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  • 1
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 2189-2189
    Abstract: Introduction Multiple myeloma is a clinically highly heterogeneous disease, which is reflected by both a complex genome and epigenome. Dynamic epigenetic changes are involved at several stages of myeloma biology, such as transformation and disease progression. Our previous genome wide epigenetic analyses identified prognostically relevant DNA hypermethylation at specific tumor suppressor genes (Kaiser MF et al., Blood 2013), indicating that specific epigenetic programming influences clinical behavior. This clinically relevant finding prompted further investigation of the epigenomic structure of myeloma and its interaction with genetic aberrations. Material and Methods Genome wide DNA methylation of CD138-purified myeloma cells from 464 patients enrolled in the NCRI Myeloma XI trial at presentation were analyzed using the high resolution 450k DNA methylation array platform (Illumina). In addition, 4 plasma cell leukemia (PCL) cases (two t(11;14) and two (4;14)) and 7 myeloma cell lines (HMCL) carrying different translocations were analysed. Analyses were performed in R Bioconductor packages after filtering and removal of low quality and non-uniquely mapping probes. Results Variation in genome wide DNA methylation was analyzed using unsupervised hierarchical clustering of the 10,000 most variable probes, which revealed epigenetically defined subgroups of disease. Presence of recurrent IGH translocations was strongly associated with specific epigenetic profiles. All 60 cases with t(4;14) clustered into two highly similar sub-clusters, confirming that overexpression of the H3K36 methyltransferase MMSET in t(4;14) has a defined and specific effect on the myeloma epigenome. Interestingly, HMCLs KMS-11 and LP-1, which carry t(4;14), MM1.S, a t(14;16) cell line with an E1099K MMSET activating mutation as well as two PCLs with t(4;14) all clustered in one sub-clade. The majority (59/85) of t(11;14) cases showed global DNA hypomethylation compared to t(4;14) cases and clustered in one subclade, indicating a epigenetic programming effect associated with CCND1, with a subgroup of t(11;14) cases showing a variable DNA methylation pattern. In addition to translocation-defined subgroups, a small cluster of samples with a distinct epigenetic profile was identified. In total 7 cases with a shared specific DNA methylation pattern (median inter-sample correlation 0.4) were identified. The group was characterized by DNA hypermethylation (4,341 hypermethylated regions vs. 750 hypomethylated regions) in comparison to all other cases. Intersection of regions hypermethylated in this subgroups with ENCODE datasets revealed mapping to poised enhancers and promoters in H1-hESC, indicating functionally relevant epigenetic changes. Gene set enrichment analysis (KEGG) demonstrated enrichment of developmental pathway genes, e.g. Hedgehog signaling (adj p=5x10exp-13), amongst others and all four HOX clusters were differentially methylated in this group. Of note, three of seven cases in this subgroup carried a t(11;14) and all t(11;14) or t(11;14)-like HMCLs clustered closely together with these patient cases, but not with the cluster carrying the majority of t(11;14) myeloma or t(11;14) PCLs. This potentially indicates that t(11;14) HMCL could be derived from a subgroup of patients with specific epigenetic characteristics. Conclusion Our results indicate that the recurrent IGH translocations are fundamentally involved in shaping the myeloma epigenome through either direct upregulation of epigenetic modifiers (e.g. MMSET) or through insufficiently understood mechanisms. However, developmental epigenetic processes seem to independently contribute to the complexity of the epigenome in some cases. This work provides important insights into the spectrum of epigenetic subgroups of myeloma and helps identify subgroups of disease that may benefit from specific epigenetic therapies currently being developed. Disclosures Walker: Onyx Pharmaceuticals: Consultancy, Honoraria.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 2
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 172-172
