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1.
Blood ; 2024 05 20.
Article in English | MEDLINE | ID: mdl-38768337

ABSTRACT

Estimating progression-free survival (PFS) and overall survival (OS) superiority during clinical trials of multiple myeloma (MM) has become increasingly challenging as novel therapeutics have improved patient outcomes. Thus, it is imperative to identify earlier endpoint surrogates that are predictive of long-term clinical benefit to expedite development of more effective therapies. Minimal residual disease (MRD)-negativity is a common intermediate endpoint that has shown prognostic value for clinical benefit in trials of patients with multiple myeloma (MM). This meta-analysis was based on the FDA guidance for considerations for a meta-analysis of MRD as a clinical endpoint and evaluates MRD-negativity as an early endpoint reasonably likely to predict long-term clinical benefit. Eligible studies were phase 2 or 3 randomized controlled clinical trials measuring MRD negativity as an endpoint in patients with MM, with follow-up of ≥6 months following an a priori defined time point of 12±3 months post-randomization. Eight newly diagnosed MM-(NDMM)-studies evaluating 4,907 patients were included. Trial-level associations between MRD-negativity and PFS were R2WLSiv (95% CI) 0.67 (0.43-0.91) and R2copula 0.84 (0.64->0.99) at the 12-month timepoint. The individual-level association between 12-month MRD negativity and PFS resulted in a global odds ratio of 4.02 (95% CI: 2.57-5.46). For relapse/refractory MM-(RRMM), there were four studies included, and the individual-level association between 12-month MRD negativity and PFS resulted in a global odds ratio of 7.67 (4.24-11.10). A clinical trial demonstrating a treatment effect on MRD is reasonably likely to eventually demonstrate a treatment effect on PFS, suggesting that MRD may be an early clinical endpoint reasonably likely to predict clinical benefit in MM, that may be used to support accelerated approval and thereby expedite the availability of new drugs to patients with MM.

2.
Blood ; 139(4): 492-501, 2022 01 27.
Article in English | MEDLINE | ID: mdl-34269818

ABSTRACT

In patients with transplant-ineligible newly diagnosed multiple myeloma (NDMM), daratumumab reduced the risk of disease progression or death by 44% in MAIA (daratumumab/lenalidomide/dexamethasone [D-Rd]) and 58% in ALCYONE (daratumumab/bortezomib/melphalan/prednisone [D-VMP]). Minimal residual disease (MRD) is a sensitive measure of disease and response to therapy. MRD-negativity status and durability were assessed in MAIA and ALCYONE. MRD assessments using next-generation sequencing (10-5) occurred for patients achieving complete response (CR) or better and after at least CR at 12, 18, 24, and 30 months from the first dose. Progression-free survival (PFS) by MRD status and sustained MRD negativity lasting ≥6 and ≥12 months were analyzed in the intent-to-treat population and among patients achieving at least CR. In MAIA (D-Rd, n = 368; lenalidomide and dexamethasone [Rd], n = 369) and ALCYONE (D-VMP, n = 350; bortezomib/melphalan/prednisone [VMP], n = 356), the median duration of follow-up was 36.4 and 40.1 months, respectively. MRD-negative status and sustained MRD negativity lasting ≥6 and ≥12 months were associated with improved PFS, regardless of treatment group. However, daratumumab-based therapy improved rates of MRD negativity lasting ≥6 months (D-Rd, 14.9% vs Rd, 4.3%; D-VMP, 15.7% vs VMP, 4.5%) and ≥12 months (D-Rd, 10.9% vs Rd, 2.4%; D-VMP, 14.0% vs VMP, 2.8%), both of which translated to improved PFS vs control groups. In a pooled analysis, patients who were MRD negative had improved PFS vs patients who were MRD positive. Patients with NDMM who achieved MRD-negative status or sustained MRD negativity had deep remission and improved clinical outcomes. These trials were registered at www.clinicaltrials.gov as #NCT02252172 (MAIA) and #NCT02195479 (ALCYONE).


Subject(s)
Antibodies, Monoclonal/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Multiple Myeloma/drug therapy , Neoplasm, Residual/drug therapy , Aged , Female , Humans , Male , Middle Aged , Multiple Myeloma/diagnosis , Neoplasm, Residual/diagnosis , Progression-Free Survival , Treatment Outcome
3.
Blood ; 139(6): 835-844, 2022 02 10.
Article in English | MEDLINE | ID: mdl-34289038

