Ploidy status rarely changes in myeloma patients at disease progression

CNV Radar: an improved method for somatic copy number alteration characterization in oncology

Background

Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it challenging to accurately detect abnormal copy number events in a cost-effective manner in clinical studies.

Results

Here we present CNV Radar, a software tool that utilizes next-generation sequencing read depth information and variant allele frequency patterns, to infer the true copy number status of genes and genomic regions from whole exome sequencing data. Evaluation of CNV Radar in a public multiple myeloma dataset demonstrated that CNV Radar was able to detect a variety of CNVs associated with risk of progression, and we observed > 70% concordance with fluorescence in situ hybridization (FISH) results. Compared to other CNV callers, CNV Radar showed high sensitivity and specificity. Similar results were observed when comparing CNV Radar calls to single nucleotide polymorphism array results from acute myeloid leukemia and prostate cancer datasets available on TCGA. More importantly, CNV Radar demonstrated its utility in the clinical trial setting: in POLLUX and CASTOR, two phase 3 studies in patients with relapsed or refractory multiple myeloma, we observed a high concordance rate with FISH for del17p, a risk defining CNV event (88% in POLLUX and 90% in CASTOR), therefore allowing for efficacy assessments in clinically relevant disease subgroups. Our case studies also showed that CNV Radar is capable of detecting abnormalities such as copy-neutral loss of heterozygosity that elude other approaches.

Conclusions

We demonstrated that CNV Radar is more sensitive than other CNV detection methods, accurately detects clinically important cytogenetic events, and allows for further interrogation of novel disease biology. Overall, CNV Radar exhibited high concordance with standard methods such as FISH, and its success in the POLLUX and CASTOR clinical trials demonstrated its potential utility for informing clinical and therapeutic decisions.

Rapid assessment of hyperdiploidy in plasma cell disorders using a novel multi-parametric flow cytometry method

Trisomies of odd numbered chromosomes are seen in nearly half of patients with multiple myeloma (MM) and typically correlate with a hyperdiploid state and better overall survival (OS). We compared DNA ploidy of monoclonal plasma cells (as a surrogate for the presence of trisomies) assessed simultaneously by PCPRO (plasma cell proliferative index), a novel method that estimates DNA index by multi-parametric flow cytometry to fluorescence in situ hybridization (FISH) in 1703 patients with plasma cell disorders. The distribution of ploidy was hyperdiploid: 759 (45%), diploid 765 (45%), hypodiploid: 71 (4%), tetraploid/near-tetraploid: 108 (6%). FISH identified trisomies in 82% (621/756) of patients with hyperdiploidy by PCPRO and no trisomy by FISH was observed in 88% (730/834) of patients without hyperdiploidy. 95% (795/834) of patients without hyperdiploidy on PCPRO had one or less trisomy by FISH. Sensitivity and specificity of PCPRO for detecting hyperdiploidy was 86% (621/725) and 84% (730/865), respectively. Sensitivity increased to 94% (579/618) for patients with more than one trisomy. Newly diagnosed MM patients with hyperdiploidy on PCPRO (147/275) had better OS compared to nonhyperdiploid patients (median not reached vs 59 months, P = 0.008) and better progression free survival (median: 33 vs 23 months, P = 0.03). Within the hyperdiploidy group, patients with high-hyperdiploidy (DNA index: 1.19-1.50) versus those with low-hyperdiploidy (DNA index: 1.05-1.18) had superior OS (3 year OS of 88% vs 68% P = 0.03). Ploidy assessment by flow cytometry can provide rapid, valuable prognostic information and also reduces the number of copy number FISH probes required and hence the cost of FISH.

Dissecting karyotypic patterns in non-hyperdiploid multiple myeloma: an overview on the karyotypic evolution

BACKGROUND

Multiple myeloma (MM) is a plasma cell disorder characterized by the presence of specific genetic and cytogenetic aberrations that define unique subgroups with different outcomes. On the basis of the ploidy status, MM can be subdivided into hyperdiploid MM (H-MM) and non-hyperdiploid MM (NH-MM). NH-MM is an entity that encompasses hypodiploid, pseudodiploid, and near tetraploid MM and is associated with a higher number of immunoglobulin heavy-chain (IgH) translocations.

MATERIALS AND METHODS

We have systematically analyzed the structure of the karyotypic evolution in NH-MM and identified several genetic features of their complex karyotypic patterns.

