Copy Number Variants Modulation and Their Clinical Impact in Multiple Myeloma

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 5304-5304
Author(s):  
Zuzana Kufova ◽  
Lucie Brozova ◽  
Pavel Nemec ◽  
Jan Smetana ◽  
Elena Kryukova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Overall Survival ◽  
Copy Number ◽  
Target Gene ◽  
Plasma Cells ◽  
Copy Number Variants ◽  
Clinical Impact ◽  
Newly Diagnosed ◽  
Total N

Abstract Background: Multiple myeloma (MM) is a lymphoproliferative disease characterized by the clonal expansion of neoplastic plasma cells within the bone marrow. The genome of the malignant plasma cells is extremely unstable characterized by a complex combination of structure and numerical abnormalities. DNA copy number variants (CNV) affects target gene expression but such affectation is not compulsory and target gene expression can be modulated. We supposed that this modulation serves as a compensatory mechanism to keep genomic homeostasis. Further compensation mechanisms exhausting leads disease aggressiveness. Aims: The objective of our study was to define and describe influence of DNA copy number variants on gene expression level in multiple myeloma. Material and methods: 66 newly diagnosed patients with MM were evaluated for this study. The patients' baseline characteristics were as follows: males/females: 34/32 (52% /48%); median age of 68 years (range 49-83 years). Type of M protein IgG/IgA/LC/other (total n=58); 36/11/10/1 (62%/19%/17%/2%); most of the patients had advanced stage of MM DS II+III (total n=58) n =58 (100%); ISS II+III (total n=53) n=42 (79%). CD138+ plasma cells separated by MACS. Gene expression profiling was performed using Affymetrix GeneChip Human Gene ST 1.0 array (Affymetrix). DNA copy number variations was evaluated using Agilent Human Genome CGH Microarray (4x44K), Agilent SurePrint G3 Human Genome CGH+SNP Microarray Kit (4x180K), OGT CytoSure Haematological Cancer +SNP (8x60K), Agilent SurePrint G3 Human CGH Microarray (8x60K) with proper platforms aggregation (Agilent technologies). Results: Each patient had at least one CNV, the most often changes were at the level of entire chromosomes. Hyperdiploid/non-hyperdiploid patients (H-MM/NH-MM) represent 53 % (31/66) and 47 % (35/66), resp. CNV considered as uncompensated, if the value of target gene expression is lower than the 25th percentile of norm (gene expression of genes without loss or gain of DNA) for gene loss, or greater than the 75th percentile of norm for gene gain. Figure 1A shows that level of CNV modulation is determined by the number of changes that occur in a given patient. Further, ROC analysis was done to determine whether certain level of compensation is related to the overall survival and CNV compensation limit 20% (p=0.026) was established. Patients with ≥20% of decompensated CNV had significantly worse OS (survival median 5.2 month) compared to patients with <20% of decompensated CNV (survival median 23.5 month). Kaplan-Meier curves for given patients' subgroups are presented in Figure 1B. Conclusion: Copy number variants in MM can be compensated on gene expression level. Compensatory capacity of genome is associated with total number of CNV. Patients with ≥20% of decompensated CNV had significantly worse OS. Acknowledgment: This study was supported by grants no. MSK 02680/2014/RRC and MSK 02692/2014/RRC; MH CZ-DRO-FNOs/2014; SGS01/LF/2014-2015, SGS02/LF/2014-2015, SGS03/LF/2015-2016, NT14575, AZV 15-29508A and AZV 15-29667A Figure 1. Copy number variants (CNV) modulation and their clinical impact in multiple myeloma A. The overall rate of CNV occurrence in proportion to the gene expression affectation (loss of CNV compensation) B. Overall survival in newly diagnosed MM patients with different level of CNV compensation. Figure 1. Copy number variants (CNV) modulation and their clinical impact in multiple myeloma A. The overall rate of CNV occurrence in proportion to the gene expression affectation (loss of CNV compensation) B. Overall survival in newly diagnosed MM patients with different level of CNV compensation. Disclosures Hajek: Janssen-Cilag: Honoraria; Celgene, Amgen: Consultancy, Honoraria.

Gene expression profiling for molecular classification of multiple myeloma in newly diagnosed patients

Blood ◽  
2010 ◽  
Vol 116 (14) ◽  
pp. 2543-2553 ◽  
Author(s):  
Annemiek Broyl ◽  
Dirk Hose ◽  
Henk Lokhorst ◽  
Yvonne de Knegt ◽  
Justine Peeters ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Plasma Cells ◽  
Medical Science ◽  
Protein Tyrosine Phosphatases ◽  
Molecular Classification ◽  
Newly Diagnosed ◽  
Expression Of Genes

Abstract To identify molecularly defined subgroups in multiple myeloma, gene expression profiling was performed on purified CD138+ plasma cells of 320 newly diagnosed myeloma patients included in the Dutch-Belgian/German HOVON-65/GMMG-HD4 trial. Hierarchical clustering identified 10 subgroups; 6 corresponded to clusters described in the University of Arkansas for Medical Science (UAMS) classification, CD-1 (n = 13, 4.1%), CD-2 (n = 34, 1.6%), MF (n = 32, 1.0%), MS (n = 33, 1.3%), proliferation-associated genes (n = 15, 4.7%), and hyperdiploid (n = 77, 24.1%). Moreover, the UAMS low percentage of bone disease cluster was identified as a subcluster of the MF cluster (n = 15, 4.7%). One subgroup (n = 39, 12.2%) showed a myeloid signature. Three novel subgroups were defined, including a subgroup of 37 patients (11.6%) characterized by high expression of genes involved in the nuclear factor kappa light-chain-enhancer of activated B cells pathway, which include TNFAIP3 and CD40. Another subgroup of 22 patients (6.9%) was characterized by distinct overexpression of cancer testis antigens without overexpression of proliferation genes. The third novel cluster of 9 patients (2.8%) showed up-regulation of protein tyrosine phosphatases PRL-3 and PTPRZ1 as well as SOCS3. To conclude, in addition to 7 clusters described in the UAMS classification, we identified 3 novel subsets of multiple myeloma that may represent unique diagnostic entities.

