Chronic exposure to simulated space conditions predominantly affects cytoskeleton remodeling and oxidative stress response in mouse fetal fibroblasts

  • Authors:
    • Michaël Beck
    • Marjan Moreels
    • Roel Quintens
    • Khalil Abou-El-Ardat
    • Hussein  El-Saghire
    • Kevin Tabury
    • Arlette Michaux
    • Ann Janssen
    • Mieke  Neefs
    • Patrick Van Oostveldt
    • Winnok H. De Vos
    • Sarah Baatout
  • View Affiliations

  • Published online on: May 22, 2014     https://doi.org/10.3892/ijmm.2014.1785
  • Pages: 606-615
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Abstract

Microgravity and cosmic rays as found in space are difficult to recreate on earth. However, ground-based models exist to simulate space flight experiments. In the present study, an experimental model was utilized to monitor gene expression changes in fetal skin fibroblasts of murine origin. Cells were continuously subjected for 65 h to a low dose (55 mSv) of ionizing radiation (IR), comprising a mixture of high‑linear energy transfer (LET) neutrons and low-LET gamma-rays, and/or simulated microgravity using the random positioning machine (RPM), after which microarrays were performed. The data were analyzed both by gene set enrichment analysis (GSEA) and single gene analysis (SGA). Simulated microgravity affected fetal murine fibroblasts by inducing oxidative stress responsive genes. Three of these genes are targets of the nuclear factor‑erythroid 2 p45-related factor 2 (Nrf2), which may play a role in the cell response to simulated microgravity. In addition, simulated gravity decreased the expression of genes involved in cytoskeleton remodeling, which may have been caused by the downregulation of the serum response factor (SRF), possibly through the Rho signaling pathway. Similarly, chronic exposure to low-dose IR caused the downregulation of genes involved in cytoskeleton remodeling, as well as in cell cycle regulation and DNA damage response pathways. Many of the genes or gene sets that were altered in the individual treatments (RPM or IR) were not altered in the combined treatment (RPM and IR), indicating a complex interaction between RPM and IR.

Introduction

In the present study, we established an in vitro model in which primary cultures of fetal fibroblasts from murine origin (PFC) were subjected for 65 h to simulated microgravity, chronic irradiation or a combination. Genome-wide gene expression changes were thereafter assessed by microarrays. For microgravity simulation, we used the random positioning machine (RPM), which is one of the most widely used instruments for this purpose and has proven valuable in many cell types (16). As far as cosmic radiation is concerned, simulating the wide variety of ions ranging from low to very high energies encountered in space is problematic, particularly if irradiation is combined with microgravity simulation models. At present, no facility offers the possibility of producing chronic exposures of very high-energy beams consisting of multiple charged particles. We therefore used a source of californium Cf-252 for low-dose rate long-term exposure consisting of a mixture of high-linear energy transfer (LET) neutrons and low-LET gamma-rays (7).

The large amount of data generated with a high-throughput technology such as microarrays constitutes a double-edged sword: whole expression pattern may be recorded, but extracting the relevant information becomes more challenging (8,9). To overcome this problem, analysis tools have been developed, such as single gene statistical analysis methods (SGA), which are widely used to determine the differentially expressed genes, and the gene set enrichment analysis (GSEA), which aims to identify gene expression differences in groups of genes, for instance in those acting synergistically in a cell process (9,10). The two analytical methods were used concomitantly in this study.

Materials and methods

Cell culture

All the animals were handled following the Belgian legislation after approval by the appropriate Ethics Committees (agreement number 08-002). BALB/cJ Rj (Janvier Laboratories, Saint-Berthevin, France) fetuses (three males and three females) originating from two different litters were dissected 17 days post-conception (day 0 being the fertilization day). Their skin was harvested and mechanically dissociated. The obtained tissue was enzymatically digested for 1 h at 37°C in phosphate-buffered saline (PBS; N.V. Invitrogen SA, Merelbeke, Belgium) solution containing 1 mg/ml of collagenase/dispase (Roche, Mannheim, Germany) and 5 mg/ml of trypsin 2,000 E/g (Merck KGaA, Darmstadt, Germany). The enzymatic reaction was subsequently stopped by adding fetal bovine serum (FBS; N.V. Invitrogen SA). The obtained cell suspension was subsequently centrifuged for 10 min at 350 × g and the cells were seeded in 6-well plates in F12 medium supplemented with 20% FBS and 1% penicillin/streptomycin (both from N.V. Invitrogen SA), one fetus skin in each well. The cells were allowed to grow for up to 3 or 4 passages at 37°C (5%, CO2) and were subsequently frozen in FBS with 10% dimethyl sulfoxide (Sigma-Aldrich, St. Louis, MO, USA). The primary cultures were then thawed and allowed to grow for two weeks. The cells were seeded at a density of ×105 cells in 12.5 cm2 flasks and allowed to adhere for 24 h prior to treatment.

Simulation of space conditions

Exposure to simulated space conditions included microgravity simulation using the desktop RPM (Dutch Space, Leiden, The Netherlands) and ionizing radiation (IR) (7). The exposure lasted for a period of 65 h. Four treatment conditions were used: controls (CTRL), microgravity simulation (RPM), irradiation and a combination of the treatment methods (RPM and IR). For microgravity simulation, the flasks were completely filled with medium, sealed and placed on the RPM at a rotational velocity between 55 and 65°/sec. Direction, speed and interval were set as random. The CTRL were placed in the same incubator under the same conditions as the treated samples. For chronic low-dose irradiation, the cells were exposed to a mixture of neutrons (98.2%) and gamma-rays (1.8%) directly or indirectly originating from a Cf-252 source were placed at 4.13 m from the incubator. The dosimetry was performed with bubble detectors as previously described (11) for neutron irradiation and with 600 cc ionization chamber (NE) coupled with a Farmer electrometer for gamma-rays. The total dose received was 55.94±19.70 mSv (862 μSv/h), which approximately corresponds to 35 times the dose rate measured on the International Space Station (ISS) (12), the total dose corresponding approximately to a stay of 100 days in the ISS.

