Project description:Microarray technology was used to monitor the level of expression of 7,657 human genes in a set of 35 nodal peripheral T-cell lymphomas.

2007-01-30 | E-TABM-191 | biostudies-arrayexpress

Genomic Analysis of Peripheral T-Cell Lymphomas

Project description:<p>Peripheral T-cell lymphomas (PTCLs) are a heterogeneous and poorly understood group of non Hodgkin lymphomas. We aim to identify new genetic alterations in PTCL transformation by using a combination of whole exome sequencing of tumor-normal DNA pairs, RNAseq analysis and targeted deep sequencing of candidate genes. Our data identified highly recurrent mutations in epigenetic factors such as TET2, DNMT3A and IDH2 as well as a new highly prevalent mutation in RHOA, the G17V allele that is present in almost 70% of angioimmunoblastic T-cell lymphomas (AITL) and almost 20% of not otherwise specified PTCL (PTCL NOS) samples. In addition, we describe new and recurrent genetic defects including mutations in FYN, ATM, B2M and CD58 implicating SRC signaling, impaired DNA damage response and escape from immune surveillance processes as key players in the pathogenesis of PTCL.</p>

| phs000689 | dbGaP

Single-nuclei gene expression profiling of human SMARCB1-deficient peripheral T cell lymphomas

Project description:Single-nuclei gene expression profiling of human SMARCB1-deficient peripheral T cell lymphomas

| PRJNA1069666 | ENA

Methylation and gene expression data obtained from Dnmt3b+/- peripheral T-cell lymphomas.

Project description:Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. However, it is poorly understood whether reduced Dnmt3b activities can initiate malignant hematopoiesis. We modulated Dnmt3b activity in vivo by generating Dnmt3b+/− mice expressing one wild-type allele. Here, we analyzed methylation and gene expression in Dnmt3b+/- peripheral T-cell lymphomas (PTCLs).

2020-12-31 | GSE154270 | GEO

Expression data from resting and activated murine T cell as well as murine peripheral T cell lymphomas

Project description:Expression data from resting and activated murine T cell as well as murine peripheral T cell lymphomas

| PRJNA728979 | ENA

B cell Lymphomas present Immunoglobulin Neoantigens

Project description:Immunoglobulin gene rearrangement and somatic hypermutation have the potential to create neoantigens in non-Hodgkin B cell lymphoma. However, the presentation of these putative immunoglobulin neoantigens by B cell lymphomas has not been proven. We used MHC immunoprecipitation followed by liquid chromatography and tandem mass spectrometry (LC-MS/MS) to define antigens presented by follicular lymphomas (FL), chronic lymphocytic leukemias (CLL), diffuse large B cell lymphoma (DLBCL) and mantle cell lymphomas (MCL). We found presentation of the clonal immunoglobulin molecule, including neoantigens by both class I and class II MHC, though more commonly in class II MHC. To determine whether B cell activation could promote presentation of immunoglobulin neoantigens, we used a toll-like receptor 9 (TLR9) agonists to upregulate expression of MHC-II. This resulted in enhanced class II MHC presentation of the immunoglobulin variable region including neoantigens. These findings demonstrate that immunoglobulin neoantigens are presented across most subtypes of B cell lymphomas. Activation of lymphoma cells to upregulate antigen presentation boosts presentation of immunoglobulin neoantigens and represents a strategy for augmenting lymphoma immunotherapies.

2019-01-07 | PXD010808 | Pride

Microarray transcriptome profiling of peripheral T-cell lymphomas in two groups differentiated by Twist and Slug protein expression

Project description:This experiment aimed to study the expression of the transcription factors Twist (TWIST1), ZEB1 and Slug (SNAI2) in peripheral T-cell lymphomas, and to see if these markers could be used to delineate lymphomas with different clinical outcomes and genetic profiles. Twist, ZEB1 and Slug expression was studied using immunohistochemistry in 67 Peripheral T-cell lymphomas and significant correlations to progression-free survival were found. Good prognosis group (high Twist, low Slug) and poor prognosis group (low Twist, high Slug) were formed for gene expression profiling. Microarray transcriptome analysis was performed on 12 cases (6 from each prognosis group) to evaluate differences in gene expression between the groups. Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue blocks using the RNeasy FFPE Kit (Qiagen, Hilden, Germany). Capillary electrophoresis was carried out to check the quality of RNA using the Agilent bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). Transcriptome was analysed using GeneChip Human Gene ST Arrays (Affymetrix, Santa Clara, CA, USA) and the WT Pico Kit (Affymetrix Santa Clara, CA, USA) in accordance with the manufacturer’s instructions. Chipster CSC software (ver 3.11) was used to process the data files.

2019-08-30 | E-MTAB-6401 | biostudies-arrayexpress

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