Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells
Abstract
:1. Introduction
2. Material and Methods
2.1. Cell Lines and Culture
2.2. Cell Treatments
2.3. Cell Viability Assays
2.4. RNA Purification
2.5. Quantitative Real-Time PCR
2.6. Next Generation Sequencing
2.7. Inmunofluorescence and Confocal Microscopy
2.8. ELISA
2.9. Statistical Analysis
3. Results
3.1. Sterculic Acid Does Not Present Cell Toxicity to Retinal Cell In Vitro
3.2. Sterculic Acid Administration is Protective Against 7KCh-Induced Cell Death In Vitro
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
7KCh | 7-ketocholesterol |
AMD | Age-related macular degeneration |
CVN | Choroidal neovascularization |
DEG | Differentially expressed genes |
DMEM | Dulbecco’s Modified Eagle medium |
ECM | Extracellular matrix |
ER | Endoplasmic reticulum |
FDR | False discovery rate |
GO | Gene ontology |
HPBCD | Hydroxypropyl-beta-cyclodextrin |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
mRPE | Monkey retinal pigment epithelium cells |
MUFA | Monounsaturated fatty acid |
RPE: | Retinal pigment epithelium |
SA | Sterculic acid |
SO | Sterculic oil |
References
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Gene Name | Oligonucleotide Sequence |
---|---|
SCD-F | 5′-ATAAGTTGGAGACGACGCCC-3′ |
SCD-R | 5′-GGCTCCCAAGTGTAGCAGAG-3′ |
SREBF1-F | 5′-CGTTTCTTCGTGGATGGGGA-3′ |
SREBF1-R | 5′-TTCAGTGCTCGCTCCAAGAG-3′ |
ITGA5-F | 5′-TCTTGCTGGACTGTGGAGAG-3′ |
ITGA5-R | 5′-AGGGCATTCTTGTCACCCAG-3′ |
APOE-F | 5′-CTGCGTTGCTGGTCACATTC-3′ |
APOE-R | 5′-CGCAGGTAATCCCAAAAGCG-3′ |
ANGPTL4-F | 5′-CAAGGCTCAGAACAGCAGGA-3′ |
ANGPTL4-R | 5′-CTCTTTCTTCGGGCAGGCTT-3′ |
CAV1-F | 5′-GCAGAACCAGAAGGGACACA-3′ |
CAV1-R | 5′-GATGCCAAAGAGGGCAGACA-3′ |
PDGFB-F | 5′-CCACTCCATCCGCTCCTTC-3′ |
PDGFB-R | 5′-CTCCTTCTTCCACGAGCCAG-3′ |
COL1A1-F | 5′-GCCAAGACGAAGACATCCCA-3′ |
COL1A1-R | 5′-GGCAGTTCTTGGTCTCGTCA-3′ |
ACC1-F | 5′-ATTGCCTTCATGGGTCCTCC-3′ |
ACC1-R | 5′-CTCCAGGGAAGAGTTGGGAT-3′ |
18S-F | 5′-ATGCTCTTAGCTGAGTGTCCCG-3′ |
18S-R | 5′-ATTCCTAGCTGCGGTATCCAGG-3′ |
Pathway | Gene | Log2 Fold Change | FDR | Gene Description |
---|---|---|---|---|
Fatty acid biosynthesis | ||||
CREB3L1 | −0.68 | 1.29 × 10−2 | cAMP responsive element binding protein 3 like 1 | |
SREBF1 | −0.79 | 1.83 × 10−2 | sterol regulatory element binding transcription factor 1 | |
FASN | −0.62 | 2.18 × 10−2 | fatty acid synthase | |
ACC1 | −0.47 | 6.86 × 10−6 | Acetyl-CoA Carboxylase Alpha | |
SCD | −1.18 | 3.18 × 10−5 | Stearoyl-CoA Desaturase | |
Steroid Biosynthesis | ||||
HMGCS1 | −0.87 | 1.13 × 10−2 | 3-Hydroxy-3-Methylglutaryl-CoA Synthase | |
MVD | −0.66 | 3.06 × 10−2 | mevalonate diphosphate decarboxylase | |
FDFT1 | −0.31 | 1.14 × 10−3 | Farnesyl-Diphosphate Farnesyltransferase 1 | |
SQLE | −0.50 | 1.41 × 10−5 | squalene epoxidase | |
LSS | −0.77 | 3.89 × 10−6 | lanosterol synthase | |
CYP51A1 | −0.47 | 2.18 × 10−2 | Cytochrome P450 Family 51 Subfamily A Member 1 | |
MSMO1 | −0.61 | 1.35 × 10−2 | Methylsterol Monooxygenase 1 | |
HSD17B7 | −0.28 | 3.60 × 10−2 | 3-keto-steroid reductase | |
NSDHL | −0.53 | 3.74 × 10−3 | NAD(P) Dependent Steroid Dehydrogenase-Like | |
EBP | −0.75 | 4.75 × 10−7 | EBP Cholestenol Delta-Isomerase | |
Fatty acid degradation and beta-oxidation | ||||
CPT1A | 0.97 | 1.07 × 10−12 | Carnitine Palmitoyltransferase 1A | |
SLC25A20 | 0.82 | 4.61 × 10−6 | solute carrier family 25 member 20 | |
ACADS | 0.50 | 5.76 × 10−3 | acyl-CoA dehydrogenase short chain | |
ACADVL | 0.58 | 1.63 × 10−5 | acyl-CoA dehydrogenase very long chain | |
