both de novo DLBCL, FL and transformed FL (tFL) comprises genes encoding histone/chromatin modifying enzymes, including methyltransferases (MLL2, EZH2) and acetyltransferases (CREBBP, EP300), which may play a central role during malignant transformation. Interestingly, sequential analysis of tumor samples during transformation of FL to tFL indicates that inactivating mutations of CREBBP and MLL2 are acquired early in the evolutionary history of a common mutated ancestral clone. The disruption of these genes by genetic alterations may thus contribute to malignant transformation by shaping the epigenetic landscape of the cancer cell as well as by perturbing specific biological programs, in part through the altered balance between acetylation-mediated activation of the p53 tumor suppressor and inactivation of the BCL6 proto-oncogene. This talk will cover recent advances in understanding the genetic basis of DLBCL, as revealed by in vitro and in vivo studies.
Citation Format: Laura Pasqualucci. The genetic basis of diffuse large B cell lymphoma. abstract. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr IA39.
Over the past two decades, genomic analyses of several B-cell lymphoma entities have identified a large number of genes that are recurrently mutated, suggesting that their aberrant function promotes ...lymphomagenesis. For many of those genes, the specific role in normal B-cell development is unknown; moreover, whether and how their deregulated activity contributes to lymphoma initiation and/or maintenance is often difficult to determine. Genetically engineered mouse models that faithfully mimic lymphoma-associated genetic alterations represent valuable tools for elucidating the pathogenic roles of candidate oncogenes and tumor suppressors in vivo, as well as for the preclinical testing of novel therapeutic principles in an intact microenvironment. Here we summarize what has been learned about the mechanisms of oncogenic transformation from accurately modeling the most common and well-characterized genetic alterations identified in mature B-cell malignancies. This information is expected to guide the design of improved molecular diagnostics and mechanism-based therapeutic approaches for these diseases.
Diffuse large B-cell lymphoma (DLBCL), the most common form of human lymphoma, is an aggressive malignancy comprising multiple phenotypically and genetically distinct subtypes, approximately 40% of ...which are incurable. These tumors may arise de novo or from the transformation of more indolent lymphomas, as observed in 30-40% of follicular lymphoma (FL) and 5-12% of chronic lymphocytic leukemia cases. Over the last decade, the introduction of next-generation sequencing technologies combined with genome-wide copy number analysis has allowed a comprehensive definition of the genetic lesions that are associated with the pathogenesis of these malignancies, leading to the identification of several previously unappreciated targets1-3. These lesions, in turn, uncovered dysregulated cellular pathways that represent potential targets for improved diagnosis and therapy. Among the most common genetic alterations found in both de novo DLBCL and transformed FL (tFL) are those targeting histone/chromatin modifiers; in particular, loss-of-function mutations in the genes encoding for the H3K4 methyltransferase MLL2 and the acetyltransferases CREBBP/EP300, together with gain-of-function mutations of the EZH2 H3K27 methyltransferase are observed in over 50% of DLBCL and 90% of tFL patients, suggesting a major role for these enzymes in altering gene expression during malignant transformation. Interestingly, sequential analysis of tumor samples isolated at FL diagnosis and at evolution to DLBCL indicates that inactivating mutations of CREBBP and MLL2 represent early events acquired during the initial expansion of a common ancestral clone4. Disruption of epigenetic modifiers by genetic alterations may thus contribute to malignant transformation by shaping the epigenetic landscape of the cancer cell as well as by perturbing specific biological programs. In line with this hypothesis, we have shown that mutations of CREBBP/EP300 disrupt the balance between acetylation-mediated activation of the p53 tumor suppressor and inactivation of the BCL6 proto-oncogene5. The lecture will cover recent advances in our understanding of the genetic basis of this disease, with emphasis on the role of epigenetic regulators in normal germinal center development and lymphomagenesis, as revealed by in vitro and in vivo studies.
References:
1. Pasqualucci L, Trifonov V, Fabbri G, et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011; 43: 830-837.
2. Morin RD, Mendez-Lago M, Mungall AJ, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011; 476: 298-303.
3. Lohr JG, Stojanov P, Lawrence MS, et al. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012; 109: 3879-3884.
4. Pasqualucci L, Khiabanian H, Fangazio M, et al., Genetics of follicular lymphoma transformation. Cell Rep. 2014; 6:130-140.
5. Pasqualucci L, Dominguez-Sola D, Trifonov V, et al. Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature. 2011; 471: 189-195.
No relevant conflicts of interest to declare.