Increased Expression of Cyclin-D1 on Trephine Bone Marrow Biopsies Independently Predicts for Shorter Overall Survival In Patients with Multiple Myeloma Treated with Novel Agents

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2965-2965
Author(s):  
Evangelos Terpos ◽  
Maria Roussou ◽  
Anna Tasidou ◽  
Magdalini Migkou ◽  
Maria Gavriatopoulou ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Overall Survival ◽  
Cyclin D1 ◽  
Plasma Cells ◽  
Univariate Analysis ◽  
Novel Agents ◽  
Positive Staining ◽  
Newly Diagnosed ◽  
Immunohistochemical Expression

Abstract Abstract 2965 The cyclin-D1 proto-oncogene is an important cell regulator of G1 to S phase progression. The overexpression of cyclin-D1 has been linked to the development and progression of several malignancies. The aim of our study was to evaluate the impact of the immunohistochemical expression of cyclin-D1on the plasma cells of trephine biopsies on survival of newly-diagnosed patients with multiple myeloma (MM) who were treated with novel agents. We evaluated formalin-fixed, paraffin-embedded, bone marrow sections of 130 consecutive patients with newly-diagnosed MM (67M/63F; median age 68 years) before any kind of therapy administration. One hundred and fifteen patients had symptomatic disease that required therapy: 29 (25%) received bortezomib-based regimens and 31 (26%) received thalidomide-based regimens as first line therapy, while all patients received regimens containing bortezomib or an IMiD at some point during the course of their disease. Immunohistochemistry was performed in all trephine biopsies using monoclonal antibodies against cyclin-D1 (Cell Marque Corp., Rocklin, CA, USA), but also against CD56 (Cell Marque Corp., Rocklin, CA, USA), CD27 (Novocastra, Newcastle upon Tyne, UK), CD117 and MUM-1 (DAKO A/S, Glostrup, Denmark), as recommended by the manufacturers. A case was considered positive if there was unequivocal positive staining of at least 20% of the plasma cells for cyclin-D1, CD56 and MUM-1 and a positive staining of at least 10% of the plasma cells for CD117 and CD27. Among patients with symptomatic myeloma (N=115), positive staining for cyclin-D1 was found in 35 (30%) patients, for CD56 in 45 (39%), for CD117 in 94 (81%) and for CD27 in 72 (62%) patients. In patients with asymptomatic myeloma, positive staining for Cyclin-D1 was found only in 1 (7%) patient, for CD56 in 9 (64%), and for CD117 in 6 (43%) (p<0.01 for all comparisons compared to symptomatic patients). There were significant positive correlations between positivity for CD27 and CD56 (p<0.001), between positivity for cyclin-D1 and CD117 (p=0.045) and a negative correlation between positivity for CD117 and CD56 (p=0.001). We also observed significant correlations between CD56 positivity and ISS-1 or ISS-2 (p=0.01) and between CD117 positivity and ISS-3 disease (p=0.002). The median overall survival (OS) for patients with symptomatic MM was 57 months (range 22–120 months). In the univariate analysis, positivity for cyclin-D1 (41 vs. 62 months, p=0.03) and for CD117 (50 vs. 75 months p=0.018) were associated with inferior survival, while positivity for CD56 (47 vs. 62 months, p=0.286), MUM-1 (52.7 vs. 63.8 months, p=0.528) and CD27 (57 vs. 50 months, p=0.445) were not. Other factors associated with inferior OS, in the univariate analysis, included ISS-3 (median OS 37 months, vs. 57 months for ISS-2 and 73 months for ISS-1, p=0.005), Hb <10 g/dl (56 vs. 73 months, p=0.044), corrected serum calcium >11.5 g/dl (29 vs. 62 months, p=0.02), serum LDH above upper normal limit (31 vs. 61 months, p=0.05), serum creatinine >2 mg/dl (26 vs. 64 months, p=0.007), low platelet counts (<100,000/ml) (22 vs. 62 months, p=0.031) and age >65 years (45 months vs. not reached for younger patients, p=0.002). In the multivariate analysis, positivity for cyclin-D1 (HR: 2.6; p=0.001), ISS stage (HR: 1.8; p=0.001) and age >65 (HR 2.7, p=0.003) were independently associated with inferior survival. Immunohistochemistry for cyclin-D1 identified subgroups of patients in ISS-2 and in ISS-3 who had extremely poor outcome. Patients with cyclin-D1 positivity had a median survival of 22 months in ISS-2 (vs. 64 months for the rest of ISS-2 patients, p=0.01) and of 13 months in ISS-3 (vs. 47 months for the rest of ISS-3, p=0.012). Our findings underline that the immunohistochemical expression of cyclin-D1 in the bone marrow trephine biopsies has independent prognostic value in MM patients, even in the era of novel agents. This marker can easily be assessed in patients who undergo a trephine biopsy as part of their initial evaluation and offers significant prognostic information. Furthermore, novel agents targeting cyclin-D1 may be of therapeutic value in MM. Disclosures: No relevant conflicts of interest to declare.

