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Browsing by Author "van Rhee, Frits"
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Item The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma(BMC, 2020-08-06) Choudhury, Samrat Roy; Ashby, Cody; Tytarenko, Ruslana; Bauer, Michael; Wang, Yan; Deshpande, Shayu; Den, Judith; Schinke, Carolina; Zangari, Maurizio; Thanendrarajan, Sharmilan; Davies, Faith E.; van Rhee, Frits; Morgan, Gareth J.; Walker, Brian A.; Medicine, School of MedicineBackground Multiple Myeloma (MM) is a hematological malignancy with genomic heterogeneity and poor survival outcome. Apart from the central role of genetic lesions, epigenetic anomalies have been identified as drivers in the development of the disease. Methods Alterations in the DNA methylome were mapped in 52 newly diagnosed MM (NDMM) patients of six molecular subgroups and matched with loci-specific chromatin marks to define their impact on gene expression. Differential DNA methylation analysis was performed using DMAP with a ≥10% increase (hypermethylation) or decrease (hypomethylation) in NDMM subgroups, compared to control samples, considered significant for all the subsequent analyses with p<0.05 after adjusting for a false discovery rate. Results We identified differentially methylated regions (DMRs) within the etiological cytogenetic subgroups of myeloma, compared to control plasma cells. Using gene expression data we identified genes that are dysregulated and correlate with DNA methylation levels, indicating a role for DNA methylation in their transcriptional control. We demonstrated that 70% of DMRs in the MM epigenome were hypomethylated and overlapped with repressive H3K27me3. In contrast, differentially expressed genes containing hypermethylated DMRs within the gene body or hypomethylated DMRs at the promoters overlapped with H3K4me1, H3K4me3, or H3K36me3 marks. Additionally, enrichment of BRD4 or MED1 at the H3K27ac enriched DMRs functioned as super-enhancers (SE), controlling the overexpression of genes or gene-cassettes. Conclusions Therefore, this study presents the underlying epigenetic regulatory networks of gene expression dysregulation in NDMM patients and identifies potential targets for future therapies.Item Ixazomib-lenalidomide-dexamethasone in routine clinical practice: effectiveness in relapsed/refractory multiple myeloma(Taylor & Francis, 2021) Hájek, Roman; Minařík, Jiří; Straub, Jan; Pour, Luděk; Jungova, Alexandra; Berdeja, Jesus G.; Boccadoro, Mario; Brozova, Lucie; Spencer, Andrew; van Rhee, Frits; Vela-Ojeda, Jorge; Thompson, Michael A.; Abonour, Rafat; Chari, Ajai; Cook, Gordon; Costello, Caitlin L.; Davies, Faith E.; Hungria, Vania T. M.; Lee, Hans C.; Leleu, Xavier; Puig, Noemi; Rifkin, Robert M.; Terpos, Evangelos; Usmani, Saad Z.; Weisel, Katja C.; Zonder, Jeffrey A.; Bařinová, Magda; Kuhn, Matyáš; Šilar, Jiří; Čápková, Lenka; Galvez, Kenny; Lu, Jin; Elliott, Jennifer; Stull, Dawn Marie; Ren, Kaili; Maisnar, Vladimír; Medicine, School of MedicineAim: To evaluate the effectiveness and safety of ixazomib-lenalidomide-dexamethasone (IRd) in relapsed/refractory multiple myeloma in routine clinical practice. Patients & methods: Patient-level data from the global, observational INSIGHT MM and the Czech Registry of Monoclonal Gammopathies were integrated and analyzed. Results: At data cut-off, 263 patients from 13 countries were included. Median time from diagnosis to start of IRd was 35.8 months; median duration of follow-up was 14.8 months. Overall response rate was 73%, median progression-free survival, 21.2 months and time-to-next therapy, 33.0 months. Ixazomib/lenalidomide dose reductions were required in 17%/36% of patients; 32%/30% of patients discontinued ixazomib/lenalidomide due to adverse events. Conclusion: The effectiveness and safety of IRd in routine clinical practice are comparable to those reported in TOURMALINE-MM1.Item Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma(American Association for Cancer Research, 2022) Sudha, Parvathi; Ahsan, Aarif; Ashby, Cody; Kausar, Tasneem; Khera, Akhil; Kazeroun, Mohammad H.; Hsu, Chih-Chao; Wang, Lin; Fitzsimons, Evelyn; Salminen, Outi; Blaney, Patrick; Czader, Magdalena; Williams, Jonathan; Zaid, Mohammad I. Abu; Ansari-Pour, Naser; Yong, Kwee L.; van Rhee, Frits; Pierceall, William E.; Morgan, Gareth J.; Flynt, Erin; Gooding, Sarah; Abonour, Rafat; Ramasamy, Karthik; Thakurta, Anjan; Walker, Brian A.; Medicine, School of MedicinePurpose: We designed a comprehensive multiple myeloma targeted sequencing panel to identify common genomic abnormalities in a single assay and validated it against known standards. Experimental design: The panel comprised 228 genes/exons for mutations, 6 regions for translocations, and 56 regions for copy number abnormalities (CNA). Toward panel