ALBERT

Description: The advent of therapeutic monoclonal antibodies (elotuzumab, daratumumab) for multiple myeloma (MM) heralded a new era of immunologic therapy for this disease. Laboratory and clinical data suggest that immune checkpoint inhibitors (ICI) targeting the PD-1/PD-L1 axis are a promising novel strategy, as PD-L1 is commonly expressed on MM cells and a phase 2 clinical trial demonstrated encouraging responses to pembrolizumab (anti-PD-1) in combination with pomalidomide and dexamethasone. However, two late stage MM clinical trials of ICI combined with either lenalidomide or pomalidomide were halted due to safety concerns and lack of efficacy, although subgroup analysis suggested that the overall response rate in subjects with immune related adverse events was higher in subjects who received pembrolizumab + pomalidomide and dexamethasone vs the control group. As a result, further investigation of ICI in MM has largely discontinued. This discrepancy with the positive findings in the early phase trial suggests that genetic or immunologic features of the tumors or immune microenvironment of the patients may influence outcome to ICI, but these factors are as yet undefined. In solid tumors, high mutation burden as assessed by microsatellite sequence instability-high (MSI-high) or mismatch repair genes deficiency (dMMR) was correlated to response to anti-PD-1 ICI, and is now an indication for these agents. Newly diagnosed MM is considered an intermediate-low mutation burden disease (

Description: This study analyzed the frequency and clinical significance of t(4;14)(p16;q32) in multiple myeloma (MM) among 208 patients with MM and 52 patients with monoclonal gammopathy of undetermined significance (MGUS); diagnosed between 1994 and 2001. Patients with the translocation were identified using reverse transcription–polymerase chain reaction (RT-PCR) to detect hybrid immunoglobulin heavy chain (IgH)–MMSET transcripts from the der(4) chromosome. We found 31 (14.9%) t(4;14)+ MM patients and 1 (1.9%) t(4;14)+ MGUS patient. IgH-MMSET hybrid transcripts were detected in bone marrow (BM) and blood. Breakpoint analysis revealed that 67.7% of t(4;14)+ patients expressed hybrid transcripts potentially encoding full-length MMSET, whereas the remainder lacked one or more amino terminal exons. Expression of fibroblast growth factor receptor 3 (FGFR3), presumptively dysregulated on der(14), was detected by RT-PCR in only 23 of 31 (74%) patients with t(4;14)+ MM. Patients lacking FGFR3 expression also lacked detectable der(14) products. Longitudinal analysis of 53 MM patients with multiple BM and blood samples showed that, over time, BM from t(4;14)+ patients remained positive and that t(4;14)− patients did not acquire the translocation. IgH-MMSET hybrid transcripts and FGFR3 transcripts disappeared from blood during response to therapy. No correlation was observed between the occurrence of t(4;14) and known prognostic indicators. However, we find the t(4;14) translocation predicts for poor survival (P = .006; median, 644 days vs 1288 days; hazard ratio [HR], 2.0), even in FGFR3 nonexpressors (P = .003). The presence of t(4;14) is also predictive of poor response to first-line chemotherapy (P = .05). These results indicate a significant clinical impact of the t(4;14) translocation in MM that is independent of FGFR3 expression.