A Comparison of Clinical FISH and Sequencing Based FISH Estimates in Multiple Myeloma: An Mmrf Commpass Analysis

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 374-374 ◽  
Author(s):  
Chase Miller ◽  
Jennifer Yesil ◽  
Mary Derome ◽  
Andrea Donnelly ◽  
Jean Marrian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Rna Sequencing ◽  
Plasma Cell ◽  
Copy Number ◽  
Target Gene ◽  
False Negative ◽  
Single Individual ◽  
Sequencing Data ◽  
Target Gene Expression

Abstract Fluorescent in situ hybridization (FISH) is commonly used in the multiple myeloma field to subtype and risk-stratify patients. There are many benefits to FISH based assays, which are widely used around the world and represent true single cell assays. However, there are significant discrepancies in the specific assays, utilization of reflex testing strategies, and enumeration requirements between clinical centers. By comparison next-generation sequencing tests can be designed to simultaneously detect the copy number abnormalities and translocations detected by clinical FISH along with gene mutations that cannot be detected by FISH. As part of the MMRF CoMMpass Study we have compared the results attained using clinical FISH assays compared to sequencing based FISH (Seq-FISH) results. Clinical FISH reports from a random subset of 339 CoMMpass patients were extraction by a single individual based on the ISCN result lines of each report. To validate the accuracy of the central data extraction, two independent cross validations of 10% of the cohort were performed, after which our data entry error rate is expected to be less than 0.348%. The Seq-FISH results were extracted from the whole genome sequencing data available from each patient using a rapid and fully automated informatics process and the results were cross-validated using the matching exome sequencing data for copy number abnormalities and by RNA sequencing data for dysregulated immunoglobulin translocation target genes. There were 230 patients with clinical FISH and Seq-FISH results. In this cohort, 151 translocations were identified by Seq-FISH. This includes translocations to MYC, CCND2, MAFA, and those involving IgK and IgL, which are not tested by clinical FISH. After filtering non-tested translocations there are 118 translocations identified by Seq-FISH. Only 97 of these translocations had a clinical FISH assay performed with 89 (91.75%) of these being detected by clinical FISH, yet spiked target gene expression was observed in all 89 cases by RNA sequencing. Conversely, 93 translocations were called by clinical FISH, of these 89 were called by Seq-FISH(95.7%). Of the 4 translocations only called by clinical FISH, 3 were t(4;14) and 1 was a t(11;14). In two of these t(4;14) cases we did observe spiked target gene expression by RNA sequencing, suggesting these are false negatives by Seq-FISH. However, the remaining two events appear to be false positive clinical FISH results. The t(4;14) event was only observed in 1/200 cells and a co-occuring t(11;14) was also called, which was confirmed by Seq-FISH and spiked gene expression. Similarly, the one t(11;14) was observed in 3/56 cells but a del13q14 was seen in 47/50 cells, unfortunately RNA sequencing data is not available to cross-validate in this case. Plasma cell enrichment or identification is commonly used to prepare myeloma samples for FISH because even in myeloma, the total plasma cell percentage can be low (median 8.3% in the MMRF CoMMpass Baseline Cohort). Therefore, performing FISH on a sample without performing purification or plasma cell identification will indiscriminately assay non-plasma cells and limit the efficacy of the assay. We looked at the two most common translocations in myeloma, t(4;14) and t(11;14), to test the effect of enrichment on sensitivity. Sensitivity was higher for both sets of translocations in the enriched cohort. There was 1 false negative in the enriched population, yielding sensitivities of 100% (32/32) and 95%(19/20) for CCND1 and WHSC1 respectively. For those reports that did not indicate enrichment was performed the observed sensitivities were 86.36% (19/22) and 92.86% (13/14). Seq-FISH identified almost all of the translocations called by clinical FISH and simultaneously; it identified 30 translocations missed by clinical FISH. The translocations that were not reported by clinical FISH can be attributed to a mixture of the correct assay not being performed and the translocation being missed even though the assay was performed. We believe that Seq-FISH is a viable alternative to clinical FISH, with similar specificity and greater sensitivity. It is important to note that a single Seq-FISH assay is sufficient to investigate all translocations, while each translocation must be investigated separately with clinical FISH. As such, Seq-FISH obviates the concern that a translocation would be missed because the correct assay was not performed. Disclosures McBride: Instat: Employment.

scholarly journals Modelization of Blood-Borne Hypercoagulability in Myeloma: A Tissue-Factor-Bearing Microparticle-Driven Process

TH Open ◽  
2019 ◽  
Vol 03 (04) ◽  
pp. e340-e347
Author(s):  
Loula Papageorgiou ◽  
Kutaiba Alhaj Hussen ◽  
Sandrine Thouroude ◽  
Elisabeth Mbemba ◽  
Héléne Cost ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Tissue Factor ◽  
Thrombin Generation ◽  
Plasma Cells ◽  
Annexin V ◽  
Factor Vii ◽  
Newly Diagnosed ◽  
Normal Human ◽  
Tf Gene

