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433 citation(s) found for "Fonseca, Rafael".

14q32 Abnormalities and 13q Deletions Are Common in Primary Systemic Amyloidosis Using Cytoplasmic Immunoglobulin Fluorescence In Situ Hybridization (cIg-FISH).
Ketterling, Rhett, Zeldenrust, Steve R., Lacy, Martha Q. , Kumar, Shaji , Hayman, Suzanne R. , Greipp, Phillip, Lust, John A., Kyle, Robert A. , Bryce, Alan H. , Gertz, Morie A. , Zeldenrust, Steven R., Buadi, Francis K. , Rajkumar, S. Vincent , Fonseca, Rafaël , Dingli, David , Dispenzieri, Angela

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2477-2477

10.1182/blood.v110.11.2477.2477 Get It

Abstract Background: Primary systemic amyloidosis is an uncommon plasma cell dyscrasia characterized by organ deposition of immunoglobulin light or heavy chain fragments. It is related to the other plasma cell dyscrasias such as multiple myeloma and monoclonal gammopathy of undetermined significance. cIg-FISH on bone marrow plasma cells has become well established in the initial evaluation of myeloma as the t(4;14), t(14;16),13q-, and the 17p- abnormality are of major prognostic value. The corresponding data does not exist in amyloidosis, as there are only three small studies published to date. Methods: Using a prospectively held dysproteinemia database, we reviewed all cases of amyloidosis seen at our institution who had cIg-FISH or cytogenetics performed as part of their routine clinical testing. Three hundred thirty nine patients were identified with amyloidosis and cytogenetic testing. Of these 69 had cIg-FISH testing results. cIg-FISH was performed with fluorescent-tagged antibodies to kappa/lambda immunoglobulin and FISH probes corresponding to the following anomalies: trisomies 3, 7, 9 and 15; del17p/-17; -13/del13q; 14q32 split; and t(11;14). CCND1/IGH. If an IGH rearrangement was detected that did not involve CCNDI, we also evaluated t(4;14) or IGH/FGFR3 and t(14;16) or IGH/c-MAF. These probes constitute the standard screening panel used in MM at our institution. Results: The study population had a median age of 61 years with a male to female ratio of 1.6:1. Median follow up time was 13.5 months. By conventional cytogenetics, 88% of patients had no detectable abnormality. In contrast, only 33% were normal by cIg-FISH. The abnormalities demonstrated were 28% 13-/del13q, 42% IgH translocation, 33% t(11;14), and 3% t(14;16). No patients had a -17/del 17p- or t(4;14). Nine patients had del13q/-13 with an IgH translocation, with 7 of these having t(11;14). Both t(14;16) patients had del 13q. A trend towards increased mortality was seen in patient with any abnormality (p=0.11), but this could not be demonstrated for any single abnormality, likely due to lack of statistical power. There was no correlation between renal involvement or cardiac involvement and cIg-FISH results. Conclusion: The majority of chromosomal abnormalities in amyloidosis are undetected by conventional cytogenetics. With further study, chromosomal abnormalities may carry the same prognostic value in amyloidosis that they currently enjoy in myeloma. This effect may be independent of currently recognized risk factors. Chromosomal abnormalities in Amyloidosis as detected by cIg-FISH Abnormality Amyloidosis % (n=69) Normal 33(23) −13/del13q 28(19) IgH Abnormality 42(29) t(4;14) 0(0) t(11;14) 33(23) t(14;16) 3(2) del 17 0(0) Other 3(2)
RB1 Haploinsufficiency Confers a Proliferation Advantage in Myeloma Cell Lines.
Henry, Travis, Carpten, John D. , Fonseca, Rafael Hinojal , Chng, Wee Joo , Bergsagel, P. Leif , Fonseca, Rafael

