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CDNA microarray assay of lymph node biopsies diagnosed as lymphoma or as reactive tissue

ABSTRACT: Gene expression profiling of biopsied human lymph node (LN) tissue comparing each patient sample against mobilised peripheral blood stem cells (PBSC), the reference channel Evaluate whether gene expression microarray can diagnose lymph node biopsies as reactive or as one of three main types of lymphoma: classical Hodgkin’s lymphoma (cHL), diffuse large B cell lymphoma (DLBCL) or follicular lymphoma (FL).

ORGANISM(S): Homo sapiens

PROVIDER: GSE23647 | GEO | 2012/11/28

SECONDARY ACCESSION(S): PRJNA130961

REPOSITORIES: GEO

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cDNA microarray assay of lymph node biopsies diagnosed as lymphoma or as reactive tissue

Project description:Gene expression profiling of biopsied human lymph node (LN) tissue comparing each patient sample against mobilised peripheral blood stem cells (PBSC), the reference channel Evaluate whether gene expression microarray can diagnose lymph node biopsies as reactive or as one of three main types of lymphoma: classical Hodgkin’s lymphoma (cHL), diffuse large B cell lymphoma (DLBCL) or follicular lymphoma (FL). Two condition experiment, LN vs mobilised PBSC, 116 cases assayed, 1 replicate per array

2012-11-28 | E-GEOD-23647 | biostudies-arrayexpress

Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients

Project description:Despite advances in Hodgkin lymphoma (HL) treatment, about 20% of patients still die due to progressive disease. Current prognostic models predict treatment outcome with imperfect accuracy, and clinically relevant biomarkers are yet to be established that improve upon the International Prognostic Scoring (IPS) system. We analyzed 130 frozen diagnostic lymph node biopsies from classical HL patients by gene expression profiling to describe cellular signatures correlated with treatment outcome. Diagnostic fresh-frozen lymph node specimens from 130 patients with cHL were selected for GEP from the tissue archive at the British Columbia Cancer Agency and the University of Nebraska Medical Center according to the following criteria: primary diagnosis of cHL following central review, representative lymph node tissue (at least 1 cmÂ² area in tissue sections), HIV-negative status and first line treatment with systemic chemotherapy ABVD (doxorubicin, bleomycin, vinblastine and dacarbazine) or ABVD-like regimen with or without radiation therapy if indicated or, in the case of seven patients with limited-stage disease, wide field radiation.

2010-03-08 | E-GEOD-17920 | biostudies-arrayexpress

The status of lymph node of resectable distant metastaticcolorectal cancer (stage Ⅳ) as a prognostic predictor

Project description:Both the univariate analysis and multivariate analysis showed that the status of primary lymph node was the strongest predict factor. The subgroup analysis confirmed that the lymph node metastasis was associated to worse prognosis only in stage T3 and T4, rather than in stage T1 and T2. We firstly proposed the hypothesis that the status of lymph node reflected delayed diagnose of the disease, rather than the biological behavior of “seed”. The mRNA profile showed that there was minimal difference between lymph node positive and negative subgroups. The status of lymph node reflected delayed diagnose of the disease, rather than the biological behavior of “seed”.

2016-04-25 | GSE63596 | GEO

Classical Hodgkin’s Lymphoma: Molecular evidence for specific alterations of circulating T lymphocytes

Project description:Gene expression profiles were performed from CD3+ T cells isolated from peripheral blood samples of untreated patients with cHL versus 2 control groups consisting of healthy donors and patients with sarcoidosis. Keywords = Hodgkin’s Lymphoma Keywords = T cell Keywords = immune regulation Keywords: repeat sample

2005-07-13 | GSE2657 | GEO

Analyzing primary Hodgkin and Reed-Sternberg cells to capture the molecular and cellular pathogenesis of classical Hodgkin lymphoma

Project description:The pathogenesis of classical Hodgkin lymphoma (cHL), the most common lymphoma in the young, is still enigmatic, largely because its Hodgkin and Reed-Sternberg (HRS) tumor cells are rare in the involved lymph node and therefore difficult to analyze. Here, by overcoming this technical challenge and performing for the first time a genome-wide transcriptional analysis of microdissected HRS cells in comparison to other B-cell lymphomas, cHL lines and normal B-cell subsets, we show that they differ extensively from the usually studied cHL cell lines, that the lost B-cell identity of cHLs is not linked to the acquisition of a plasma cell-like gene expression program, and that Epstein-Barr virus infection of HRS cells has a minor transcriptional influence on the established cHL clone. Moreover, although cHL appears a distinct lymphoma entity overall, HRS cells of its histological subtypes diverged in their similarity to other related lymphomas. Unexpectedly, we identified two molecular subgroups of cHL associated to differential strengths of the transcription factor activity of the NOTCH1, MYC and IRF4 proto-oncogenes. Finally, HRS cells display deregulated expression of several genes potentially highly relevant to lymphoma pathogenesis, including silencing of the apoptosis-inducer BIK and of INPP5D, an inhibitor of the PI3K-driven oncogenic pathway. The present study complements the GSE12453 and GSE14879 records by adding the following 10 samples: 5 primary tumor samples and 5 cell line samples. The 5 primary tumor samples represent 1000-2000 neoplastic cells microdissected from frozen biopsies of 5 cases of primary mediastinal B-cell lymphoma (PMBL). The 5 cell line samples represent 500-1000 living neoplastic cells isolated by fluorescence-activated cell sorting from growing cultures of the classical Hodgkin lymphoma (cHL) cell lines L1236, L428, KMH2 and HDLM2 and the lymphocyte-predominant Hodgkin lymphoma (lpHL) cell line DEV.

2012-09-17 | E-GEOD-40160 | biostudies-arrayexpress

Analyzing primary Hodgkin and Reed-Sternberg cells to capture the molecular and cellular pathogenesis of classical Hodgkin lymphoma

2012-09-17 | GSE40160 | GEO

Homo sapiens

Project description:Follicular lymphoma lymph node

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Clinical proteomics analysis using Data Independent Acquisition-Mass Spectrometry (DIA-MS) identified classifiers for molecular characterization of Lymphoma

Project description:In this study, we conducted a proteomics analysis on 109 fresh-frozen lymph node samples from clinical patients, covering a comprehensive suite of lymphoma subtypes including B-NHL, T-NHL, HL, Lymphadenitis, Tumor metastatic lymph node (TLN), and Non-neoplastic lymph node (TNM: N0).

2020-01-15 | PXD017096 | iProX

Single-cell RNA-seq data of the tumor microenvironment of lymphocyte-rich Hodgkin lymphoma and other Hodgkin lymphoma subtypes

Project description:Lymphocyte-rich classic Hodgkin lymphoma (LR-CHL) is a rare subtype of Hodgkin lymphoma. Recent technical advances have allowed for the characterization of specific crosstalk mechanisms between malignant Hodgkin Reed-Sternberg (HRS) cells and different normal immune cells in the tumor microenvironment (TME) of CHL. However, the TME of LR-CHL has not yet been characterized at single cell resolution. Here, using single cell RNA sequencing, we examined the immune cell profile of 8 cell suspension samples of LR-CHL in comparison to 20 samples of the mixed cellularity (9 cases) and nodular sclerosis (11 cases) subtypes of CHL, as well as 5 reactive lymph node controls.

| EGAS00001005541 | EGA

Expression data from human lymphoma endothelium and reactive lymph node-derived endothelium

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

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