RNA extraction

Immediately after treatment, adherent cells were washed in PBS, lysed in 350 ml of AllPrep DNA/RNA/Protein Mini kit lysis buffer (Qiagen, Hilden, Germany) and frozen at −80°C. RNA was extracted using the same kit and its concentration was measured using the Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) while its quality (RNA integrity number, RIN) was determined with Agilent’s lab-on-chip Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). All the RNA samples had a RIN value of >9.0.

Affymetrix microarrays and data analysis

The RNA was treated using the GeneChip WT cDNA Synthesis and Amplification kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting RNA was hybridized onto Affymetrix Mouse Gene 1.0 ST arrays.

Raw data (.cel-files) were imported at exon level in Partek Genomics Suite v6.5 (Partek Incorporated, St. Louis, MO, USA). Briefly, robust Multi-array Average (RMA) background correction was applied, data were normalized by quantile normalization and probe set summarization was performed using the median polish method. Gene summarization was performed using One-Step Tukey’s Biweight method. These data were further analyzed with the Partek Genomics Suite software for SGA and by the GSEA software (v2.0, Broad Institute of Harvard and MIT, Cambridge, MA, USA).

For the single gene method, taking into consideration the scan date (also available for the litter), the fetus, the gender and the treatment as factors, a four-way ANOVA was performed to determine the genes that had a significantly altered expression for different conditions. For the pathway analysis, KEGG and PathArt databases were analyzed with ArrayTrack v3.3.0 (National Center for Toxicological Research, Jefferson, AR, USA).

For the GSEA, a selection of 144 gene sets from gene ontology (GO) databases was based on biological relevance (Table I). Gene sets were considered to be significantly differently regulated with a false discovery rate (FDR) when q<0.05.

Table I

List of the 144 gene sets selected for GSEA.

Table I

List of the 144 gene sets selected for GSEA.

Gene set descriptionGene Ontology
Actin bindingGO:0003779
Actin cytoskeletonGO:0015629
Activation of JNK activityGO:0007257
Activation of MAPK activityGO:0000187
Adherens junctionGO:0005912
Anti-apoptosisGO:0006916
Antioxidant activityGO:0016209
Apoptosis GOGO:0006915
Base excision repairGO:0006284
Calcium ion bindingGO:0005509
Calcium ion transportGO:0006816
Caspase activationGO:0006919
Cell-cell adhesionGO:0016337
Cell-cell signalingGO:0007267
Cell cycle arrestGO:0007050
Cell cycleGO:0007049
Cell cycle processGO:0022402
Cell junctionGO:0030054
Cell matrix adhesionGO:0007160
Cellular respirationGO:0045333
CentrosomeGO:0005813
Chaperone bindingGO:0051087
ChromatinGO:0000785
ChromosomeGO:0005694
CollagenGO:0005581
Cortical cytoskeletonGO:0030863
Cytokine activityGO:0005125
Cytoskeletal protein bindingGO:0008092
CytoskeletonGO:0005856
DNA damage checkpointGO:0000077
DNA integrity checkpointGO:0031570
DNA repairGO:0006281
Double-strand break repairGO:0006302
Electron transportGO:0006118
Embryonic developmentGO:0009790
Endoplasmic reticulumGO:0005783
ExcretionGO:0007588
Extracellular matrixGO:0031012
Focal adhesionGO:0005925
G-protein coupled receptor activityGO:0004930
G-protein coupled receptor protein signaling pathwayGO:0007186
G-protein signaling coupled to IP3 second messenger phospholipase C activatingGO:0007200
G1 phaseGO:0051318
G1/S transition of mitotic cell cycleGO:0000082
G2/M transition of mitotic cell cycleGO:0000086
Glutathione transferase activityGO:0004364
Golgi apparatusGO:0005794
GTPase regulator activityGO:0030695
Histone modificationGO:0016570
Hormone activityGO:0005179
Inositol or phosphatidylinositol kinase activityGO:0004428
Inositol or phosphatidylinositol phosphatase activityGO:0004437
Inositol or phosphatidylinositol phosphodiesterase activityGO:0004434
Insulin receptor signaling pathwayGO:0008286
Integrin bindingGO:0005178
Intercellular junctionGO:0005911
Ion channel activityGO:0005216
JAK/STAT cascadeGO:0007259
JNK cascadeGO:0007254
LamellipodiumGO:0030027
Lipid bindingGO:0008289
M phaseGO:0000279
Magnesium ion bindingGO:0000287
MAP kinase activityGO:0004707
MAPKKK cascadeGO:0000165
MicrotubuleGO:0005874
Microtubule cytoskeletonGO:0015630
Mitochondrial inner membraneGO:0005743
Mitochondrial respiratory chainGO:0005746
MitochondrionGO:0005739
Motor activityGO:0003774
Negative regulation of apoptosisGO:0043066
Negative regulation of cell adhesionGO:0007162
Negative regulation of cell cycleGO:0045786
Negative regulation of cell proliferationGO:0008285
Negative regulation of cellular metabolic processGO:0031324
Negative regulation of signal transductionGO:0009968
Negative regulation of transcriptionGO:0016481
Negative regulation of translationGO:0017148
Nuclear poreGO:0005643
NucleolusGO:0005730
NucleusGO:0005634
Oligosaccharide metabolic processGO:0009311
Phosphoinositide-mediated signalingGO:0048015
Phospholipase activityGO:0004620
Phospholipid bindingGO:0005543
PhosphorylationGO:0016310
Positive regulation of caspase activityGO:0043280
Positive regulation of cell adhesionGO:0045785
Positive regulation of cell cycleGO:0045787
Positive regulation of cell proliferationGO:0008284
Positive regulation of JNK activityGO:0043507
Positive regulation of MAP kinase activityGO:0043406
Positive regulation of protein metabolic processGO:0051247
Positive regulation of signal transductionGO:0009967
Positive regulation of transcriptionGO:0045941
Positive regulation of translationGO:0045727
Post-translational protein modificationGO:0043687
Potassium ion transportGO:0006813
Programmed cell deathGO:0012501
Protein foldingGO:0006457
Protein kinase activityGO:0004672
Protein kinase cascadeGO:0007243
Protein metabolic processGO:0019538
Protein modification processGO:0006464
Protein/RNA complex assemblyGO:0022618
Protein serine/threonine kinase activityGO:0004674
Protein ubiquitinationGO:0016567
ProteolysisGO:0006508
RAS GTPase activator activityGO:0005099
RAS GTPase bindingGO:0017016
Receptor bindingGO:0005102
Regulation of apoptosisGO:0042981
Replication forkGO:0005657
Respiratory chain complex IGO:0045271
Response to DNA damage stimulusGO:0006974
Response to ionizing radiationGO:0010212
Response to radiationGO:0009314
Response to stressGO:0006950
RHO GTPase activator activityGO:0005100
RHO protein signal transductionGO:0007266
Rhodopsin-like receptor activityGO:0001584
RNA helicase activityGO:0003724
RNA processingGO:0006396
RNA splicingGO:0008380
RuffleGO:0001726
S phaseGO:0051320
Second messenger-mediated signalingGO:0019932
Small conjugated protein ligase activityGO:0019787
Small GTPase-mediated signal transductionGO:0007264
Sodium channel activityGO:0005272
SpindleGO:0005819
SpliceosomeGO:0005681
Structural constituent of cytoskeletonGO:0005200
Structural constituent of ribosomeGO:0003735
Tight junctionGO:0005923
TranscriptionGO:0006350
TranslationGO:0006412
Transmembrane receptor protein kinase activityGO:0019199
Transmembrane transporter activityGO:0022857
T-RNA metabolic processGO:0006399
Ubiquitin cycleGO:0006512
Ubiquitin protein ligase activityGO:0004842
Voltage-gated channel activityGO:0022832