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2489-2489

10.1182/blood.v110.11.2489.2489 Get It

Abstract The retinoblastoma 1 (RB1) gene is a frequent target of mutation or inactivation in neoplastic diseases. However, the current model for RB1-mediated malignancy requires inactivation of both alleles for tumor progression. Single–copy loss of RB1 has been shown to correlate with an approximate 50% reduction in RB1 mRNA expression in patients diagnosed with multiple myeloma and survival in this cohort of patients is significantly reduced. Using siRNA to reduce Rb protein levels to 50% and Rb-expressing adenovirus to restore RB1, variations in proliferation and cell cycle were observed. The KMS–11 adherent cell line with normal Rb protein expression was labeled with carboxyfluorescein succinimidyl ester (CFSE) for tracking of cellular division and RB1 siRNA added to silence 50% of protein expression. Transfection efficiency for siRNA was measured at 95% or greater. Flow cytometric analysis was performed at 72 hours to identify changes in proliferation between controls and Rb knock–down. Using CFSE proliferation analysis software, reduction of Rb protein levels by 50% caused an average increase in the proliferation index from 2.05 to 2.50. Additionally, reduction of Rb protein levels caused an increase in the percentage of cells in S–phase, from 24 to 29%. CFSE and cell cycle experiments were performed in triplicate. Conversely, addition of Rb–expressing adenovirus to MM.1R and U266 cell lines, with mono-allelic and bi-allelic loss of RB1 respectively, resulted in a decrease in proliferation assayed by CFSE and an average decrease in the percentage of cells in S-phase from 29 to 23% compared to controls. No changes in proliferation or cell cycle compared to untreated controls were observed following null adenovirus infection. Western blot and quantitative RT–PCR (qPCR) were used to confirm reduction or addition of RB1 to cell lines. Further, qPCR was used to identify potential activation of the interferon response following addition of siRNA and adenovirus. No changes in annexin V expression were observed following reduction or replacement of Rb as compared to controls. These results suggest the addition of proliferation advantages to tumors with single copy loss of RB1. For malignancies such as multiple myeloma characterized by deletion of 13q14 coupled with an extended period of development, the proliferation advantage associated with RB1 haploinsufficiency may contribute to decreased survival in the deletion 13 cohort.
A Phase II Trial of Myeloma Induction Therapy with Cyclophosphamide, Bortezomib, and Dexamethasone (Cybor-D): Improved Response over Historical Lenalidomide-Dexamethasone Controls.
Reeder, Craig B. , Reece, Donna , Hentz, Joseph G. , Pirooz, Nicholas, Boesiger, Jacy E., Pisa, Jesus G., Kukreti, Vishal , Chen, Christine , Trudel, Suzanne , Lacy, Martha Q. , Stewart, A. Keith, Fonseca, Rafaël , Bergsagel, P. Leif , Mıkhael, Joseph , Rajkumar, S. Vincent

