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Abstract Events mediating transformation from pre-malignant MGUS to MM is currently not well defined. Recurrent genetic abnormalities such as t(11;14), t(4;14), hyperdiploidy and chromosome 13 deletion are already present in MGUS at relatively similar frequency to MM. The unified deregulation of D-type cyclins is also already present in MGUS. Previous GEP studies have revealed little differences between MGUS and MM. A more recent study using a large patient cohort and new generation Affymetrix genechip identifies an MGUS signature but the functional and biological significance underlying this signature is unknown. In the current study, we analyze a cohort of 22 MGUS and 101 MM from the Mayo Clinic with GEP performed on Affymetrix U133A genechip using gene set enrichment analysis, a method that analyze differentially expressed gene between 2 phenotypes of interest in the context of published or curated genesets that represent specific biological, chemical, or molecular perturbation to cells. This method increases the sensitivity of identifying low but significant changes in gene expression. We made further modification to the original method that allows assessment in individual samples rather than the average across a phenotype further increasing the specificity of the output. In this analysis, 313 genesets were significant enriched for genes over-expressed in MM compared to MGUS, representing potential activated pathways that mediate transformation. When MM samples and genesets were clustered using the enrichment score for each genesets and samples, 4 cluster of genesets emerged, one including a number of MYC genesets, one including a number of cell cycle related genesets, one including genesets related to metabolic activity and another including a number of IFN related genesets. Further dissection of these correlated genesets to identify common enriched genes (leading edge genes) led to identification of a MYC core signature, tRNA core signature, Proteosome core signature and metabolic core signature which are highly correlated. From known literature and biology, it is likely that MYC activation leads to downstream activation of protein synthesis (tRNA signature), degradation (proteasome signature), and metabolic pathway (metabolic signature). This is verified by GEP results from in vitro modulation of MYC activation in cell lines. In addition, a cell cycle core signature and IFN core signature was identified. Activation of IFN and MYC core signatures accounts for almost 90% of MM patients. The remaining patients have a metabolic signature without MYC or IFN activation. The activation of the different core signatures is significantly correlated with certain TC classes when assessed by Chi-Square test. IFN activation is significantly correlated with D1 subtypes and negatively correlated with D2 subtypes. MYC activation is negatively correlated with t(11;14). Similar patterns were observed in a validation dataset of 351 MM patients from UAMS (GSE2677) with GEP performed on the U133plus2.0 chip. These results are validated at the protein level using IHC on TMA of the Mayo cohort. The activation of the IFN and MYC pathway may represent predominant mechanism in MGUS to MM progression.

Abstract Background Multiple myeloma (MM) is presently an incurable plasma cell (PC) malignancy which involves 16 000 new patients per year in US. In spite of the abundance of cytogenetic information, with more than 600 published karyotypes in Non-hyperdiploid MM (NHMM), very little is known about the mode of karyotypic evolution or of the presence of possible cytogenetic pathways. In our investigation, we have used 647 NHMM karyotypes, to identify the most frequently occurring imbalances. Patients and Methods The Mitelman database of Chromosome aberrations in cancer (Mitelman et al., 2007) was searched, and myelomas with modal chromosome number less than 48 were selected. All karyotypes were described using ISCN nomenclature (ISCN, 1995). Only the main clones were analyzed and incomplete karyotypes were excluded. The following information was obtained from each karyotype: chromosome number, imbalances including whole chromosome gains and losses; specific translocations and breakpoints, including add chromosomes. An Excel spreadsheet in which the rows of the first column were labeled to represent each band of a 360-band human chromosome ideogram was created as previously described (Hoglund et al., 2001; Horsman et al., 2003) All karyotypes were scored individually in successive columns for net gain and loss of each chromosome band. The total number of gains and losses affecting each chromosome band for the total