    Abstract: Introduction Co-segregation of two or more adverse structural genetic aberrations in myeloma is associated with a particularly bad outcome and defines a molecular high risk subgroup of patients that is in urgent need of innovative treatment approaches (Boyd, Leukemia 2012). Interphase in situ fluorescence hybridization(iFISH) is the current clinical standard for detecting structural genetic aberrations in myeloma. However, iFISH is labor-intensive, slow and dependent on investigator expertise, which makes standardization difficult. There is an urgent need to develop a standardized and easily accessible all-molecular diagnostic test to enable the design of risk-stratified trials and, finally, risk-adapted precision medicine treatments for high risk patients. Material and Methods Bone marrow material from 1596 patients was received by a central laboratory for patients enrolled in the NCRI Myeloma XI trial (NCT01554852) at diagnosis from over 80 centers throughout the UK. Myeloma cells were purified to a purity of 〉 98% (median across samples) using an AutoMACS (Miltenyi Biotech) system and DNA and RNA were extracted using AllPrep columns (QIAGEN). Recurrent translocations were predicted by gene expression using a sensitive and specific TC-classification based multiplex qRT-PCR assay on a standard TaqMan (Life Technologies) real-time cycler (Kaiser et al., Leukemia 2013). Myeloma specific copy number alterations were assayed using the sensitive and specific multiplex ligation-dependent probe amplification assay (MLPA P425; MRC Holland; Alpar et al, Gen Chrom Cancer 2013) on a standard thermocycler and a standard ABI 3730 capillary electrophoresis Genetic Analyzer. Analysis of qRT-PCR and MLPA results was performed on a desktop computers using standard software without need for bioinformatics expertise or infrastructure. Results Translocation status was successfully analyzed for 1201 cases and copy number aberrations were successfully analyzed for 1232 cases. Matched translocation and copy number aberration data was available for 1044 cases. Genetic lesions associated with an adverse prognosis were detected with the following frequencies among the 1044 cases: t(4;14): 13%; t(14;16): 4%; t(14;20): 1%; del(1p32): 9%; gain(1q): 27%; amp(1q): 8%; del(17p): 9%. Non-high risk recurrent IGH translocations as well as copy number aberrations were assayed through both tests as well. Co-segregation analysis of all detected abnormalities using Fisher’s exact test, corrected for multiple testing, revealed co-occurrence more than expected by chance of the following lesions: t(4;14) and gain(1q): q=6.2x10-4; t(4;14) and amp(1q): q=2.1x10-7; del(1p32) and gain(1q): 1.1x10-3. Statistically significant co-occurrence was also observed for del(12p) and del(17p): q=2.1x10-5 as well as del(12p) and t(4;14): q=1.8x10-5. Survival data at the timepoint of analysis was available for 450 patients with a median follow-up of 25 months. Patients were classified as previously described (Boyd et al, Leukemia 2013) into molecular risk groups with standard risk defined by absence of adverse genetic lesions (n=224), intermediate risk with presence of one adverse genetic lesion (n=161) and high risk with presence of two adverse lesions (n=65). On Cox analysis, there was a significant difference in terms of PFS between these groups with a median PFS of 31.3 months (95% CI 28.5-35.2), 25.8 months (CI 22.1-27.6) and 16.2 months (CI 10.6-23.7) for groups with none, one, two or more genetic lesions, respectively. The 2-year OS was also significantly different between the groups with 84% (CI 79-89%) in standard risk, 78% (CI 71-85%) in intermediate risk and 65% (CI 53-78%) in high risk patients. Conclusion This all-molecular diagnostic approach for recurrent structural aberrations in myeloma offers a fast, robust and high throughput alternative to iFISH that can be run in any molecular diagnostic laboratory on standard equipment. The methods described here enable standardized and specific identification of a high risk subgroup of patients without the need for a bioinformatics infrastructure or expertise. The clinical applicability of this method makes it an ideal candidate method for prospective molecular risk-stratified clinical trials. Disclosures Walker: Onyx Pharmaceuticals: Consultancy, Honoraria. Savola:MRC-Holland: Employment.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 3
