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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| Overall design |
RNA-seq; four conditions in quadruplicates, 16 samples in total.
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| 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
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| Department |
Department of Medical Sciences
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| Street address |
Husargatan 3
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| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
SE-752 37 |
| Country |
Sweden |
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| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL22245 |
Illumina HiSeq 2500 (Homo sapiens; Mus musculus) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA388663 |
| SRA |
SRP108358 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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