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| Status |
Public on Dec 13, 2018 |
| Title |
Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [THE1B RACE-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported that a member of the THE1B class of LTR elements in classical Hodgkin Lymphoma (cHL) acted as a promoter for the growth factor receptor gene CSF1R and that expression of this gene is required for tumor survival. However, to which extent and how such elements participate in globally shaping the unique cHL gene expression program is unknown. To address this question we mapped the genome-wide activation of THE1-LTRs in cHL cells using a targeted next generation sequencing approach (RACE-Seq). Integration of these data with global gene expression data from cHL and control B cell lines showed a unique pattern of LTR activation impacting on gene expression, including genes associated with the cHL phenotype. We also show that global LTR activation is induced by strong inflammatory stimuli. Together these results demonstrate that LTR activation provides an additional layer of gene deregulation in classical Hodgkin lymphoma and highlight the potential impact of genome-wide LTR activation in other inflammatory diseases.
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| Overall design |
Sequencing of THE1B 5’ RACE assays in HL, WT NHL, NHL+PMA, NHL+IKK+-dox, NHL+GFP+dox cell lines
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| Contributor(s) |
Edginton-White B, Cauchy P, Assi SA, Hartmann S, Riggs AG, Mathas S, Cockerill PN, Bonifer C |
| Citation(s) |
30546079 |
| Submission date |
Sep 21, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Pierre Daniel Cauchy |
| E-mail(s) |
cauchy@ie-freiburg.mpg.de
|
| Phone |
+49 (0)761 270-77576
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| Organization name |
University Medical Center Freiburg
|
| Department |
Zentrum für Translationale Zellforschung
|
| Lab |
AG Onco-Immunology
|
| Street address |
Breisacher Str. 115
|
| City |
Freiburg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (27)
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| This SubSeries is part of SuperSeries: |
| GSE120331 |
Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma |
|
| Relations |
| BioProject |
PRJNA492490 |
| SRA |
SRP162357 |
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