    In: Blood, American Society of Hematology, Vol. 125, No. 5 ( 2015-01-29), p. 831-840
    Abstract: Coexistent hyperdiploidy or t(11;14) does not abrogate the poor prognosis associated with adverse cytogenetics in myeloma patients. Single-cell analysis reveals that hyperdiploidy may precede IGH translocation in the clonal history of a proportion of patients with both.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
    detail.hit.zdb_id: 1468538-3
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  • 4
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 640-640
    Abstract: Multiple myeloma (MM) is a disease characterized by the abnormal proliferation of plasma cells in the bone marrow. We and others have recently demonstrated the existence of different myeloma subclones phylogenetically related to the founding clone. This intra-clonal heterogeneity is the basis for disease progression, treatment resistance, and relapse. However, the clinical and biological relevance of the presence and diversity of different myeloma subclones has not been fully established. In this study, we used whole exome sequencing (WES) plus a pull down of the MYC, IGH, IGL and IGK loci as a tool to analyze the largest series of presenting cases of myeloma (463 patients) to date, which were entered into the Myeloma XI trial (NCT01554852). DNA from both tumor and peripheral blood samples were used in the exome capture protocol following the SureSelect Target Enrichment System for Illumina Paired-End Sequencing Library v1.5. Exome reads were used to call single nucleotide variants (SNVs), indels, translocations, and copy number aberrations. The proportion of tumor cells containing an SNV was inferred. The presence and proportion of subclones were defined in a subset of 437 patients using a genetic algorithm based-tool (GAUCHO), which also calculated different indices of clonal diversity: number of clones, mean pairwise genetic divergence, Shannon and Inverse Simpson diversity index and Berger-Parker dominance index. Based on these results, we aimed to determine the clinical implications of the number of mutations and the subclonal diversity of MM at presentation in progression free (PFS) and overall survival (OS). We found that MM patients with t(14;16) and t(14;20) had more exonic mutations (not including Ig variants) than the rest of samples (median 87 versus 43, p 〈 0.001). Additionally, we found that MM patients with an APOBEC signature or with mutations in ATM/ATR had significantly more mutations than patients without these genetic lesions with a median number of 137 mutations (range 20-569) and 84.5 (range 33-319) respectively (p 〈 0.001). Subsequently, we identified patients with high number of mutations ( 〉 59 mutations) that had a worse outcome in terms of OS (2-year OS rate of 71% (95% CI, 63-80%) vs. 82% (95% CI, 78-87%), p=0.02), but not progression free survival (median 22.5 (95% CI 18.7-30.2) vs. 27.5 (95% CI, 25.8-30.5) months, p=0.1) We reported recurrent mutated genes in myeloma with mutations being present at both clonal and subclonal levels (IRF4, RB1, DIS3, BRAF, KRAS, and NRAS), whereas other genes were mutated only at clonal (HIST1H1E, LTB, TP53 or EGR1), or subclonal levels (CYLD, TRAF3, MAX). These results give insights about the differences in mutation acquisition times and potential subclonal fitness. We inferred that the median number of clones present in this myeloma series was 5, and determined the prognostic value of the number and diversity of subclones in MM patients. The prognostic impact of having high number of clones was unclear as no significant differences were found. On the contrary, there was a significant difference in terms of outcome when calculating distinct measurements of subclonal diversity. Briefly, MM patients with high values of inverse Simpson diversity index had a significantly poorer PFS (median 13.2 (95% CI, 9.4-∞) vs. 26.9 months (95% CI, 24-30.2) months, p=0.02) and OS (66% (95% CI, 52-82%) vs. 81% (95% CI, 77-85%) alive at 2-years, p=0.01); and, alternatively, MM patients who did not have a dominant subclone accounting for 〉 25% of MM cells (low values of Berger-Parker