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 3601-3601

10.1182/blood.v110.11.3601.3601 Get It

Abstract Background: We previously reported an 85% response rate with 54% CR/nCR using a combination of cyclophosphamide (Cy), prednisone, and bortezomib (BZ) in relapsed myeloma (MM). We now report a Phase II clinical trial using a combination of Cy, BZ, and dexamethasone (Dex) [Cybor-D] in newly-diagnosed MM. We then compare the activity of this combination with historical controls treated with our current induction standard of Lenalidomide-Dexamethasone (L-Dex). Methods: 30 patients have been enrolled on Cybor-D. Treatment consists of Cy 300mg/m2 p.o. days 1, 8, 15, and 22; BZ 1.3 mg/m2 days 1, 4, 8, and 11, and Dex 40mg p.o. days 1–4, 9–12, 17–20. Prophylactic use of acyclovir, a quinolone and antifungal prophylaxis was highly recommended for all patients on study. Growth factors were allowed. As a relevant contemporaneous control for speed and depth of response, we used 33 patients treated on a recent Mayo Clinic trial of L-Dex (Rajkumar. Blood: 2005 106;4050–3). Response was defined according to IMWG criteria although in the current trial, bone marrows for confirmation of CR are not yet available on all patients. Results: At time of current analysis, 17 patients on Cybor-D were evaluable through at least one cycle for response and toxicity. Baseline characteristics included mean age of 57, 29% female, 41/24% ISS stage II/III. There were statistically more early stage patients on L-Dex; otherwise, baseline patient characteristics were similar. The mean % decline in monoclonal (M) protein from baseline following cycles 1–4 of Cybor-D were 71%, 90%, 93%, 96%. This compares favorably with L-Dex where equivalent % decline in M proteins were 66%, 77%, 80%, and 79%. Thus, in preliminary results, Cybor-D produces a more rapid initial decline and mean % reduction in M protein than L-Dex. Overall response rate (≥ PR) after one cycle of Cybor-D was 77% with 36% obtaining ≥VGPR (L-Dex 73% and 18% respectively). The % of patients obtaining ≥VGPR after each cycle was 36%, 64%, 77%, and 100% for Cybor-D as compared to 18%, 36%, 42%, and 33% for L-Dex. The overall ≥VGPR at the end of four cycles of Cybor-D is currently100% (≥ 66%nCR using older nomeclature). Major toxicities ≥ grade 3 for Cybor-D included hematologic (37%), hyperglycemia (15%) and neuropathy (11%). Conclusions: In summary, for newly-diagnosed MM patients, four cycles of Cybor-D produces more frequent, rapid and deep responses when contrasted with historical L-Dex controls. Further confirmation of response rates and effect on TTP will be required.
Inactivation of Tumor Necrosis Factor 3 Gene (TRAF3) Is Frequently Identified in Waldenström’s Macroglobulinemia Patients.
Wier, Scott Van, Price-Troska, Tammy, Henderson, Kimberly J., Chesi, Marta , Carpten, John D. , Bergsagel, Leif P., Braggio, Esteban , Keats, Jonathan J. , Bergsagel, P. Leif , Fonseca, Rafaël

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2476-2476

10.1182/blood.v110.11.2476.2476 Get It

Abstract Constitutive activation of NF-κB signaling pathways has been identified in a variety of malignancies, however the molecular basis has remained largely unknown. Recently, we have shown mutations in 10 genes encoding positive and negative regulators of NF-κB signaling pathways in 20% of multiple myeloma (MM) patients, with TRAF3 being the most commonly affected gene. TRAF3 is a negative regulator of NF-κB signal and its inactivation results in the constitutive activation of the alternative or noncanonical NF-κB signaling pathway. With the exception of two recent studies in MM, there is no available data regarding the mechanisms that dysregulate NF-κB in other B-cell malignancies. The aim of this study was to analyze the TRAF3 status in a cohort of Waldenström’s macroglobulinemia (WM) patients. Forty-nine WM were analyzed by using a combination of array-based comparative genomic hybridization (aCGH) and cIgM-FISH. Genome sequencing from 28 of these patients was performed on all coding exons of TRAF3 and the adjacent intron-exon junctions. A NF-κB index, as a measure of NF-κB transcription activity, was calculated from 21 patients with gene expression data. The index is the mean expression level of four probe sets differentially expressed between human myeloma cell lines with identified mutations compared to those without identified NF-κB pathway mutations (CD74, IL2RG and 2x TNFAIP3). By performing aCGH we identified a small monoallelic deletion (∼460 Kb), including the TRAF3 locus in one of 22 patients. Genome sequencing identified a missense mutation (D483N) in the remaining allele. This substitution affects a highly conserved amino acid throughout vertebrate evolution, suggesting its functional relevance. We used cIgM-FISH to screen 27 patients with no available aCGH data and we found one biallelic TRAF3 deletion and one chromosome 14 monosomy. In the later case, no DNA was available to sequence the remaining allele. Both samples with biallelic inactivation of TRAF3 possess the two highest NFKB index values of our WM cohort, suggesting NF-κB transcription activity. Moreover, the case with biallelic deletion showed the lowest level of TRAF3 gene expression. Additionally, the entire TRAF3 coding region was sequenced in 28 of these 49 patients and one homozygous nonsense mutation (K286X) was identified. No GEP was available in this sample to calculate the NF-κB index. TRAF3 was only recently implicated in a malignant process, when inactivating mutations and biallelic deletions were reported in approximately 13% of MM patients, making it the most frequently inactivated tumor suppressor in MM. Our study has identified biallelic TRAF3 inactivation in at least 3 of 49 WM patients, suggesting that the constitutive activation of NF-κB signaling pathways may be involved in the pathogenesis of WM. Recent findings showing an association between TRAF3 loss of function and good response to bortezomib in MM patients suggest that proteasome inhibitor-based therapy may be an attractive option in the treatment of the WM patients with constitutive activation of NF-κB signaling pathways. Additional mutational screening of TRAF3 and other regulators of these pathways are ongoing to determine the extent of constitutive activation present in WM and other B-cell malignancies.
Immunoglobulin Free Light Chain Ratio Is an Independent Risk Factor for Progression of Smoldering Multiple Myeloma.
Kyle, Robert A. , Katzmann, Jerry A., Benson, Joanne, Clark, Raynell, Melton, L. Joseph, Kumar, Shaji , Jelinek, Diane F., Dispenzieri, Angela , Larson, Dirk R. , Benson, Joanne T., Gertz, Morie A. , Fonseca, Rafaël , Rajkumar, S. Vincent