Abstract Introduction Hypercoagulability is a common blood alteration in newly diagnosed chemotherapy naïve patients with multiple myeloma. The identification of the procoagulant potential of cancer cells, which is principally related to tissue factor (TF) expression, attracts particular interest. The mechanisms by which myeloma plasma cells (MPCs) activate blood coagulation have been poorly investigated. Aim To identify the principal actors related with MPCs that boost thrombin generation (TG). Methods TF and annexin V expression by MPCs and MPC-derived microparticles (MPC-dMPs) was analyzed by flow cytometry. TF activity (TFa) and TF gene expression were also determined. TG in the presence of MPCs or MPC-dMPs was assessed with the calibrated automated thrombogram assay (CAT) in normal human PPP and in plasma depleted of factor VII or XII. TG was also assessed in plasma spiked with MPCs and MPC-dMPs. Results MPC-dMPs expressed approximately twofold higher levels of TF as compared with MPCs. The TFa expressed by MPC-dMPs was significantly higher compared with that expressed by MPCs. MPCs and MPC-dMPs enhanced TG of human plasma. TG was significantly higher with MPC-dMPs compared with MPCs. Conclusion MPCs indirectly induce blood-borne hypercoagulability through the release of MPC-dMPs rich in TF. Since MPCs, expressing low TFa, represent a weak procoagulant stimulus, the hypercoagulability at the microenvironment could be the resultant of MPC-dMPs rich in TF.

Gene Expression Profiling of Myeloma Cells To Predict Response to Primary Therapy with Thalidomide-Dexamethasone for Newly Diagnosed Multilple Myeloma.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1494-1494
Author(s):  
Abderrahman Abdelkefi ◽  
John de Vos ◽  
Said Assou ◽  
Tarek Ben Othman ◽  
Jean-Francois Rossi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Gene Expression Profiling ◽  
Treatment Strategy ◽  
Expression Profiling ◽  
Plasma Cells ◽  
Gene List ◽  
Microarray Platform ◽  
Primary Therapy ◽  
Newly Diagnosed

Abstract Background: Thalidomide which represents an effective treatment strategy for relapsed/refractory multiple myeloma, actually represents a standard of care also for newly diagnosed multiple myeloma patients. Methods: In the present study, we adopted a gene expression profiling (GEP) strategy in an attempt to predict response (&gt; 50% reduction in serum M protein) to primary therapy with thalidomide-dexamethasone for newly diagnosed multiple myeloma. Plasma cells (CD138+) were purified from bone marrow aspirates from 17 patients at diagnosis, before initiation of treatment with thalidomide-dexamethasone. GEP was performed using the Affymetrix U133 Plus_2 microarray platform. The Affymetrix output (CEL files) was imported into Genespring 7.3 (Agilent technologies) microarray analysis software, where data files were normalized across chips using GCRMA and to the 50th percentile, followed by per gene normalization to median. Criteria of response were those established by Bladè et al. Results: After sufficient follow-up, responders (n=9) and nonresponders (n=8) were identified, and gene expression differences in baselines samples were examined. Of the 11000 genes surveyed, Wilcoxon rank sum test identified 149 genes that distinguished response from non response. A multivariate step-wise discriminant analysis (MSDA) revealed that 14 of the 149 genes could be used in a response predictor model (see table). Of interest, the gene list encompasses WXSC1, known to be involved in the chromosomal translocation t(4;14) (p16.3;q32.3) in multiple myeloma. Conclusion: These results could be the first step to adopt microfluidic cards, in an attempt to select at diagnosis patients who will respond favourably to a particular treatment strategy. List of 14 genes able to predict response to primary therapy with thalidomide-dexamethasone for newly diagnosed multiple myeloma. Gene ID Gene Name Chromosomal location 212771_at C10orf38 10p13 229874_x_at LOC400741 1p36.13 219690_at U2AF1L4 19q13.12 202207_at ARL7 2q37.1 243819_at GNG2 14q21 203753_at TCF4 18q21.1 235400_at FCRLM1 1q23.3 211474_s_at SERPINB6 6p25 226785_at ATP11C Xq27.1 215440_s_at BEXL1 Xq22.1–q22.3 209054_s_at WXSC1 4p16.3 227168_at FLJ25967 22p12.1 213355_at ST3GAL6 3q12.1 223218_s_at NFKBIZ 3p12–q12

MAGE-A3 or NY-ESO1 Expression and Spontaneous Antibody Responses to NY-ESO1 in Newly Diagnosed Multiple Myeloma Patients Are Associated with Worse Overall Survival

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 5110-5110
Author(s):  
Adam D Cohen ◽  
Ping Lu ◽  
Sacha Gnjatic ◽  
James Hoffman ◽  
Erika Ritter ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Overall Survival ◽  
Soft Tissue ◽  
Induction Therapy ◽  
Plasma Cells ◽  
Prognostic Significance ◽  
Antibody Responses ◽  
Newly Diagnosed ◽  
Bone Marrow Plasma

