ILyAD (Indolent Lymphoma And vitamin D)
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ABSTRACT:
PROVIDER: PRJNA1055198 | ENA |
REPOSITORIES: ENA
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Project description:ILyAD (Indolent Lymphoma And vitamin D)
| PRJNA1055197 | ENA
Project description:Mantle cell lymphoma (MCL) is an aggressive neoplasm with poor outcome. However, some patients have an indolent disease (iMCL) and may not require intensive treatment at initial diagnosis. Diagnostic criteria to recognize these patients are not available. We hypothesized that the analysis of the genetic and expression features of the tumors may help to identify patients with an indolent clinical evolution and provide biomarkers that could be used in the clinical setting. Seven patients with an iMCL that did not require chemotherapy for more than 2 years were compared to 15 conventional MCL (cMCL) that needed systemic therapy at diagnosis. MCL were compared with other leukemic lymphoid neoplasms including 17 CLL, 7FL, HCL and 2HCLv.
2010-03-04 | E-GEOD-16455 | biostudies-arrayexpress
Project description:Of the 142 patients enrolled in Study CHRONOS-1, an open-label, single-arm, Phase II study evaluating the efficacy and safety of single-agent copanlisib in patients with relapsed or refractory, indolent B-cell lymphoma (NCT01660451; Part B), 96 archival formalin-fixed paraffin-embedded tumor tissues were collected under relevant consent and available for tumor macro-dissection, mRNA extraction and gene expression profiling using Affymetrix GeneChip Gene ST 1.0 Arrays (AltheaDx, Inc., San Diego, CA, USA). Of these, only 78 samples were with high quality and passed Affymetrix positive versus negative controls AUC ≥ 0.62. Affymetrix CEL files were processed with RMA (R package affy) using a custom CDF from Brainarray (version 20.0.0). 71 patients with indolent non-Hodgkin lymphoma (iNHL), including 54 with follicular lymphoma (FL), had both response data and evaluable gene expression data with high quality array data sets (array positive versus negative controls AUC ≥ 0.62) and were included in this biomarker analysis. In this study, with the exception of subject # 16349B-53, for which expression values were averaged from three equal aliquots that were amplified and scanned on 3 separate days in order to control for day-to-day batch effect, there was only one sample per subject. Affymetrix raw data (CEL files) and the gene expression matrix generated with RMA for the 78 high quality tumor samples are submitted.
2017-12-01 | E-MTAB-6088 | biostudies-arrayexpress
Project description:Mantle cell lymphoma (MCL) is an aggressive neoplasm with poor outcome. However, some patients have an indolent disease (iMCL) and may not require intensive treatment at initial diagnosis. Diagnostic criteria to recognize these patients are not available. We hypothesized that the analysis of the genetic and expression features of the tumors may help to identify patients with an indolent clinical evolution and provide biomarkers that could be used in the clinical setting.
2010-03-04 | GSE16455 | GEO
Project description:Primary outcome(s): a)To study the association of baseline vitamin D level with Overall Response Rate(ORR) in patients with newly diagnosed lymphoma.
b)To study the effect of vitamin D supplementation on Overall Response Rate (ORR) in the vitamin D deficient patients with newly diagnosed lymphoma.