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 1487-1487

10.1182/blood.v110.11.1487.1487 Get It

Abstract Background: Smoldering multiple myeloma (SMM) is an asymptomatic plasma cell proliferative disorder with a high risk of progression to symptomatic multiple myeloma. Identification of risk factors that predict progression of SMM to symptomatic MM could identify higher risk patients who might benefit from chemoprevention or more intensive surveillance. We hypothesized that increased monoclonal free kappa or lambda immunoglobulin light chains in smoldering myeloma (SMM), as detected by the serum free light chain (FLC) assay, indicates an increased the risk of progression to active myeloma. Methods: Of 276 pathologically confirmed SMM patients seen at the Mayo Clinic from 1970 to 1995, baseline serum samples obtained within 30 days of diagnosis were available in 273. Results: At a median follow-up of surviving patients of 12.4 years, transformation to active disease has occurred in 161 (59%) patients. An abnormal FLC ratio was present at baseline in 90% of patients. The best break-point for predicting risk of progression was a FLC ratio less than or equal to 0.125 or greater than or equal to 8 (hazard ratio, 2.3; 95% CI, 1.6–3.2) [Figure 1]. The extent of abnormality of FLC ratio was independent of SMM risk categories defined by number of plasma cells in the bone marrow and size of serum M-proteins (bone marrow plasma cells ≥ 10% and serum M protein ≥ 3 g/dL; bone marrow plasma cells ≥ 10% but serum M protein < 3 g/dL; and serum M protein ≥ 3 g/dL but bone marrow plasma cells < 10%). Incorporating the FLC ratio into the risk model, the division of patients into high-, intermediate-, and low-risk groups is 28, 42, and 30% with 5 year progression rates of 76, 51, and 25%, respectively [Figure 2]. Conclusions: The serum immunoglobulin FLC ratio is an important additional determinant of clinical outcome in patients with SMM. Figure Figure Figure Figure
The Multiple Myeloma Research Consortium Genomics Initiative.
Trent, Jeffrey M. , Carpten, John D. , Liefeld, Ted , Mousses, Spyro, Hahn, William C. , Trudel, Suzanne , Alsina, Melissa , Richardson, Paul G. , Auclair, Daniel , Giusti, Kathy, Golub, Todd R. , Reich, Michael M. , Keats, Jonathan J. , Siegel, David S. , Rajkumar, S. Vincent , Richardson, Paul Gerard Guy , Anderson, Kenneth C. , Perkins, Louise M. , Fonseca, Rafaël