Abstract The cancer-testis antigens (CTA) are highly immunogenic antigens expressed in various tumors but not in normal tissues (except during gametogenesis), making them an attractive target for cancer immunotherapy. Expression of CTAs such as MAGE-A3, MAGE-C1 (CT7), MAGE-C2 (CT10), NY-ESO1 and the SSX antigens has been previously reported in multiple myeloma (MM). To date, however, these reports have included a heterogeneous group of newly diagnosed and relapsed/refractory patients, all in different stages of treatment. Therefore, the extent and prognostic significance of CTA expression, and of de novo immune responses against CTA in newly-diagnosed MM patients are not known. We now report on both CTA expression and antibody responses in MM patients at diagnosis and on their prognostic significance. From 8/00-11/04, we treated 67 newly-diagnosed, symptomatic patients with a thalidomide, doxorubicin, and dexamethasone-based induction regimen. (Brit J Haematol2006;132:155). Median age was 58; 54% were ISS stage I, 28% ISS II, and 18% ISS III. Nine of 63 tested (14%) had deletion 13q by FISH, while 24% had soft tissue involvement by MM. Responses to induction therapy included 10 (15%) CR, 16 (24%) VGPR, 26 (39%) PR, 6 (8%) stable or progressive disease, and 9 (13%) inevaluable. Post-induction 54 underwent autoSCT and 9 also underwent alloSCT.. Median overall survival (OS) has not been reached with 61% alive at median follow up of 65 months. Cryopreserved pre-treatment bone marrow plasma cells were used to assess CTA expression by RT-PCR. Pre- and post-treatment sera were used to assess antibody (Ab) responses against CTA proteins by ELISA. Fifty-two patients had sufficient RNA for PCR, and 46 had baseline serum for ELISA. OS of these groups did not differ significantly from the entire cohort. At least 1 CTA was expressed in 77% of cases, including MAGE-A3 (52%), SSX1 (40%), CT7 (29%), CT10 (25%), NY-ESO1 (21%), and SSX5 (17%). Three or more CTA were expressed in 29% of cases. Individually MAGE-A3 or NY-ESO1 expression at diagnosis conferred a poorer prognosis (MAGE-A3: median OS 66 mos. vs. not reached, p=0.02 by log-rank; NY-ESO1: median OS 65 mos. vs. not reached, p=0.09). These poorer outcomes were independent of ISS stage, presence of del 13q, or response to induction therapy. No other CTA was associated with an OS difference, nor was the total number of CTA expressed prognostically significant. Baseline Ab responses, all at titers &gt; 1:1600, were noted to NY-ESO1 in 6/46 (13%) patients, 5 of whom also had Ab to the NY-ESO1 homologue LAGE-1. Ab responses were also noted to CT7 (n=2), CT10 (n=1) and SSX4 (n=1). No Ab responses were noted to MAGE-A3. The effect of induction therapy on antibody titers was inconsistent, with increases, decreases, and no changes seen. Interestingly, 2 of the 6 NY-ESO1 Ab+ patients had no NY-ESO1 expression in bone marrow plasma cells. Both, however, had extensive soft tissue (ST) plasmacytomas, suggesting another source of NY-ESO1 antigen. Presence of NY-ESO1 Ab correlated significantly with baseline ST involvement, with 67% of Ab+ patients having ST disease compared with 20% of Ab− patients (p=0.05). NY-ESO1 Ab+ patients also had significantly poorer OS (med 21 mos. vs. not reached, p=0.009), independent of other prognostic factors. In sum, CTA expression is frequent in newly diagnosed MM patients, and expression of MAGE-A3 or NY-ESO1 is associated with worse long-term survival. Spontaneous antibody responses against NY-ESO1 are seen in untreated patients, and are associated with ST involvement and poorer survival. Further exploration of biologic differences between CTA+ and CTA-MM, as well as immunotherapeutic strategies which target these antigens, are warranted.

CXCR3 Binding Chemokines MIG, IP-10 and ITAC Are Predictors of Overall Survival in Newly Diagnosed Multiple Myeloma

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2052-2052
Author(s):  
Arnold Bolomsky ◽  
Niklas Zojer ◽  
Martin Schreder ◽  
Heinz Ludwig
Keyword(s):  
Multiple Myeloma ◽  
Overall Survival ◽  
Plasma Cells ◽  
In Silico Analysis ◽  
Serum Levels ◽  
Newly Diagnosed ◽  
Myeloma Cells ◽  
Detection Call ◽  
Silico Analysis