validation, targeted sequencing was conducted on 233 patient samples and further validated using clinical FISH (translocations), multiplex ligation probe analysis (MLPA; CNAs), whole-genome sequencing (WGS; CNAs, mutations, translocations), or droplet digital PCR (ddPCR) of known standards (mutations). Results: Canonical immunoglobulin heavy chain translocations were detected in 43.2% of patients by sequencing, and aligned with FISH except for 1 patient. CNAs determined by sequencing and MLPA for 22 regions were comparable in 103 samples and concordance between platforms was R2 = 0.969. Variant allele frequency (VAF) for 74 mutations were compared between sequencing and ddPCR with concordance of R2 = 0.9849. Conclusions: In summary, we have developed a targeted sequencing panel that is as robust or superior to FISH and WGS. This molecular panel is cost-effective, comprehensive, clinically actionable, and can be routinely deployed to assist risk stratification at diagnosis or posttreatment to guide sequencing of therapies.Item PHF19 inhibition as a therapeutic target in Multiple Myeloma(Elsevier, 2021) Schinke, Carolina D.; Bird, Jordan T.; Qu, Pingping; Yaccoby, Shmuel; Lyzogubov, Valeriy V.; Shelton, Randal; Ling, Wen; Boyle, Eileen M.; Deshpande, Sharyu; Byrum, Stephanie D.; Washam, Charity; Mackintosh, Samuel; Stephens, Owen; Thanendrarajan, Sharmilan; Zangari, Maurizio; Shaughnessy, John, Jr.; Zhan, Fenghuang; Barlogie, Bart; van Rhee, Frits; Walker, Brian A.; Medicine, School of MedicineEpigenetic deregulation is increasingly recognized as a contributing pathological factor in multiple myeloma (MM). In particular tri-methylation of H3 lysine 27 (H3K27me3), which is catalyzed by PHD finger protein 19 (PHF19), a subunit of the Polycomb Repressive Complex 2 (PRC2), has recently shown to be a crucial mediator of MM tumorigenicity. Overexpression of PHF19 in MM has been associated with worse clinical outcome. Yet, while there is mounting evidence that PHF19 overexpression plays a crucial role in MM carcinogenesis downstream mechanisms remain to be elucidated. In the current study we use a functional knock down (KD) of PHF19 to investigate the biological role of PHF19 and show that PHF19KD leads to decreased tumor growth in vitro and in vivo. Expression of major cancer players such as bcl2, myc and EGR1 were decreased upon PHF19KD further underscoring the role of PHF19 in MM biology. Additionally, our results highlighted the prognostic impact of PHF19 overexpression, which was significantly associated with worse survival. Overall, our study underscores the premise that targeting the PHF19-PRC2 complex would open up avenues for novel MM therapies.Item Plasma cells expression from smouldering myeloma to myeloma reveals the importance of the PRC2 complex, cell cycle progression, and the divergent evolutionary pathways within the different molecular subgroups(Springer, 2022-02) Boyle, Eileen M.; Rosenthal, Adam; Ghamlouch, Hussein; Wang, Yan; Farmer, Phillip; Rutherford, Michael; Ashby, Cody; Bauer, Michael; Johnson, Sarah K.; Wardell, Christopher P.; Wang, Yubao; Hoering, Antje; Schinke, Carolina; Thanendrarajan, Sharmilan; Zangari, Maurizio; Barlogie, Bart; Dhodapkar, Madhav V.; Davies, Faith E.; Morgan, Gareth J.; van Rhee, Frits; Walker, Brian A.; Medicine, School of MedicineSequencing studies have shed some light on the pathogenesis of progression from smouldering multiple myeloma (SMM) and symptomatic multiple myeloma (MM). Given the scarcity of smouldering samples, little data are available to determine which translational programmes are dysregulated and whether the mechanisms of progression are uniform across the main molecular subgroups. In this work, we investigated 223 SMM and 1348 MM samples from the University of Arkansas for Medical Sciences (UAMS) for which we had gene expression profiling (GEP). Patients were analysed by TC-7 subgroup for gene expression changes between SMM and MM. Among the commonly dysregulated genes in each subgroup, PHF19 and EZH2 highlight the importance of the PRC2.1 complex. We show that subgroup specific differences exist even at the SMM stage of disease with different biological features driving progression within each TC molecular subgroup. These data suggest that MMSET SMM has already transformed, but that the other precursor diseases are distinct clinical entities from their symptomatic counterpart.Item Rates of Influenza and Pneumococcal Vaccination and Correlation With Survival in Multiple Myeloma Patients(Elsevier, 2023) Thompson, Michael A.; Boccadoro, Mario; Leleu, Xavier; Vela-Ojeda, Jorge; van Rhee, Frits; Weisel, Katja C.; Rifkin, Robert M.; Usmani, Saad Z.; Hájek, Roman; Cook, Gordon; Abonour, Rafat; Armour, Mira; Morgan, Kathryn E.; Yeh, Su-Peng; Costello, Caitlin L.; Berdeja, Jesus G.; Davies, Faith