ABSTRACT

We explored minimal residual disease (MRD) in relapsed/refractory multiple myeloma (RRMM) and transplant-ineligible (TIE) newly diagnosed multiple myeloma (NDMM) using data from 4 phase 3 studies (POLLUX, CASTOR, ALCYONE, and MAIA). Each study previously demonstrated that daratumumab-based therapies improved MRD negativity rates and reduced the risk of disease progression or death by approximately half vs standards of care. We conducted a large-scale pooled analysis for associations between patients achieving complete response or better (≥CR) with MRD-negative status and progression-free survival (PFS). MRD was assessed via next-generation sequencing (10-5 sensitivity threshold). Patient-level data were pooled from all 4 studies and for patients with TIE NDMM and patients with RRMM who received ≤2 prior lines of therapy (≤2 PL). PFS was evaluated by response and MRD status. Median follow-up (months) was 54.8 for POLLUX, 50.2 for CASTOR, 40.1 for ALCYONE, and 36.4 for MAIA. Patients who achieved ≥CR and MRD negativity had improved PFS vs those who failed to reach CR or were MRD positive (TIE NDMM and RRMM hazard ratio [HR] 0.20, P < .0001; TIE NDMM and RRMM ≤2 PL HR 0.20, P < .0001). This benefit occurred irrespective of therapy or disease setting. A time-varying Cox proportional hazard model confirmed that ≥CR with MRD negativity was associated with improved PFS. Daratumumab-based treatment was associated with more patients reaching ≥CR and MRD negativity. These findings represent the first large-scale analysis with robust methodology to support ≥CR with MRD negativity as a prognostic factor for PFS in RRMM and TIE NDMM. These trials were registered at www.clinicaltrials.gov as #NCT02076009, #NCT02136134, #NCT02195479, and #NCT02252172.


Subject(s)
Multiple Myeloma/diagnosis , Neoplasm, Residual/diagnosis , Aged , Antibodies, Monoclonal/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Disease-Free Survival , Humans , Multiple Myeloma/drug therapy , Neoplasm Recurrence, Local/diagnosis , Neoplasm Recurrence, Local/drug therapy , Neoplasm, Residual/drug therapy , Prognosis , Progression-Free Survival , Treatment Outcome
4.
Haematologica ; 107(10): 2408-2417, 2022 10 01.
Article in English | MEDLINE | ID: mdl-35354247

ABSTRACT

In the primary analysis of the phase III COLUMBA study, daratumumab by subcutaneous administration (DARA SC) demonstrated non-inferiority to intravenous administration (DARA IV) for relapsed or refractory multiple myeloma (RRMM). Here, we report the final analysis of efficacy and safety from COLUMBA after a median of 29.3 months follow-up (additional 21.8 months after the primary analysis). In total, 522 patients were randomized (DARA SC, n=263; DARA IV, n=259). With longer follow-up, DARA SC and DARA IV continued to show consistent efficacy and maximum trough daratumumab concentration as compared with the primary analysis. The overall response rate was 43.7% for DARA SC and 39.8% for DARA IV. The maximum mean (standard deviation [SD]) trough concentration (cycle 3, day 1 pre-dose) of serum DARA was 581 (SD, 315) µg/mL for DARA SC and 496 (SD, 231) µg/mL for DARA IV. Median progression-free survival was 5.6 months for DARA SC and 6.1 months for DARA IV; median overall survival was 28.2 months and 25.6 months, respectively. Grade 3/4 treatment-emergent adverse events occurred in 50.8% of patients in the DARA SC group and 52.7% in the DARA IV group; the most common (≥10%) were thrombocytopenia (DARA SC, 14.2%; DARA IV, 13.6%), anemia (13.8%; 15.1%), and neutropenia (13.1%; 7.8%). The safety profile remained consistent with the primary analysis after longer follow-up. In summary, DARA SC and DARA IV continue to demonstrate similar efficacy and safety, with a low rate of infusion-related reactions (12.7% vs. 34.5%, respectively) and shorter administration time (3-5 minutes vs. 3-7 hours) supporting DARA SC as a preferable therapeutic choice. (Clinicaltrials gov. Identifier: NCT03277105.


Subject(s)
Multiple Myeloma , Administration, Intravenous , Antibodies, Monoclonal , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Dexamethasone , Humans , Multiple Myeloma/drug therapy , Neoplasm Recurrence, Local/drug therapy , Treatment Outcome
5.
Ann Hematol ; 100(4): 1065-1077, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33599794