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2498-2498

10.1182/blood.v110.11.2498.2498 Get It

Abstract The Multiple Myeloma Research Consortium (MMRC) Genomics Initiative is a three-year program to analyze tumor tissue from hundreds of multiple myeloma (MM) patients via gene expression profiling (GEP), comparative genomic hybridization (aCGH), and exon re-sequencing. In addition, RNAi knockdown of selected genes in MM tumor cell lines is being evaluated to identify potential new targets. All genomic data generated is scheduled for placement in an open-access Multiple Myeloma Genomics Portal pre-publication and in near real-time (www.broad.mit.edu/mmgp). Additionally, samples are also destined for drug validation and correlative science on clinical protocols as this study moves forward. This comprehensive project is spearheaded by the MMRC and conducted via collaboration with the Eli and Edythe L. Broad Institute of MIT and Harvard, the Translational Genomics Research Institute (TGen), Mayo Clinic Arizona, and The Dana-Farber Cancer Center. The study is supported by the collection from member institutions of the MMRC of bone marrow aspirates and matched peripheral blood samples from over 1000 patients. Specific genomic technologies that are currently being employed across this sample set include GEP using Affymetrix Human Genome U133A 2.0 Plus Arrays, and, in parallel, efforts to identify regions of genomic gain and loss are using Agilent Human Genome CGH arrays. In contrast to other large-scale genomic projects based on exon-sequencing of targeted gene sets, this project will be the first to perform genome-scale single molecule sequencing (SMS) of DNA from patient specimens. Results will be targeted against candidate classes of genes (e.g. kinases, phosphatases, known oncogenes and tumor suppressors), and genes from GEP or within candidate regions of copy gain or loss identified by the aCGH experiments. Mutations will be further validated in an independent set of patient specimens. Finally we will attempt to identify points of vulnerability of MM through systematic loss-of-function screens in myeloma cell lines using high-throughput RNA interference (using both shRNA and siRNA platforms). Importantly, data generated from this genomics initiative will ultimately be made public pre-publication through the established MMRC Multiple Myeloma Genomics Portal. Data from all aspects of this project (sample collection and analyte isolation, GEP, aCGH, SMS, RNAi and bioinformatics) will be described in this presentation. The power of this study is the comprehensive collection of gene expression, CGH, and genome sequencing on a single reference set of clinically annotated samples. The addition of RNAi screens makes this a very important and unique data resource, which we hope will help expedite the discovery of novel targeted agents for MM scientific community.
Proteomic Analysis of Multiple Myeloma Identifies Potential Targets for Drug Therapy.
Eckel, Jeanette E., Leontovich, Alexey A. , Timm, Michael, Ahmann, Gregory , Hoering, Antje , Ziesmer, Stephen, Cabanela, Miguel E., Nehme, Alex, Greipp, Philip R., Ghobrial, Irene M. , Fonseca, Rafaël , Witzig, Thomas E.