[i] GSEA, gene set enrichment analysis.

Results

Single gene analysis revealed that 119 genes were downregulated and 55 genes were upregulated by >1.5-fold change (unadjusted p-value <0.01) across all the treatments (Fig. 1 and an exhaustive list of the differentially expressed genes can be found in Table II). KEGG and PathArt databases indicated that the 54 genes that were downregulated only by RPM treatment were mostly involved in cell cycle regulation (p53- and p21-mediated pathways), in cytoskeleton modeling, cell junctions and cell signaling via integrins, IL-1, and TGF-β. Within the list of individual genes that were downregulated after IR or RPM and IR treatments, no clear pathway was found. On the other hand, in the 52 genes that were upregulated following RPM and RPM and IR treatments, interleukin signaling (IL-11 and MMP) and glutathione metabolism were the most prominent pathways affected. Some genes were differentially expressed by RPM and RPM and IR, however, only a few genes were common between IR and RPM and IR. Six genes were upregulated (S1p3, Rab11b, Ptger3, Vldlr, Cnn1 and Serping1) and only one predicted gene of unknown function was downregulated (Gm13668) in both irradiated treatments (IR and RPM and IR). The upregulated genes were mostly membrane proteins, G-protein coupled (S1p3 and Ptger3) or involved in ligand endocytosis (Rab11b and Vldlr). Cnn1 and Serping1, involved in cytoskeleton organization and peptidase inhibition, respectively, were both upregulated in all the treatments, including RPM.

Table II

Down- and upregulated genes following IR, RPM or RPM and IR treatments (p<0.001, fold change >1.5).

Table II

Down- and upregulated genes following IR, RPM or RPM and IR treatments (p<0.001, fold change >1.5).

A, Down- and upregulated genes following IR

Gene symbolGenBankp-valueFC
Rab11bNM_0089975,48E-03−2,026
Csgalnact1NM_1727539,04E-03−1,989
Smarca5NM_0531244,08E-03−1,986
Tceb3NM_0137366,85E-03−1,953
Serping1NM_0097761,39E-03−1,948
Ppp1r2NM_0258009,20E-03−1,801
PtgfrnNM_0111974,38E-03−1,801
Dnaja1NM_0082986,13E-03−1,772
Arhgap24NM_0292706,13E-03−1,767
ThraNM_1780603,67E-04−1,728
Itga8NM_0010013099,74E-03−1,718
Gpr108NM_0300842,40E-03−1,696
Zfp346NM_0120171,54E-04−1,672
RbmxNM_0112521,04E-03−1,655
B4galt6NM_0197379,25E-03−1,638
BC003331NM_1455115,04E-03−1,637
VldlrNM_0137033,68E-03−1,636
Unc93b1NM_0194495,57E-04−1,625
Pip4k2aNM_0088453,79E-04−1,622
MgllNM_0011662512,52E-03−1,620
BC005624NM_1448852,10E-03−1,619
S1pr3NM_0101012,64E-03−1,613
PrkcdNM_0111033,32E-03−1,583
Cnn1NM_0099224,26E-03−1,575
P2ry2NM_0087736,80E-03−1,566
Saps1NM_1728948,65E-03−1,566
Casc4NM_1770544,45E-03−1,559
Opa1NM_1337527,47E-03−1,552
EmbNM_0103305,84E-04−1,551
Cyb5d1NM_0010455255,23E-03−1,549
Ptger3NM_0111961,41E-03−1,549
Usp30NM_0010332021,36E-03−1,543
Tbc1d2bNM_1943346,00E-03−1,539
CyldNM_0011281692,57E-03−1,530
Trip4NM_0197978,21E-03−1,520
Luzp1NM_0244529,75E-03−1,502
Gm13668XR_0327576,87E-041,856
Hist1h2aoNM_0011775443,69E-031,710
BmycNM_0233263,25E-031,575
4930458L03RikNM_0300471,32E-031,523