ABSTRACT

The phase 3 COLUMBA study demonstrated noninferiority of subcutaneous daratumumab (DARA SC) to intravenous daratumumab (DARA IV) in relapsed or refractory multiple myeloma. We present a subgroup analysis of Asian patients from COLUMBA. Eligible patients had ≥ 3 prior lines of therapy, including a proteasome inhibitor and an immunomodulatory drug, or were double refractory. Co-primary endpoints were overall response rate (ORR) and maximum trough concentration (Ctrough). Secondary endpoints included rates of infusion-related reactions, progression-free survival, and patient-reported satisfaction with therapy. Sixty-seven Asian patients (DARA SC, n = 30; DARA IV, n = 37) were randomized, including 42 Japanese patients (DARA SC, n = 18; DARA IV, n = 24). Comparable ORRs for DARA SC versus DARA IV were seen in the Asian cohort (66.7% vs 43.2%) and Japanese-only cohort (61.1% vs 54.2%), including patients weighing ≤ 65 kg. Similarity of Ctrough was seen in both Asian and Japanese-only cohorts; the ratio of the geometric mean of the Ctrough concentrations for DARA SC/DARA IV was 143.96% (90% confidence interval (CI), 112.03-185.00%) and 148.02% (90% CI, 113.32-193.34%), respectively. The Asian cohort (both treatment groups) and Japanese-only cohort (DARA SC group) experienced higher rates of grade 3/4 cytopenias compared with the global COLUMBA population, occurring predominantly in patients of low bodyweight; no patients discontinued treatment due to cytopenias. The Cancer Therapy Satisfaction Questionnaire results generally favored DARA SC. In the Asian and Japanese-only cohorts, DARA SC was comparable to DARA IV. The efficacy, pharmacokinetic, safety, and satisfaction results were generally consistent with the global COLUMBA population regardless of patient bodyweight. ClinicalTrials.gov Identifier: NCT03277105.


Subject(s)
Antibodies, Monoclonal/therapeutic use , Antineoplastic Agents, Immunological/therapeutic use , Asian People/statistics & numerical data , Multiple Myeloma/drug therapy , Salvage Therapy , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Monoclonal/administration & dosage , Antibodies, Monoclonal/adverse effects , Antibodies, Monoclonal/pharmacokinetics , Antineoplastic Agents, Immunological/administration & dosage , Antineoplastic Agents, Immunological/adverse effects , Antineoplastic Agents, Immunological/pharmacokinetics , Asian People/psychology , Body Weight , Disease-Free Survival , Female , Follow-Up Studies , Humans , Injections, Subcutaneous , Japan/epidemiology , Kaplan-Meier Estimate , Male , Middle Aged , Multiple Myeloma/ethnology , Multiple Myeloma/mortality , Multiple Myeloma/therapy , Neutropenia/chemically induced , Patient Satisfaction , Progression-Free Survival , Republic of Korea/epidemiology , Taiwan/epidemiology , Young Adult
6.
Blood ; 128(13): 1735-44, 2016 09 29.
Article in English | MEDLINE | ID: mdl-27516441

ABSTRACT

To elucidate the mechanisms underlying relapse from chemotherapy in multiple myeloma, we performed a longitudinal study of 33 patients entered into Total Therapy protocols investigating them using gene expression profiling, high-resolution copy number arrays, and whole-exome sequencing. The study illustrates the mechanistic importance of acquired mutations in known myeloma driver genes and the critical nature of biallelic inactivation events affecting tumor suppressor genes, especially TP53, the end result being resistance to apoptosis and increased proliferation rates, which drive relapse by Darwinian-type clonal evolution. The number of copy number aberration changes and biallelic inactivation of tumor suppressor genes was increased in GEP70 high risk, consistent with genomic instability being a key feature of high risk. In conclusion, the study highlights the impact of acquired genetic events, which enhance the evolutionary fitness level of myeloma-propagating cells to survive multiagent chemotherapy and to result in relapse.


Subject(s)
Clonal Evolution , Genes, Tumor Suppressor , Multiple Myeloma/genetics , Mutation , Adult , Aged , Cell Proliferation , DNA Copy Number Variations , Disease Progression , Female , Gene Expression Profiling , Genes, p53 , Genes, ras , Genomic Instability , Humans , Longitudinal Studies , Male , Middle Aged , Models, Genetic , Multiple Myeloma/pathology , Multiple Myeloma/therapy , Phosphatidylinositol 3-Kinases/genetics , Recurrence , Risk Factors , Stem Cell Transplantation , Transplantation, Autologous
7.
Biometrics ; 74(1): 313-320, 2018 03.
Article in English | MEDLINE | ID: mdl-28498490

ABSTRACT

This article proposes an efficient approach to screening genes associated with a phenotypic variable of interest in genomic studies with subgroups. In order to capture and detect various association profiles across subgroups, we flexibly estimate the underlying effect size distribution across subgroups using a semi-parametric hierarchical mixture model for subgroup-specific summary statistics from independent subgroups. We then perform gene ranking and selection using an optimal discovery procedure based on the fitted model with control of false discovery rate. Efficiency of the proposed approach, compared with that based on standard regression models with covariates representing subgroups, is demonstrated through application to a randomized clinical trial with microarray gene expression data in multiple myeloma, and through a simulation experiment.