RESULTS

On the basis of statistical models used in complex karyotypes, we were able to identify the temporal order in which the genetic aberrations occur in NH-MM. In this analysis, whole chromosome losses and IgH translocations were commonly seen, and -13/13q- and t14q32 were defined as early genetic events in the karyotypic evolution of NH-MM. Furthermore, chromosome 1 and 17 abnormalities were associated with a late karyotypic phase of evolution consistent with the recognized pattern of acquired events deemed to be associated with these type of genetic aberrations.

CONCLUSION

Accumulation of genetic aberrations in NH-MM above a threshold results in malignant transformation.

Relapsed/Refractory multiple myeloma: defining refractory disease and identifying strategies to overcome resistance

Despite the development of more effective therapies for multiple myeloma (MM) over the past decade, nearly all patients will eventually experience disease relapse and require further therapy. Designing the next generation of therapies for relapsed and refractory disease will depend on understanding the complex molecular pathogenesis of MM and mechanisms of resistance. Oncogenomic studies have identified many potential therapeutic targets and have led to emerging models of the multistep molecular pathogenesis of MM. The key to overcoming resistance may depend on interrupting the complex interactions between MM cells and the bone microenvironment. Direct interaction between MM cells and bone marrow cells activates pleiotropic signaling pathways that mediate growth, survival, and migration of MM cells as well as resistance to chemotherapy (known as cell adhesion-mediated drug resistance). The bone marrow also secretes growth factors and cytokines that maintain MM cells and inhibit apoptosis. Therefore, successful therapeutic strategies must target not only the MM plasma cell but also the bone microenvironment. The benefit of immunomodulatory drugs such as thalidomide and lenalidomide and the proteasome inhibitor bortezomib in relapsed/refractory MM is related to their ability to target both. Novel agents and combination strategies are building on the success of these agents and targeting synergistic pathways.

The t(4;14) translocation and FGFR3 overexpression in multiple myeloma: prognostic implications and current clinical strategies

Multiple myeloma (MM) is a heterogeneous plasma cell disorder characterized by genetic abnormalities, including chromosomal translocations, deletions, duplications and genetic mutations. Translocations involving the immunoglobulin heavy chain region at chromosome 14q32 are observed in approximately 40% of patients with MM. Translocation of oncogenes into this region may lead to their increased expression, contributing to disease initiation, disease progression and therapeutic resistance. The t(4;14) translocation is associated with upregulation of the fibroblast growth factor receptor 3 (FGFR3) and the myeloma SET domain protein. Patients with t(4;14) demonstrate an overall poor prognosis that is only partially mitigated by the use of the novel agents bortezomib and lenalidomide; as such, an unmet medical need remains for patients with this aberration. Preclinical studies of inhibitors of FGFR3 have shown promise in t(4;14) MM, and these studies have led to the initiation of clinical trials. Data from these trials will help to determine the clinical utility of FGFR3 inhibitors for patients with t(4;14) MM and may pave the way for personalized medicine in patients with this incurable disease.

Pathogenesis of myeloma

Multiple myeloma (MM) is a neoplasm of post-germinal center, terminally differentiated B cells. It is characterized by a multifocal proliferation of clonal, long-lived plasma cells within the bone marrow (BM) and associated skeletal destruction, serum monoclonal gammopathy, immune suppression, and end-organ sequelae. MM is preceded by an age-progressive premalignant condition termed monoclonal gammopathy of undetermined significance. Unlike the genomes of most hematological malignancies, and similar to those of solid-tissue neoplasms, MM genomes are typified by numerous structural and numerical chromosomal aberrations as well as mutations in a number of oncogenes and tumor-suppressor genes, some of which have been linked to disease pathogenesis and clinical behavior. Recent studies have also defined the importance of interactions between the MM cells and their BM microenvironment, dysregulation in signaling pathways and in a specialized subpopulation of cells within the tumor (termed myeloma cancer stem cells) for tumor cell growth and survival, and the development of resistance to therapy.