E.; Zonder, Jeffrey A.; Lee, Hans C.; Omel, Jim; Spencer, Andrew; Terpos, Evangelos; Hungria, Vania T. M.; Puig, Noemi; Fu, Chengcheng; Ferrari, Renda H.; Ren, Kaili; Stull, Dawn Marie; Chari, Ajai; Medicine, School of MedicineBackground: Infections are a common reason for hospitalization and death in multiple myeloma (MM). Although pneumococcal vaccination (PV) and influenza vaccination (FV) are recommended for MM patients, data on vaccination status and outcomes are limited in MM. Materials and methods: We utilized data from the global, prospective, observational INSIGHT MM study to analyze FV and PV rates and associated outcomes of patients with MM enrolled 2016-2019. Results: Of the 4307 patients enrolled, 2543 and 2500 had study-entry data on FV and PV status. Overall vaccination rates were low (FV 39.6%, PV 30.2%) and varied by region. On separate multivariable analyses of overall survival (OS) by Cox model, FV in the prior 2 years and PV in the prior 5 years impacted OS (vs. no vaccination; FV: HR, 0.73; 95% CI, 0.60-0.90; P = .003; PV: HR, 0.51; 95% CI, 0.42-0.63; P < .0001) when adjusted for age, region, performance status, disease stage, cytogenetics at diagnosis, MM symptoms, disease status, time since diagnosis, and prior transplant. Proportions of deaths due to infections were lower among vaccinated versus non-vaccinated patients (FV: 9.8% vs. 15.3%, P = .142; PV: 9.9% vs. 18.0%, P = .032). Patients with FV had generally lower health resource utilization (HRU) versus patients without FV; patients with PV had higher or similar HRU versus patients without PV. Conclusion: Vaccination is important in MM and should be encouraged. Vaccination status should be recorded in prospective clinical trials as it may affect survival.Item The molecular make up of smoldering myeloma highlights the evolutionary pathways leading to multiple myeloma(Springer Nature, 2021-01-12) Boyle, Eileen M.; Deshpande, Shayu; Tytarenko, Ruslana; Ashby, Cody; Wang, Yan; Bauer, Michael A.; Johnson, Sarah K.; Wardell, Christopher P.; Thanendrarajan, Sharmilan; Zangari, Maurizio; Facon, Thierry; Dumontet, Charles; Barlogie, Bart; Arbini, Arnaldo; Rustad, Even H.; Maura, Francesco; Landgren, Ola; Zhan, Fenghuang; van Rhee, Frits; Schinke, Carolina; Davies, Faith E.; Morgan, Gareth J.; Walker, Brian A.; Medicine, School of MedicineSmoldering myeloma (SMM) is associated with a high-risk of progression to myeloma (MM). We report the results of a study of 82 patients with both targeted sequencing that included a capture of the immunoglobulin and MYC regions. By comparing these results to newly diagnosed myeloma (MM) we show fewer NRAS and FAM46C mutations together with fewer adverse translocations, del(1p), del(14q), del(16q), and del(17p) in SMM consistent with their role as drivers of the transition to MM. KRAS mutations are associated with a shorter time to progression (HR 3.5 (1.5-8.1), p = 0.001). In an analysis of change in clonal structure over time we studied 53 samples from nine patients at multiple time points. Branching evolutionary patterns, novel mutations, biallelic hits in crucial tumour suppressor genes, and segmental copy number changes are key mechanisms underlying the transition to MM, which can precede progression and be used to guide early intervention strategies.Item The spatio-temporal evolution of multiple myeloma from baseline to relapse-refractory states(Springer, 2022-08-03) Rasche, Leo; Schinke, Carolina; Maura , Francesco; Bauer , Michael A.; Ashby, Cody; Deshpande , Shayu; Poos , Alexandra M.; Zangari , Maurizio; Thanendrarajan, Sharmilan; Davies, Faith E.; Walker, Brian A.; Barlogie, Bart; Landgren, Ola; Morgan, Gareth J.; van Rhee, Frits; Weinhold , Niels; Medicine, School of MedicineDeciphering Multiple Myeloma evolution in the whole bone marrow is key to inform curative strategies. Here, we perform spatial-longitudinal whole-exome sequencing, including 140 samples collected from 24 Multiple Myeloma patients during up to 14 years. Applying imaging-guided sampling we observe three evolutionary patterns, including relapse driven by a single-cell expansion, competing/co-existing sub-clones, and unique sub-clones at distinct locations. While we do not find the unique relapse sub-clone in the baseline focal lesion(s), we show a close phylogenetic relationship between baseline focal lesions and relapse disease, highlighting focal lesions as hotspots of tumor evolution. In patients with ≥3 focal lesions on positron-emission-tomography at diagnosis, relapse is driven by multiple distinct sub-clones, whereas in other patients, a single-cell expansion is typically seen (p < 0.01). Notably, we observe resistant sub-clones that can be hidden over years, suggesting that a prerequisite for curative therapies would be to overcome not only tumor heterogeneity but also dormancy.