Abstract Background. The chemokine receptor CXCR3 and its binding molecules MIG, IP-10 and ITAC have been associated with tumor progression, immune escape and angiogenesis in several human malignancies. In multiple myeloma (MM), CXCR3 binding molecules were shown to induce migration of MM cells without effecting proliferation. More recent results suggest a tumor suppressive activity of IP-10. Presently, information about the precise role of CXCR3 binding chemokines in MM is limited and evidence for their clinical significance is lacking. Therefore we aimed to evaluate the prognostic relevance of CXCR3 binding chemokines in patients with MM. Patients and Methods. Serum levels of MIG, IP-10 and ITAC were analyzed by FACS-CBA array in 65 newly diagnosed MM patients. Expression of CXCR3 and its binding molecules was also analyzed by quantitative PCR in 7 human MM cell lines (HMCLs) and in a publically available gene expression dataset (GSE2658). Further analysis of MIG serum levels was performed by ELISA in an extended cohort of MM (n=105) and MGUS patients (n=17), and in healthy volunteers (n=37). Results. Determination of serum levels by FACS-CBA revealed significant expression of MIG (range: 33.4 – 157 960 pg/ml) and IP-10 (12 - 4418.8 pg/ml), while ITAC (0 - 351.5 pg/ml) was only detectable in a subset (20 of 65) of patients. Interestingly, serum levels of all three molecules showed a positive correlation with each other (MIG vs. IP-10, R=0.38, P=0.002; MIG vs. ITAC, R=0.62, P<0.0001; ITAC vs. IP-10, R=0.41, P=0.0007). We also observed a significant correlation with beta 2 microglobulin (B2M) (MIG: R=0.45, P<0.0001; IP-10: R=0.36, P=0.003; ITAC: R=0.3, P=0.016) and a trend regarding ISS stage (MIG: R=0.23, P=0.06; IP-10: R=0.24, P=0.05; ITAC: R=0.11, P=0.39). Importantly, a significant association with overall survival (OS) was observed as well. Survival was significantly worse in patients with high compared to low MIG (median OS 25.3 months vs. not reached, P=0.003) and IP-10 (19.97 months vs. not reached, P=0.0006) as well as in patients with detectable compared to absent ITAC serum levels (19.97 vs. 65.8 months, P=0.019). In multivariate analysis, MIG (P=0.03) and ITAC (P=0.013) along LDH and calcium were revealed as independent predictors of survival. Expression of CXCR3 binding chemokines was rarely detected in HMCLs (1 of 7 expressed MIG, 3 of 7 IP-10 and 2 of 7 ITAC, respectively). In line with this, in-silico analysis of previously published primary MM cell samples (n=414) (GSE2658), showed a present detection call of MIG, IP-10 and ITAC in 51 (12.3%), 11 (2.7%) and 0 (0%) patients, respectively. In contrast, all three cytokines were detectable in 100% of bone marrow plasma cells of healthy donors, MGUS and smoldering MM patients in this dataset. Hence, CXCR3 binding chemokines are silenced in myeloma cells indicating that the increased serum levels of CXCR3 binding chemokines are derived from other cell types. As MIG serum concentration was identified as one of the most important predictors for OS, we studied the prognostic relevance of this molecule in an extended cohort (n=105) of MM patients by ELISA. Median MIG levels (161.3 pg/ml, range: 9.4-1966) were significantly elevated in newly diagnosed MM patients compared to MGUS (92.7 pg/ml, range: 6.29-1303.1) and healthy volunteers (106.2, range: 51–390.6 pg/ml). MIG levels were significantly correlated with B2M, ISS stage, calcium, albumin, LDH, hemoglobin and with age (R=0.466, P<0.001). Importantly, high MIG levels predicted adverse survival (17.0 months vs. not reached, P<0.001), which was upheld when age-adjusted cut-off levels were used. In accordance with our findings, in-silico analysis of MIG expression in purified plasma cells of MM patients (n=559) treated within the total therapy 2 and 3 protocol (GSE2658) revealed shorter OS in patients with a present compared to those with an absent detection call for MIG (P=0.004). Conclusion. Our findings depict MIG, IP-10 and ITAC as novel prognostic markers for shorter survival in newly diagnosed MM patients. High serum levels of CXCR3 binding chemokines in conjunction with silenced expression in MM cells may shield myeloma cells from immune attack as previously shown for T cell lymphomas. Further experiments will aim to confirm these initial results by extending our patient cohort and define the source as well as functional role of CXCR3 chemokines in MM. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

scholarly journals Presence of Extrachromosomal DNA (ecDNA) Impacts Both Progression Free and Overall Survival and Is an Independent Poor Prognostic Marker in Multiple Myeloma

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 461-461
Author(s):  
Parth Shah ◽  
Anil Aktas-Samur ◽  
Mariateresa Fulciniti ◽  
Raphael Szalat ◽  
Masood A. Shammas ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Overall Survival ◽  
Board Of Directors ◽  
Copy Number ◽  
Research Funding ◽  
P Value ◽  
Newly Diagnosed ◽  
Extrachromosomal Dna ◽  
Publicly Traded ◽  
Advisory Committees