Subject(s)
Genetic Testing , Models, Statistical , Gene Expression Profiling , Humans , Multiple Myeloma/genetics , Oligonucleotide Array Sequence Analysis , Randomized Controlled Trials as Topic
8.
Blood ; 125(24): 3756-9, 2015 Jun 11.
Article in English | MEDLINE | ID: mdl-25943786

ABSTRACT

Multiple myeloma is a B-cell malignancy stratified in part by cytogenetic abnormalities, including the high-risk copy number aberrations (CNAs) of +1q21 and 17p(-). To investigate the relationship between 1q21 CNAs and DNA hypomethylation of the 1q12 pericentromeric heterochromatin, we treated in vitro peripheral blood cultures of 5 patients with balanced constitutional rearrangements of 1q12 and 5 controls with the hypomethylating agent 5-azacytidine. Using G-banding, fluorescence in situ hybridization, and spectral karyotyping, we identified structural aberrations and copy number gains of 1q21 in the treated cells similar to those found in patients with cytogenetically defined high-risk disease. Aberrations included 1q12 triradials, amplifications of regions juxtaposed to 1q12, and jumping translocations 1q12. Strikingly, all 5 patients with constitutional 1q12 rearrangements showed amplifications on the derivative chromosomes distal to the inverted or translocated 1q12 region, including MYCN in 1 case. At the same time, no amplification of the 1q21 region was found when the 1q12 region was inverted or absent. These findings provide evidence that the hypomethylation of the 1q12 region can potentially amplify any genomic region juxtaposed to it and mimic CNAs found in the bone marrow of patients with high-risk disease.


Subject(s)
Chromosomes, Human, Pair 1/genetics , Gene Dosage , Multiple Myeloma/genetics , Chromosome Aberrations , DNA Methylation , Epigenesis, Genetic , Humans , Translocation, Genetic
9.
Blood ; 123(16): 2504-12, 2014 Apr 17.
Article in English | MEDLINE | ID: mdl-24497533

ABSTRACT

Multiple myeloma (MM) is a B-cell malignancy driven in part by increasing copy number alterations (CNAs) during disease progression. Prognostically significant CNAs accumulate during clonal evolution and include gains of 1q21 and deletions of 17p, among others. Unfortunately, the mechanisms underlying the accumulation of CNAs and resulting subclonal heterogeneity in high-risk MM are poorly understood. To investigate the impact of jumping translocations of 1q12 (JT1q12) on receptor chromosomes (RCs) and subsequent clonal evolution, we analyzed specimens from 86 patients selected for unbalanced 1q12 aberrations by G-banding. Utilizing spectral karyotyping and locus-specific fluorescence in situ hybridization, we identified 10 patients with unexpected focal amplifications of an RC that subsequently translocated as part of a sequential JT1q12 to one or more additional RCs. Four patients exhibited amplification and translocation of 8q24 (MYC), 3 showed amplification of 16q11, and 1 each displayed amplification of 18q21.3 (BCL2), 18q23, or 4p16 (FGFR3). Unexpectedly, in 6 of 14 patients with the combination of the t(4;14) and deletion of 17p, we identified the loss of 17p as resulting from a JT1q12. Here, we provide evidence that the JT1q12 is a mechanism for the simultaneous gain of 1q21 and deletion of 17p in cytogenetically defined high-risk disease.


Subject(s)
Chromosome Deletion , Chromosomes, Human, Pair 17/genetics , Chromosomes, Human, Pair 1/genetics , Multiple Myeloma/genetics , Translocation, Genetic , Bone Marrow Cells/metabolism , Bone Marrow Cells/pathology , Cytogenetic Analysis , Disease Progression , Humans , In Situ Hybridization, Fluorescence , Interspersed Repetitive Sequences , Karyotype , Multiple Myeloma/pathology , Risk
10.
BMC Bioinformatics ; 16 Suppl 13: S7, 2015.
Article in English | MEDLINE | ID: mdl-26424171

