Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. Alternating Current (AC) Electric Field (EF) Stimulation
2.3. Microarray Hybridization
2.4. Microarray Data Analysis
2.5. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR)
2.6. Antibody MicroarrayAanalysis
3. Results
3.1. Stimulation of Telomerase-Immortalized Human Corneal Epithelial (hTCEpi) Cells with Alternate Current (AC) Electric Fields (EFs)
3.2. Gene Expession Profiling (GEP) of AC EF-Stimulated hTCEpi Cells
3.3. Validation of Trancriptome Analysis Data by qRT-PCR
3.4. Antibody Microarray Analysis of Differentially Expressed Proteins in hTCEpi Cells
4. Discussion and Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Target | Primer | Primer Sequence (5′-3′) | GenBank Accession |
---|---|---|---|
Twist1 | Fwd | CAGCCTGAGCAACAGCGAGGA | NM_000474 |
Rev | CGAACGCCTCGTTCAGCGAC | ||
Notch1 | Fwd | GCAGTGCTTCCAGAGTGCCACC | NM_017617 |
Rev | AACCGGAACTTCTTGGTCTCCAGG | ||
Notch3 | Fwd | GGCCAGGCCATGGTCTTCC | NM_000435 |
Rev | TCAGGGAACCAGAGGGTGCTG | ||
Notch4 | Fwd | AGGCTGGAGCCAACCCCAAC | NM_004557 |
Rev | CAGCCCCTTCCAGCAGCGT | ||
Jag2 | Fwd | CCTGATTGGCGGCTATTACTGTGA | NM_002226 |
Rev | CCCGCAGCCATCGATCACTC | ||
Zeb1 | Fwd | GCAGGGCACACCAGAAGCCA | NM_001128128 |
Rev | GTGAGCTATAGGAGCCAGAATGGGAA | ||
Numb | Fwd | CAAGCTAATGGCACTGACTCAGCC | NM_001005743 |
Rev | CTGAGGGTGGCCTGCAGTGC | ||
NFkB | Fwd | GCACCTAGCTGCCAAAGAAGGAC | NM_001165412 |
Rev | GCTCCTGCTGCTTTGAGAAGAGC | ||
E-cadherin | Fwd | GCTTGGATTTTGAGGCCAAGCA | NM_004360 |
Rev | AATCTCCAGCCAGTTGGCAGTGTC | ||
IL8 | Fwd | CGTGGCTCTCTTGGCAGCC | NM_000584 |
Rev | TGTGTTGGCGCAGTGTGGTC | ||
IL18 | Fwd | CCAAGGAAATCGGCCTCTATTTG | NM_001562 |
Rev | TCAGGAGGATTCATTTCCTTAAAGGA | ||
IL21 | Fwd | GCCACATGATTAGAATGCGTCAAC | NM_021803 |
Rev | TGTATTTGCTGACTTTAGTTGGGCC | ||
IL27 | Fwd | CGGAGCGTCTCTGCTTCATCTC | NM_145659 |
Rev | AGGTTGAATCCTGCAGCCAGC | ||
Ker9 | Fwd | CTCTCCTGGACATTGACAACACTCGC | NM_000226 |
Rev | AGCACCTGCCGCAGGCCAT | ||
Ker27 | Fwd | GCGAGCTGAGTACGAAGCCCTCG | NM_181537 |
Rev | CTCATTCCGGGCTGAGGTGGTG | ||
GAPDH | Fwd | GGATATTGTTGCCATCAATGACCC | NM_002046 |
Rev | TCTCGCTCCTGGAAGATGGTGA |
KEGG Pathway | Pathway Description | Observed Gene Count | False Discovery Rate |
---|---|---|---|
hsa00520 | Amino sugar and nucleotide sugar metabolism | 13 of 48 | 0.0036 |
hsa04010 | MAPK signaling pathway | 35 of 293 | 0.0036 |
hsa04978 | Mineral absorption | 13 of 51 | 0.0036 |
hsa05162 | Measles | 21 of 133 | 0.0036 |
hsa05164 | Influenza A | 25 of 168 | 0.0036 |
hsa05202 | Transcriptional misregulation in cancer | 25 of 169 | 0.0036 |