Dominance index, n=56) had a significantly shorter PFS than those with a dominant clone accounting for more than 25% of cells with a median of 22 (95% CI, 12.3-26.3) vs. 27.5 months (95% CI, 23.9-30.9) respectively, p=0.02. Our results show that mutational load and subclonal diversity are poor prognostic factors in myeloma. Previous studies from massive-parallel sequencing and single cell analyses of myeloma plasma cells already revealed that myeloma had the features of an evolutionary ecosystem, where different tumour subclones coexist and have differential response to treatment. We have demonstrated in this study that measures of tumor diversity have important clinical consequences. To our knowledge, this is the first time that the use of clonal diversity indices as predictive biomarkers of progression is proposed in haematological malignancies, and more specifically, myeloma. Disclosures Walker: Onyx Pharmaceuticals: Consultancy, Honoraria.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 5
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 2981-2981
    Abstract: Introduction Identifying molecular high risk myeloma remains a diagnostic challenge. We previously reported co-segregation of 〉 1 adverse lesion [t(4;14), t(14;16), t(14;20), gain(1q), del(17p)] by iFISH to specifically characterise a group of high risk patients (Boyd et al., Leukemia 2012). However, implementation of this approach is difficult using FISH because of its technical limitations. We recently developed and validated a novel high-throughput all-molecular testing strategy against FISH (MyMaP- Myeloma MLPA and translocation PCR; Kaiser MF et al., Leukemia 2013; Boyle EM et al., Gen Chrom Canc 2015). Here, we molecularly characterised 1,036 patients from the NCRI Myeloma XI trial using MyMaP and validated the co-segregation approach. Materials, Methods and Patients Recurrent translocations and copy number changes were assayed for 1,036 patients enrolled in the NCRI Myeloma XI (NCT01554852) trial using CD138+ selected bone marrow myeloma cells taken at diagnosis. The trial included an intensive therapy arm for younger and fitter and a non-intense treatment arm for elderly and frail patients. Analysis was performed using MyMaP, which comprises TC-classification based multiplex qRT-PCR and multiplex ligation-dependent probe amplification (MLPA; MRC Holland). Median follow up for the analysis was 24 months. Results Adverse translocations [t(4;14), t(14;16), t(14;20)] were present in 18.2% of cases, del(17p) in 9.3%, gain(1q) in 34.5% and del(1p32) in 9.4% of cases. All adverse lesions were associated with significantly shorter PFS and OS by univariate analysis (P 〈 0.05 for all). Of the 1,036 analysed cases, 13.5% carried 〉 1 adverse lesion, 33.9% had one isolated adverse lesion and 52.6% had no adverse lesion. Presence of 〉 1, 1 or no adverse lesion was associated with a median PFS of 17.0, 23.9 and 30.6 months (P =3.0x10-9) and OS at 24 months of 67.9%, 75.0% and 86.0% (P =1.8x10-7), respectively. Del(1p) was associated with shorter PFS and OS for the intensive, but not for the non-intensive therapy arm and was independent of the co-segregation model by multivariate analysis regarding OS (P =0.006). We thus included del(1p) as an additional adverse lesion in the model for younger patients. The groups with 〉 1 (19.4% of cases), 1 (31.1%) and no adverse lesions (49.5%) were characterised by median PFS of 19.4, 29.4 and 39.1 months (P =1.2x10-10) and median 24-months survival of 73.8%, 86.4% and 91.5% (P =1.4x10-6), respectively. Hazard Ratio for 〉 1 adverse lesion was 3.0 (95% CI 2.1-4.1) for PFS and 3.8 (95% CI 2.2-6.5) for OS. By multivariate analysis, co-segregation of adverse lesions was independent of ISS for PFS/OS in the entire group of 1,036 cases and in the intensive treatment arm. We integrated adverse lesions and ISS into a combined model defining High Risk ( 〉 1 adv les + ISS 2 or 3; 1 adv les + ISS 3) and Low Risk (no adv les + ISS 1 or 2; 1 adv les + ISS 1) and the remainder as Intermediate Risk. The High Risk, Intermediate Risk and Low Risk groups of the total cohort included 11.2%, 41.2% and 41.6% of cases with median PFS of 15.8, 19.8 and 35.2 months (P 〈 2.2x10-16) and median OS at 24 months of 62.9%, 73.7%, and 90.7% (P =4.0x10-14), respectively. Integration of ISS into the model for younger patients resulted in highly specific identification of a High Risk group (15.6% of cases) with HR 3.8 (CI 2.6-5.4) for PFS and 6.2 (CI 3.3-11.6) for OS. Conclusions Co-segregation analysis of adverse genetic lesions is a specific molecular risk stratification tool which has now been validated in two large independent trials including a real-world population of all age groups (UK MRC Myeloma IX; NCRI Myeloma XI; total 1,905 patients). MyMaP is a validated all-molecular analysis approach that makes the otherwise technically challenging assessment of multiple genetic regions by FISH accessible using standard laboratory equipment without bioinformatics requirements. Disclosures Kaiser: BristolMyerSquibb: Consultancy; Chugai: Consultancy; Janssen: Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Amgen: Consultancy, Honoraria. Pawlyn:Celgene: Honoraria, Other: Travel support; The Institute of Cancer Research: Employment. Jones:Celgene: Other: Travel support, Research Funding. Savola:MRC Holland: Employment. Owen:Celgene: Honoraria, Research Funding; Janssen: Honoraria. Cook:Celgene: Consultancy, Research Funding, Speakers Bureau; BMS: Consultancy; Sanofi: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; Takeda Oncology: Consultancy, Research Funding, Speakers Bureau; Janssen: Consultancy, Research Funding, Speakers Bureau. Gregory:Celgene: Honoraria; Janssen: Honoraria. Davies:Takeda-Milenium: Honoraria; Onyx-Amgen: Honoraria; Celgene: Honoraria; University of Arkansas for Medical Sciences: Employment. Jackson:Celgene: Honoraria; Takeda: Honoraria; Amgen: Honoraria. Morgan:Weisman Institute: Honoraria; Takeda-Millennium: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; University of Arkansas for Medical Sciences: Employment; CancerNet: Honoraria; MMRF: Honoraria.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 6
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 37, No. 15_suppl ( 2019-05-20), p. 1051-1051
    Abstract: 1051 Background: PI3K and CDK4/6 inhibitors synergise in ER+ve and –ve PIK3CA-mt breast cancer (BC) models. Escalation phase of this study set recommended phase 2 dose (RP2D) at P 125mg on a 3/1 scheme plus T 2mg daily ( Lim, ASCO 2017). Here we present the results of expansion cohorts for PIK3CA-mt BC patients (pts). Methods: The primary objective was to assess the confirmed objective response rate (ORR) of the P + T + FUL triplet in pts with measurable PIK3CA-mt ER+ve HER2-ve advanced BC, with up to two prior lines of chemotherapy for advanced disease. PIK3CA mutation was assessed in tissue or plasma DNA analysis. Exploratory objectives included assessment of efficacy of P + T in a cohort of pts with PIK3CA-mt advanced ER-ve BC. Safety is reported overall for 44 patients including an additional cohort of 7 PIK3CA-unknown ER+ve BC pts treated with P + T + letrozole (LET). For the P + T + FUL triplet a Simon minmax design was used, with 6 responses in 25 patients required to declare efficacy. Results: We recruited 24 assessable patients with PIK3CA-mt ER+ve HER2-ve advanced BC, median age 57 (42-74), median 3 (1-9) prior therapy lines for advance disease, with 24 (100%) receiving prior endocrine therapy and 23 (96%) prior aromatase inhibitor. ORR was 33% (8/24, 95% CI 16-55%), with median progression free survival (PFS) 7.9m (95% CI 5.6-11.8). For the 11 assessable PIK3CA-mt ER-ve pts (8 HER2-ve, 3 HER2+ve) receiving P + T, ORR was 0% (0/11), clinical benefit rate (CBR) 27% (3/11) and median PFS 4.3m (95% CI 1.8-6.1). Most common AEs across all cohorts were neutropenia (80%), fatigue (50%), mucositis (50%) and thrombocytopenia (30%). Most common grade 3/4 AEs were neutropenia (57%) and rash (11%). Translational research is ongoing. Conclusions: The triplet of P + T + FUL has promising efficacy in pre-treated PIK3CA-mt ER+ve advanced BC. A subset of patients with PIK3CA-mt ER-ve advanced BC had clinical benefit from P + T. The combination of P + T +/- FUL/LET was well tolerated with anticipated AEs. Clinical trial information: NCT02389842.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2019
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  • 7
    In: Cancer Discovery, American Association for Cancer Research (AACR), Vol. 13, No. 3 ( 2023-03-01), p. 654-671