ABSTRACT

INTRODUCTION: It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural capability of cancer to adapt dynamically in a Darwinian manner is a primary reason for therapeutic failures. Survival advantages may be induced by cancer therapies and also occur as a result of inherent cell and microenvironmental factors. The selected "more fit" clones outmatch their competition and then become dominant in the tumor via propagation of progeny. This clonal expansion leads to relapse, therapeutic resistance and eventually death. The goal of this study is to develop and demonstrate a more detailed clonality approach by utilizing integrative genomics. METHODS: Patient tumor samples were profiled by Whole Exome Sequencing (WES) and RNA-seq on an Illumina HiSeq 2500 and methylation profiling was performed on the Illumina Infinium 450K array. STAR and the Haplotype Caller were used for RNA-seq processing. Custom approaches were used for the integration of the multi-omic datasets. RESULTS: Reported are major enhancements to CloneViz, which now provides capabilities enabling a formal tumor multi-dimensional clonality analysis by integrating: i) DNA mutations, ii) RNA expressed mutations, and iii) DNA methylation data. RNA and DNA methylation integration were not previously possible, by CloneViz (previous version) or any other clonality method to date. This new approach, named iCloneViz (integrated CloneViz) employs visualization and quantitative methods, revealing an integrative genomic mutational dissection and traceability (DNA, RNA, epigenetics) thru the different layers of molecular structures. CONCLUSION: The iCloneViz approach can be used for analysis of clonal evolution and mutational dynamics of multi-omic data sets. Revealing tumor clonal complexity in an integrative and quantitative manner facilitates improved mutational characterization, understanding, and therapeutic assignments.


Subject(s)
Clonal Evolution/genetics , Epigenomics/methods , Genomics/methods , Neoplasms/genetics , Epigenesis, Genetic , Humans
11.
Blood ; 121(23): 4753-7, 2013 Jun 06.
Article in English | MEDLINE | ID: mdl-23603914

ABSTRACT

Lenalidomide has been linked to myelodysplastic syndrome (MDS) after autotransplants for myeloma. Total therapy trials (TT; TT2(-/+) thalidomide) and TT3 (TT3a with bortezomib, thalidomide; TT3b with additional lenalidomide) offered the opportunity to examine the contribution of these immune-modulatory agents to MDS-associated cytogenetic abnormalities (MDS-CA) and clinical MDS or acute leukemia ("clinical MDS/AL"). Of 1080 patients with serial cytogenetic studies, MDS-CA occurred in 11% and clinical MDS/AL in 3%. Risk features of MDS-CA included TT3b, age ≥65 years, male gender, levels of ß-2-microglobulin >5.5 mg/L, and multiple myeloma relapse. Clinical MDS/AL occurred less frequently in the control arm of TT2 and more often with TT3a and TT3b. Since MDS-CA often antedated clinical disease, periodic cytogenetic monitoring is recommended. Larger CD34 quantities should be collected upfront as the risk of MDS could be reduced by applying higher CD34 doses with transplant. Thus, treatment, host, and myeloma features could be linked to MDS development after therapy for this malignancy. This trial was registered at www.clinicaltrials.gov: TT3A: NCT00081939, TT3B: NCT00572169.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/adverse effects , Chromosome Aberrations , Leukemia/epidemiology , Multiple Myeloma/drug therapy , Myelodysplastic Syndromes/epidemiology , Neoplasm Recurrence, Local/epidemiology , Acute Disease , Adolescent , Adult , Aged , Boronic Acids/administration & dosage , Bortezomib , Female , Follow-Up Studies , Humans , Incidence , Lenalidomide , Leukemia/chemically induced , Leukemia/genetics , Male , Middle Aged , Multiple Myeloma/complications , Myelodysplastic Syndromes/chemically induced , Myelodysplastic Syndromes/genetics , Neoplasm Recurrence, Local/chemically induced , Neoplasm Recurrence, Local/genetics , Prognosis , Pyrazines/administration & dosage , Risk Factors , Thalidomide/administration & dosage , Thalidomide/analogs & derivatives , Young Adult
12.
Haematologica ; 100(9): 1214-21, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26022710

ABSTRACT

Multiple myeloma is preceded by an asymptomatic phase, comprising monoclonal gammopathy of uncertain significance and smoldering myeloma. Compared to the former, smoldering myeloma has a higher and non-uniform rate of progression to clinical myeloma, reflecting a subset of patients with higher risk. We evaluated the gene expression profile of smoldering myeloma plasma cells among 105 patients enrolled in a prospective observational trial at our institution, with a view to identifying a high-risk signature. Baseline clinical, bone marrow, cytogenetic and radiologic data were evaluated for their potential to predict time to therapy for symptomatic myeloma. A gene signature derived from four genes, at an optimal binary cut-point of 9.28, identified 14 patients (13%) with a 2-year therapy risk of 85.7%. Conversely, a low four-gene score (< 9.28) combined with baseline monoclonal protein < 3 g/dL and albumin ≥ 3.5 g/dL identified 61 patients with low-risk smoldering myeloma with a 5.0% chance of progression at 2 years. The top 40 probe sets showed concordance with indices of chromosome instability. These data demonstrate high discriminatory power of a gene-based assay and suggest a role for dysregulation of mitotic checkpoints in the context of genomic instability as a hallmark of high-risk smoldering myeloma.