The molecular mechanism involved in the process of antigen-driven somatic hypermutation of Ig genes is unknown, but it is commonly believed that this mechanism is restricted to the Ig loci. B cell ...lymphomas commonly display multiple somatic mutations clustering in the 5′-regulatory region of BCL-6, a proto-oncogene encoding for a POZ/Zinc finger transcriptional repressor expressed in germinal center (GC) B cells and required for GC formation. To determine whether BCL-6 mutations represent a tumor-associated phenomenon or reflect a physiologic mechanism, we screened single human tonsillar GC B cells for mutations occurring in the BCL-6 5′-noncoding region and in the Ig variable heavy chain sequences. Thirty percent of GC B cells, but not naive B cells, displayed mutations in the 742 bp region analyzed within the first intron of BCL-6 (overall frequency: 5× 10-4/bp). Accordingly, an expanded survey in lymphoid malignancies showed that BCL-6 mutations are restricted to B cell tumors displaying GC or post-GC phenotype and carrying mutated Ig variable heavy chain sequences. These results indicate that the somatic hypermutation mechanism active in GC B cells physiologically targets non-Ig sequences.
IRTA1 (immunoglobulin superfamily receptor translocation-associated 1) is a novel surface B-cell receptor related to Fc receptors, inhibitory receptor superfamily (IRS), and cell adhesion molecule ...(CAM) family members and we mapped for the first time its distribution in human lymphoid tissues, using newly generated specific antibodies. IRTA1 was selectively and consistently expressed by a B-cell population located underneath and within the tonsil epithelium and dome epithelium of Peyer patches (regarded as the anatomic equivalents of marginal zone). Similarly, in mucosa-associated lymphoid tissue (MALT) lymphomas IRTA1 was mainly expressed by tumor cells involved in lympho-epithelial lesions. In contrast, no or a low number of IRTA1+ cells was usually observed in the marginal zone of mesenteric lymph nodes and spleen. Interestingly, monocytoid B cells in reactive lymph nodes were strongly IRTA1+. Tonsil IRTA1+ cells expressed the memory B-cell marker CD27 but not mantle cell-, germinal center-, and plasma cell-associated molecules. Polymerase chain reaction (PCR) analysis of single tonsil IRTA1+ cells showed they represent a mixed B-cell population carrying mostly mutated, but also unmutated, IgV genes. The immunohistochemical finding in the tonsil epithelial areas of aggregates of IRTA1+ B cells closely adjacent to plasma cells surrounding small vessels suggests antigen-triggered in situ proliferation/differentiation of memory IRTA1+ cells into plasma cells. Collectively, these results suggest a role of IRTA1 in the immune function of B cells within epithelia. (Blood. 2003;102: 3684-3692)
Non-Hodgkin's lymphomas (NHL) form a heterogeneous group of diseases, with diffuse large B-cell lymphoma (DLBCL) comprising the largest subgroup. The commonest chromosomal translocations found in ...DLBCL are those affecting band 3q27. In 35% of DLBCL cases, as well as in a small fraction of follicular lymphomas, the normal transcriptional regulation of Bcl-6 is disrupted by these chromosomal translocations. In addition, about three-quarters of cases of DLBCL display multiple somatic mutations in the 5′ non-coding region of Bcl-6, which occur independently of chromosomal translocations and appear to be due to the IgV-associated somatic hypermutation process. Bcl-6 is a 95-kD nuclear phosphoprotein belonging to the BTB/POZ (bric-a-brac, tramtrack, broad complex/Pox virus zinc finger) zinc finger family of transcription factors. It has been suggested that Bcl-6 is important in the repression of genes involved in the control of lymphocyte activation, differentiation, and apoptosis within the germinal center, and that its down-regulation is necessary for normal B-cells to exit the germinal center. Bcl-6 remains constitutively expressed in a substantial proportion of B-cell lymphomas. Recently, acetylation has been identified as a mode for down-regulating Bcl-6 activity by inhibition of the ability of Bcl-6 to recruit complexes containing histone deacetylases (HDAC). The pharmacologic inhibition of two recently identified deacetylation pathways, HDAC- and silent information regulator (SIR)-2-dependent deacetylation, results in the accumulation of inactive acetylated Bcl-6 and thus in cell cycle arrest and apoptosis in B-cell lymphoma cells. These results reveal a new method of regulating Bcl-6, with the potential for therapeutic exploitation. These studies also indicate a novel mechanism by which acetylation promotes transcription, not only by modifying histones and activating transcriptional activators, but also by inhibiting transcriptional repressors.
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Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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