Ontology highlight
ABSTRACT:
PROVIDER: PRJNA727804 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14457300_1.fastq.gz | Fastqsanger.gz | |||
| SRR14457300_2.fastq.gz | Fastqsanger.gz | |||
| SRR14457301_1.fastq.gz | Fastqsanger.gz | |||
| SRR14457301_2.fastq.gz | Fastqsanger.gz | |||
| SRR14457302_1.fastq.gz | Fastqsanger.gz |
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Project description:Angiogenesis plays a key role in tumor metastasis. Many genes may act in this process including formation of vessels, immune evasion,etc. Different gene expression profiles between lymphoma endothelium cells and reactive lymph node-derived endothelium cells may uncover these genes. And intensive mechanism researches on such key genes may explain the mechanisim of tumor-specific angiogenesis and help to explore effective treatment strategies to prevent/reverse tumor metastasis. We use microarrays to detail gene expression profiles of human lymphoma endothelium and reactive lymph node-derived endothelium. Lymph nodes were taken from surgery samples of cases pathologically diagnosed DLBCL (diffuse large B-cell lymphoma), PTL (peripheral T cell lymphoma) and reactive lymph nodes. The pure endothelium cells were isolated by LCM after immunohistochemical staining of CD34. We found Tim-3 was preferentially expressed on lymphoma-derived ECs via different expression profiles between lymphoma ECs and reactive lymph node-derived ECs. Intensive researches were carried out on Tim-3-expressing -ECs and we found that Tim-3 -expressing-Ecs may play important role on EC-mediated tumor evasion.
2010-01-14 | E-GEOD-19882 | biostudies-arrayexpress
Project description:CAR T-cell therapy has led to tremendous successes in the treatment of B-cell malignancies. However, 30%-50% of treated patients relapse – often with reduced target antigen expression. We report that anti-CD19 CAR T-cells cause a rapid reduction of CD19 expression within hours in CAR-T exposed CD19+ B-ALL cells. Initially, anti-CD19 CAR T-cells cause CD19 clusters at the T-cell – leukemia cell interface followed by CD19 internalization and decreased CD19 surface expression. Subsequently, CD19 expression is repressed by transcriptional rewiring. Using single-cell RNA-seq and single-cell ATAC-seq we demonstrate that a subset of CD19low cells that are refractory to CAR T-cell killing employ transcriptional programs of physiological B-cell activation and germinal center reaction in order to sustain decreased CD19 expression. Inhibiting B-cell activation programs with the BTK inhibitor ibrutinib increased the cytotoxic efficacy of anti-CD19 CAR T-cells without effecting CAR T-cell viability. These results demonstrate transcriptional plasticity as an underlying mechanism of CAR T-resistance and highlight the importance of combining CAR T-cell therapy with targeted therapies that aim to overcome this plasticity.
2022-06-09 | GSE176418 | GEO
Project description:Individualized diagnosis prediction classifiers were successfully constructed through expression profiling of a total of 8,644 genes in 49 patients with relapse/refractory diffuse large B cell lymphoma, prospectively treated in a randomized trial. keyword(s): Diagnosis prediction
2011-09-29 | GSE26812 | GEO
Project description:Individualized diagnosis prediction classifiers were successfully constructed through expression profiling of a total of 8,644 genes in 49 patients with relapse/refractory diffuse large B cell lymphoma, prospectively treated in a randomized trial. keyword(s): Diagnosis prediction All lymphoma cases were predicted as belonging either to germical center B-cell like DLBCL or activated B cell like DLBCL based on the expression of a set of 54 genes (140 probes).
2011-09-28 | E-GEOD-26812 | biostudies-arrayexpress
Project description:<p>Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy for relapsed or refractory (r/r) large B-cell lymphoma (LBCL) results in durable response in only a subset of patients. MYC overexpression in LBCL tumors is associated with poor response to treatment. We tested whether a MYC-driven polyamine signature, as a liquid biopsy, is predictive of response to anti-CD19 CAR-T therapy in patients with r/r LBCL. Elevated plasma acetylated polyamines were associated with non-durable response. Concordantly, increased expression of spermidine synthase, a key enzyme which regulates levels of acetylated spermidine, was prognostic for survival in r/r LBCL. A broad metabolite screen identified additional markers which resulted in a 6-marker panel (6MetP) consisting of acetylspermidine, diacetylspermidine and lysophospholipids which was validated in an independent set from another institution as predictive of non-durable response to CAR T therapy. A polyamine centric metabolomics liquid biopsy panel has predictive value for response to CAR-T therapy in r/r LBCL. </p>
2022-10-31 | MTBLS5381 | MetaboLights
Project description:We used DNA microarray technology to assess changes in gene expression after treatment of 11 lymphoma cell lines with epigenetic drugs. We identified genes with upregulated expression in treated cell lines and with downregulated expression in B-cell lymphoma patient samples when compared to normal B cells. CD19+ b cells were isolated from buffy coats from diffrent healthy donors. Gene expression of healthy controls (CD19+ b cells) was used as a normal counterpart for lymphoma samples (GSE4732, GSE10846).