Subject(s)
Genes, Neoplasm , Genomic Instability , Multiple Myeloma/genetics , Neoplasm Proteins/genetics , Aged , Aged, 80 and over , Bone Marrow/pathology , Female , Humans , Male , Multiple Myeloma/pathology , Prospective Studies
13.
J Immunol ; 190(6): 2966-75, 2013 Mar 15.
Article in English | MEDLINE | ID: mdl-23408834

ABSTRACT

Epigenetic changes play important roles in carcinogenesis and influence initial steps in neoplastic transformation by altering genome stability and regulating gene expression. To characterize epigenomic changes during the transformation of normal plasma cells to myeloma, we modified the HpaII tiny fragment enrichment by ligation-mediated PCR assay to work with small numbers of purified primary marrow plasma cells. The nano-HpaII tiny fragment enrichment by ligation-mediated PCR assay was used to analyze the methylome of CD138(+) cells from 56 subjects representing premalignant (monoclonal gammopathy of uncertain significance), early, and advanced stages of myeloma, as well as healthy controls. Plasma cells from premalignant and early stages of myeloma were characterized by striking, widespread hypomethylation. Gene-specific hypermethylation was seen to occur in the advanced stages, and cell lines representative of relapsed cases were found to be sensitive to decitabine. Aberrant demethylation in monoclonal gammopathy of uncertain significance occurred primarily in CpG islands, whereas differentially methylated loci in cases of myeloma occurred predominantly outside of CpG islands and affected distinct sets of gene pathways, demonstrating qualitative epigenetic differences between premalignant and malignant stages. Examination of the methylation machinery revealed that the methyltransferase, DNMT3A, was aberrantly hypermethylated and underexpressed, but not mutated in myeloma. DNMT3A underexpression was also associated with adverse overall survival in a large cohort of patients, providing insights into genesis of hypomethylation in myeloma. These results demonstrate widespread, stage-specific epigenetic changes during myelomagenesis and suggest that early demethylation can be a potential contributor to genome instability seen in myeloma. We also identify DNMT3A expression as a novel prognostic biomarker and suggest that relapsed cases can be therapeutically targeted by hypomethylating agents.


Subject(s)
Cell Transformation, Neoplastic/immunology , DNA Methylation/genetics , DNA Methylation/immunology , Multiple Myeloma/genetics , Multiple Myeloma/immunology , Cell Transformation, Neoplastic/genetics , Cohort Studies , Early Diagnosis , Gene Expression Regulation, Neoplastic/immunology , Humans , Multiple Myeloma/pathology , Neoplasm Staging , Polymerase Chain Reaction , Recurrence , Remission Induction , Reproducibility of Results , Syndecan-1/biosynthesis , Syndecan-1/genetics , Tumor Cells, Cultured
14.
Genes Chromosomes Cancer ; 53(7): 549-57, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24638926

ABSTRACT

In studies of patients with multiple myeloma (MM), gene expression profiling (GEP) of myeloma cells demonstrates substantially higher expression of MMSET, FGFR3, CCND3, CCND1, MAF, and MAFB--the partner genes of 14q32 translocations--than GEP of plasma cells from healthy individuals. Interphase fluorescent in situ hybridization (FISH) was used to discriminate between chromosomal translocations involving different regions of the immunoglobulin heavy chain (IGH) genes at 14q32. With special probes designed for the constant region (IGHC) and the variable region (IGHV), IGH translocations were shown to be definite, nonrandom chromosomal fusions of IGHC with the loci of FGFR3, CCND1, CCND3, MAF, and MAFB genes; and IGHV with the locus of MMSET gene. When correlated with GEP results, the IGH translocations were found to drive expression levels of the partner genes to significantly higher levels (spikes) than copy-number variations. Hence, 42% of IGH translocations were identified among newly diagnosed MM patients (448/1,060). As GEP has become essential for assessing cancer risk, this novel approach is highly consistent with the cytogenetic features of the chromosomal translocations to effectively stratify molecular subgroups of MM on the basis of gene expression profiles of the IGH translocation partner genes in myeloma cells. © 2014 Wiley Periodicals, Inc.


Subject(s)
Chromosomes, Human, Pair 14/genetics , Multiple Myeloma/genetics , Translocation, Genetic , Gene Expression Profiling , Gene Fusion , Humans , Multiple Myeloma/metabolism
15.
BMC Bioinformatics ; 15 Suppl 11: S9, 2014.
Article in English | MEDLINE | ID: mdl-25350589

ABSTRACT

Tumors are heterogeneous in composition. They are composed of cancer cells proper, along with stromal elements that collectively form a microenvironment, all of which are necessary to nurture the malignant process. In addition, many of the stromal cells are modified to support the unique needs of the malignant state. Tumors are composed of a variety of clones or subpopulations of cancer cells, which may differ in karyotype, growth rate, expression of cell surface markers, sensitivity to therapeutics, etc. New tools and methods to provide an improved understanding of tumor clonal architecture are needed to guide therapy.