    Abstract: Malignant peripheral nerve sheath tumor (MPNST), an aggressive soft-tissue sarcoma, occurs in people with neurofibromatosis type 1 (NF1) and sporadically. Whole-genome and multiregional exome sequencing, transcriptomic, and methylation profiling of 95 tumor samples revealed the order of genomic events in tumor evolution. Following biallelic inactivation of NF1, loss of CDKN2A or TP53 with or without inactivation of polycomb repressive complex 2 (PRC2) leads to extensive somatic copy-number aberrations (SCNA). Distinct pathways of tumor evolution are associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumors with H3K27me3 loss evolve through extensive chromosomal losses followed by whole-genome doubling and chromosome 8 amplification, and show lower levels of immune cell infiltration. Retention of H3K27me3 leads to extensive genomic instability, but an immune cell-rich phenotype. Specific SCNAs detected in both tumor samples and cell-free DNA (cfDNA) act as a surrogate for H3K27me3 loss and immune infiltration, and predict prognosis. Significance: MPNST is the most common cause of death and morbidity for individuals with NF1, a relatively common tumor predisposition syndrome. Our results suggest that somatic copy-number and methylation profiling of tumor or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. This article is highlighted in the In This Issue feature, p. 517
    Type of Medium: Online Resource
    ISSN: 2159-8274 , 2159-8290
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 8
    In: European Journal of Cancer, Elsevier BV, Vol. 162 ( 2022-02), p. 209-220
    Type of Medium: Online Resource
    ISSN: 0959-8049
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
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  • 9
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 3097-3097
    Abstract: Obtaining reliable information about the molecular subtype of myeloma is and will become ever more important in a number of clinical settings, such as alternative treatment strategies for high risk or ultra high risk disease (Boyd KD et al., Leukemia 2011), or patient selection for small molecule inhibitors, that are currently under development, targeting myeloma subtype specific proteins (e.g. MMSET or MAF). We report here our experience with a novel, highly applicable and high throughput diagnostic approach in a large sample set of 1016 myeloma presentation cases, using a combination of qRT-PCR and Multiplex Ligation-dependent Probe Amplification (MLPA) for molecular patient characterization of Ig loci translocations and well-defined copy number abnormalities. Material and Methods Recurrent translocations were assessed for 1016 presentation NCRI Myeloma XI trial cases and 41 matched relapse samples, using a previously published and interphase fluorescence in situ hybridization (iFISH)-validated in house qRT-PCR assay on purified bone marrow plasma cell material. The assay measures expression of translocation partner genes and their downstream effectors (e.g. CCND1, MMSET, FGFR3, MAF, MAFB, CCND2) with subsequent interpretation and categorization of results based on the translocation/cyclin D (TC) classification. This allows prediction of presence of the recurrent translocations with high sensitivity and specificity (Kaiser MF et al., Leukemia 2013) and evaluation of overexpression of potential drug targets independent of translocations (e.g. MAF). For selected cases, the myeloma specific SALSA MLPA assay (MRC-Holland) was performed, containing 46 probes that inform about prognostically relevant copy number alterations, such as del(1p), gain(1q), or del(17p). High correlation between MLPA and FISH results for clinically relevant copy number aberrations has been previously reported (Alpar D et al., Genes Chrom Canc 2013). Results The TC classification based translocation qRT-PCR assay worked reliably even for poor quality input RNA, providing results for 〉 96% of analyzed samples. Predicted translocation frequencies among the 1016 evaluable cases were comparable to previously reported results [t(11;14): 16.6%; t(4;14): 12.6%, of which 21.1% lacked FGFR3 expression; t(14;16): 2.6%; t(14;20): 0.5%; t(6;14): 0.7%]. Relapse samples