B, Down- and upregulated genes following RPM

DmpkNM_0324182,73E-05−2,522
Myh10NM_1752601,51E-03−2,485
Myh9NM_0224102,08E-03−2,432
MaobNM_1727781,48E-04−2,335
Slc38a4NM_0270529,81E-04−2,270
Cnn1NM_0099224,53E-05−2,147
Adh1NM_0074092,01E-04−2,126
Serping1NM_0097765,85E-04−2,095
Actg2NM_0096103,08E-05−2,089
Ccnb2NM_0076302,94E-04−2,071
Kif20aNM_0011664061,35E-04−2,023
Gjb2NM_0081251,16E-04−2,014
AnlnNM_0283908,66E-04−2,001
NfixNM_0010819813,95E-03−1,964
Itga8NM_0010013092,19E-03−1,963
PygbNM_1537811,46E-03−1,913
Bub1NM_0011131793,71E-05−1,881
Ly6c1NM_0107419,89E-04−1,879
ND4L ENSMUST000000840132,03E-05−1,843
Myl9NM_1721181,95E-04−1,830
Actn4NM_0218958,48E-03−1,819
Itgbl1NM_1454678,49E-03−1,814
Efemp1NM_1460156,17E-04−1,801
D17H6S56E-5L787882,29E-07−1,791
Plk1NM_0111211,55E-03−1,774
ND4L ENSMUST000000840133,76E-05−1,750
Susd2NM_0278902,62E-04−1,736
Ly6c2NM_0010992177,26E-04−1,731
Ucp2NM_0116714,37E-04−1,717
CenpaNM_0076813,25E-03−1,713
Nuf2NM_0232846,69E-04−1,711
RbmxNM_0112527,19E-04−1,692
Kif2cNM_1344712,28E-03−1,687
Rpl22l1NM_0265179,88E-03−1,678
Ly6aNM_0107388,47E-03−1,671
Pkp2NM_0261631,21E-04−1,667
Tgfb1i1NM_0093656,54E-03−1,652
Acta1NM_0096067,19E-06−1,644
Gas2l3NM_0010333315,26E-04−1,643
Lrrc17NM_0289774,37E-03−1,642
2810417H13RikNM_0265153,58E-03−1,640
Lpar4NM_1752713,20E-03−1,639
Dlgap5NM_1445531,76E-03−1,622
HgfNM_0104271,71E-03−1,611
Trp53inp2NM_1781111,30E-03−1,605
Cyb5r3NM_0297871,06E-03−1,603
Mfap2NM_0085466,77E-04−1,600
Cyp1b1NM_0099945,70E-03−1,597
Trpv2NM_0117064,75E-03−1,596
Kif23NM_0242451,56E-03−1,591
Sh3pxd2aNM_0080181,37E-03−1,566
ND2 ENSMUST000000823961,35E-03−1,564
Tgfb3NM_0093681,15E-03−1,562
Scd2NM_0091285,24E-03−1,554
DnerNM_1529151,80E-03−1,546
PdgfrlNM_0268404,88E-04−1,543
CenpmNM_0256396,47E-03−1,539
Ppp1r3cNM_0168541,04E-03−1,536
Fam114a1NM_0266671,68E-03−1,533
D2Ertd750eNM_0264127,48E-04−1,533
Nkd2NM_0281867,87E-03−1,531
NovNM_0109309,41E-03−1,529
Tgm2NM_0093732,62E-03−1,525
Nucb2NM_0011304797,36E-03−1,518
5730469M10RikBC0566351,03E-03−1,516
Ccna2NM_0098288,65E-03−1,514
Maged2NM_0307006,56E-03−1,512
Eif4bNM_1456257,83E-03−1,512
Sepx1NM_0137592,65E-04−1,506
Shisa4NM_1752595,60E-03−1,503
St3gal5NM_0113758,29E-03−1,502
Fhl5NM_0213182,32E-04−1,502
Serpinb9eNM_0114562,02E-032,514
Gstα1NM_0081811,59E-052,232
Taf1dBC0569641,32E-032,223
Gstα1NM_0081812,15E-052,210
Prl2c3NM_0111182,70E-052,209
Snhg1AK0510455,45E-062,192
Prl2c5NM_1818522,79E-042,179
Malat1NR_0028471,90E-042,139
Il1rl1NM_0010256022,81E-042,061
Snhg1AK0510451,78E-051,967
Gm10639NM_0011226602,00E-041,908
Sema7aNM_0113525,57E-041,870
Lce1hNM_0263356,44E-031,841
Taf1dBC0569647,18E-041,812
Crct1NM_0287983,49E-041,802
Gm8074XM_9835013,90E-041,799
Lsm1NM_0260321,31E-031,794
2310002L13Rik ENSMUST000000253904,85E-041,771
Sirt7NM_1530564,15E-041,760
Serpinb9bNM_0114524,07E-061,734
Snord14eNR_0282757,22E-041,704
Gstα2NM_0081827,50E-071,700
PpbpNM_0237855,04E-031,691
Hsd3b6NM_0138211,21E-041,684
Snord14dNR_0282747,27E-041,679
Hmox1NM_0104425,24E-061,678
Clcf1NM_0199521,97E-041,671
Snord14dNR_0282747,39E-041,667
ProcrNM_0111712,00E-031,649
Hist1h4iNM_1756564,77E-031,635
Dusp4NM_1769334,07E-031,626
Mmp10NM_0194716,51E-041,587
Cops3NM_0119911,24E-031,584
Gas5NR_0028403,87E-031,573
Chrna1NM_0073891,19E-031,565
Ifrd1NM_0135621,44E-031,556
D4Wsu53eBC0430572,60E-031,515
S100a7aNM_1994228,26E-031,513
Scarna17NR_0285606,25E-041,512
Scarna17NR_0285606,25E-041,512