Abstract Background Focal amplifications and rearrangements drive tumor growth and evolution in cancer. Focally amplified regions often involve the juxtaposition of rearranged segments of DNA from distinct chromosomal loci into a single amplified region and nearly half of these regions can be explained by circular, extrachromosomal DNA (ecDNA) formation. Cancer-associated ecDNA shows a unique circular placing ecDNA at the interface of cancer genomics and epigenetics. As formation of ecDNA represents a manifestation of genomic instability, we have investigated presence and prognostic impact of ecDNA in multiple myeloma (MM). Methods Whole genome (WGS) and transcriptome (RNAseq) sequencing data from CD138 purified MM cells from 191 uniformly-treated newly diagnosed MM patients were used for this analysis. Copy number variants (CNV), single nucleotide variants (SNV) and structural variants (SV) were identified on all WGS samples using Facets, Mutect2 and Manta. Seed data from these CNV results was passed to the AmpliconArchitect tool to determine presence of focally amplified and rearranged segments of DNA. Seed CNV thresholds were set for a minimum CNV size of 100kb and a copy number of equal or greater to 5. Extrachromosomal calls were then annotated using the Amplicon Classifier to determine the presence of ecDNA. Multivariate survival analysis was performed after segregating samples into the conventional myeloma risk classifications including translocations, copy number alterations, ISS, age and mutations associated with risk. Differential expression analysis was performed on transcriptomic data using DEseq2. Results We identified 6.8% of the newly diagnosed patients with ecDNA, 12.5% with complex non-cyclic DNA amplifications and 10.1% with linear amplifications. ecDNA and complex events were targeting MM dependent genes, including MYC/PVT1, IRF4 as well as known driver genes such as CDYL and TRAF2. We further evaluated association between ecDNA, complex rearrangements, linear amplification and patients with none of these amplification types and found that patients with ecDNA had significantly poor PFS (median PFS 22 months vs. 41 months) and OS (median OS 41 months vs. 105 months). Patients having ecDNA in their MM cells did not show any significant enrichment for known translocations, double hit or TP53 mutations. In a multivariate model including ecDNA and all other known MM risk features, ecDNA was found to be an independent predictor of progression free survival.(HR 2.6, CI: 1.26 -5.6, p=0.0082) and overall survival (HR 7.94 CI:3.5-17.9 p &lt; 0.0001). Patients with ecDNA have higher mutational load probability(8798 vs 6982, effect size = 0.64 , probability is 91.1). However, this was not reflected in heterogeneity by using MATH score. We found that patients with ecDNA are likely to have BRAF mutations (OR= 25.07 [2.57 - 330 95% CI], p value = 0.002), however overall RAS/RAF pathway mutations were similar to other patients. Patients with ecDNA showed fragile DNA with more breaks (median segments 197 vs. 125.5, p value = 0.001). Although ecDNA is defined as copy number gain with fragments having 5 or more copies, overall genomic gain between ecDNA and other patients were similar. However, overall genomic loss in patients with ecDNA were higher than others (7% vs. 4.2%, p = 0.06). By differential gene expression analysis we noted 98 differentially expressed genes in MM cells with ecDNA. The downregulated geneset involved pathways responsible for cell death as well as the RAS pathway. Interestingly, CD38 was upregulated in the ecDNA dataset suggesting greater potential for CD38 targeting therapies in these patients. Conclusions ecDNA, as an unique marker of perturbed genomic integrity, is observed in a subset of patients and is an independent prognostic marker in newly diagnosed MM patients. As patients with ecDNA are not fully captured by other risk features its incorporation in an expanded definition of a high risk group of multiple myeloma should be investigated. Future studies will endeavor to explore the biological mechanism through which ecDNA are formed and influences outcomes in myeloma. Figure 1 Figure 1. Disclosures Richardson: Sanofi: Consultancy; GlaxoSmithKline: Consultancy; Karyopharm: Consultancy, Research Funding; AstraZeneca: Consultancy; AbbVie: Consultancy; Oncopeptides: Consultancy, Research Funding; Takeda: Consultancy, Research Funding; Janssen: Consultancy; Protocol Intelligence: Consultancy; Celgene/BMS: Consultancy, Research Funding; Secura Bio: Consultancy; Regeneron: Consultancy; Jazz Pharmaceuticals: Consultancy, Research Funding. Perrot: Abbvie: Honoraria; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene/BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees; GSK: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Honoraria; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Moreau: Abbvie: Honoraria; Amgen: Honoraria; Janssen: Honoraria; Sanofi: Honoraria; Celgene BMS: Honoraria; Oncopeptides: Honoraria. Thakurta: Oxford University: Other: Visiting Professor; BMS: Current Employment, Current equity holder in publicly-traded company. Anderson: Gilead: Membership on an entity's Board of Directors or advisory committees; Millenium-Takeda: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Sanofi-Aventis: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Membership on an entity's Board of Directors or advisory committees; Scientific Founder of Oncopep and C4 Therapeutics: Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company; Mana Therapeutics: Membership on an entity's Board of Directors or advisory committees. Munshi: Legend: Consultancy; Karyopharm: Consultancy; Takeda: Consultancy; Janssen: Consultancy; Novartis: Consultancy; Bristol-Myers Squibb: Consultancy; Amgen: Consultancy; Abbvie: Consultancy; Adaptive Biotechnology: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Celgene: Consultancy; Pfizer: Consultancy.

XBP1 Expression Is An Important Prognostic Factor for Newly Diagnosed Myeloma Patients.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1686-1686
Author(s):  
Tina Bagratuni ◽  
Ping Wu ◽  
David Gonzalez de Castro ◽  
Emma L Davenport ◽  
Brian A Walker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Plasma Cells ◽  
Critical Role ◽  
Clinical Samples ◽  
Newly Diagnosed ◽  
Expression Levels ◽  
Downstream Target ◽  
Lower Ratio ◽  
Gene Expression Levels

Abstract The immunoglobulin production of myeloma plasma cells means they are dependent on the unfolded protein response process (UPR), which controls protein production and ensures its proper translation and folding. Knockout mouse studies have highlighted the importance of IRE1, a transducer of the UPR signal and XBP1 its downstream target, in B cell development. Gene expression studies show that XBP1 is highly expressed in myeloma plasma cells and it is consistently deregulated in clinical samples. XBP1s, the active moiety, is a known myeloma survival factor and IgVH-XBP1s transgenic mice develop myeloma. In this work we demonstrate that XBP1s levels correlate with survival of myeloma patients and that targeting it with small molecules may be a useful therapeutic strategy. We have re-sequenced IRE1 and determined the gene expression levels of IRE1, total XBP1, XBP1 unspliced (XBP1u), and XBP1 spliced (XBP1s) in a large series of myeloma patients (n=260), and correlated biological findings with clinical characteristics and patient outcome. To quantitatively assess the expression of XBP1s and XBP1u variants, we have designed a novel real time PCR method (Lux Technology, Invitrogen) capable of determining the ratio of these transcripts within a sample. These results show that total IRE1 and XBP1 are highly expressed in all patients. In addition all patients expressed higher levels of XBP1s, the active transcription factor which is anti-apoptotic, compared to the inactive precursor XBP1u. We correlated XBP1s/u gene expression levels with clinical parameters in 159 newly diagnosed patients. This group of patients contained 68 females and 91 males with a median age of 64 years (range 39–89), B2M median = 7.45mg/mL (range 1.1–30mg/mL), haemoglobin median = 10.2g/dL (range 5.7–14.7g/dL) and ISS status stage 1 = 21%, stage 2 = 36%, and stage 3 = 36%. The XBP1s/u ratio demonstrated a statistically significant effect on overall survival (OS) in patients with high B2M (B2M &gt;5), with a cut-off ratio of 2.8 for the XBP1s/u expression (assigned using the quartile method). In this group of patients those with higher XBP1s/u have shorter survival (28 months) compared to those with lower XBP1s/u (not reached, 50+ months). (p = 0.033). The cause for the high and variable XBP1s levels is uncertain but could be mediated by IRE activity. Sequence analysis of the kinase and endoribonuclease domain of IRE1 identified 3/50 patients with an inactivating mutation in the endoribonuclease domain (G923V): patients with this mutation had a lower ratio of XBP1s to XBP1u and a longer survival. In conclusion, this study is the first to demonstrate the clinical significance of high XBP1s levels in myeloma and shows that patients with high levels of XBP1s have a shorter overall survival. Coupled with our previous study highlighting the critical role of the UPR in myeloma and the report of the XBP1s transgenic mouse model, the importance of the IRE1-XBP1 axis myeloma is now established, and its role as a therapeutic target needs to be explored.