Cell Death | ||||
CASP8 | −0.36 | 3.20 × 10−2 | caspase 8 | |
CASP1 | −0.86 | 3.38 × 10−2 | caspase-1 | |
GSDMD | −0.59 | 2.21 × 10−3 | gasdermin D | |
TNFRSF10A | −0.52 | 6.56 × 10−4 | TNF receptor superfamily member 10a | |
ECM-Receptor interaction, cell adhesion, Cell junction | ||||
COL1A1 | −1.37 | 9.76 × 10−5 | collagen type I alpha 1 chain | |
COL1A2 | −0.96 | 2.61 × 10−7 | collagen type I alpha 2 chain | |
COL3A1 | −1.66 | 2.74 × 10−21 | collagen type III alpha 1 chain | |
COL5A2 | −0.73 | 3.23 × 10−20 | collagen type V alpha 2 chain | |
COL7A1 | −1.04 | 2.25 × 10−5 | Collagen Type VII Alpha 1 Chain | |
COL8A1 | −0.62 | 3.38 × 10−5 | collagen type VIII alpha 1 chain | |
COL9A1 | −2.11 | 1.27 × 10−4 | Collagen Type IX Alpha 1 Chain | |
COl11A1 | −0.63 | 1.45 × 10−4 | collagen type XI alpha 1 chain | |
COL16A1 | −1.82 | 2.78 × 10−10 | collagen type XVI alpha 1 chain | |
COL17A1 | −2.91 | 9.06 × 10−4 | collagen type XVII alpha 1 chain | |
LAMA3 | −0.98 | 8.32 × 10−7 | laminin subunit alpha 3 | |
LAMC1 | −0.32 | 2.90 × 10−2 | laminin subunit gamma 1 | |
THBS3 | −0.50 | 1.73 × 10−2 | thrombospondin 3 | |
FN1 | −0.86 | 4.27 × 10−4 | fibronectin 1 | |
CHST2 | 1.14 | 3.64 × 10−5 | carbohydrate sulfotransferase 2 | |
CHST12 | 0.68 | 4.09 × 10−2 | carbohydrate sulfotransferase 12 | |
CHST15 | 0.56 | 6.66 × 10−4 | carbohydrate sulfotransferase 15 | |
CD274 | −0.82 | 1.39 × 10−2 | CD274 Molecule | |
ITGA5 | −0.64 | 1.29 × 10−2 | integrin subunit alpha 5 | |
ITGB2 | −0.36 | 1.41 × 10−2 | integrin subunit beta 2 | |
CLDN16 | −1.46 | 3.74 × 10−2 | claudin 16 | |
IGFBP3 | −0.93 | 2.69 × 10−6 | insulin like growth factor binding protein 3 | |
IGFBP4 | −0.59 | 1.50 × 10−2 | insulin like growth factor binding protein 4 | |
IGFBP5 | −2.31 | 1.62 × 10−50 | insulin like growth factor binding protein 5 | |
IGFBP8 | 1.01 | 4.49 × 10−5 | insulin like growth factor binding protein 8 | |
IGFBP9 | −1.74 | 8.74 × 10−08 | insulin like growth factor binding protein 9 | |
SDC2 | −0.44 | 7.97 × 10−3 | syndecan 2 | |
CDH1 | −1.38 | 4.37 × 10−4 | cadherin 1 | |
CDH3 | −2.29 | 3.50 × 10−15 | cadherin 3 | |
CDH10 | −1.50 | 1.60 × 10−2 | cadherin 10 | |
CDH15 | −1.22 | 4.74 × 10−2 | cadherin 15 | |
VCAN | −1.18 | 1.14 × 10−2 | versican | |
NCAM1 | −0.27 | 3.20 × 10−3 | neural cell adhesion molecule 1 | |
Actin cytoskeleton reorganization | ||||
FLNB | −0.48 | 4.16 × 10−2 | filamin B | |
PARVA | −0.33 | 2.97 × 10−4 | parvin alpha | |
MYLPF | −1.31 | 1.05 × 10−3 | myosin light chain, phosphorylatable, fast skeletal muscle | |
MLCP | −0.59 | 2.39 × 10−2 | Protein Phosphatase 1 Regulatory Subunit 12A | |
RHOJ | −1.21 | 1.32 × 10−2 | ras homolog family member J |
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Pariente, A.; Pérez-Sala, Á.; Ochoa, R.; Peláez, R.; Larráyoz, I.M. Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells. Cells 2020, 9, 1187. https://doi.org/10.3390/cells9051187
Pariente A, Pérez-Sala Á, Ochoa R, Peláez R, Larráyoz IM. Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells. Cells. 2020; 9(5):1187. https://doi.org/10.3390/cells9051187
Chicago/Turabian StylePariente, Ana, Álvaro Pérez-Sala, Rodrigo Ochoa, Rafael Peláez, and Ignacio M. Larráyoz. 2020. "Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells" Cells 9, no. 5: 1187. https://doi.org/10.3390/cells9051187
APA StylePariente, A., Pérez-Sala, Á., Ochoa, R., Peláez, R., & Larráyoz, I. M. (2020). Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells. Cells, 9(5), 1187. https://doi.org/10.3390/cells9051187