Gene expression analysis of hematological malignancies and healthy (non-)hematopoietic cell types

·发布 2016年9月1日 ·更新 2016年9月12日

166

样本数

166

实验数

芯片平台

相关文献

实验描述

Cellular immunotherapy has proven to be effective in the treatment of hematological cancers by donor lymphocyte infusion after allogeneic hematopoietic stem cell transplantation and more recently by targeted therapy with chimeric antigen or T-cell receptor-engineered T-cells. However, dependent on the tissue distribution of the antigens that are targeted, anti-tumor responses can be accompanied by undesired side effects. Therefore, detailed tissue distribution analysis is essential to estimate efficacy and toxicity of candidate targets for immunotherapy of hematological malignancies. In this study, we performed microarray gene expression analysis of hematological malignancies of different origins, healthy hematopoietic cells and various non-hematopoietic cell types from organs that are often targeted in detrimental immune responses after allogeneic stem cell transplantation leading to graft-versus-host disease. Non-hematopoietic cells were also cultured in the presence of IFN-γ to analyze gene expression under inflammatory circumstances. Gene expression was investigated by Illumina HT12.0 microarrays and quality control analysis was performed to confirm the cell-type origin and exclude contamination of non-hematopoietic cell samples with peripheral blood cells. Microarray data were validated by quantitative RT-PCR showing strong correlation between both platforms. Detailed gene expression profiles were generated for various minor histocompatibility antigens and B-cell surface antigens to illustrate the value of the microarray dataset to estimate efficacy and toxicity of candidate targets for immunotherapy. In conclusion, our microarray database provides a relevant platform to analyze and select candidate antigens with hematopoietic (lineage)-restricted expression as potential targets for immunotherapy of hematological cancers. Microarray gene expression analysis was performed on hematological malignancies of different origins and their healthy hematopoietic counterparts as well as on healthy non-hematopoietic cell types from organs that are often targeted in Graft-versus-Host Disease (166 samples in total). Various non-hematopoietic cell types were cultured in the presence of IFN-γ or T-cell culture supernatant to allow gene expression analysis under inflammatory conditions. Malignant and healthy hematopoietic cells were isolated by flow cytometry based on expression of specific surface markers and healthy non-hematopoietic cell types were isolated or cultured from tissue biopsies or surgically removed specimen. Various non-hematopoietic cell types were in vitro cultured for 4 days in the presence of IFN-γ or T-cell culture supernatant to mimic inflammation. The dataset allows comparison of gene expression between hematological malignancies and healthy non-hematopoietic cell types to estimate efficacy and toxicity of immunotherapeutic targets for hematological malignancies. Total RNA was isolated from (malignant) hematopoietic cells isolated by flow cytometry based on expression of specific surface markers and from healthy non-hematopoietic cell types isolated or cultured from tissue biopsies or surgically removed specimen. From various non-hematopoietic cell types, total RNA was also isolated after 4 days of in vitro culture in the presence of IFN-γ or T-cell culture supernatant.

参考文献

Integrated Whole Genome and Transcriptome Analysis Identified a Therapeutic Minor Histocompatibility Antigen in a Splice Variant of ITGB2.

Pont MJ, van der Lee DI, van der Meijden ED, van Bergen CA, Kester MG, Honders MW, Vermaat M, Eefting M, Marijt EW, Kielbasa SM, Hoen PA, Falkenburg JH, Griffioen M

PMID: 26964570

芯片平台

A-MEXP-1171

Illumina HumanHT-12 v3.0 Expression BeadChip（97 例）

A-GEOD-10558

Illumina HumanHT-12 V4.0 expression beadchip（69 例）

样本属性

cell line

AML-193, Daudi, HELA TK-, Jurkat, Jurkat-76, K562, Raji, T2, THP-1

cell type

Acute lymphoblastic leukemia cells, Acute myeloid leukemia cells, B-Cells, Chronic lymphoblastic leukemia cells, Chronic myeloid leukemia cells, Colon epithelial cells, Cornea epithelial cells, Cornea stroma cells, Fibroblasts, hematopoietic stem cell, Hepatocytes, Immature dendritic cells, Intrahepatic biliary epithelial cells, Juvenile myelomonocytic leukemia (JMML) formerly referred to as juvenile chronic myeloid leukemia, Keratinocytes, Mature dendritic cells, mature dendritic cells, Melanocytes, monocytes, mononuclear cell, Multiple myeloma cells, PHA-T blasts, Primary bronchial epithelial cells, Proximal tubular epithelial cells, Small intestine epithelial cells, T-cells, Type 2 macrophages, Type I macrophages, umbilical vein endothelial cell