C, Down- and upregulated genes following RPM and IR

Cnn1NM_0099226,32E-06−2,494
Serping1NM_0097761,65E-04−2,337
DmpkNM_0324181,36E-04−2,206
Actg2NM_0096101,44E-05−2,203
Adh1NM_0074092,24E-04−2,107
Rab11bNM_0089974,88E-03−2,051
Itgbl1NM_1454672,48E-03−2,041
Gjb2NM_0081251,20E-04−2,009
SrpxNM_0169111,74E-05−1,882
Myl9NM_1721181,72E-04−1,844
S1pr3NM_0101014,04E-04−1,824
MaobNM_1727782,99E-03−1,814
Tmem45aNM_0196313,16E-04−1,793
PdgfrlNM_0268403,28E-05−1,7722
NovNM_0109301,36E-03−1,749
PigcNM_0260785,96E-03−1,691
Il1r1NM_0083625,64E-03−1,690
VldlrNM_0137032,37E-03−1,687
Susd2NM_0278906,17E-04−1,652
Ptger3NM_0111964,43E-04−1,651
Lysmd3NM_0302572,93E-03−1,650
Fhl1NM_0010773611,90E-08−1,629
Cyp1b1NM_0099944,48E-03−1,625
Plk1NM_0111216,41E-03−1,600
St3gal5NM_0113753,71E-03−1,583
Rab13NM_0266777,09E-04−1,581
Snta1NM_0092284,11E-05−1,577
Aqp1NM_0074725,14E-03−1,556
Cpa6NM_1778344,01E-03−1,554
NosipNM_0255331,35E-03−1,540
Pla2g16NM_1392695,13E-03−1,532
Lmod1NM_0531063,01E-03−1,523
Zcchc17NM_1531604,13E-03−1,519
IslrNM_0120431,27E-03−1,509
6330406I15RikBC1162461,22E-04−1,502
Serpinb9eNM_0114567,91E-042,818
Slc40a1NM_0169171,83E-052,670
Taf1dBC0569642,85E-042,595
Snhg1AK0510458,57E-062,126
Prl2c3NM_0111188,34E-052,037
Gstα1NM_0081811,21E-041,938
ProcrNM_0111711,83E-041,935
Gstα1NM_0081811,60E-041,921
Mmp13NM_0086075,88E-041,894
Malat1NR_0028471,05E-031,873
Serpinb9gNM_0114555,62E-031,865
Snhg1AK0510455,03E-051,848
Serpinb9gNM_0114555,24E-031,801
310002L13Rik ENSMUST000000253904,28E-041,785
Gm8074XM_9835016,00E-041,750
MycNM_0108491,98E-051,748
Peg10NM_1308771,83E-031,746
Mamdc2NM_1748577,44E-041,744
Il11NM_0083509,82E-031,728
Mmp3NM_0108098,35E-031,724
Fabp7NM_0212722,79E-031,693
Serpinb9bNM_0114527,99E-061,681
Taf1dBC0569642,40E-031,667
GmnnAF0687807,71E-031,620
Gm10639NM_0011226602,64E-031,610
Dusp4NM_1769335,31E-031,596
Bcl2l11NM_2076809,00E-031,595
Ctu1NM_1455821,01E-031,594
Gstα2NM_0081823,74E-061,591
Hsd3b6NM_0138215,25E-041,561
Gm13668XR_0327578,44E-031,553
Ang2NM_0074491,54E-031,548
Scarna17NR_0285603,97E-041,545
Scarna17NR_0285603,97E-041,545
Hmox1NM_0104423,84E-051,541
Serpinb9fNM_1831979,11E-041,540
Opa3NM_2075251,23E-031,540
Ormdl3NM_0256618,94E-031,505

[i] IR, ionizing radiation; RPM, random positioning machine.

In contrast to the results obtained by SGA, GSEA revealed a high impact of IR on coordinately differentially expressed genes. A total of 63 gene sets were significantly downregulated following chronic low-dose irradiation. Of the 63 genes, 30 were exclusively enriched in irradiated samples (Fig. 2), although this number may be an overestimation due to redundancy between some of the gene sets. The gene sets that were specifically downregulated after irradiation conditions are mostly involved in DNA damage response, cell signaling, cell cycle, RNA processing and protein turnover (Table III). Moreover, we detected significantly downregulated gene sets involved in cell signaling, cell cycle, transcription, protein turnover, cell shape, adhesion, motility and communication for all the treatments. Of note, two gene sets involved in oxidative phosphorylation were significantly downregulated solely in the RPM and IR samples. No gene set was significantly upregulated in any of the treatments.

Table III

Downregulated gene sets revealed by GSEA, based on the list of gene sets provided by Fig. 2.

Table III

Downregulated gene sets revealed by GSEA, based on the list of gene sets provided by Fig. 2.

TreatmentCell processGene set (GO)
IRDNA damageDNA damage checkpoint
DNA repair
Histone modification
Response to DNA damage stimulus
Response to radiation
Response to stress
Cell signalingNegative regulation of signal transduction
Inositol or phosphatidylinositol kinase activity
Ras GTPase binding
Positive regulation of JNK activity
RHO GTPase activator activity
Protein kinase cascade
Magnesium ion binding
Protein serine/threonine kinase activity
Phosphorylation
Cell cycleCell cycle arrest (GO 0007050)
Negative regulation of cell cycle
RNA processingRNA processing
RNA splicing
Spliceosome
Nuclear pore
Protein turnovertRNA metabolic process
Post translational protein modification
Endoplasmic reticulum
Golgi apparatus
Portein ubiquitination
Ubiquitin cycle
Ubiquitin protein ligase activity
Small conjugating protein ligase activity
Cell motilityLamellipodium
IR + RPMCell signalingG protein signaling coupled to IP3
Phosphoinositide-mediated signaling
RAS GTPase activator activity
GTPase regulator activity
Small GTPase-mediated signal transduction
Transmembrane receptor
protein kinase activity
Protein kinase activity
Cell cycleCell cycle (GO 0007049)
Centrosome
Cell shape, adhesion, motility and communicationMicrotubule
Cytoskeletal protein binding
Ruffle
Cell junction
Collagen
Extracellular matrix
TranscriptionPositive regulation of transcription
Negative regulation of transcription
RNA helicase activity
Chromosome
Nucleolus
Cellular metabolismNegative regulation of cellular metabolic process
IR + RPMIR + RPM and IRProtein turnoverProtein/RNA complex assembly
IR + RPM + RPM + IRCell shape, adhesion, motility and communicationCytoskeleton
Actin binding
Actin cytoskeleton
Adherens junction
Cell matrix adhesion
Motor activity
Microtubule cytoskeleton
Cell signalingInsulin receptor signaling pathway
Cell cycleCell cycle process
M phase
Spindle
RPMCell shape, adhesion, motility and communicationStructural constituent of cytoskeleton
Integrin binding
Receptor binding
RPM + IROxidative phosphorylationElectron transport (GO 0006118)
Mitochondrion

[i] ‘+’ shows the gene sets commonly differentially expressed between the treatments cited; IR, ionizing radiation; RPM, random positioning machine.