cohort of karyotypes was then calculated using the Excel countif function. Recurrent abnormalities were defined as those that were involved in >5% of cases. Histograms of the number of abnormalities per tumor were then plotted, and the modal value extracted as variable called time to occurrence. Statistics correlation between the presence and absence of different abnormalities was analyzed using Spearman correlation matrices. P value of <0.05 was considered as statistical significant. Results In total 647 cases of newly diagnosed NHMM were included in the analysis. The median chromosome number was 43. Few cases had chromosome numbers under 40. The median NAPT was 12 (1–49) with a normal distribution (Fig 1). The most common abnormalities were monosomies of the chromosomes 13 and 14 (32.44% and 14.88% respectively). Out of 647 cases, more than 300 NHMM cases contained translocations in their karyotypes. The most common translocation was t(11;14), which occurs in 17% of cases followed by t(1;16) in 2.7% of cases and t(4;14) and t(8;14) in 1.5% respectively. The most recurrent breakpoints in our series include: 14q32 (32%), 11q13 (20%), 1q10 (10.5%), 1q12 (8%), 8q24 (6.9%), 1p11 (6.6%) and 1q21 (5.5%). Discussion Although only about 40% of MM has informative karyotypes, karyotyping has the advantage of representing global genetic changes at the cellular level. In this comprehensive survey, loss of chromosome 13 and 14 were the most common abnormalities. The NAPT analysis suggests that most NHMM patients have at least 12 abnormalities at diagnosis. It is possible that accumulation of abnormalities above a threshold results in malignant transformation. In our series the t(11;14) translocation appears to be the most recurrent translocation and exceeds the rate reported in Hyperdiploid-MM (17% vs 3.8%). Figure 1. NAPT Distribution in NH-MM Figure 1. NAPT Distribution in NH-MM

Abstract Background: Venous thrombotic events (VTE) are a common complication of therapy with the lenalidomide plus dexamethasone regimen. The incidence of VTE with RD is approximately 20%, and can be lowered with the use of effective thromboprophylaxis, avoidance of erythropoietin, and the use of lower doses of dexamethasone. The goal of this study was to determine the impact of VTE on overall survival of patients with newly diagnosed myeloma by studying events occurring in ECOG E4A03 phase III trial of lenalidomide plus high (standard) dose dex (RD) versus lenalidomide plus low dose dex (Rd) in newly diagnosed myeloma (MM). Methods: Pts with untreated, symptomatic MM were eligible. Pts in the RD arm (Arm A) received lenalidomide 25 mg/day PO days 1–21 every 28 days plus dex 40 mg days 1–4, 9–12, and 17–20 PO every 28 days; pts in the Rd arm (Arm B) received lenalidomide at the same dose plus dex 40 mg days 1, 8, 15, and 22 PO every 28 days. The trial initially did not mandate routine thromboprophylaxis, but recommended that such treatment be considered. After the first 264 patients were enrolled the trial was amended to require mandatory thromboprophylaxis of aspirin for all patients, with a recommendation to use stronger thromboprophylaxis with either warfarin (target INR 2–3) or low molecular weight heparin among patients in the RD arm. Results: 445 pts (median age, 65 yrs) were accrued; 223 randomized to RD, 222 to Rd. Median follow-up time is 30 months. Overall VTE including deep vein thrombosis (DVT) and pulmonary embolism (PE) occurred in 18.5% of patients; 25.6% in Arm A and 11.4% in Arm B. Rates for the first 4 cycles of treatment were 20.2% in Arm A and 8.2% in Arm B, P<0.01. Rates did not change substantially before and after the prophylaxis amendment. A partial response (PR) or higher was seen in 82.1% of pts who experienced VTE compared with 74.6% of pts who did not experience VTE, P=0.19. Overall VGPR rates also were not inferior. Pts who had VTE, however, had significantly higher other grade 3–5 toxicities such as hyperglycemia (14.6% vs 7.5%, P=0.051), cardiac ischemia (4.9% vs 0.8%, P=0.002), non-neuropathic weakness (13.4% vs 6.4%, P=0.039), infection/pneumonia (17.1% vs 11.1%, P=0.138) and fatigue (18.3% vs 10.5%, P=0.060). In a Cox PH model, VTE status as a time-varying covariate was marginally significant: HR 1.54 95%CI (0.96–2.47), P=0.074, suggesting patients that develop VTE have a higher hazard of death. Conclusions: The occurrence of VTE may adversely affect the survival of patients with newly diagnosed myeloma receiving Rev-Dex. VTE was associated with a higher frequency of other serious adverse events. Prevention of VTE events is a priority. Besides lowering the dose of dexamethasone, studies investigating optimum thromboprophylaxis are needed.

