Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure
- PDF / 1,231,430 Bytes
- 13 Pages / 595.276 x 790.866 pts Page_size
- 37 Downloads / 156 Views
RESEARCH ARTICLE
Molecular Medicine
Open Access
Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation Lara Kim Brackmann1† , Alicia Poplawski2† , Caine Lucas Grandt1 , Heike Schwarz1, Thomas Hankeln3, Steffen Rapp3, Sebastian Zahnreich4 , Danuta Galetzka4 , Iris Schmitt4, Christian Grad4, Lukas Eckhard5 , Johanna Mirsch6, Maria Blettner2 , Peter Scholz-Kreisel2 , Moritz Hess7 , Harald Binder7 , Heinz Schmidberger4 and Manuela Marron1*
Abstract Background: Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points. Methods: Fibroblasts from skin biopsies of 15 cell donors were exposed to a high (2Gy) and a low (0.05Gy) dose of X-rays. RNA was extracted and sequenced 2 h and 4 h after exposure. Differentially expressed genes with an adjusted p-value < 0.05 were flagged and used for pathway analyses including prediction of upstream and downstream effects. Principal component analyses were used to examine the effect of two different sequencing runs on quality metrics and variation in expression and alignment and for explorative analysis of the radiation dose and time point of analysis. Results: More genes were differentially expressed 4 h after exposure to low and high doses of radiation than after 2 h. In experiments with high dose irradiation and RNA sequencing after 4 h, inactivation of the FAT10 cancer signaling pathway and activation of gluconeogenesis I, glycolysis I, and prostanoid biosynthesis was observed taking p-value (< 0.05) and (in) activating z-score (≥2.00 or ≤ − 2.00) into account. Two hours after high dose irradiation, inactivation of small cell lung cancer signaling was observed. For low dose irradiation experiments, we did not detect any significant (p < 0.05 and z-score ≥ 2.00 or ≤ − 2.00) activated or inactivated pathways for both time points. (Continued on next page)
* Correspondence: [email protected] † Lara Kim Brackmann and Alicia Poplawski contributed equally to this work. 1 Leibniz Institute for Prevention Research and Epidemiology – BIPS, Achterstr. 30, 28359 Bremen, Germany Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and
Data Loading...