Discussion

In this study, primary cultures of murine fetal fibroblasts were chronically exposed (65 h) to simulated space conditions including simulated microgravity via RPM and a low-dose mixture of neutrons and gamma-rays (IR). The duration of the experiment was chosen to allow cellular adaptation to the simulated microgravity environment for instance for cytoskeleton remodeling (13,14), in order to decrease the primary stress response mechanisms and to better characterize the effects of chronic exposure to these conditions. Microarrays were performed on RNA harvested from CTRL, IR, RPM and RPM and IR conditions. Microarrays generate a substantial amount of information on the gene expression pattern of cells subjected to a defined treatment. However, a <2-fold difference in the gene expression is often not sufficient to meet the requirements for statistical significance (8). Identification of moderate gene expression differences in groups of genes acting together in a cell process can nevertheless be achieved by means of GSEA. For this reason, we analyzed our microarray output data using the single gene analysis method as well as GSEA.

The RPM has a dominant impact on single gene expression

The SGA method revealed a significant impact of 65 h of simulated microgravity on gene expression in murine fetal fibroblasts. The combination of RPM and IR triggered a differential expression of fewer genes than RPM alone. Only a few genes had an altered expression in IR samples, suggesting that such a low dose of radiation exerted a moderate impact on the expression of individual genes. It was also noted that only a few genes were commonly differentially expressed in all irradiated treatments (IR and RPM and IR), of which there were only six known genes, all upregulated (S1p3, Rab11b, Ptger3, Vldlr, Cnn1 and Serping1), with most of them being involved in cell signaling. No explanation can be provided for the fact that few genes were commonly up- or downregulated in the irradiated treatments (with or without RPM). However the strong effect of RPM may have concealed a more subtle effect of IR, making it statistically less significant.

Among the upregulated genes following RPM treatment, glutathione-S-transferases α 1 and 2 (Gstα1 and Gstα2) were prominent enzymes for the detoxification of breakdown products of oxidative stress (15). However, since the Affymetrix arrays cannot distinguish between the two isoforms due to their very high sequence homology (97%), we cannot dismiss the possibility that only one of the two isoforms was actually affected by the treatment. The modifier subunit of glutathione-cysteine ligase (Gclm) was significantly upregulated as well. The protein encoded by this gene was shown to play an important role in controlling the rate of glutathione synthesis in murine fetal fibroblasts (16). We also report upregulation of the heme oxygenase 1 (Hmox1), a cytoprotective enzyme against oxidative stress (17). In murine fibroblasts, its upregulation by curcumin was found to block radiation-induced reactive oxygen species (ROS) generation (18). Notably, these three genes are targets of the nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) which induces transcription of cytoprotective genes containing antioxidant response elements (19). The transcription factor Nrf2 may therefore play a cytoprotective role against a possible oxidative stress induced by the RPM, which is in line with previous observations of increased oxidative stress in simulated microgravity (2022).

After RPM treatment, two members of the actin filament family, Actg2 and Acta1 were downregulated. These genes were described in smooth (23) or skeletal muscles (24), respectively. Calponin 1 (Cnn1), a gene coding for a protein involved in the cytoskeleton organization (25), and four and a half LIM domains 1 (Fhl1), which functions in adherens junctions signaling to the cytoskeleton (26), were also downregulated. Notably, the four genes were shown to be regulated by the serum response factor (SRF). SRF was shown to be mediated by the Rho signaling pathway (2527), which may have been triggered by the RPM. Rho signaling is believed to be an important pathway for focal adhesion assembly and cytoskeleton remodeling in response to cellular tension stress (28) and has been suggested to play a role in the microgravity response (21,2931). Furthermore, Rho GTPase activities were shown to be increased in dermal fibroblasts subjected to simulated microgravity for 30 and 120 min, thereafter decreasing to reach similar values to those of the CTRL at 48 h of treatment (32). Our hypothesis is that a 65-h exposure to RPM induced downregulation of the Rho signaling pathway, which decreased the activity of the transcription factor SRF, decreasing in turn the expression of genes involved in cytoskeleton organization (Cnn1) and adherens junctions (Fhl1).

IR has a dominant effect on gene sets

At the gene set level, GSEA did not detect any upregulation, except for the structural constituents of the ribosome in IR-treated samples. This result is noteworthy as it did not occur with SGA. Since SGA and GSEA are purely statistical methods, it is unlikely that this result originates from an experimental issue, which may have affected both methods. We also examined the gene set selection, however, a screening of all the gene sets of GO provided the same result. Since the experimental design involved long-term irradiation, it is possible that a feedback loop occurred and decreased the expression pattern of the gene sets.

We identified a significant downregulation of 63 gene sets in response to low-dose IR, although single gene analysis did not reveal any important effects. Of the 63 gene sets, 30 were specifically enriched in IR-treated samples (Fig. 2). These latter gene sets are involved in DNA damage response, cell signaling, cell cycle, RNA processing, protein turnover or cell motility. Of note, the DNA damage response gene sets were downregulated, which may be explained by the long duration of continuous irradiation at an extremely slow-dose rate. It is possible that an adaptation mechanism of the cells to irradiation triggered a feedback loop to decrease the expression of these pathways, as was observed at the gene level (SGA) for SRF responsive genes in response to the RPM. Various other gene sets involved in the same cell processes were also enriched in the RPM, and RPM and IR treatments.

Many of the downregulated gene sets are involved in cell signaling, including Rho and Ras GTPases, inositol and phosphatidylinositol, JNK and insulin receptor-mediated pathways. The downregulation of these signaling pathways may lead to an alteration of the cell cycle (33). In addition to its major role in the cell response to radiation (34,35), the regulation of the cell cycle has been shown to be affected by simulated microgravity (36). GSEA revealed that gene sets involved in the positive regulation of the cell cycle were downregulated in all treatments. However, cells that were only irradiated exhibited a significant downregulation of gene sets involved in cell cycle arrest, indicating no trend towards a pro- or anti-proliferative expression profile, while both RPM and RPM and IR showed an anti-proliferative expression profile. We suggest that all the treatments may have induced a general stress response that decreased the expression of cell cycle progression pathways, while irradiation alone also reduced the expression of genes involved in cell cycle arrest. This hypothesis is in agreement with the decreased expression of DNA damage response pathways that we also detected. In RPM and IR, the effect of the RPM may have concealed the cell cycle arrest gene set downregulation.