hsa05418 | Fluid shear stress and atherosclerosis | 22 of 133 | 0.0036 |
hsa01100 | Metabolic pathways | 100 of 1250 | 0.0074 |
hsa01212 | Fatty acid metabolism | 11 of 48 | 0.0074 |
hsa05160 | Hepatitis C | 19 of 131 | 0.0074 |
hsa05200 | Pathways in cancer | 49 of 515 | 0.0074 |
hsa05203 | Viral carcinogenesis | 24 of 183 | 0.0074 |
hsa05206 | MicroRNAs in cancer | 21 of 149 | 0.0074 |
hsa05219 | Bladder cancer | 10 of 41 | 0.0074 |
hsa04110 | Cell cycle | 18 of 123 | 0.0076 |
hsa05168 | Herpes simplex infection | 23 of 181 | 0.0076 |
hsa04360 | Axon guidance | 22 of 173 | 0.0093 |
hsa04657 | IL-17 signaling pathway | 14 of 92 | 0.0194 |
hsa04060 | Cytokine-cytokine receptor interaction | 28 of 263 | 0.0206 |
hsa04914 | Progesterone-mediated oocyte maturation | 14 of 94 | 0.021 |
hsa00970 | Aminoacyl-tRNA biosynthesis | 9 of 44 | 0.0213 |
hsa05161 | Hepatitis B | 18 of 142 | 0.0229 |
hsa01040 | Biosynthesis of unsaturated fatty acids | 6 of 23 | 0.0426 |
hsa05322 | Systemic lupus erythematosus | 13 of 94 | 0.0454 |
hsa04217 | Necroptosis | 18 of 155 | 0.0474 |
KEGG Pathway | Pathway Description | Protein Count | False Discovery Rate | Matching Proteins in Network |
---|---|---|---|---|
hsa04668 | TNF signaling pathway | 17 | 1.95 × 10−13 | MAPK12, MAPK1, AKT3, ICAM1, VCAM1, IL15, CSF2, FOS, CASP3, CFLAR, SELE, FAS, MAPK9, TNF, MAP2K4, PGAM5, CCL5 |
hsa05200 | Pathways in cancer | 27 | 2.95 × 10−11 | MAPK1, HGF, IFNG, CCND2, AKT3, IL7, FGF2, STAT3, TP53, ERBB2, IL15, HSP90B1, IL7R, FOS, CASP3, GSTM1, KLK3, MET, MMP1, CASP9, FAS, RAC1, IL2RA, ETS1, JAK3, MAPK9, CUL2 |
hsa05418 | Fluid shear stress and atherosclerosis | 16 | 2.95 × 10−11 | MAPK12, IFNG, AKT3, KDR, ICAM1, TP53, VCAM1, HSP90B1, FOS, GSTM1, SELE, CAV3, RAC1, MAPK9, TNF, MAP2K4 |
hsa04010 | MAPK signaling pathway | 21 | 3.06 × 10−11 | MAPK12, MAPK1, HGF, HSPB1, AKT3, KDR, FGF2, TP53, ERBB2, CD14, FOS, CASP3, MET, FAS, RAC1, HSPA1A, MAPK9, TNF, MAP2K4, DDIT3, NTF4 |
hsa04060 | Cytokine-cytokine receptor interaction | 20 | 3.06 × 10−11 | HGF, IFNG, TNFSF10, CCR7, IL7, KDR, CXCL13, IL15, CSF2, CCL11, IL7R, MET, FAS, IL2RA, CCL8, TNF, IL10, TNFSF14, CCL5, TNFRSF9 |
hsa04657 | IL-17 signaling pathway | 13 | 2.29 × 10−10 | MAPK12, MAPK1, IFNG, CSF2, HSP90B1, CCL11, FOS, CASP3, MMP1, MAPK4, MAPK9, TNF, MUC5B |
hsa04151 | PI3K-Akt signaling pathway | 21 | 3.07 × 10−10 | MAPK1, HGF, VTN, CCND2, AKT3, IL7, KDR, FGF2, TP53, ERBB2, ITGA5, HSP90B1, IL7R, MET, CASP9, RAC1, THBS3, IL2RA, JAK3, PPP2R5D, NTF4 |
hsa04933 | AGE-RAGE signaling pathway in diabetic complications | 11 | 4.79 × 10−8 | MAPK12, MAPK1, AKT3, STAT3, ICAM1, VCAM1, CASP3, SELE, RAC1, MAPK9, TNF |