Description: The genetic and transcriptional program of multiple myeloma has identified novel markers of high-risk disease and mechanisms of pathogenesis. However, there remains a significant gap between prospective identification of high-risk patients and our ability to determine all patients that experience poor outcomes. Epigenetic alterations in myeloma have been less studied, but have significant potential as a translatable biomarker. To better understand how epigenetic programming may contribute to myeloma pathogenesis, we characterized the myeloma DNA methylome. DNA from CD138+ enriched myeloma specimens from the Multiple Myeloma Research Foundation (MMRF) CoMMpass study (NCT01454297) were obtained after receiving permission from the CoMMpass Tissue Use Committee and Emory IRB. Whole genome bisulfite sequencing (WGBS) was performed by adapter ligation (Kapa HyperPrep) using fully methylated sequencing adapters followed by bisulfite conversion (Qiagen Epitect), library amplification (Kapa Uracil+ HiFi polymerase), and sequencing (NovaSeq 6000 S4 150bp paired-end reads). Sequencing data were mapped with Bismark and CpG methylation calls were extracted using R. WGBS DNA methylation data was generated for 120 specimens, including 87 baseline, 24 paired relapse, and 9 paired peripheral blood specimens. This yielded ≥5x coverage at 21,393,650 CpGs in 90% of samples with an average coverage of 20x. Myeloma exhibited extensive genomic hypomethylation such that the median level was 42% (range 21-67%) as compared to 64% in plasma cells from healthy individuals. Principle component analysis indicated most variation corresponded with hypomethylation, which occurred in megabase domains devoid of gene expression. In contrast, DNA methylation was retained in the bodies of expressed genes. Principle components 2 and 3 separated samples with t(4;14) translocations from others. This may be due to overexpression of WHSC1 driving excessive histone 3 lysine 36 di-methylation (H3K36me2), which in turn impacts the function of PWWP-domain containing DNA methyltransferases (DNMT3A, DNMT3B). Given the 3-fold variability observed in average methylation, we sought to understand if this was indicative of outcome. Analysis of 87 baseline specimens identified 23,386 loci where DNA methylation (or lack thereof) was prognostic of outcome (FDR ≤0.01) (Figure 1a). These prognostic loci were clustered into contiguous regions often found in gene bodies and could be used to stratify patients by progression-free and overall survival (P-value 8) (Figure 1b). Importantly, the prognostic value of these CpG were independent of t(4;14) status and ISS stage, indicating these high-risk patients would not have otherwise been identified. Furthermore, analysis of 24 relapse specimens from 22 patients indicated epigenetic remodeling occurred at these prognostic loci. Specifically, loci where the presence of DNA methylation was indicative of poor outcome gained DNA methylation in relapsed samples, and loci where lack of DNA methylation was indicative of poor outcome lost DNA methylation in relapse samples (Figure 1c). These relapse/refractory DNA methylation changes occurred in contiguous regions proximal to genes including PRKCE, MGMT, FHIT, WWOX, and HDAC9 (Figure 1d and data not shown). Cumulatively, these data identify myeloma epigenetic markers of outcome that undergo reprogramming in relapsed samples suggesting they may be indicative of therapeutic resistance. Disclosures Lonial: Genentech: Consultancy; Takeda: Consultancy, Research Funding; Amgen: Consultancy; BMS: Consultancy; Janssen: Consultancy, Research Funding; GSK: Consultancy; Karyopharm: Consultancy; Celgene Corporation: Consultancy, Research Funding. Boise:AstraZeneca: Honoraria, Research Funding; Genentech Inc.: Membership on an entity's Board of Directors or advisory committees.