Molecular pathogenesis of multiple myeloma: chromosomal aberrations, changes in gene expression, cytokine networks, and the bone marrow microenvironment

This chapter focuses on two aspects of myeloma pathogenesis: (1) chromosomal aberrations and resulting changes in gene and protein expression with a special focus on growth and survival factors of malignant (and normal) plasma cells and (2) the remodeling of the bone marrow microenvironment induced by accumulating myeloma cells. We begin this chapter with a discussion of normal plasma cell generation, their survival, and a novel class of inhibitory factors. This is crucial for the understanding of multiple myeloma, as several abilities attributed to malignant plasma cells are already present in their normal counterpart, especially the production of survival factors and interaction with the bone marrow microenvironment (niche). The chapter closes with a new model of pathogenesis of myeloma.

The basis and rational use of molecular genetic testing in mature B-cell lymphomas

An increasing number of neoplasms are associated with variably specific genetic abnormalities. This is best exemplified by hematological malignancies, in which there is a growing list of entities that are defined by their genetic lesion(s); this is not (yet) the case in mature B-cell lymphomas. However, enhanced insights into the pathogenesis of this large and diverse group of lymphomas have emerged with the ongoing unraveling of a plethora of fascinating genetic abnormalities. The purpose of this review is to synthesize well-recognized data and nascent discoveries in our understanding of the genetic basis of a spectrum of mature B-cell lymphomas, and how this may be applied to contemporary clinical practice. Despite the explosion of new and exciting knowledge in this arena, with the potential for enhanced diagnostic and prognostic strategies, it is essential to remain cognizant of the limitations (and complexity) of genetic investigations, so that assays can be developed and used both judiciously and rationally.

International Myeloma Working Group molecular classification of multiple myeloma: spotlight review

Myeloma is a malignant proliferation of monoclonal plasma cells. Although morphologically similar, several subtypes of the disease have been identified at the genetic and molecular level. These genetic subtypes are associated with unique clinicopathological features and dissimilar outcome. At the top hierarchical level, myeloma can be divided into hyperdiploid and non-hyperdiploid subtypes. The latter is mainly composed of cases harboring IgH translocations, generally associated with more aggressive clinical features and shorter survival. The three main IgH translocations in myeloma are the t(11;14)(q13;q32), t(4;14)(p16;q32) and t(14;16)(q32;q23). Trisomies and a more indolent form of the disease characterize hyperdiploid myeloma. A number of genetic progression factors have been identified including deletions of chromosomes 13 and 17 and abnormalities of chromosome 1 (1p deletion and 1q amplification). Other key drivers of cell survival and proliferation have also been identified such as nuclear factor- B-activating mutations and other deregulation factors for the cyclin-dependent pathways regulators. Further understanding of the biological subtypes of the disease has come from the application of novel techniques such as gene expression profiling and array-based comparative genomic hybridization. The combination of data arising from these studies and that previously elucidated through other mechanisms allows for most myeloma cases to be classified under one of several genetic subtypes. This paper proposes a framework for the classification of myeloma subtypes and provides recommendations for genetic testing. This group proposes that genetic testing needs to be incorporated into daily clinical practice and also as an essential component of all ongoing and future clinical trials.

Role of genetics in prognostication in myeloma

As in other hematological malignancies, cytogenetics is becoming a major prognostic parameter in myeloma. Myeloma differs from other hemopathies particularly in technical aspects related to low proliferation and partial infiltrates. Thus, fluorescence in-situ hybridization (FISH) is probably the best method for cytogenetic assessment in myeloma, but it requires the identification of the malignant cells (morphologically, immunologically or through sorting). Several chromosomal abnormalities have been identified. Among them, the t(4;14) and t(14;16) translocations and the del(17p) are the most important for outcome prediction, all of them predicting a short overall survival. However, even in these genetically defined subgroups, an outcome heterogeneity is observed, suggesting the role of other factors (genetic or otherwise) in disease evolution.

Chromosome 13q deletion and IgH abnormalities may be both masked by near-tetraploidy in a high proportion of multiple myeloma patients: A combined morphology and I-FISH analysis