Abstract Table 1. Samples to p53 deletions p 53 deletion FISH aCGH FISH and aCGH MGUS 142 - - SMM 108 - - Newly diagnosed MM - 182 - Relapsed/refractory MM 62 156 19 HMCLs - 48 - Total 312 386 19 Background: Inactivation of p53 by mutation or allelic loss is a rare event in multiple myeloma (MM) at the time of disease diagnosis and believed to be more common in the late stages of the disease. Here we defined the prevalence of p53 deletions in monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), newly diagnosed MM, relapsed MM and human myeloma cell lines (HMCLs). Indirect mechanisms of p53 inactivation such as amplification of MDM2, or deletion of CDKN2A (p14ARF) were also investigated. Patients and Methods: A total of 631 MM samples and 48 HMCLs were analyzed for p53 abnormalities (Table 1) and compared with a cohort of plasma cell leukemia (PCL) previously published by us. Interphase fluorescence in situ hybridization (FISH) and highresolution array-based comparative genomic hybridization (aCGH) were used to detect p53 deletions. MDM2 amplification and p14ARF loss were evaluated by aCGH. Overall survival (OS) was estimated through Kaplan Meier method. Results: The prevalence of p53 deletions was 1.4%, 3.7%, 8.9%, 20% and 87.5% in MGUS, SMM, newly diagnosed MM, relapsed MM and HMCLs respectively (Figure 1). Of interest patients in first relapse showed a p53 deletion prevalence of 18% in comparison with 33% for patients in second relapse or more. We obtained p53 deletion status in 8 patients noted to have deletion at the time of relapse and in whom we had previous samples stored. In 7 of 8 cases deletions had been acquired (absent in the previous samples). The median OS for relapsed MM patients with or without p53 deletion were 4.2 months and 37.8 months respectively (p <0.001). MDM 2 amplification and p14ARF loss was detected in 0.4% and 2% of new diagnosed MM, 0.6% and 5.1% of relapsed MM and 2% and 29% of HMCLs respectively. Discussion: Emergence of p53 deletion/mutations denotes progression genetic events in MM. Importantly we show for the first time the overriding importance of p53 deletions as prognostic markers in relapsed MM. A molecular staging system that is based on the presence of p53 inactivation may be more powerful than classifying patients based on the loss of p53. Other abnormalities involving p53 pathway regulators like MDM2 gain and p14ARF loss are infrequent events in MM, even in advanced disease. Figure 1. Prevalence of p53 deletions Figure 1. Prevalence of p53 deletions

Abstract The Multiple Myeloma Research Consortium (MMRC) Genomics Initiative was instigated to harness the power of multiple genomic approaches to further the understanding of multiple myeloma. To date, 137 samples from patients with newly diagnosed and relapsed myeloma (out of an estimated final total of 250 by the end of the year) have been subjected to expression profiling and array comparative genomic hybridization. To identify regions of recurrent copy number alteration with a high degree of confidence, we have used the Genomic Identification of Significant Targets In Cancer (GISTIC) algorithm, which detects such regions and assigns a probability to each. Application of GISTIC to the MMRC collection identified 14 significant regions of amplification and 15 significant regions of deletion. The algorithm further detects peaks of copy number change that contribute to each region’s significance. Of genes that were expressed in our dataset, a total of 64 across the genome were found to lie within the boundaries of significant amplification peaks and 30 were found to lie within significant deletion peaks. Given the likelihood that this gene collection is highly enriched for genes important in the pathogenesis of myeloma and potential therapeutic targets, it has been prioritized for further validation with the amplified genes submitted for arrayed RNAi and the deleted genes expedited for re-sequencing. In order to define a poor prognosis group, we developed and applied a model based on the gene expression dataset of Shaughnessy and colleagues. To identify pathways activated in poor prognosis disease, we applied Gene Set Enrichment Analysis with the Molecular Signatures Database. This demonstrated enrichment of multiple canonical pathways within the poor prognosis group, including those associated with proliferation, cell cycle progression and DNA repair. A search for recurrent copy number events associated with poor prognosis disease revealed that by far the most significant event, and the only one surviving correction for multiple hypothesis testing, was mono- or bi-allelic deletion of CDKN2C (p18). Interestingly, the poor prognosis group also demonstrated higher expression of p18 in those samples without bi-allelic deletion and of CDKN2A (p16). Deletion and increased expression of p18 in high proliferation index myeloma samples has previously been described. However, our analyses demonstrate the pre-eminence of p18 loss for defining poor prognosis disease compared to other recurrent copy number changes. Furthermore, it expands on work in other tumors demonstrating feedback mechanisms between cyclin dependent kinase inhibitor pathways, suggesting a more complex model of interplay between the pathways than previously described. In conclusion, the MMRC reference collection is proving an important tool in the fight to understand key genetic events in multiple myeloma and would ultimately be anticipated to contribute towards development of improved therapy for the disease.