Description: Multiple Myeloma (MM) is a genetically heterogeneous disease of plasma cells that generally exhibits chromosomal abnormalities and distinct gene expression signatures. Previous studies have sought to identify gene expression indices using microarray technology to discern genes associated with survival outcomes to predict whether a newly diagnosed patient has an aggressive form of the disease. One such MM-specific index is the UAMS 70 gene index, which is composed of 51 over- and 19 under-expressed genes. This index was developed using Affymetrix U133Plus2.0 microarray data from 532 MM patients at diagnosis by computing log-rank test statistics on gene expression quartiles. Despite consistently achieving a high performance across a variety of MM datasets, issues arise when applying this index to RNAseq data. Here we address those issues, deriving an independent index based on the RNAseq data from the Multiple Myeloma Research Foundation (MMRF) CoMMpass Study (NCT01454297), and benchmark its performance to an implementation of the UAMS 70 gene index. UAMS index scores are computed by taking the difference between the average log2-scale expression of the 51 over- and 19 under-expressed genes. We applied this calculation to RNAseq data analyzed using Sailfish, Salmon v7.2, and HTseq counts collected from 41 Multiple Myeloma Genomics Initiative samples and compared the results to scores from matching GCRMA, MAS5, RMA, and PLIER16 Affymetrix U133Plus2.0 microarray data. Differences in the distribution of index values across data types led to nonconforming classification of high-risk individuals. Additionally, when applied to RNAseq data, several Affymetrix probesets did not uniquely match to gene annotations from Ensembl-v74. This reduced the number of genes upon which our UAMS score was calculated to 61 genes. Of the original 51 over-expressed probes, only 44 uniquely mapped genes remained after 7 multi-mapped probes are removed and similarly, out of the 19 under-expressed genes only 17 were uniquely mapped. Given the complication of probe-gene mismatch and inconsistencies identifying high-risk individuals when applied to RNAseq data, we developed an independent index using the baseline RNAseq data from the MMRF CoMMpass Study IA13 dataset. From a training set (n=375) of RNAseq data measuring 56430 genes, we performed univariate log-rank tests on expression quartiles associated with disease-related survival while controlling for an FDR of 2.5%, resulting in 23 under- and 332 over-expressed genes. Subsequent multivariate Cox regression analysis and backward stepwise selection culminated in the identification of the CoMMpass RNAseq index, which is based on the ratio of mean expression values of 87 genes (19 under- and 68 over-expressed) predictive of high risk (hazard ratio [HR] = 8.7341, 95% CI = 5.615-13.58, p 〈 0.001). Validation on the test set (n=251) yielded a HR of 5.612 (95% CI = 3.066-10.27, p 〈 0.001) as compared to a HR of 4.753 (95% CI = 2.688-8.403, p 〈 0.001) achieved with the adapted UAMS index. Adjusting for a patient's International Staging System (ISS) stage revises these hazard ratios to 6.236 (95% CI = 3.345-11.627, p 〈 0.001) and 3.6420 (95% CI = 1.9726-6.724, p 〈 0.001) for the CoMMpass RNAseq and the adapted UAMS indices, respectively. Furthermore, the distribution of CoMMpass RNAseq index values across the training and test set show no observable bias with respect to three main therapy arms, suggesting it is predictive of high risk independent of treatment. Our newly derived CoMMpass RNAseq index shares one gene in common with the UAMS 61 gene index (CENPW) and recovers two over-expressed genes (FABP5, TAGLN2), which were removed from the UAMS 70 gene index due to probe multimapping. When the recovered genes are added back to the UAMS index, the unadjusted and adjusted hazard ratios measured for the test set are 5.173 (CI = 2.926-9.146, p 〈 0.001) and 4.022 (CI = 2.1840-7.408, p 〈 0.001), respectively. Of the original 70 genes in the UAMS index, 21 (30%) map to chromosome 1, which frequently exhibits copy number gains in MM. Only 11 of the 87 (13%) genes in our proposed index map to chr1, which indicates that, given its performance, the newly derived list of genes may represent a more diverse index to predict, and provide novel insights into, high risk MM. Altogether, the CoMMpass RNAseq index identifies a high risk signature in 13% of MM patients and outperforms the UAMS index. Disclosures Lonial: Amgen: Research Funding.

Description: Multiple myeloma (MM) plasma cells (PCs) express receptor for hyaluronan-mediated motility (RHAMM), a hyaluronan-binding, cytoskeleton and centrosome protein. The most abundant RHAMM isoforms in MM are full-length RHAMM (RHAMMFL) and the splice variant RHAMM-exon4. We separately examined the significance of RHAMM expression, and isoform balance, in 2 groups of MM patients. In oligonucleotide microarray experiments (n = 210, Arkansas), increasing RHAMM mRNA expression in MM PCs is strongly associated with osteolytic bone lesions (P 〈 .001), and event-free (P = .05) and overall (P = .04) survival. Semiquantitative determination of RHAMM isoform expression (Alberta, Canada) used capillary electrophoretic detection and measurement of RHAMM-exon4/RHAMMFL reverse-transcriptase-polymerase chain reaction (RT-PCR) products. RHAMM isoforms are rarely expressed concurrently in single MM PCs; the pattern of isoform expression, at the single-cell level, is approximated in larger numbers of cells by the RHAMM-exon4/RHAMMFL ratio. Absolute RHAMM expression and the RHAMM-exon4/RHAMMFL ratio are only partially correlated in MM PCs; in cell lines, absolute RHAMM expression is elevated in mitosis, while RHAMM ratios remain stable. Temporal examination of MM patients' peripheral blood reveals that the RHAMM-exon4/RHAMMFL ratio increases with disease burden. The RHAMM-exon4/RHAMMFL ratio in diagnostic bone marrow samples (n = 101, Alberta) is an independent prognostic factor. Thus, expression and splicing of RHAMM are important molecular determinants of disease severity in MM. (Blood. 2004;104:1151-1158)