Blood | April 18, 2020 | Volume: 104 | Issue: 11 | Pages: 2446-2446

10.1182/blood.v104.11.2446.2446 Get It

Abstract The objective of this study was to investigate the underlying molecular alteration in multiple myeloma at the protein level in order to identify regulators of pathogenesis, discover novel targets of therapy, and compare genetic and proteomic alterations. We employed antibody protein microarrays (BD Clonetech, CA) to measure changes in the patterns of protein expression between MM and normal plasma cells. The antibody array is a new technique enabling protein differences to be assayed directly by hybridizing fluorescently labeled protein mixtures from cell extracts onto glass slides spotted with 512 different monoclonal antibodies. CD138+purified plasma cells were obtained from cryopreserved bone marrow samples of 12 newly diagnosed patients with MM. The labeling index was high (1% cutoff) in 7 samples and low in the other 5. Control plasma cells were obtained from 9 pooled CD138+ purified normal donor bone marrow plasma cells. Interphase FISH analysis for 17p deletion, 13q deletion, and t(11:14) were performed. To assess differential expression, the mean of the ratios of Cy5/Cy3 for each sample were analyzed using the Clontech software to calculate an internally normalized ratio. The normalized data were analyzed by the Genespring software. Unsupervised clustering identified 4 groups of MM. Changes of protein expression ≥2 fold in 70% of the samples as compared to control were identified. There were 6 proteins differentially expressed between all MM samples and control cells including proteins in the ras signaling pathway (KSR-1), the ubiquitin pathway (Ubc-H6), cyclin-dependent kinases (CDK4), cytokines (IL-6), DNA toposisomerase II, and the rho-interacting serine-threonine kinase CRIK. Proteins differentially expressed in MM groups 1 and 2 compared to normal control included cell cycle regulators (cul-2, MCM6, PCNA, TGFb1), kinases (p70S6K, PKC), and chromatin regulators (Ran, AKAP450, Rad50). Protiens differentially expressed in MM group 3 included cell cycle regulators (CDK2, CLK1, MENA), apoptosis regulators (XIAP, caspase 4, perforin) kinases (IKKa and RAC1 in the Wnt signaling pathway) and P53 regulators, while proteins identified in MM group 4 included NFkB/ubiquitin proteins (IKKa and Ubch6), cell cycle regulators (c-myc, CDK4), p53 pathway proteins (53bp2), ras-signaling proteins (KSR1), and the kinase CRIK. There were no differences in protein expression between the high and low labeling index groups. 13q was identified in 5 (42%), 17 p in 1(8%) and t(11:14) in 1(8%) patients. 80% of the 13 q deletion cases clustered in MM group 1 and 2 patients. Cyclin D-1 was upregulated in 5 (42%) patients including the patient with (11:14) translocation. This is the first proteomic study of patients with MM. The results are consistent with previously identified genetic alterations in MM indicating that this novel technique could be used in identifying molecular changes in MM. It identifies novel proteins dysregulated in MM that differ between the 4 MM groups. These results may be used in the future to individualize therapy based on the proteins dysregulated in each group. For example, IKK inhibitors may be useful in group 3 MM patients, while mTOR inhibitors (upstream of p70S6K) could be used in groups 1 and 2 patients. Future correlations with gene expression arrays and prognosis in a larger cohort of patients is warranted.
Waldenström Macroglobulinaemia: The Impact of Cytogenetic Analysis.
Jiménez‐Zepeda, Víctor H. , Chng, Wee Joo , Fonseca, Rafaël

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2490-2490

10.1182/blood.v110.11.2490.2490 Get It

Abstract Background Waldenström macroglobulinaemia (WM) is an uncommon indolent B-cell lymphoproliferative characterized by bone marrow infiltration by lymphoplasmacytic cells and an IgM paraproteinemia. This study analyzed the impact of cytogenetics in WM and the pattern of evolution in 73 cases from the Mitelman database and 14 cases evaluated at the Mayo Clinic Arizona (MCA). Patients and Methods The Mitelman database of Chromosome aberrations in cancer (Mitelman et al., 2007) was searched, and 73 WM karyotypes were selected. We also evaluated 14 cases seen at MCA with karyotype analysis at diagnosis. 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 (loss=0 and gain=1). Recurrent abnormalities were defined as those that were involved in >5% of cases. Histograms of the number of abnormalities per tumor (NAPT) 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 significan Results In total 73 cases of newly diagnosed WM from the Mitelman database were included in the analysis. The median chromosome number was 46 (Range 40 to 49).The most common abnormalities were loss of 6q21 (10%) (Fig 1), +3 (7.1%), loss of X (6%) and −10, −20, −21, +12, +18 and +5 (5.71% respectively). The most common translocation was t(8;14) (4%).The most recurrent breakpoints in our series include: 14q32 (6%), 6q21 (5%), 8q24 (5%), 18q21 (4%) and 19q13 (4%). In the MCA cohort, 14 karyotypes were reviewed and only 3 cases exhibited an abnormal result. Deletion of 6q21, 20q11 and a Robertsonian translocation t(13;14) were reported (3/11, 21%). In the 6q21 case, FISH analysis confirmed the deletion of BLIMP1 on 6q. One case exhibited a 20q deletion in a WM with kidney amyloidosis patient. Discussion In this comprehensive analysis we show a very small complexity of recurrent abnormalities expressed by conventional karyotype analysis in WM. The incidence of 6q21 deletion was 10% by conventional cytogenetics and it is been reported as high as 34% when analysed by FISH (54% when cytoplasmic immunoglobulin M-FISH was used). Interestingly we report the case of a patient with 20q deletion at diagnosis in the MCA cohort. To date, only a limited number of cases with del(20q) as a sole cytogenetic anomaly have been reported in plasma cell dyscrasias, either at diagnosis or later in the disease course. The recurrent immunoglobulin gene translocation is known to be involved in the initial oncogenetic events in plasma cell dyscrasias and, so it is important to identify whether there are any masked translocations involving immunoglobulin genes and 20q in these cases. Figure 1. 6q21 deletion and Waldenstrom Macroglobulinaemia Figure 1. 6q21 deletion and Waldenstrom Macroglobulinaemia
Identification of Survival Critical Genomic Gains or Losses in Myeloma (MM) Using Array-Comparative Genomic Hybridization (aCGH).
Chung, Tae-Hoon , Baker, Angela , Carpten, John D. , Chng, Wee Joo , Keats, Jonathan J. , Bergsagel, P. Leif , Fonseca, Rafaël