organism

Homo sapiens

organism part

bile duct, bone marrow, cervix, colon, eye, G-CSF mobilized peripheral blood, kidney, liver, lung, lymphoblast, peripheral blood, peripheral blood/bone marrow, skin, small intestine, umbilical cord

protocol

cultured from a skin derived biopsy in DMEM with low glucose, cultured from a skin derived biopsy in DMEM with low glucose and IFN-γ (100 IU/mL) for 4 days, cultured from a skin derived biopsy in DMEM with low glucose, cultured with IFN-γ, cultured from a skin derived biopsy in DMEM with low glucose, cultured with IFN-γ for 4 days, cultured from a skin derived biopsy in DMEM with low glucose, cultured with T cell culture supernatant, cultured from CD14 isolated monocytes with GM-CSF for 7 days, cultured from CD14 isolated monocytes with M-CSF for 7 days, cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days, cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days. TNF-α, IL-1β, IL-6, prostaglandin E2 and IFN-γ was added during the final 2 days for maturation., cultured from surgically removed nevi in F10 supplemented medium, cultured from surgically removed nevi in F10 supplemented medium and IFN-γ (100 IU/mL) for 4 days, cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone, cultured in serum-free DMEM/HAM-F12 with insulin, transferrin, selenium, triiodothyronine, epidermal growth factor and hydrocortisone and IFN-γ (100 IU/mL) for 4 days, generated by stimulating PBMC with IL-2 and PHA, immortalized by Epstein Barr Virus, isolated by flow cytometry based on CD14 surface expression, isolated by flow cytometry based on CD19 surface expression, isolated by flow cytometry based on CD3 surface expression, isolated by flow cytometry based on CD34 surface expression, isolated from bone marrow after Ficoll-Isopaque separation, isolated from colon tissue biopsies and cultured in Matrigel and advanced DMEM-F12 with murine EGF, murine noggin, human R-spondin-1, recombinant human Wnt-3A, gastrin, nicotinamide, A83-01, SB202190, isolated from cornea and cultured in CnT-20 medium, isolated from cornea and cultured in DMEM/HAM-F12, isolated from liver, isolated from liver and cultured on collagen I-coated plates in William's Medium E with insulin, transferrin, selenium and hydrocortisone, isolated from lung cultured under submerged conditions and mucociliary differentation was achieved by culture at the air-liquid interface, isolated from peripheral blood after Ficoll-Isopaque separation, isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and CD14 surface expression, isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and lack of CD14 surface expression, isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression, isolated from samples with >30% plasma cells (range 30-95%) based on CD38 surface expression, isolated from samples with >5% hematopoietic progenitor cells based on CD34 surface expression, isolated from samples with >85% leukemic blasts (range 85-98%) based on CD19 surface expression, isolated from samples with >90% malignant cells based on CD19 and CD5 surface expression, isolated from small intestine tissue biopsies and cultured in Matrigel and advanced DMEM-F12 with murine EGF, murine noggin, human R-spondin-1, recombinant human Wnt-3A, gastrin, nicotinamide, A83-01, SB202190, isolated from umbilical cords and cultured in EGM-2 bullit kit supplemented EGM-2 medium, isolated from umbilical cords and cultured in EGM-2 bullit kit supplemented EGM-2 medium and IFN-γ (100 IU/mL) for 4 days

实验信息

登记号

E-GEOD-76340

GEO 编号

GSE76340

实验类型

transcription profiling by array

物种

Homo sapiens

发布日期

2016年9月1日

更新日期

2016年9月12日

提交者

Marieke Griffioen、 Margot J Pont、 Marieke Griffioen

外部链接

ArrayExpress 原始页 NCBI GEO：GSE76340

分析服务

Gene expression analysis of hematological malignancies and healthy (non-)hematopoietic cell types

联系地址

微信公众号