hsa04660 | T cell receptor signaling pathway | 11 | 4.95 × 10−8 | MAPK12, MAPK1, IFNG, AKT3, CSF2, FOS, CD28, MAPK9, TNF, PTPRC, IL10 |
hsa04620 | Toll-like receptor signaling pathway | 11 | 6.21 × 10−8 | MAPK12, MAPK1, AKT3, CD14, FOS, CD86, RAC1, MAPK9, TNF, MAP2K4, CCL5 |
hsa04510 | Focal adhesion | 14 | 6.84 × 10−8 | MAPK1, HGF, VTN, CCND2, AKT3, KDR, ERBB2, ITGA5, MET, CAV3, RAC1, THBS3, ACTN1, MAPK9 |
hsa05164 | Influenza A | 13 | 8.98 × 10−8 | MAPK12, MAPK1, IFNG, TNFSF10, AKT3, ICAM1, CASP9, FAS, HSPA1A, MAPK9, TNF, MAP2K4, CCL5 |
hsa04630 | Jak-STAT signaling pathway | 12 | 3.49 × 10−7 | IFNG, CCND2, AKT3, IL7, STAT3, IL15, CSF2, IL7R, AOX1, IL2RA, JAK3, IL10 |
hsa04068 | FoxO signaling pathway | 11 | 3.99 × 10−7 | MAPK12, MAPK1, TNFSF10, CCND2, AKT3, STAT3, ATM, IL7R, BNIP3, MAPK9, IL10 |
hsa05162 | Measles | 11 | 4.63 × 10−7 | IFNG, TNFSF10, CCND2, AKT3, STAT3, TP53, CD28, FAS, HSPA1A, IL2RA, JAK3 |
hsa05161 | Hepatitis B | 11 | 8.35 × 10−7 | MAPK1, AKT3, STAT3, TP53, FOS, CASP3, CASP9, FAS, MAPK9, TNF, MAP2K4 |
hsa04664 | Fc epsilon RI signaling pathway | 8 | 2.19 × 10−6 | MAPK12, MAPK1, AKT3, CSF2, RAC1, MAPK9, TNF, MAP2K4 |
hsa05168 | Herpes simplex infection | 11 | 6.12 × 10−6 | CDC34, IFNG, TP53, IL15, FOS, CASP3, FAS, MAPK9, TNF, TNFSF1, CCL5 |
hsa04514 | Cell adhesion molecules (CAMs) | 10 | 4.92 × 10−6 | SELP, ICAM1, VCAM1, CD28, SELE, CD86, VTCN1, CD99, PDCD1LG2, PTPRC |
hsa04370 | VEGF signaling pathway | 7 | 9.52 × 10−6 | MAPK12, MAPK1, HSPB1, AKT3, KDR, CASP9, RAC1 |
hsa04217 | Necroptosis | 10 | 1.05 × 10−5 | IFNG, TNFSF10, STAT3, CFLAR, FAS, FAF1, JAK3, MAPK9, TNF, PGAM5 |
hsa04115 | p53 signaling pathway | 7 | 1.92 × 10−5 | CCND2, TP53, ATM, CASP3, CASP9, FAS, CHEK2 |
hsa04917 | Prolactin signaling pathway | 7 | 2.02 × 10−5 | MAPK12, MAPK1, CCND2, AKT3, STAT3, FOS, MAPK9 |
hsa04062 | Chemokine signaling pathway | 10 | 3.16 × 10−5 | MAPK1, CCR7, AKT3, STAT3, CXCL13, CCL11, RAC1, CCL8, JAK3, CCL5 |
hsa04512 | ECM-receptor interaction | 7 | 5.07 × 10−5 | VTN, ITGA5, GP1BA, CD47, THBS3, HMMR, CD44 |
hsa04071 | Sphingolipid signaling pathway | 8 | 5.57 × 10−5 | MAPK12, MAPK1, AKT3, TP53, RAC1, MAPK9, TNF, PPP2R5D |
hsa04064 | NF-kappa B signaling pathway | 7 | 0.00011 | ICAM1, ATM, VCAM1, CD14, CFLAR, TNF, TNFSF14 |
hsa04066 | HIF-1 signaling pathway | 7 | 0.00013 | MAPK1, IFNG, ENO1, AKT3, STAT3, ERBB2, CUL2 |
hsa04014 | Ras signaling pathway | 10 | 0.00016 | MAPK1, HGF, AKT3, KDR, FGF2, MET, RAC1, ETS1, MAPK9, NTF4 |
hsa04722 | Neurotrophin signaling pathway | 7 | 0.00034 | MAPK12, MAPK1, AKT3, TP53, RAC1, MAPK9, NTF4 |