2013-04-18 | E-GEOD-46062 | biostudies-arrayexpress
Project description:Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. Although 60-70% of the patients can be cured with standard chemoimmunotherapy, a substantial number of patients die from the disease due to relapse or primary refractory disease. To better understand the biological processes behind the treatment resistance, we characterized the microRNA (miRNA) expression profiles of matched primary and relapsed DLBCL by next-generation sequencing. A total of 492 known miRNAs were expressed in the DLBCL samples (n=7 pairs). A majority of these showed similar expression at diagnosis and relapse; we identified 24 highly expressed and 177 lowly expressed miRNAs in the DLBCL samples as compared to a control set of non-malignant cells. Interestingly, only 13 miRNAs had differential expression between the primary–relapse pairs. MiRNA-mRNA target pair analysis combined with pathway enrichment analysis revealed the putative targets of differentially expressed miRNAs to be significantly enriched for several cancer-associated pathways that included phosphatidylinositol, MAPK and B-cell receptor signaling, suggesting activation of these pathways during progression. Additionally, Kaplan-Meier survival analyses indicated higher expression of genes from these pathways to be associated with shorter survival in immunochemotherapy-treated patients (n=92). Taken together, our data demonstrate that the miRNA expression profile remains relatively constant during the disease progression, but a small set of differentially expressed miRNAs may contribute to the relapse by regulating key cell survival pathways, thus representing potential novel therapeutic targets.
2018-02-23 | GSE69810 | GEO
Project description:Here we characterize an association between disease progression and DNA methylation in Diffuse Large B cell Lymphoma (DLBCL). By profiling genome-wide DNA methylation at single base-pair resolution in thirteen DLBCL diagnosis-relapse sample pairs, we show DLBCL patients exhibit heterogeneous evolution of tumor methylomes during relapse. We identify differentially methylated regulatory elements and determine a relapse–associated methylation signature converging on key pathways such as transforming growth factor beta (TGF-beta) receptor activity. We also observe decreased intra-tumor methylation heterogeneity from diagnosis to relapsed tumor samples. Relapse-free patients display lower intra-tumor methylation heterogeneity at diagnosis compared to relapsed patients in an independent validation cohort. Furthermore, intra-tumor methylation heterogeneity is predictive of time to relapse. Therefore, we propose that epigenomic heterogeneity may support or drive the relapse phenotype and can be used to predict DLBCL relapse. Using ERRBS, we profiled genome-wide DNA methylation patterns of non-relapse DLBCL tumor samples at diagnosis, relaspe DLBCL patient samples at diagnosis and relaspe.
2015-04-14 | E-GEOD-66329 | biostudies-arrayexpress
Project description:Interventions: Group 1: Patients with relapsed or refractory diffuse large B-cell lymphoma (DLBCL) and patients with relapsed or refractory acute lymphocytic leukemia (ALL) who have been selected for treatment with CD19-targeting CAR-T cells will be recruited. Stool samples are collected at multiple timepoints (before lymphodepletion, before T-cell infusion, and after T-cell infusion).
Primary outcome(s): The main outcome is bacterial alpha diversity according to Simpson (AD) at the time of CAR-T cell therapy, which should be associated with survival within 24 months.
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: treatment
| 2436511 | ecrin-mdr-crc
Project description:Purpose: Despite recent advances in the treatment of patients with aggressive lymphomas, still a significant fraction of patients will succumb to their disease. Thus, novel therapeutic strategies are urgently needed. As the anti-CD20 antibody rituximab and the CD19-targeting antibody tafasitamab share distinct modes of actions, we investigated if dual-targeting of aggressive lymphoma B-cells by combining rituximab and tafasitamab might increase cytotoxic effects. Experimental Design: Antibody single and combination efficacy was determined investigating different modes of action including direct cytotoxicity, antibody-dependent cell-mediated cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) in vitro and in vivo models of aggressive B-cell lymphoma comprising diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). Results: Overall, three different sensitivity profiles to antibody monotherapy or combination treatment were observed in in vitro models: while 2/11 cell lines were primarily sensitive to tafasitamab and 2/11 were predominantly sensitive to rituximab treatment, the combination of tafasitamab and rituximab resulted in enhanced cell death in 7/11 cell lines in at least one mode of action. Treatment with either antibody or the combination resulted in decreased expression of the oncogenic transcription factor MYC and inhibition of AKT signaling which mirrored the cell line-specific sensitivities to direct cytotoxicity. At last, the combinatorial approach of the two antibodies resulted in a synergistic survival benefit in a PBMC-humanized Ramos NOD/SCID mouse model. Conclusions: This study demonstrates that the combination of tafasitamab and rituximab improves efficacy compared to antibody mono treatment in models of aggressive B-cell lymphoma in vitro and in vivo. Translational Relevance: The immunochemotherapy of rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) remains the standard of care for newly diagnosed DLBCL patients. However, 30-40% of patients are refractory or relapse after initial response to the immunochemotherapy, indicating a high-unmet medical need for these patients. Tafasitamab and rituximab target the B-cell surface proteins CD19 and CD20, respectively, and both antibodies feature overlapping modes of action , namely direct cytotoxicity, ADCC and ADCP. In this study, we show that the combination of tafasitamab and rituximab had additive and synergistic efficacy both in vitro and in vivo. Our findings shed new light on the underlying mechanism of the combination of both antibodies and lay the ground to translate the results into improved outcome for patients with aggressive lymphoma in future clinical trials.
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