scholarly journals Dissecting the Epigenetic Landscape of Smoldering, Newly Diagnosed and Relapsed Multiple Myeloma Revealed IRAK3 As a Marker of Disease Progression

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3896-3896
Author(s):  
Mahshid Rahmat ◽  
Nicholas Haradhvala ◽  
Romanos Sklavenitis-Pistofidis ◽  
Jihye Park ◽  
Daisy Huynh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Multiple Myeloma ◽  
Disease Progression ◽  
Plasma Cells ◽  
Whole Genome ◽  
Newly Diagnosed ◽  
Promoter Regions ◽  
Healthy Donors ◽  
Precursor States

Abstract Introduction. Multiple myeloma (MM) is a complex and heterogeneous malignancy of plasma cells that has two precursor states: monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). MGUS and SMM are asymptomatic states that eventually give rise to overt MM, with some patients progressing, while others do not. Recent studies in MM pathobiology have highlighted epigenetic alterations that contribute to the onset, progression and heterogeneity of MM. Global hypomethylation of DNA, including tumor suppressor genes, and hypermethylation of B-cell specific enhancers, abnormal histone methylation patterns due to the overexpression of histone methyltransferases such as MMSET, and deregulation of non-coding RNAs along with mutations in different classes of chromatin modulators underline a potential for epigenetic biomarkers in disease prognosis and treatment. This study aimed to define epigenetic pathways that lead to the dynamic regulation of gene expression in MM pathogenesis. Methods. We performed ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and RNA-seq on 10 MM cell lines and CD138+ plasma cells isolated from bone marrow aspirates of 3 healthy donors, 9 SMM, 8 newly diagnosed MM (NDMM) and 9 relapsed (RRMM) patients. ATAC-seq reads were trimmed of adapters, aligned to hg19 using bowtie2, and filtered for mapping quality >=Q30 using the ENCODE ATAC-seq pipeline. Reads mapping to promoter regions, defined as -400 to +250 bases from a refseq transcription start site, were counted using bedtools for each sample. Promoter read counts were then normalized by the total number of reads in promoters in the sample, scaled to 1 million total reads, and converted to log10(x+1) space. Results. To characterize the epigenetic contribution to disease progression in MM, we first identified accessible promoter regions in normal plasma cells (NPC), SMM, NDMM and RRMM patients and found regions displaying differential accessibility in MM progression. Next, we intersected the list of differential accessible regions (DARs) with matched transcriptome data and observed two main clusters: genes with unaltered transcription profiles and genes in which the dynamics of open chromatin regions (OCRs) correlated with gene expression. Transcriptomic analysis revealed that a large portion of the differentially expressed (DE) genes in SMM remain DE in NDMM as compared to NPCs (882 genes out of 1642 and 1150 DE genes in SMM and NDMM, respectively). Those genes were significantly enriched for pathways like epithelial mesenchymal transition, cell cycle checkpoints and mitosis, KRAS signaling and interleukin-JAK-STAT pathways. To investigate the genes that behaved differently among the stages of disease, we looked at differential accessibility and expression in NDMM and SMM samples, and integrated them with Whole-Genome Bisulfite-Sequencing and 450K DNA-methylation data from MM patients and healthy donors (BLUEPRINT). This analysis led to the identification of novel genes in MM progression, such as the transcriptional repressor ZNF254 and IRAK3, a negative regulator of the TLR/IL1R signaling pathway. Although gene expression data for these genes showed comparable mRNA levels in SMM and NPCs, followed by a significant decrease in NDMM/ RRMM, ATAC-seq revealed a striking drop in promoter accessibility in SMM, NDMM and RRMM cases. Comparison of ATAC-seq peaks to DNA methylation and ChIP-seq data revealed that the altered OCR of IRAK3 is actually hypermethylated in MM patients and marked by H3K4me3, a marker of active promoters, in MM cell lines. Hypermethylation of IRAK3 has been described in hepatocellular carcinoma, where it is associated with poor prognosis. Together, our data suggest that the identified IRAK3 OCR may act as a bivalent domain that loses accessibility in the precursor states and gains DNA methylation in MM progression. Hence, IRAK3 methylation could be a novel prognostic marker in MM. Conclusion. We have generated a global epigenetic map of primary tumors from patients at the smoldering, newly diagnosed and relapsed/refractory stage of multiple myeloma. Integrative analysis of ATAC-seq data with DNA methylome, transcriptome and whole-genome map of active and repressive histone marks in our study led to the identification of IRAK3 as a novel epigenetic biomarker of disease progression. Disclosures Licht: Celgene: Research Funding. Ghobrial:Takeda: Consultancy; BMS: Consultancy; Celgene: Consultancy; Janssen: Consultancy.

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