hsa04926 | Relaxin signaling pathway | 7 | 0.00066 | MAPK12, MAPK1, AKT3, FOS, MMP1, MAPK9, MAP2K4 |
hsa04015 | Rap1 signaling pathway | 8 | 0.0015 | MAPK12, MAPK1, HGF, AKT3, KDR, FGF2, MET, RAC1 |
hsa05219 | Bladder cancer | 4 | 0.0017 | MAPK1, TP53, ERBB2, MMP1 |
hsa04110 | Cell cycle | 6 | 0.0025 | CCND2, TP53, ATM, CDC25C, CHEK2, CDKN1C |
hsa04012 | ErbB signaling pathway | 5 | 0.0027 | MAPK1, AKT3, ERBB2, MAPK9, MAP2K4 |
hsa04550 | Signaling pathways regulating pluripotency of stem cells | 6 | 0.0042 | MAPK12, MAPK1, AKT3, FGF2, STAT3, JAK3 |
hsa04920 | Adipocytokine signaling pathway | 4 | 0.0089 | AKT3, STAT3, MAPK9, TNF |
hsa04919 | Thyroid hormone signaling pathway | 5 | 0.0094 | MAPK1, AKT3, NCOR1, TP53, CASP9 |
hsa04662 | B cell receptor signaling pathway | 4 | 0.0096 | MAPK1, AKT3, FOS, RAC1 |
hsa04915 | Estrogen signaling pathway | 5 | 0.0154 | MAPK1, AKT3, HSP90B1, FOS, HSPA1A |
hsa04024 | cAMP signaling pathway | 6 | 0.0179 | MAPK1, SOX9, AKT3, FOS, RAC1, MAPK9 |
hsa04912 | GnRH signaling pathway | 4 | 0.0179 | MAPK12, MAPK1, MAPK9, MAP2K4 |
hsa04310 | Wnt signaling pathway | 5 | 0.0197 | MMP7, CCND2, TP53, RAC1, MAPK9 |
hsa04810 | Regulation of actin cytoskeleton | 6 | 0.0213 | MAPK1, FGF2, ITGA5, CD14, RAC1, ACTN1 |
hsa04141 | Protein processing in endoplasmic reticulum | 5 | 0.0298 | AMFR, HSP90B1, HSPA1A, MAPK9, DDIT3 |
hsa04621 | NOD-like receptor signaling pathway | 5 | 0.0329 | MAPK12, MAPK1, MAPK9, TNF, CCL5 |
hsa04622 | RIG-I-like receptor signaling pathway | 3 | 0.0468 | MAPK12, MAPK9, TNF |
hsa03320 | PPAR signaling pathway | 3 | 0.0497 | FABP2, FABP5, MMP1 |
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Kowtharapu, B.S.; Damaraju, J.; Singh, N.K.; Ziebart, J.; Bader, R.; Koczan, D.; Stachs, O. Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields. Genes 2021, 12, 299. https://doi.org/10.3390/genes12020299
Kowtharapu BS, Damaraju J, Singh NK, Ziebart J, Bader R, Koczan D, Stachs O. Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields. Genes. 2021; 12(2):299. https://doi.org/10.3390/genes12020299
Chicago/Turabian StyleKowtharapu, Bhavani S., Jyoti Damaraju, Nitesh Kumar Singh, Josefin Ziebart, Rainer Bader, Dirk Koczan, and Oliver Stachs. 2021. "Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields" Genes 12, no. 2: 299. https://doi.org/10.3390/genes12020299
APA StyleKowtharapu, B. S., Damaraju, J., Singh, N. K., Ziebart, J., Bader, R., Koczan, D., & Stachs, O. (2021). Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields. Genes, 12(2), 299. https://doi.org/10.3390/genes12020299