Blood | April 18, 2020 | Volume: 110 | Issue: 11 | Pages: 2471-2471

10.1182/blood.v110.11.2471.2471 Get It

Abstract Genetic abnormalities are important in the pathobiology of myeloma and established prognostic factors. High-density aCGH allow global unbiased detection of genomic gains and losses. In this study, we attempt to identify survival critical genomic aberrations by correlating aCGH-defined abnormalities with survival in 2 different cohorts of patients. aCGH was performed in 64 MM patients treated with high dose therapy from the Mayo Clinic using Agilent’s 44k DNA microarray genechip. In addition, a publicly available aCGH dataset performed in 67 MM patients treated with total therapy from the University of Arkansas Medical School using the lower density Agilent 22k chip (Human 1A v2) was also analyzed. Base 2 logarithms of the ratios between red and green intensities (log-ratios) were treated as a primary measure of copy number ratio between tumor and normal samples. To detect the regions of genomic aberration, values of a sliding window of 15 consecutive log-ratios were compared with those of an artificial ‘reference’ chromosome using the Wilcoxon rank sum test. The reference chromosome, constructed for each sample, was assembled by collecting log-ratio values close to zero. For this, 15 randomly sampled log-ratios from autosomal regions whose p-value of Wilcoxon signed rank test against 0 was larger than 0.05 were recursively accepted until the number of log-ratios in the assembled reference chromosome reached 1000. The p-values and their corresponding false discovery rates (q-values) for the copy number gain or loss were calculated independently for each sliding window and assigned to the center position of corresponding sliding window. The survival difference was examined between samples that had gained or lost a chromosomal region (sliding window) and samples that had not using the method of Kaplan-Meier and the statistical significance was assessed by the log-rank test. The sliding window was identified as gained or lost if P-value < 10 −4 and Q-value < 10[suo]-3. Sliding windows whose gains or losses led to poor survival with log-rank test p-value < 0.5, corresponding q-value < 0.5, and happened to ≥ 10% of all samples were retained. Several regions of genomic gains and losses were significantly associated with poorer survival with 5 deletion hotspots common between the 2 datasets (Table). We validated the prognostic significance of these survival critical loci using FISH in an independent dataset of 169 patients treated with high dose therapy. Clustering of these survival critical loci revealed clusters of MM characterized by low, intermediate or high number of these abnormalities, which are independent of ploidy and translocations subtypes. These subgroups have significantly different survival. In addition, the clustering analysis suggests the chromosome 13 loss is an early event whereas chromosome 1 abnormalities are late events. Our strategy therefore identified novel regions of genomic aberration that are important prognostically. However, it is likely that these regions are manifestation of genomically unstable tumors with complex abnormalities that have poorer prognosis. Chr Start End Length Cytoband 1 74,137,824 75,972,544 1,834,720 p31.1 1 62,433,123 84,792,809 22,359,686 p31.3 – p22.3 20 4,100,452 6,189,410 2,088,958 p13 – p12.3 20 6,717,170 13,142,205 6,425,035 p12.3 – p12.1 20 4,708,668 10,566,333 5,857,665 p13 – p12.2
Deletion 13 by FISH Provides Prognostic Information on Overall Survival and Time to Progression Independent of Serum Beta 2 Microglobulin and Bone Marrow Plasma Cell Labeling Index in Myeloma Patients Undergoing Stem Cell Transplantation.
Lacy, Martha Q. , Greipp, Philip R., Litzow, Mark R. , Henderson, Kim, VanWier, Scott, Ahmann, Greg, Gertz, Morie A. , Dispenzieri, Angela , Henderson, Kimberly J., Fonseca, Rafaël