In addition, many gene sets involved in the composition of the cytoskeleton (actin and microtubule) and inter- (cell junctions) and extracellular connections (extracellular matrix) were affected by all the treatments. While it has been shown in various cell types that cytoskeleton remodeling starts immediately after exposure to simulated or real microgravity (21,2931), few studies investigated the effects of IR on the cytoskeleton. However, therapeutic doses of irradiation were shown to affect cell permeability of microvascular endothelial cells through Rho-mediated cytoskeleton remodeling (37). More recently, Rho-mediated focal adhesion and fibronectin adhesion were shown to be increased in endothelial cells in response to radiation (38). As Rho GTPases intervene in a number of additional cell pathways (e.g., cell cycle arrest, and regulation of apoptosis) (39), Rho GTPases potentially play a pivotal role in the cell response to simulated space conditions. In agreement with this hypothesis, GSEA revealed that Rho GTPases activity was downregulated in IR-treated samples. Notably, gene sets involved in integrin and receptor binding were specifically downregulated following treatment using the RPM. The results of this study confirm therefore that integrins play a significant role in the cellular response to simulated microgravity.

In conclusion, this study has shown that continuous exposure to simulated microgravity affects fetal murine fibroblasts, especially at the single gene level, by increasing the expression of oxidative stress responsive genes and decreasing the expression of genes involved in cytoskeleton remodeling. As far as irradiation is concerned, we detected a decreased expression of gene sets involved in cytoskeleton mechanisms, in cell signaling and DNA damage response after a chronic low-dose rate of irradiation, particularly at the gene set level. The results indicate that the effects of the combination of the two treatments did not result in a synergism between the two separate effects, since many genes or gene sets that were altered by RPM or IR treatment, were not changed by the combined treatment (RPM and IR).

Acknowledgements

This study was supported by the ESA Topical Team on ‘Developmental Biology in Vertebrates’ and 4 PRODEX/ESA contracts [C90-303, C90-380, C90-391 and 42-000-90-380].

References

1 

Huijser RH: Desktop RPM: new small size microgravity simulator for the bioscience laboratory. Fokker Space FS-MG-R00-017. 1–5. 2000.

2 

van Loon JJWA: Some history and use of the random positioning machine, RPM, in gravity related research. Adv Space Res. 39:1161–1165. 2007.

3 

Borst A and van Loon J: Technology and developments for the random positioning machine, RPM. Microgravity Sci Technol. 21:287–292. 2009. View Article : Google Scholar

4 

Kraft TF, van Loon JJ and Kiss JZ: Plastid position in arabidopsis columella cells is similar in microgravity and on a random-positioning machine. Planta. 211:415–422. 2000. View Article : Google Scholar : PubMed/NCBI

5 

Villa A, Versari S, Maier JA and Bradamante S: Cell behavior in simulated microgravity: a comparison of results obtained with RWV and RPM. Gravit Space Biol Bull. 18:89–90. 2005.

6 

Grimm D, Bauer J, Ulbrich C, et al: Different responsiveness of endothelial cells to vascular endothelial growth factor and basic fibroblast growth factor added to culture media under gravity and simulated microgravity. Tissue Eng Part A. 16:1559–1573. 2010. View Article : Google Scholar

7 

Mastroleo F, Van Houdt R, Leroy B, et al: Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight. ISME J. 3:1402–1419. 2009. View Article : Google Scholar : PubMed/NCBI

8 

Shi J and Walker MG: Gene set enrichment analysis (GSEA) for interpreting gene expression profiles. Curr Bioinform. 2:133–137. 2007. View Article : Google Scholar

9 

Subramanian A, Tamayo P, Mootha VK, et al: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 102:15545–15550. 2005. View Article : Google Scholar : PubMed/NCBI

10 

El-Saghire H, Thierens H, Monsieurs P, Michaux A, Vandevoorde C and Baatout S: Gene set enrichment analysis highlights different gene expression profiles in whole blood samples X-irradiated with low and high doses. Int J Radiat Biol. 89:628–638. 2013. View Article : Google Scholar : PubMed/NCBI

11 

Vanhavere F, Loos M, Plompen AJM, Wattecamps E and Thierens H: A combined use of the BD-PND and BDT bubble detectors in neutron dosimetry. Radiat Meas. 29:573–577. 1998. View Article : Google Scholar

12 

Cucinotta FA, Kim MH, Willingham V and George KA: Physical and biological organ dosimetry analysis for international space station astronauts. Radiat Res. 170:127–138. 2008. View Article : Google Scholar : PubMed/NCBI

13 

Crawford-Young SJ: Effects of microgravity on cell cytoskeleton and embryogenesis. Int J Dev Biol. 50:183–191. 2006. View Article : Google Scholar : PubMed/NCBI

14 

Meloni MA, Galleri G, Pani G, Saba A, Pippia P and Cogoli-Greuter M: Space flight affects motility and cytoskeletal structures in human monocyte cell line J-111. Cytoskeleton (Hoboken). 68:125–137. 2011. View Article : Google Scholar : PubMed/NCBI

15 

Hayes JD and McLellan LI: Glutathione and glutathione-dependent enzymes represent a co-ordinately regulated defence against oxidative stress. Free Radic Res. 31:273–300. 1999. View Article : Google Scholar : PubMed/NCBI

16 

Chen Y, Johansson E, Fan Y, et al: Early onset senescence occurs when fibroblasts lack the glutamate-cysteine ligase modifier subunit. Free Radic Biol Med. 47:410–418. 2009. View Article : Google Scholar : PubMed/NCBI

17 

Haines DD, Lekli I, Teissier P, Bak I and Tosaki A: Role of haeme oxygenase-1 in resolution of oxidative stress-related pathologies: Focus on cardiovascular, lung, neurologic and kidney disorders. Acta Physiol (Oxf). 204:487–501. 2012. View Article : Google Scholar

18 

Lee JC, Kinniry PA, Arguiri E, et al: Dietary curcumin increases antioxidant defenses in lung, ameliorates radiation-induced pulmonary fibrosis, and improves survival in mice. Radiat Res. 173:590–601. 2010. View Article : Google Scholar : PubMed/NCBI

19 

Hayes JD and McMahon M: NRF2 and KEAP1 mutations: permanent activation of an adaptive response in cancer. Trends Biochem Sci. 34:176–188. 2009. View Article : Google Scholar : PubMed/NCBI

20 

Wang J, Zhang J, Bai S, et al: Simulated microgravity promotes cellular senescence via oxidant stress in rat PC12 cells. Neurochem Int. 55:710–716. 2009. View Article : Google Scholar : PubMed/NCBI

