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Series GSE99501 Query DataSets for GSE99501
Status Public on Jun 12, 2018
Title Mixed-species RNAseq analysis of human lymphoma cell adhesion to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of MCL and CLL patients.
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Background:A subset of hematological cancer patients is refractory to treatment or suffer relapse, due in part to minimal residual disease, whereby some cancer cells survive treatment via microenvironment interaction. Cell-adhesion mediated drug resistance is an important mechanism, whereby cancer cells receive survival signals via interaction with e.g. stromal cells. No genome-wide studies of in vitro systems have yet been performed to compare gene expression in different cell subsets within a co-culture and cells grown separately. Results: Using RNAseq and species-specific read mapping, we compared transcript levels in human Jeko-1 mantle cell lymphoma (MCL) cells stably adhered to stromal cells or in suspension within a co-culture and in separate culture as well as mouse MS-5 stromal cells in co-culture or in separate culture. 1050 differentially expressed transcripts in adherent MCL cells identified 24 functional categories that together represent four main functional themes, anti-apoptosis, B-cell signaling, cell adhesion/migration and early mitosis. Comparison with previous MCL and chronic lymphocytic leukemia (CLL) patient data identified 116 genes that are differentially regulated in all three studies. From these genes we suggest a gene signature (CCL3, CCL4, DUSP4, ETV5, ICAM1, IL15RA, IL21R, IL4I1, MFSD2A, NFKB1, NFKBIE, SEMA7A, TMEM2) characteristic of cells undergoing cell-adhesion mediated microenvironment signaling in MCL/ CLL cells. Conclusions: The model system developed and characterized here together with suggested signature genes can be used in future studies of pathways that mediate increased cancer cell survival and drug resistance mechanisms.
Overall design RNA-seq; four conditions in quadruplicates, 16 samples in total.
Contributor(s) Arvidsson G, Wright A, Sander B
Citation(s) 29449436, 32370190
Submission date May 31, 2017
Last update date Sep 09, 2021
Contact name Gustav Arvidsson
Organization name Uppsala Universitet
Department Department of Medical Sciences
Street address Husargatan 3
City Uppsala
State/province Uppsala
ZIP/Postal code SE-752 37
Country Sweden
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (16)
GSM2644880 MS-5_1
GSM2644881 SEP_1
GSM2644882 ADH_1
BioProject PRJNA388663
SRA SRP108358

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Supplementary file Size Download File type/resource
GSE99501_hg19_count_table.csv.gz 542.7 Kb (ftp)(http) CSV
GSE99501_mm10_count_table.csv.gz 477.3 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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