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| Status |
Public on Jan 27, 2016 |
| Title |
Gene expression analysis in the peripheral blood of baboons for early prediction of the later occurring hematological ARS using human Agilent SurePrint G3 Microarrays, v2 (8x60K) |
| Platform organism |
Homo sapiens |
| Sample organism |
Papio papio |
| Experiment type |
Expression profiling by array
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| Summary |
Based on gene expression changes measured in the peripheral blood within the first 2 days after irradiation we aimed to predict the later occurring hematological acute radiation syndrome (HARS). Altogether 18 baboons were irradiated simulating different patterns of partial body irradiation or total body irradiation corresponding to an equivalent dose of 2.5 or 5 Gy. According to changes in blood cell counts (BCC) they were either suffering from H1-2 (n=4) or H2-3 (n=13) degree HARS. One animal was deleted from analysis due to unusual changes in BCC and early death. Blood samples taken before irradiation served as H0 (n=17). A two stage study design was applied. During first stage we screened the whole genome (mRNA microarrays) using one part of the samples (H0 n=5, H1-2 n=4, H2-3 n=5). Candidate genes differentially up- or down-regulated during the first two days after irradiation were forwarded for validation in stage II using the remaining samples and changing the methodology (qRT-PCR). Differential gene expression was defined as a significant (p<0.05) and > 2-fold difference in gene expression over H0. From about 20,000 genes on average 46% appeared expressed. At H2-3 and day 1 about 2-3 times more genes appeared up-regulated (1,418 versus 550) or down-regulated (1,603 versus 735) compared to H1-2 an effect which became pronounced at day 2 while the number of differentially expressed genes decreased. These genes did show an enrichment regarding biological processes coding for immune system processes, natural killer cell activation and immune response (p= 1xE-06 up to 9xE-14). Based on the p-value, the height and constant differential gene expression over time, 89 candidate genes were selected for validation using qRT-PCR. Finally, 22 genes for identification of H1-3 and 7 genes for identification of H2-3 were confirmed using qRT-PCR. For H1-3 most genes were constantly and 3-5 fold down-regulated relative to H0 over both days, but some genes appeared 10.3-fold (VSIG4) or even 30.7-fold up-regulated (CD177) over H0. For H2-3 some genes appeared 4-7-fold up-regulated relative to H0 (RNASE3, DAGLA, ARG2), but other genes showed a strong and 14-33-fold down-regulation relative to H0 (WNT3, POU2AF1, CCR7). Each of the genes allowed an almost complete separation of HARS categories. Taken together, clinical relevant HARS can be independently predicted with each of 29 radiation-induced genes examined in the peripheral blood of baboons within the first two days after irradiation.
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| Overall design |
A two stage study design was applied. During first stage we screened the whole genome (mRNA microarrays) using one part of the samples (H0 n=5, H1-2 n=4, H2-3 n=5). Candidate genes differentially up- or down-regulated during the first two days after irradiation were forwarded for validation in stage II using the remaining samples and changing the methodology (qRT-PCR, n=35). This database contains the Agilent micorarray data only.
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| Contributor(s) |
Port M, Herodin F, Valente M, Drouet M, Lamkowski A, Majewski M, Abend M |
| Citation(s) |
27333084, 30337559, 28257102 |
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| Submission date |
Jan 26, 2016 |
| Last update date |
Jul 10, 2019 |
| Contact name |
Michael Abend |
| E-mail(s) |
michaelabend@bundeswehr.org
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| Phone |
+49-89-992692- 2280
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| Organization name |
Bundeswehr Institute of Radiobiology
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| Street address |
Neuherbergstr. 11
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| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
80937 |
| Country |
Germany |
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| Platforms (1) |
| GPL17077 |
Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version) |
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| Samples (23)
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| GSM2046686 |
H0 HARS category, before irr., baboon 1 |
| GSM2046687 |
H0 HARS category, before irr., baboon 2 |
| GSM2046688 |
H0 HARS category, before irr., baboon 3 |
| GSM2046689 |
H0 HARS category, before irr., baboon 4 |
| GSM2046690 |
H0 HARS category, before irr., baboon 5 |
| GSM2046691 |
H1-2° HARS category, 1st day after irr., baboon 1 |
| GSM2046692 |
H1-2° HARS category, 1st day after irr., baboon 2 |
| GSM2046693 |
H1-2° HARS category, 1st day after irr., baboon 3 |
| GSM2046694 |
H1-2° HARS category, 1st day after irr., baboon 4 |
| GSM2046695 |
H1-2° HARS category, 2nd day after irr., baboon 1 |
| GSM2046696 |
H1-2° HARS category, 2nd day after irr., baboon 2 |
| GSM2046697 |
H1-2° HARS category, 2nd day after irr., baboon 3 |
| GSM2046698 |
H1-2° HARS category, 2nd day after irr., baboon 4 |
| GSM2046699 |
H2-3° HARS category, 1st day after irr., baboon 1 |
| GSM2046700 |
H2-3° HARS category, 1st day after irr., baboon 2 |
| GSM2046701 |
H2-3° HARS category, 1st day after irr., baboon 3 |
| GSM2046702 |
H2-3° HARS category, 1st day after irr., baboon 4 |
| GSM2046703 |
H2-3° HARS category, 1st day after irr., baboon 5 |
| GSM2046704 |
H2-3° HARS category, 2nd day after irr., baboon 1 |
| GSM2046705 |
H2-3° HARS category, 2nd day after irr., baboon 2 |
| GSM2046706 |
H2-3° HARS category, 2nd day after irr., baboon 3 |
| GSM2046707 |
H2-3° HARS category, 2nd day after irr., baboon 4 |
| GSM2046708 |
H2-3° HARS category, 2nd day after irr., baboon 5 |
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| Relations |
| BioProject |
PRJNA309872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77254_RAW.tar |
283.0 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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