Subject(s)
Clonal Evolution , Mutation , Neoplasms/genetics , Clone Cells , Computational Biology/methods , Humans , Software
16.
BMC Bioinformatics ; 15 Suppl 11: S3, 2014.
Article in English | MEDLINE | ID: mdl-25350881

ABSTRACT

Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. However, the scientific discovery offered by NGS also includes challenges concerning the interpretation of large and non-trivial experimental results. This task is potentially further complicated when a multitude of molecular profiling modalities are available, with the goal of a more integrative and comprehensive analysis of the cancer biology.


Subject(s)
Gene Expression Profiling/methods , High-Throughput Nucleotide Sequencing/methods , Neoplasms/genetics , Oligonucleotide Array Sequence Analysis , Humans , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins p21(ras) , Sequence Analysis, DNA/methods , Sequence Analysis, RNA/methods , Software , ras Proteins/genetics
17.
Blood ; 120(8): 1597-600, 2012 Aug 23.
Article in English | MEDLINE | ID: mdl-22674807

ABSTRACT

Thalidomide and lenalidomide constitute an important part of effective myeloma therapy. Recent data from the Intergroup Francophone du Myélome, Cancer and Leukemia Group B, and Gruppo Italiano Malattie Ematologiche dell Adulto MM-015 trials suggest that lenalidomide maintenance therapy is associated with a higher incidence of second primary malignancies (SPMs), including both hematologic and solid malignancies. In the present study, we analyzed data from the Total Therapy 2 (TT2) trial, along with the 2 Total Therapy 3 (TT3) trials. TT2 patients were assigned randomly to either a control group (no thalidomide) or to the experimental group (thalidomide during induction, between transplantations, and during consolidation and maintenance). The 2 TT3 trials used thalidomide and bortezomib during induction, before and in consolidation after tandem melphalan-based transplantation; TT3A applied VTD (bortezomib, thalidomide, dexamethasone) in the first year of maintenance and TD for 2 more years, whereas TT3B used VRD (bortezomib, lenalidomide, dexamethasone) maintenance for 3 years. The cumulative incidence of SPMs did not differ significantly among the TT trial components when measured from enrollment (P = .78) or from initiation of maintenance (P = .82). However, a pairwise comparison of the TT2 arms suggested a lower incidence of hematologic SPMs in the thalidomide maintenance arm (hazard ratio = 0.38; P = .09). These trials are registered at www.clinicaltrials.gov as NCT00573391 (TT2), NCT00081939 (TT3A), and NCT00572169 (TT3B).


Subject(s)
Antineoplastic Agents/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Maintenance Chemotherapy/methods , Multiple Myeloma/drug therapy , Neoplasms, Second Primary/drug therapy , Thalidomide/analogs & derivatives , Thalidomide/therapeutic use , Aged , Antineoplastic Agents/administration & dosage , Antineoplastic Combined Chemotherapy Protocols/administration & dosage , Boronic Acids/administration & dosage , Boronic Acids/therapeutic use , Bortezomib , Dexamethasone/administration & dosage , Dexamethasone/therapeutic use , Female , Humans , Incidence , Induction Chemotherapy , Lenalidomide , Male , Multiple Myeloma/diagnosis , Multiple Myeloma/epidemiology , Neoplasms, Second Primary/diagnosis , Neoplasms, Second Primary/epidemiology , Pyrazines/administration & dosage , Pyrazines/therapeutic use , Thalidomide/administration & dosage
18.
Blood ; 119(21): e148-50, 2012 May 24.
Article in English | MEDLINE | ID: mdl-22496154

ABSTRACT

Cytogenetic abnormalities are important clinical parameters in various types of cancer, including multiple myeloma. We developed a model to predict cytogenetic abnormalities in patients with multiple myeloma using gene expression profiling and validated it by different cytogenetic techniques. The model has an accuracy rate up to 0.89. These results provide proof of concept for the hypothesis that gene expression profiling is a superior genomic method for clinical molecular diagnosis and/or prognosis.