Ploidy status and chromosomal aberrations involving chromosome 13q and the immunoglobulin heavy chain locus (IgH) are important prognostic features in multiple myeloma (MM). However, conventional cytogenetic studies are often not reveling and determination of plasma cells (PC) ploidy status in MM is technically difficult. We have used a combined cell morphology and interphase FISH (I-FISH) analysis in 184 consecutive BM samples from 136 MM patients for the diagnosis of chromosome 13q deletion [del (13q)] and IgH abnormalities. We have found a high prevalence (37%) of near-tetraploid (NT) PC in the BM samples studied. NT status of PC was verified with DNA index (DI) measurements. del (13q) was found in 69% and a total absence of one IgH copy (loss of IgH) in 20% of NT samples. We have shown that the presence of del (13q) and loss of IgH can be masked in NT cases: in 12 NT samples originally identified as normal for del (13q) the abnormality was obscured in the majority of plasma cells due to the presence of NT. Similarly, loss of IgH was masked in four samples with a large population of NT cells. Moreover, in one case the appearance of a 100% tetraploidy during disease progression masked the presence of del (13q), originally present, and could therefore falsely appear as disappearance of this prognostic marker. In conclusion, we have shown that a combination of three abnormalities, i.e., del (13q), loss of IgH and NT, all of potential prognostic significance, can be overlooked unless NT is specifically searched for and ruled out. Therefore, we suggest that a search for NT should be added to the routine BM assessment in MM patients.

Understanding multiple myeloma pathogenesis in the bone marrow to identify new therapeutic targets

Multiple myeloma is a plasma cell malignancy characterized by complex heterogeneous cytogenetic abnormalities. The bone marrow microenvironment promotes multiple myeloma cell growth and resistance to conventional therapies. Although multiple myeloma remains incurable, novel targeted agents, used alone or in combination, have shown great promise to overcome conventional drug resistance and improve patient outcome. Recent oncogenomic studies have further advanced our understanding of the molecular pathogenesis of multiple myeloma, providing the framework for new prognostic classification and identifying new therapeutic targets.

Sequential analysis of chromosome aberrations in multiple myeloma during disease progression

PURPOSE

Several chromosomal aberrations have been associated with molecular pathogenesis and classification of multiple myeloma. It is not known whether the expression of abnormal karyotypes is consistent in patients during disease progression. Herein, we report on sequential analysis of conventional cytogenetics as well as fluorescence in situ hybridization (FISH) data of 79 bone marrow specimens from 38 patients with myeloma who were longitudinally followed.

PATIENTS AND METHODS

We determined and characterized the development of additional chromosomal aberrations during progressive disease.

RESULTS

Overall, conventional cytogenetics detected an abnormal karyotype in 42% of the samples, whereas this increased to 69% by FISH. Among the cases with an abnormal conventional karyotype, 52% had a hyperdiploid subtype of myeloma. Progressive disease was correlated with an increased complexity of genetic abnormalities, which in the majority, consisted of structural aberrations acquired in later stages of disease. Using conventional cytogenetics, rearrangements of chromosome 1 were the most common structural abnormality (15%). In the majority, these rearrangements consisted of unbalanced translocations of 1p and 1q; however, no specific locus was predominantly affected. Second in frequency were structural aberrations of chromosomes 8 and 17 (6%). The frequency of del(13q) by FISH was 40% and did not increase in later stages of the disease, suggesting that del(13q) is not a genetic event associated with disease progression. Change of ploidy category during disease progression occurred in a minority of the cases.

CONCLUSION

This study supports the notion that cytogenetic abnormalities in multiple myeloma are not random. Particular chromosomal alterations are associated with disease progression, whereas others show a stable pattern during the course of the disease.

A practical guide to defining high-risk myeloma for clinical trials, patient counseling and choice of therapy

Clinical outcomes for multiple myeloma (MM) are highly heterogeneous and it is now clear that pivotal genetic events are the primary harbingers of such variation. These findings have broad implications for counseling, choice of therapy and the design and interpretation of clinical investigation. Indeed, as in acute leukemias and non-hodgkins lymphoma, we believe it is no longer acceptable to consider MM a single disease entity. As such, the accurate diagnosis of MM subtypes and the adoption of common criteria for the identification and stratification of MM patients has become critical. Herein, we provide a consensus high-risk definition and offer practical guidelines for the adoption of routine diagnostic testing. Although acknowledging that more refined classifications will continue to be developed, we propose that the definition of high-risk disease (any of the t(4;14), t(14;16), t(14;20), deletion 17q13, aneuploidy or deletion chromosome 13 by metaphase cytogenetics, or plasma cell labeling index >3.0) be adopted. This classification will identify most of the 25% of MM patients for whom current therapies are inadequate and for whom investigational regimens should be vigorously pursued. Conversely, the 75% of patients remaining have more favorable outcomes using existing - albeit non-curative - therapeutic options.