Blood | April 18, 2020 | Volume: 104 | Issue: 11 | Pages: 4852-4852

10.1182/blood.v104.11.4852.4852 Get It

Abstract INTRODUCTION The bone marrow plasma cell labeling index (PCLI) and the beta 2 microglobulin (β2M) when combined provide a powerful staging system highly predictive of outcomes in myeloma patients (Greipp et. al., Blood, 81:3382–87, 1993). This staging system lacks information on cytogenetics and it has been demonstrated that deletion 13 (Δ13) by conventional cytogenetics is associated with poor outcomes. In conventionally treated patients Δ13 by FISH is an independent prognostic variable. We analyzed the importance of Δ13 by FISH in a cohort of patients receiving high dose therapy and assessed its value relative to known prognostic parameters, PCLI and β2M. PATIENTS AND METHODS 238 patients undergoing high dose therapy between January 1990 and September 2001 were studied. The minimum follow-up of patients was 34 months. The median age of the cohort 56 years. Interphase fluorescence in situ hybridization with Probes LSI13/D13S319 was performed with simultaneous immunofluorescent detection of bone marrow plasma cells by the presence of cytoplasmic immunoglobulin. PCLI was done by a slide-based immunofluorescence method with antibodies to bromodeoxyuridine. RESULTS Of the 238 patients studied 215 had a successful FISH analysis and 212 of these had a bone marrow labeling index. Deletion 13 was absent in 104 patients (48%) and present in 111 patients. The overall survival and time to progression for patients lacking and having deletion 13 was 47.8 vs 26.4 (OS) and 19.0 vs 11.7 (TTP)months respectively. A Cox model was constructed with the PCLI, the presence or absence of deletion 13 and serum β2M. Although all three variables were independently predictive of survival and time to progression, the β2M was the weakest of these three variables. The hazard function for survival for PCLI, deletion 13 and β2M was 1.4, 1.6 and 1.1 respectively. A staging system was constructed assigning 1 point for the presence of deletion 13 or a PCLI ≥ 1%. Patients fell into 3 categories of 0 points (N=69), 1 point (N=104) and 2 points (N=39). The overall survival for the three groups respectively were 56.5, 36.6 and 13.7 months (figure). The time to progression for the three groups were 22.3, 15.4 and 8 months (P<0.001). When analysis was limited to those patients transplanted within 12 months of diagnosis the results remained significant (P<0.003) with median survivals of stage 0, 1 and 2 of 72.5, 59.1 and 15.4 months respectively. TTP for stage 0, 1 & 2 in this same cohort of patients transplanted < 12 mos after diagnosis is 30.6, 21.5 & 8.2 months respectively. CONCLUSION Deletion 13 by FISH is an independent predictor of survival and time to progression providing information independent of the β2M and the PCLI. Combining the PCLI with FISH del 13 identifies patients who following transplant have a median time to progression of 8 months and a median OS of 13.7 months. This group may not benefit from autologous transplant and are candidates for novel therapeutic approaches. Figure Figure