A high-risk, Double-Hit, group of newly diagnosed myeloma identified by genomic analysis

Patients with newly diagnosed multiple myeloma (NDMM) with high-risk disease are in need of new treatment strategies to improve the outcomes. Multiple clinical, cytogenetic, or gene expression features have been used to identify high-risk patients, each of which has significant weaknesses. Inclusion of molecular features into risk stratification could resolve the current challenges. In a genome-wide analysis of the largest set of molecular and clinical data established to date from NDMM, as part of the Myeloma Genome Project, we have defined DNA drivers of aggressive clinical behavior. Whole-genome and exome data from 1273 NDMM patients identified genetic factors that contribute significantly to progression free survival (PFS) and overall survival (OS) (cumulative R2 = 18.4% and 25.2%, respectively). Integrating DNA drivers and clinical data into a Cox model using 784 patients with ISS, age, PFS, OS, and genomic data, the model has a cumlative R2 of 34.3% for PFS and 46.5% for OS. A high-risk subgroup was defined by recursive partitioning using either a) bi-allelic TP53 inactivation or b) amplification (≥4 copies) of CKS1B (1q21) on the background of International Staging System III, comprising 6.1% of the population (median PFS = 15.4 months; OS = 20.7 months) that was validated in an independent dataset. Double-Hit patients have a dire prognosis despite modern therapies and should be considered for novel therapeutic approaches

A high-risk, Double-Hit, group of newly diagnosed myeloma identified by genomic analysis

Patients with newly diagnosed multiple myeloma (NDMM) with high-risk disease are in need of new treatment strategies to improve the outcomes. Multiple clinical, cytogenetic, or gene expression features have been used to identify high-risk patients, each of which has significant weaknesses. Inclusion of molecular features into risk stratification could resolve the current challenges. In a genome-wide analysis of the largest set of molecular and clinical data established to date from NDMM, as part of the Myeloma Genome Project, we have defined DNA drivers of aggressive clinical behavior. Whole-genome and exome data from 1273 NDMM patients identified genetic factors that contribute significantly to progression free survival (PFS) and overall survival (OS) (cumulative R2 = 18.4% and 25.2%, respectively). Integrating DNA drivers and clinical data into a Cox model using 784 patients with ISS, age, PFS, OS, and genomic data, the model has a cumlative R2 of 34.3% for PFS and 46.5% for OS. A high-risk subgroup was defined by recursive partitioning using either a) bi-allelic TP53 inactivation or b) amplification ( 654 copies) of CKS1B (1q21) on the background of International Staging System III, comprising 6.1% of the population (median PFS = 15.4 months; OS = 20.7 months) that was validated in an independent dataset. Double-Hit patients have a dire prognosis despite modern therapies and should be considered for novel therapeutic approaches

Quantifying the Biodiversity Values of Reforestation: Perspectives, design issues and outcomes in Australian rainforest landscapes

Following two centuries of land clearing, the past two decades have seen growing efforts to re-establish forest on formerly-cleared sites. While the immediate goals of reforestation vary, there is also a widespread expectation that one of its effects will be an improvement in "biodiversity value". However, agreed standards concerning how this can be measured, and against what benchmarks it should be judged, are lacking. This paper describes a study of biodiversity development in different types of rainforest reforestation in tropical and subtropical eastern Australia. It provides information on the responses of rainforest fauna and also discusses key issues of survey design and methodology that, if ignored, may limit the effectiveness of monitoring programs.The nature of rainforest, its history within Australia, and its role as fauna habitat are briefly reviewed. Modern deforestation and human land use, and various reforestation pathways (including regrowth, timber plantation, and ecological restoration projects) are described. Then design principles, biodiversity measurements, and issues relating to their choice are discussed.These include: spatial scale; site selection and replication in relation to environmental variation; reference sites; the array of potentially measurable biotic and process variables, and spatio-temporal measurement scales. Finally we explore analytical options and present selected findings, using univariate and multivariate approaches, and comparing simple species richness, functional groupings, and analyses of taxonomic composition. Rainforest biodiversity value is defined as the development of a rainforest-like set of biota and ecological processes. Reforested sites were generally intermediate between pasture and rainforest reference sites in the measured components of rainforest biodiversity value. Many components had been rapidly (by around 10 years) acquired by ecological restoration sites, although it is clear that some components will take decades or longer to develop. The results also show: (1) the existence of production/ biodiversity trade-offs, in that sites managed for timber production acquired less biodiversity value than those planted for ecological restoration; (2) moderate correspondence across different indicator taxa when they are analysed as functional groups; (3) very little agreement among indicator taxa when overall richness is used; (4) a likelihood of important landscape and context effects. Long-term conservation of rainforest fauna will require rainforest restoration over substantial areas of currently denuded land. However, although rainforest restoration may often show reasonable success, it should not be viewed as an alternative to conserving existing remnants and advanced regrowth

Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients

Secondary MYC translocations in myeloma have been shown to be important in the pathogenesis and progression of disease. Here, we have used a DNA capture and massively parallel sequencing approach to identify the partner chromosomes in 104 presentation myeloma samples. 8q24 breakpoints were identified in 21 (20%) samples with partner loci including IGH, IGK and IGL, which juxtapose the immunoglobulin (Ig) enhancers next to MYC in 8/23 samples. The remaining samples had partner loci including XBP1, FAM46C, CCND1 and KRAS, which are important in B-cell maturation or myeloma pathogenesis. Analysis of the region surrounding the breakpoints indicated the presence of superenhancers on the partner chromosomes and gene expression analysis showed increased expression of MYC in these samples. Patients with MYC translocations had a decreased progression-free and overall survival. We postulate that translocation breakpoints near MYC result in colocalization of the gene with superenhancers from loci, which are important in the development of the cell type in which they occur. In the case of myeloma these are the Ig loci and those important for plasma cell development and myeloma pathogenesis, resulting in increased expression of MYC and an aggressive disease phenotyp

Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma.

We have used whole exome sequencing to compare a group of presentation t(4;14) with t(11;14) cases of myeloma to define the mutational landscape. Each case was characterized by a median of 24.5 exonic nonsynonymous single-nucleotide variations, and there was a consistently higher number of mutations in the t(4;14) group, but this number did not reach statistical significance. We show that the transition and transversion rates in the 2 subgroups are similar, suggesting that there was no specific mechanism leading to mutation differentiating the 2 groups. Only 3% of mutations were seen in both groups, and recurrently mutated genes include NRAS, KRAS, BRAF, and DIS3 as well as DNAH5, a member of the axonemal dynein family. The pattern of mutation in each group was distinct, with the t(4; 14) group being characterized by deregulation of chromatin organization, actin filament, and microfilament movement. Recurrent RAS pathway mutations identified subclonal heterogeneity at a mutational level in both groups, with mutations being present as either dominant or minor subclones. The presence of subclonal diversity was confirmed at a single-cell level using other tumor-acquired mutations. These results are consistent with a distinct molecular pathogenesis underlying each subgroup and have important impacts on targeted treatment strategies. The Medical Research Council Myeloma IX trial is registered under ISRCTN68454111. (Blood. 2012; 120(5): 1077-1086

Co-existent hyperdiploidy does not abrogate poor prognosis in myeloma with adverse cytogenetics and may precede IGH-translocations

The acquisition of the cytogenetic abnormalities hyperdiploidy or translocations into the immunoglobulin gene loci are considered as initiating events in the pathogenesis of myeloma and were often assumed to be mutually exclusive. These lesions have clinical significance with hyperdiploidy or the presence of the t(11;14) translocation associated with a favorable outcome whilst t(4;14), t(14;16) and t(14;20) are unfavorable. Poor outcomes are magnified when lesions occur in association with other high-risk features, del17p and +1q. Some patients have co-existence of both good and poor prognostic lesions and there has been no consensus on their risk status. To address this we have investigated their clinical impact using cases in the Myeloma IX study (ISRCTN68454111) and shown that the co-existence of hyperdiploidy or t(11;14) does not abrogate the poor prognosis associated with adverse molecular lesions, including translocations. We have also used single cell analysis to study cases with co-existent translocations and hyperdiploidy, to determine how these lesions co-segregate within the clonal substructure, and demonstrated that hyperdiploidy may precede IGH translocation in a proportion of patients. These findings have important clinical and biological implications as we conclude patients with coexistence of adverse lesions and hyperdiploidy should be considered high-risk and treated accordingly