showed consistent results with matched presentation samples, with one t(4;14) case losing initial high FGFR3 expression at relapse. Correlation with clinical data will be available for presentation at the meeting. Measurement and analysis of the samples was performed by a single lab technician in a short time, demonstrating the high throughput capability of the method. This makes rapid analysis of very large sample collections possible, revealing novel findings. When the assayed group was split by median age, the younger group (22-66 years) contained relatively more t(4;14) [15.7% vs. 9.4%; p=0.003] cases than the older group (67-88 years), consistent with recent reports on iFISH data (Avet-Loiseau H, 2013). We also found a lower frequency of t(11;14) [13.6% vs. 19%;p=0.022] in the younger vs. the older group, which has not been reported. MLPA results were generated for a subset of 30 samples for which iFISH and copy number array data were available. The previously reported high level of correlation with iFISH results (Alpar D et al., Genes Chrom Canc 2013) was confirmed and extended for copy number array data, with 〉 85% sensitivity and 〉 95% specificity for del(1p), gain(1q), del(13p) and del(17p). MLPA assessments will be extended in the coming months to include a large group of Myeloma XI cases, and results and their associations with qRT-PCR results and clinical features will be presented at the meeting. Conclusion Precision medicine approaches in myeloma require fast, robust and practicable molecular diagnostic tools. The current diagnostic standard iFISH doesn’t fulfill any of these criteria. Other approaches such as microarray analyses have never found acceptance outside of highly specialized centers due to practicability issues. With the approach presented here, clinically relevant molecular features can be assessed within 48 hours with standard molecular laboratory equipment. This approach is a suitable candidate for a novel standard for routine clinical molecular analysis of multiple myeloma. Disclosures: Savola: MRC-Holland: Employment.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
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  • 10
    In: Molecular Cancer, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2022-12)
    Abstract: Development of resistance to targeted therapies has tempered initial optimism that precision oncology would improve poor outcomes for cancer patients. Resistance mechanisms, however, can also confer new resistance-specific vulnerabilities, termed collateral sensitivities. Here we investigated anaplastic lymphoma kinase (ALK) inhibitor resistance in neuroblastoma, a childhood cancer frequently affected by activating ALK alterations. Methods Genome-wide forward genetic CRISPR-Cas9 based screens were performed to identify genes associated with ALK inhibitor resistance in neuroblastoma cell lines. Furthermore, the neuroblastoma cell line NBLW-R was rendered resistant by continuous exposure to ALK inhibitors. Genes identified to be associated with ALK inhibitor resistance were further investigated by generating suitable cell line models. In addition, tumor and liquid biopsy samples of four patients with ALK -mutated neuroblastomas before ALK inhibitor treatment and during tumor progression under treatment were genomically profiled. Results Both genome-wide CRISPR-Cas9-based screens and preclinical spontaneous ALKi resistance models identified NF1 loss and activating NRAS Q61K mutations to confer resistance to chemically diverse ALKi. Moreover, human neuroblastomas recurrently developed de novo loss of NF1 and activating RAS mutations after ALKi treatment, leading to therapy resistance. Pathway-specific perturbations confirmed that NF1 loss and activating RAS mutations lead to RAS-MAPK signaling even in the presence of ALKi. Intriguingly, NF1 loss rendered neuroblastoma cells hypersensitive to MEK inhibition. Conclusions Our results provide a clinically relevant mechanistic model of ALKi resistance in neuroblastoma and highlight new clinically actionable collateral sensitivities in resistant cells.
    Type of Medium: Online Resource
    ISSN: 1476-4598
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2091373-4
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