21 

Nikawa T, Ishidoh K, Hirasaka K, et al: Skeletal muscle gene expression in space-flown rats. FASEB J. 18:522–524. 2004.PubMed/NCBI

22 

Liu Y and Wang E: Transcriptional analysis of normal human fibroblast responses to microgravity stress. Genomics Proteomics Bioinformatics. 6:29–41. 2008. View Article : Google Scholar : PubMed/NCBI

23 

Carson JA, Culberson DE, Thompson RW, Fillmore RA and Zimmer W: Smooth muscle gamma-actin promoter regulation by RhoA and serum response factor signaling. Biochim Biophys Acta. 1628:133–139. 2003. View Article : Google Scholar

24 

Philippar U, Schratt G, Dieterich C, et al: The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF. Mol Cell. 16:867–880. 2004. View Article : Google Scholar : PubMed/NCBI

25 

Beamish JA, He P, Kottke-Marchant K and Marchant RE: Molecular regulation of contractile smooth muscle cell phenotype: implications for vascular tissue engineering. Tissue Eng Part B Rev. 16:467–491. 2010. View Article : Google Scholar : PubMed/NCBI

26 

Olson EN and Nordheim A: Linking actin dynamics and gene transcription to drive cellular motile functions. Nat Rev Mol Cell Biol. 11:353–365. 2010. View Article : Google Scholar

27 

Sun Q, Chen G, Streb JW, et al: Defining the mammalian CArGome. Genome Res. 16:197–207. 2006. View Article : Google Scholar : PubMed/NCBI

28 

Ingber DE: Tensegrity II. How structural networks influence cellular information processing networks. J Cell Sci. 116:1397–1408. 2003. View Article : Google Scholar : PubMed/NCBI

29 

Meloni MA, Galleri G, Pippia P and Cogoli-Greuter M: Cytoskeleton changes and impaired motility of monocytes at modelled low gravity. Protoplasma. 229:243–249. 2006. View Article : Google Scholar : PubMed/NCBI

30 

Servotte S, Zhang Z, Lambert CA, et al: Establishment of stable human fibroblast cell lines constitutively expressing active rho-GTPases. Protoplasma. 229:215–220. 2006. View Article : Google Scholar

31 

Nichols HL, Zhang N and Wen X: Proteomics and genomics of microgravity. Physiol Genomics. 26:163–171. 2006. View Article : Google Scholar : PubMed/NCBI

32 

Loesberg WA, Walboomers XF, van Loon JJWA and Jansen JA: Simulated microgravity activates MAPK pathways in fibroblasts cultured on microgrooved surface topography. Cell Motil Cytoskeleton. 65:116–129. 2008. View Article : Google Scholar : PubMed/NCBI

33 

Hall A: Rho GTPases and the control of cell behaviour. Biochem Soc Trans. 33:891–895. 2005. View Article : Google Scholar : PubMed/NCBI

34 

Jeggo P: The role of the DNA damage response mechanisms after low-dose radiation exposure and a consideration of potentially sensitive individuals. Radiat Res. 174:825–832. 2010. View Article : Google Scholar : PubMed/NCBI

35 

Jeggo P and Lavin MF: Cellular radiosensitivity: how much better do we understand it? Int J Radiat Biol. 85:1061–1081. 2009. View Article : Google Scholar : PubMed/NCBI

36 

Grimm D, Wise P, Lebert M, Richter P and Baatout S: How and why does the proteome respond to microgravity? Expert Rev Proteomics. 8:13–27. 2011. View Article : Google Scholar : PubMed/NCBI

37 

Gabryś, Greco O, Patel G, Prise KM, Tozer GM and Kanthou C: Radiation effects on the cytoskeleton of endothelial cells and endothelial monolayer permeability. Int J Radiat Oncol Biol Phys. 69:1553–1562. 2007.PubMed/NCBI

38 

Rousseau M, Gaugler MH, Rodallec A, Bonnaud S, Paris F and Corre I: Rhoa GTPase regulates radiation-induced alterations in endothelial cell adhesion and migration. Biochem Biophys Res Commun. 414:750–755. 2011. View Article : Google Scholar : PubMed/NCBI

39 

Etienne-Manneville S and Hall A: Rho GTPases in cell biology. Nature. 420:629–635. 2002. View Article : Google Scholar

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August-2014
Volume 34 Issue 2

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Online ISSN:1791-244X

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Beck M, Moreels M, Quintens R, Abou-El-Ardat K, El-Saghire H, Tabury K, Michaux A, Janssen A, Neefs M, Van Oostveldt P, Van Oostveldt P, et al: Chronic exposure to simulated space conditions predominantly affects cytoskeleton remodeling and oxidative stress response in mouse fetal fibroblasts. Int J Mol Med 34: 606-615, 2014
APA
Beck, M., Moreels, M., Quintens, R., Abou-El-Ardat, K., El-Saghire, H., Tabury, K. ... Baatout, S. (2014). Chronic exposure to simulated space conditions predominantly affects cytoskeleton remodeling and oxidative stress response in mouse fetal fibroblasts. International Journal of Molecular Medicine, 34, 606-615. https://doi.org/10.3892/ijmm.2014.1785
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Beck, M., Moreels, M., Quintens, R., Abou-El-Ardat, K., El-Saghire, H., Tabury, K., Michaux, A., Janssen, A., Neefs, M., Van Oostveldt, P., De Vos, W. H., Baatout, S."Chronic exposure to simulated space conditions predominantly affects cytoskeleton remodeling and oxidative stress response in mouse fetal fibroblasts". International Journal of Molecular Medicine 34.2 (2014): 606-615.
Chicago
Beck, M., Moreels, M., Quintens, R., Abou-El-Ardat, K., El-Saghire, H., Tabury, K., Michaux, A., Janssen, A., Neefs, M., Van Oostveldt, P., De Vos, W. H., Baatout, S."Chronic exposure to simulated space conditions predominantly affects cytoskeleton remodeling and oxidative stress response in mouse fetal fibroblasts". International Journal of Molecular Medicine 34, no. 2 (2014): 606-615. https://doi.org/10.3892/ijmm.2014.1785