Ontology highlight
ABSTRACT:
PROVIDER: PRJNA887394 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21814600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21814600_2.fastq.gz | Fastqsanger.gz | |||
| SRR21814700_1.fastq.gz | Fastqsanger.gz | |||
| SRR21814700_2.fastq.gz | Fastqsanger.gz | |||
| SRR21814800_1.fastq.gz | Fastqsanger.gz |
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Project description:Double-deletion of 1p32 defines ultra-high-risk myeloma, but monoallelic del(1p32) remains a strong prognostic factor
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Project description:Cytogenetics abnormalities (CA) are known to be the preponderant prognostic factor in multiple myeloma (MM). Our team has recently developeda prognostic score based on 6 CA, where del(1p32) appears to be the second worst abnormality after del(17p). The aim of this study was to confirm the adverse impact of 1p32 deletion on newly-diagnosed multiple myeloma (NDMM) patients. Among 2551 NDMM patients, 11% were harboring del(1p32). Their overall survival (OS) was half as long as the OS of patients without del(1p32) (49 months vs. 124 months). Likewise, progression-free survival was significantly shorter. More importantly, double-deletion of the 1p32 locus conferred a dramatically poorer prognosis than a monoallelic del(1p32) (OS: 25 months vs. 60 months). As expected, the OS of del(1p32) patients significantly decreased when this abnormality was associated with other high-risk CA (del(17p), t(4;14) or gain(1q)). In the multivariate analysis, del(1p32) appeared as a negative prognostic factor; after adjustment for age and treatment, the risk of progression was 1.3 times higher among patients harboring del(1p32), and the risk of death was 1.9 times higher. At the dawn of risk-adapted treatment strategies, we have confirmed the adverse impact of del(1p32) in MM and the relevance of its assessment at diagnosis.
2022-12-14 | GSE216574 | GEO
Project description:Purpose Chromosomal aberrations are a hallmark of multiple myeloma but their global prognostic impact is largely unknown. Methods We performed a genome-wide analysis of malignant plasma cells from 192 newly myeloma patients using high-density, single-nucleotide polymorphism (SNP) arrays to identify genetic lesions associated with prognosis. Results Our analyses revealed deletions and amplifications in 98% of cases. Amplifications in 1q and deletions in 1p, 12p, 14q, 16q, and 22q were the most frequent lesions associated with adverse prognosis while recurrent amplifications of chromosomes 5, 9, 11, 15 and 19 conferred a favorable prognosis. Multivariate analysis retained three independent lesions: amp(1q23.3), amp(5q31.3) and del(12p13.31). When adjusted to the established prognostic variables ie t(4;14), and serum beta2-microglobulin (Sb2M), del(12p13.31) remained the most powerful independent marker (P <.0001; hazard ratio = 3.17) followed by Sb2M (P <.0001; hazard ratio = 2.78) and amp(5q31.3) (P =.0005; hazard ratio = 0.37). Cases with amp(5q31.3) alone and low Sb2M had an excellent prognosis (5-year overall survival = 87%) conversely cases with del(12p13.31) alone or amp(5q31.3) and del(12p13.31) and high Sb2M had a very poor outcome (5-year overall survival = 20%). Moreover, integration of SNP mapping and gene expression identified CD27 as potential critical gene responsible for poor prognosis of del(12p) myeloma patients. Conclusion These findings demonstrate the power and accessibility of molecular karyotyping to identify novel strong independent prognostic markers: amp(5q31.3) and del(12p13.31) and to provide insights into putative pathways deregulated in sub classes of cancer patients. Keywords: Human chromosome copy-number alterations study 192 myeloma patients at diagnosis examined with 500K Set Affymetrix chips
2009-08-19 | E-GEOD-12896 | biostudies-arrayexpress
Project description:Purpose Chromosomal aberrations are a hallmark of multiple myeloma but their global prognostic impact is largely unknown. Methods We performed a genome-wide analysis of malignant plasma cells from 192 newly myeloma patients using high-density, single-nucleotide polymorphism (SNP) arrays to identify genetic lesions associated with prognosis. Results Our analyses revealed deletions and amplifications in 98% of cases. Amplifications in 1q and deletions in 1p, 12p, 14q, 16q, and 22q were the most frequent lesions associated with adverse prognosis while recurrent amplifications of chromosomes 5, 9, 11, 15 and 19 conferred a favorable prognosis. Multivariate analysis retained three independent lesions: amp(1q23.3), amp(5q31.3) and del(12p13.31). When