Description: Improving outcomes in multiple myeloma will involve not only development of new therapies but also better use of existing treatments. We performed RNA sequencing on samples from newly diagnosed patients enrolled in the phase 2 PADIMAC (Bortezomib, Adriamycin, and Dexamethasone Therapy for Previously Untreated Patients with Multiple Myeloma: Impact of Minimal Residual Disease in Patients with Deferred ASCT) study. Using synthetic annealing and the large margin nearest neighbor algorithm, we developed and trained a 7-gene signature to predict treatment outcome. We tested the signature in independent cohorts treated with bortezomib- and lenalidomide-based therapies. The signature was capable of distinguishing which patients would respond better to which regimen. In the CoMMpass data set, patients who were treated correctly according to the signature had a better progression-free survival (median, 20.1 months vs not reached; hazard ratio [HR], 0.40; confidence interval [CI], 0.23-0.72; P = .0012) and overall survival (median, 30.7 months vs not reached; HR, 0.41; CI, 0.21-0.80; P = .0049) than those who were not. Indeed, the outcome for these correctly treated patients was noninferior to that for those treated with combined bortezomib, lenalidomide, and dexamethasone, arguably the standard of care in the United States but not widely available elsewhere. The small size of the signature will facilitate clinical translation, thus enabling more targeted drug regimens to be delivered in myeloma.

Description: As multiple myeloma tumors universally dysregulate cyclin D genes we conducted high-throughput chemical library screens for compounds that inhibit signaling pathways driving cyclin D2 promoter transactivation, assaying more than 4,000 compounds. The top-ranked compound from these studies was a natural triterpenoid, pristimerin. Pristimerin markedly suppressed cyclin D2 promoter activity (〉90%) in 3T3 fibroblast cells and inhibited cyclin D1, D2 and D3 protein expression in myeloma tumor cells. Strikingly, the early (4 hour) transcriptional response of myeloma cells treated with pristimerin closely resembles cellular responses elicited by proteosome inhibitors (P90-fold), activating transcription factor (ATF) 3 and CHOP. Enzymatic assays performed with purified 20S proteosome, or with total cellular extract, confirm that pristimerin rapidly and specifically inhibits chymotrypsin-like 20S proteosome activity at low concentration (6 hours. Consistent with inhibition of proteosome function, pristimerin causes rapid and sustained accumulation of high molecular weight poly-ubiquitinated protein in myeloma cell lines. Notably, related cytotoxic triterpenoid drugs, such as the methyl ester of 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO-Me, RTA 402) or betulinic acid or the ginsenosides - all of which show promising anti-cancer activities and are currently in clinical trials for advanced lymphoma, leukemia or solid malignancies - commonly inhibit NF-kB activation via direct inhibition of IKKα or IKKβ. In contrast drugs that function as proteosome inhibitors also commonly suppress NF-kB function instead by impairing degradation of ubiquitinated IkB. Immunoblotting for phosphorylated IkB confirms that pristimerin, like other triterpenoids, acts upstream of IkB to inhibit its phosphorylation, although pristimerin simultaneously inhibits proteosome activity with marked potency to diminish the clearance of ubiquitinated IkB. As a result of this two-fold stabilization of IkB, pristimerin causes overt and specific suppression of NF-kB mediated transcription, measured by a panel of transcriptional reporters with synthetic promoters containing 5x repeats of generic binding sites for NF-kB, AP-1, CREB or TCF4. Importantly, specific suppression of constitutive NF-kB transcriptional activity was pronounced in myeloma cells with inherent NF-kB pathway activation resulting from bi-allelic deletion of the TRAF3 tumor suppressor. Constitutive activation of the NF-kB pathway occurs in a significant proportion of primary myeloma tumors, most commonly via inactivation of TRAF3. Selective silencing of NF-kB driven transcription in myeloma cells may mediate the potent suppression of cyclin D proteins induced by this compound. Significantly, multiple myeloma cells are exquisitely sensitive to both proteosome inhibition or NFkB pathway inhibition. Consistent with these twin vulnerabilities, pristimerin is potently and selectively lethal to primary myeloma cells from patients (IC50