Abstract Melphalan (M), Prednisone (P) and Lenalidomide (R) are active in the treatment of multiple myeloma (MM). We evaluated the toxicity and efficacy of MPR in a phase I/II trial. Results of phase I part were previously reported (Blood2006, 108(11) abst 3558). M 5 mg/m2 on days (d) 1–4, 60 mg/m2 d 1–4 and R 10 mg d 1–21 of a 28 day cycle was determined as MTD for the phase II study. Methods: Patients with previously untreated MM who were not candidates for stem cell transplantation, age ≥18 yr, ECOG PS 0–3, evaluable or measurable disease, ANC >1500, platelets > 100,000 and creatinine ≤ 3.0 mg/dL were eligible. All patients received aspirin 325 mg/d as DVT prophylaxis. Routine antibacterial prophylaxis was not used. G/GM-CSF was used at the discretion of the treating physician for neutropenia. Response rate (RR), confirmed on two consecutive determinations was the primary end-point. The study had 90% power to detect a RR of at least 45%. Results: Twenty-six patients were accrued between July ’06 and Feb ’08. The median age was 74 y (64 – 87y), 17 (65%) were men. Six, 13, 6, 1 (23%, 50%, 23%, and 4%) patients had ECOG PS 0, 1, 2, and 3, respectively. Three (12%), 11 (42%) and 10 (38%) patients were ISS stage 1, 2 and 3. A total of 106 cycles were administered; median 4.5 (1–13). Seventy-seven % patients experienced at least 1 grade 3 or 4 toxicity. Neutropenia (42%/8%) and thrombocytopenia (20%/8%) were the most common grade 3/4 adverse events followed by anemia (16%/0%), fatigue (8%/4%), rash (11%/0%), and hyperglycemia (4%/0%). There were 20 treatment delays in 9 patients, and 18 dose reductions (9 in R, 11 in M and 1 P) occurred in 7 patients, most commonly because of neutropenia or thrombocytopenia. Eleven patients (42%) required G-CSF treatment. Eleven patients are currently receiving treatment; 15 have gone off study (4 completed per protocol, 3 refused, 3 adverse effects, 3 unrelated illnesses, 2 other). Median follow up of survivors is 8 m (0 – 22m). Eighteen (69 %; 95%CI 48–86) patients had a PR or better according to International Myeloma Working Group Uniform Response criteria; 3 (12 %) CR, 5 (19 %) VGPR and 10 (38%) PR. Median number of cycles before achieving a response was 2 (1 – 11). Median Progression Free and Overall Survival is 16.7m (95% CI 11.2–23.0), and 23 m (95% CI: 22 – 23), respectively. Conclusions: MPR combination is feasible with a manageable toxicity profile and has significant activity in the treatment of patients with MM who are not candidates for stem cell transplant, with an overall response rate of 69%, and a CR plus VGPR rate of 31%. Grade 3 or 4 neutropenia and thrombocytopenia was the most common toxicity, seen in up to 50% of patients in this cohort of predominantly elderly patients. Dose reduction in R and/or M was required in 27% patients. No patient developed neuropathy or thromboembolic complications.