Timepoint: August 2018 to May 2020
| 2588839 | ecrin-mdr-crc
Project description:BACKGROUND AND OBJECTIVES: Low-grade B-cell lymphomas include several subtypes of tumors with different degrees of histological, biological or clinical features. Differential diagnosis is frequently compromised by the lack of specific cytogenetic or molecular features. As a consequence, therapies remain in many lymphoma types largely based in common protocols with largely variable success. Our objectives were to describe and to compare the genomic profile of a series of samples from the most prevalent low-grade lymphoma subtypes; all of them systematically analyzed with the same approach. DESIGN-AND-METHODS: We carried out a high-resolution genomic DNA analysis (44K probes) in 87 low grade B cell lymphoma tumor samples that unambiguously presented the clinical picture, analytical features, and peripheral blood morphology and phenotype described for each entity. RESULTS: The genomic integrity of the samples was heavily compromised (80% of the tumors presented at least one aberration). This phenomenon also involved lymphoplasmocytic and marginal zone lymphomas that have not been previously studied by this genomic approach. New aberrations have been described for almost every subtype. We have also generated reports of the extension of the genomic instability, detecting distinct patterns of genomic instability within subtypes. INTERPRETATION-AND-CONCLUSIONS: The genomic profile of each subgroup showed substantive differences. The bioinformatic analysis of the data detected a set of new aberrations which were present in the majority of the subgroups and that pointed out to specific pathways, such as NF-kB (gains that involved REL, BCL11A and COMMD1) or DNA repair checkpoint pathways (deletion of 16q24 involving CDT1). Keywords: Comparative Genomic Hybridization - array; Genomic Instability
2008-01-01 | GSE8918 | GEO
Project description:Follicular lymphoma is the most common indolent non-Hodgkin's lymphoma involving germinal centre B cells, with a subset of patients undergoing transformation to a diffuse large B-cell lymphoma (DLBCL) morphology for which the clinical outcomes are poor. To elucidate the differences in copy number profiles between FL and tFL groups, we performed Affymetrix SNP 6.0 Array analysis on 31 paired FL-tFL cases. We wanted to identify and compare recurrent somatic copy number alterations (CNAs) between the two groups (FL vs. tFL). In addition, the concordance and discordance in the copy neutral loss of heterozygosity (cnLOH) between the two groups were also investigated to identify recurrent target gene regions.
2013-10-01 | GSE42525 | GEO
Project description:Primary cutaneous B-cell lymphomas comprise a heterogeneous group of extranodal non-Hodgkin lymphomas. While primary cutaneous diffuse large B cell lymphoma - leg type (pcDLBCL-LT) is highly aggressive, the two other subtypes, primary cutaneous follicle centre lymphoma (pcFCL) and primary cutaneous marginal zone lymphoma (pcMZL), also termed primary cutaneous marginal zone lymphoproliferative disorder, usually follow an indolent disease course. To better characterise these most common types of primary cutaneous B cell lymphomas, we performed a comprehensive, single-cell RNA-sequencing based analysis of biopsies from pcFCL, pcMZL, and pcDLBCL-LT skin lesions, in comparison to samples from benign reactive B-cell rich lymphoid proliferation (rB-LP) lesions, as well as gastric MALT lymphoma, nodal FCL and nodal DLBCL. Our data show that all non-aggressive forms of primary cutaneous B cell lymphoma, as well as rB-LP, show a persistent germinal centre reaction, with all accessory germinal centre-support cells and continuous somatic hypermutation within the expanded B cell clone. By contrast, malignant clones of pcDLBCL-LT lesions and gastric MALT showed absence of all of these features. Our data further shows that pcMZL originates from naïve and not post-germinal centre B cells as currently believed and observed in gastric MALT. The modest clonal expansion in pcMZL may therefore be the result of a recognition of a distinct (unknown) antigen. Conversely, in pcFCL, B cells show an (antigen-driven) expansion of a single clone with a germinal centre phenotype, presumably through acquisition of a driving mutation. The lack of further differentiation of B cells in pcFCL, in contrast to nodal FCL, may explain its indolent clinical course. Our data indicates that in contrast to highly aggressive cutaneous B cell lymphoma (pcDLBCL-LT), pcMZL, and pcFCL, similar to rB-LP are characterised by a functional germinal centre reaction driven by antigen recognition and supports the classification of pcMZL as a lymphoproliferative disease.
2025-12-30 | GSE218861 | GEO
Project description:Profiling of indolent and aggressive mammary lesions
| PRJNA680303 | ENA
Project description:Vitamin D deficiency has been associated with decreased overall survival in patients with diffuse large B-cell lymphoma treated with rituximab. Natural killer cell-mediated antibody-dependent cytotoxicity is one of the main mechanisms of action of rituximab, and it has been shown to be enhanced after in vivo vitamin D supplementation. We aimed to explore molecular mechanisms behind these findings using whole transcriptome analysis of natural killer cells after vitamin D supplementation
2023-08-30 | GSE239308 | GEO