Subject(s)
Chromosome Aberrations , Cytogenetic Analysis/methods , Gene Expression Profiling , Multiple Myeloma/diagnosis , Multiple Myeloma/genetics , Biopsy, Needle , Bone Marrow/metabolism , Bone Marrow/pathology , Case-Control Studies , Comparative Genomic Hybridization , Female , Gene Expression Profiling/methods , Humans , Male , Microarray Analysis/methods , Models, Statistical , Multiple Myeloma/mortality , Multiple Myeloma/pathology , Prognosis , Sensitivity and Specificity
19.
Blood ; 120(10): 2076-86, 2012 Sep 06.
Article in English | MEDLINE | ID: mdl-22753872

ABSTRACT

Even though hematopoietic stem cell (HSC) dysfunction is presumed in myelodysplastic syndrome (MDS), the exact nature of quantitative and qualitative alterations is unknown. We conducted a study of phenotypic and molecular alterations in highly fractionated stem and progenitor populations in a variety of MDS subtypes. We observed an expansion of the phenotypically primitive long-term HSCs (lineage(-)/CD34(+)/CD38(-)/CD90(+)) in MDS, which was most pronounced in higher-risk cases. These MDS HSCs demonstrated dysplastic clonogenic activity. Examination of progenitors revealed that lower-risk MDS is characterized by expansion of phenotypic common myeloid progenitors, whereas higher-risk cases revealed expansion of granulocyte-monocyte progenitors. Genome-wide analysis of sorted MDS HSCs revealed widespread methylomic and transcriptomic alterations. STAT3 was an aberrantly hypomethylated and overexpressed target that was validated in an independent cohort and found to be functionally relevant in MDS HSCs. FISH analysis demonstrated that a very high percentage of MDS HSC (92% ± 4%) carry cytogenetic abnormalities. Longitudinal analysis in a patient treated with 5-azacytidine revealed that karyotypically abnormal HSCs persist even during complete morphologic remission and that expansion of clonotypic HSCs precedes clinical relapse. This study demonstrates that stem and progenitor cells in MDS are characterized by stage-specific expansions and contain epigenetic and genetic alterations.


Subject(s)
Chromosome Aberrations , Chromosomes, Human, Pair 7/genetics , Hematopoietic Stem Cells , Myelodysplastic Syndromes/genetics , STAT3 Transcription Factor/genetics , Antigens, CD/genetics , Antigens, CD/metabolism , Azacitidine/administration & dosage , Case-Control Studies , Cell Lineage , DNA Methylation , Epigenesis, Genetic , Flow Cytometry , Gene Expression , Hematopoietic Stem Cells/metabolism , Hematopoietic Stem Cells/pathology , Humans , Karyotyping , Myelodysplastic Syndromes/diagnosis , Myelodysplastic Syndromes/drug therapy , Myelodysplastic Syndromes/pathology , Primary Cell Culture , Recurrence , STAT3 Transcription Factor/metabolism
20.
Blood Cancer J ; 14(1): 24, 2024 02 02.
Article in English | MEDLINE | ID: mdl-38307865

ABSTRACT

Multiple myeloma is a genetically complex and heterogenous malignancy with a 5-year survival rate of approximately 60%. Despite advances in therapy, patients experience cycles of remission and relapse, with each successive line of therapy associated with poorer outcomes; therefore, therapies with different mechanisms of action against new myeloma antigens are needed. G protein-coupled receptor class C group 5 member D (GPRC5D) has emerged as a novel therapeutic target for the treatment of multiple myeloma. We review the biology and target validation of GPRC5D, and clinical data from early phase trials of GPRC5D-targeting bispecific antibodies, talquetamab and forimtamig, and chimeric antigen receptor T cell (CAR-T) therapies, MCARH109, OriCAR-017, and BMS-986393. In addition to adverse events (AEs) associated with T-cell-redirection therapies irrespective of target, a consistent pattern of dermatologic and oral AEs has been reported across several trials of GPRC5D-targeting bispecific antibodies, as well as rare cerebellar events with CAR-T therapy. Additional studies are needed to understand the underlying mechanisms involved in the development of skin- and oral-related toxicities. We review the strategies that have been used to manage these GPRC5D-related toxicities. Preliminary efficacy data showed overall response rates for GPRC5D-targeting T-cell-redirecting therapies were ≥64%; most responders achieved a very good partial response or better. Pharmacokinetics/pharmacodynamics showed that these therapies led to cytokine release and T-cell activation. In conclusion, results from early phase trials of GPRC5D-targeting T-cell-redirecting agents have shown promising efficacy and manageable safety profiles, including lower infection rates compared with B-cell maturation antigen- and Fc receptor-like protein 5-targeting bispecific antibodies. Further clinical trials, including those investigating GPRC5D-targeting T-cell-redirecting agents in combination with other anti-myeloma therapies and with different treatment modalities, may help to elucidate the future optimal treatment regimen and sequence for patients with multiple myeloma and improve survival outcomes. Video Summary.


Subject(s)
Antibodies, Bispecific , Multiple Myeloma , Receptors, Chimeric Antigen , Humans , Multiple Myeloma/drug therapy , Antibodies, Bispecific/therapeutic use , Neoplasm Recurrence, Local/drug therapy , Immunotherapy, Adoptive/methods , Receptors, G-Protein-Coupled
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