Abstract Multiple Myeloma (MM) is the second most prevalent haematological disorder in the US with great recent progress propelled by various technological and therapeutic advances. Nevertheless, the complexity of MM genomes remains inadequately characterized. We have combined high-resolution (44K Agilent) array comparative genomic hybridization (aCGH) and gene expression data with clinical outcomes in an initial attempt at indexing genomic complexity in MM and its clinical implication in 100 MM patients. We enumerated the Number of Aberrations per Tumor (NAPT) as defined by the ADM-1 algorithm available within CGH Analytics. There appear to be no difference in degree of genetic complexity between hyperdiploid and non-hyperdiploid myeloma. Generally, t(11;14) have low NAPT whereas D2 tumors have high NAPT. Amongst the high-risk genetic subtypes, tumors with maf translocations have relatively low NAPT whereas t(4;14) have high NAPT. Whilst a Multivariate Cox Proportional Hazards regression of survival outcome showed little statistical support for popular indicators such as ploidy and TC classification, results for NAPT were considerably more encouraging (p~ 0.07, median survival of 40 months in low complexity vs 18 months in high). Log-rank tests further supported prognosis based on NAPT independent of clinical status and ploidy. To characterize complexity, we clustered aCGH profiles by clinical status, ploidy and TC classification. Clear patterns of aggregation and recurrent aberration were observed suggesting that they were possibly instrument to aberrant gene expression. Indeed, expression of a large proportion of genes approximately 2Mb of the recurrent breakpoints varied significantly between patients carrying aberrations vis-a-viz others that did not. Comparison against known gene sets showed an enrichment for cell-cycle and apoptosis genes. We are presently characterizing several such breakpoint-associated genes for their functional significance.

Abstract Background: The combination of lenalidomide and dexamethasone (Rev/Dex) has been shown to be a highly effective therapy for multiple myeloma (MM). Over half of the patients with newly diagnosed MM achieve a complete response with prolonged therapy. More recently, a phase III trial demonstrated improved survival with use of lenalidomide and low dose dexamethasone with one year survival in excess of 90%. We report the initial results from a phase II trial combining lenalidomide and low dose dexamethasone with cyclophosphamide (CRd) as initial therapy of newly diagnosed MM. Methods: The trial was initiated in July 2006 and completed the target accrual of 33 patients by July 2007. The treatment protocol consisted of lenalidomide given orally at a dose of 25 mg daily on days 1–21 of a 28-day cycle. Dexamethasone (dex) was given orally at a dose of 40 mg on days 1, 8, 15, and 22 of each cycle. Cyclophosphamide at a dose of 300 mg/m2 was given on days 1, 8, and 15 of each cycle. Patients also received an aspirin once daily as thromboprophylaxis. Response was defined as a decrease in serum monoclonal (M) protein by 50% or higher and a decrease in urine M protein by at least 90% or to a level less than 200 mg/24 hours, confirmed at least 4 weeks apart. Results: The median age was 63 years (range, 44–79). Eight patients (24%) had ISS stage III disease. At this time, 19 of the 33 patients are evaluable for confirmed responses (i.e., off-study or completed at least 4 cycles of therapy). Of these, 2 achieved VGPR and 13 had a partial response giving an overall response rate of 79%. The response rate was affected by 5 of 19 patients who went off study within three cycles due to toxicities [interstitial nephritis (1 pt), multiple grade 3 toxicities including infection (1 pt) atrial fibrillation and infection (1 pt)] or alternative treatment [no response and possible renal toxicity (1 pt) and progression at 4 cycles (1 pt)]. Overall, hematological toxicity was the most common with grade 4 toxicity seen in 6 patients (20%). Non-hematological grade 3 or higher toxicities included fatigue (4 pts), thrombosis (3 pts) and renal failure (2 pts). One patient with thrombosis came off study for other toxicities, and the other two continued on study with anticoagulation. Thirteen patients (43%) had dose reductions of both cyclophosphamide and lenalidomide, most commonly due to hematological toxicity. So far, 12 patients have gone off study, 6 went to stem cell transplant, 3 due to adverse events, 1 due to disease progression and 2 patients went to alternate treatment. Conclusions: CRd has excellent activity in newly diagnosed myeloma with an estimated overall response rate of 79%. Response evaluation of the entire 33 patients will be presented at the meeting. We believe that the initial use of a 300 mg/m2 dose of cyclophosphamide resulted in 5 of the first 19 pts experiencing early toxicity and withdrawal. As a result, an expansion of the current trial is evaluating lower doses of cyclophosphamide (300 mg fixed dose). Full analysis of this study will be needed to determine if CRd can improve outcome compared to Rd.