adjusted to the established prognostic variables ie t(4;14), and serum beta2-microglobulin (Sb2M), del(12p13.31) remained the most powerful independent marker (P <.0001; hazard ratio = 3.17) followed by Sb2M (P <.0001; hazard ratio = 2.78) and amp(5q31.3) (P =.0005; hazard ratio = 0.37). Cases with amp(5q31.3) alone and low Sb2M had an excellent prognosis (5-year overall survival = 87%) conversely cases with del(12p13.31) alone or amp(5q31.3) and del(12p13.31) and high Sb2M had a very poor outcome (5-year overall survival = 20%). Moreover, integration of SNP mapping and gene expression identified CD27 as potential critical gene responsible for poor prognosis of del(12p) myeloma patients. Conclusion These findings demonstrate the power and accessibility of molecular karyotyping to identify novel strong independent prognostic markers: amp(5q31.3) and del(12p13.31) and to provide insights into putative pathways deregulated in sub classes of cancer patients. Keywords: Human chromosome copy-number alterations study
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Project description:DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q.
2021-03-09 | GSE138438 | GEO
Project description:DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q.
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Project description:DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q. We validated these findings in serially sorted primary AML patient blasts at day 0 and day 8 of DNMTi treatment (within the DECIDER trial).
2021-03-09 | GSE138696 | GEO
Project description:Multiple myeloma is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, multiple myeloma remains incurable and better risk stratification as well as new therapies are therefore highly needed. The proteome of multiple myeloma has not been systematically assessed before and holds the potential to uncover additional insight into disease biology and improved prognostic models. Here, we provide a comprehensive multi-omics analysis including deep tandem mass tags (TMT)-based quantitative global (phospho)proteomics, RNA sequencing and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive multiple myeloma patients treated in clinical trials, plasma cell leukemia, and the premalignancy monoclonal gammopathy of undetermined significance (MGUS), as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells is highly deregulated as compared to healthy plasma cells and is both defined by chromosomal alterations and extensive post-transcriptional regulation. A protein signature was identified that is associated with aggressive disease and more predictive for outcome than cytogenetic-based risk assessment in newly diagnosed multiple myeloma. Integration with functional genetics and single-cell sequencing revealed generally and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include novel potential targets for (immuno)therapies. These findings provide new insights in the biology of multiple myeloma and will be a unique resource for investigating new therapeutic approaches.
2024-07-09 | PXD038437 | Pride
Project description:Multiple myeloma is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, multiple myeloma remains incurable and better risk stratification as well as new therapies are therefore highly needed. The proteome of multiple myeloma has not been systematically assessed before and holds the potential to uncover additional insight into disease biology and improved prognostic models. Here, we provide a comprehensive multi-omics analysis including deep tandem mass tag (TMT)-based quantitative global (phospho)proteomics, RNA sequencing and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive multiple myeloma patients treated in clinical trials, plasma cell leukemia, and the premalignancy monoclonal gammopathy of undetermined significance (MGUS), as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells is highly deregulated as compared to healthy plasma cells and is both defined by chromosomal alterations and extensive post-transcriptional regulation. A protein signature was identified that is associated with aggressive disease and more predictive for outcome than cytogenetic-based risk assessment in newly diagnosed multiple myeloma. Integration with functional genetics and single-cell sequencing revealed generally and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include novel potential targets for (immuno)therapies. These findings provide new insights in the biology of multiple myeloma and will be a unique resource for investigating new therapeutic approaches.
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