Abstract Waldenström’s Macroglobulinemia (WM) is a low-grade lymphoplasmacytic disorder associated with an IgM monoclonal protein that may present with anemia, lymphadenopathy, and hepatosplenomegaly. Since combination chemotherapy and Rituximab are both active in this disease, it is possible the response rate can be enhanced by using a combined modality of Rituximab and CHOP. This approach has been used in indolent lymphoma with remarkable results and limited toxicity. Objective: To determine the response rate in previously untreated patients with Waldenström’s Macroglobulinemia receiving rituximab and CHOP. Methods: This was a phase II study of standard R-CHOP in symptomatic WM patients. The study was activated on June 15, 2004 and closed on April 26, 2007 due to poor accrual. The median age of the sixteen patients enrolled was 60 (44–79 years), β2M 3 ug/ml (2.1–7.6), median hemoglobulin was 9 g/dl (7.7–10.9), Viscosity 3.4(1.6–10), and IgM 6389 (3229–13300 mg/dl). The most common symptoms were Fatigue (13/16), visual disturbance (7/16) and parasthesias or painful/numb feet (6/16). Only one patient had bulky adenopathy (6.3%). Results: Of 16 patients treated, 5 patients have no response data available (it will be presented at the meeting). Objective response was 91% (90% CI: 63.5% ∼ 99.5%) and 1 patient had a minor response with an overall response rate of 100%. Median time to response was 1.6 months from registration and median time to maximum response was 2.1 months. Median duration of response has not been reached. The median follow up time of the 16 patients was 18.3 months with a range of 3.6–24.8 months. Among the 16 treated patients, there were 8 (50%, 90% exact binomial CI: 27.9%∼72.1%) grade 4 neutropenia. 8 patients experienced grade 3 lymphopenia (50%, 90% exact binomial CI: 27.9%∼72.1%). Only 2 grade 3 febrile neutropenia were noted. As of August 4, 2007, none of the 16 patients has died. R-CHOP is a promising regimen in the treatment of patients with Waldenström’s Macroglobulinemia. To succeed in completing clinical trials in this rare disease better international collaboration and involvement in advocacy groups are required.

Abstract Background B-cell chronic lymphocytic leukemia (B-CLL) is a well-defined clinical entity with heterogeneous molecular and cytogenetic features. Chromosome aberrations could be associated to specific CLL clinical features and outcomes and their impact on clonal evolution should have been addressed by using temporal analysis. In order to demonstrate the role of temporal analysis in CLL we conducted a comprehensive karyotypic survey of a large number of CLL cases with already known genetic aberrations to fully describe their meaning in terms of biological evolution. Methods A total of 1749 karyotypes were retrieved from the Mitelman Database of Chromosome Aberrations in Cancer. A matrix depicting the 360-band human chromosome ideogram was created. Regions that were either lost or gained in more than 3% of the cases were retained and identified as recurrent imbalances. Early and late imbalances were defined according to the appearance on the complex karyotypes. Descriptive statistics were used to summarize the genetic abnormalities. Results The median chromosome number and the median number of abnormalities per tumor (NAPT) were 46 and 1 respectively. (Figure 1 A and 1B) The most common abnormality seen was trisomy 12 which occurred in 29% (508 cases) followed by 13q14del (10.34%), 13q13del (6.63%) and add14q32 (6.63%). The temporal analysis revealed +12, 13q-, −17, 17p-, −Y and −X to be early imbalances (TO<5), followed predominately by a late loss with TO=5–10.5 (11q-). Hierarchical clustering suggested there are different groups including: trisomy 12, 13q-, 11q-, and 6q-, which at least in this clustering analysis appeared to be mutually exclusive. In summary, we can conclude that overall CLL is a neoplasia that shows remarkable chromosome stability even when only abnormal karyotypes are evaluated. Interestingly, clustering analysis suggests there are non-overlapping, unique subsets of CLL cases where trisomy 12 is the most common and along with 13q-emerged as early events on CLL clonal evolution. Figure 1A. Chromosomes distribution in chronic Lymphocytes Leukemia karyotypes Figure 1A. Chromosomes distribution in chronic Lymphocytes Leukemia karyotypes Figure 1b. Chronic Lymphocytes Leukemia and Number of Abnormalities Per Tumor (NAPT) distribution Figure 1b. Chronic Lymphocytes Leukemia and Number of Abnormalities Per Tumor (NAPT) distribution Figure Figure