A Regulator Role for the ATP-Binding Cassette Subfamily C Member 6 Transporter in HepG2 Cells: Effect on the Dynamics of Cell–Cell and Cell–Matrix Interactions
Abstract
:1. Introduction
2. Results
2.1. Whole Transcriptome of the ABCC6-Silenced HepG2 Cell Line
2.2. Functional Enrichment Analysis of Differentially Expressed Genes
2.3. The Silencing of ABCC6 Changes the Expression of Some Proteins Involved in Cell–Cell and Cell–Matrix Interactions
2.4. ABCC6-Silenced Cells Modify Their Clonogenic Potential and Ability to Invade the Extracellular Matrix
2.5. ABCC6 Silencing Dysregulates Genes Involved in the Epithelial–Mesenchymal Transition
3. Discussion
4. Materials and Methods
4.1. Cell Lines and Maintenance of Cell Culture
4.2. Gene Knockdown of Stable Cell Lines
4.3. RNA Sequencing
4.4. Functional and Pathway Analysis of Differentially Regulated Genes
4.5. Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR)
4.6. Western Blot Analysis
4.7. Cell Adhesion Assay
4.8. Migration and Invasion Assays
4.9. SDS–Gelatin Gel Zymogram
4.10. Colony Formation Assay
4.11. Statistical Analyses
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Symbol | Fold Change | padj | Regulation |
---|---|---|---|
MATN2 | −6.52 | 2.08 × 10−4 | |
ABCG8 | −6.48 | 1.55 × 10−2 | Down |
PITPNM3 | −6.46 | 9.42 × 10−3 | |
FADS6 | −5.71 | 1.60 × 10−2 | |
FLNC | −5.64 | 5.94 × 10−7 | |
JAM3 | −5.12 | 3.35 × 10−2 | |
ICAM2 | −4.88 | 8.39 × 10−3 | |
UNC13C | −4.66 | 5.54 × 10−4 | |
PLCB2 | −4.63 | 5.55 × 10−4 | |
SLC22A7 | −4.46 | 4.40 × 10−2 | |
GLIPR1 | 6.14 | 2.30 × 10−5 | |
NXPH3 | 6.63 | 1.62 × 10−5 | Up |
ISM1 | 6.99 | 1.50 × 10−10 | |
CDH17 | 7.68 | 1.94 × 10−3 | |
RAB27B | 7.72 | 1.32 × 10−3 | |
RIPPLY3 | 8.08 | 4.54 × 10−10 | |
PAUPAR | 11.81 | 3.53 × 10−4 | |
LYVE1 | 16.55 | 4.57 × 10−9 | |
MMP7 | 19.08 | 1.17 × 10−17 | |
DHRS9 | 22.97 | 2.90 × 10−5 |
ID | Term Description | Fold- Enrichment | Occurrence | Support | Lowest_p | Highest_p | Up_Regulated | Down_Regulated |
---|---|---|---|---|---|---|---|---|
hsa05414 | Dilated cardiomyopathy | 5.36 | 10 | 0.12 | 5.41 × 10−9 | 3.54 × 10−7 | ITGA2, ITGA6, ITGB1, ACTG1, TPM4, ADCY7, TGFB1 | ITGA3, TTN, ADCY9 |
hsa04510 | Focal adhesion | 3.36 | 10 | 0.14 | 1.68 × 10−6 | 8.16 × 10−6 | LAMB3, SPP1, ITGA2, ITGA6, ITGB1, ARHGAP5, ACTG1, CAPN2, FLNA | VTN, ITGA3, PPP1CC, FLNC |
hsa05410 | Hypertrophic cardiomyopathy | 4.58 | 10 | 0.09 | 3.04 × 10−7 | 9.07 × 10−6 | ITGA2, ITGA6, ITGB1, ACTG1, TPM4, TGFB1 | ITGA3, TTN |
hsa05205 | Proteoglycans in cancer | 3.26 | 10 | 0.14 | 3.28 × 10−6 | 1.23 × 10−5 | ACTG1, FLNA, ITPR3, CD63, TGFB1, PLAUR, ITGA2, ITGB1, RDX | FLNC, PPP1CC, TIMP3, VTN |
hsa05132 | Salmonella infection | 2.06 | 10 | 0.03 | 3.86 × 10−5 | 3.86 × 10−5 | DYNLL2, DYNLRB1, TUBA1A, TUBB2A, FLNA, ACTG1, SNX9 | FLNC, CYFIP2, CD14 |
hsa04610 | Complement and coagulation cascades | 5.99 | 10 | 0.04 | 4.46 × 10−5 | 4.46 × 10−5 | F2R, SERPINE1, PLAUR | FGG, KNG1, MBL2, MASP2, C3, CLU, VTN |
hsa05412 | Arrhythmogenic right ventricular cardiomyopathy | 4.02 | 10 | 0.07 | 2.07 × 10−5 | 4.53 × 10−5 | ITGA2, ITGA6, ITGB1, ACTG1, DSP | ITGA3 |
hsa04512 | ECM–receptor interaction | 4.63 | 10 | 0.05 | 2.09 × 10−5 | 8.19 × 10−5 | LAMB3, SPP1, NPNT, ITGA2, ITGA6, ITGB1 | VTN, ITGA3 |
hsa05145 | Toxoplasmosis | 2.27 | 10 | 0.03 | 8.49 × 10−5 | 1.02 × 10−4 | LAMB3, ITGA6, ITGB1, LDLR, TGFB1 | |
hsa05222 | Small-cell lung cancer | 3.32 | 10 | 0.05 | 2.61 × 10−5 | 1.02 × 10−4 | CDKN2B, LAMB3, ITGA2, ITGA6, ITGB1 | ITGA3 |
Gene | Accession Number | Forward Primer | Reverse Primer |
---|---|---|---|
β-actin | NM_001101.3 | 5′-CCTGGCACCCAGCACAAT-3′ | 5′-GCCGATCCACACGGAGTACT-3′ |
ABCC6 | NM_001171.5 | 5′-AAGGAACCACCATCAGGAGGAG-3′ | 5′-ACCAGCGACACAGAGAAGAGG-3′ |
CDH1 | NM_001317184.2 | 5′-CTCCCTTCACAGCAGAACTAACAC-3′ | 5′-GTCCTCTTCTCCGCCTCCTTC-3′ |
CDH2 | NM_001308176.2 | 5′-GGATCAAAGCCTGGAACATAT-3′ | 5′-TTGGAGCCTGAGACACGATT-3′ |
CDH17 | NM_004063.4 | 5′-TCAAAATCACTCAGGTGCGG-3′ | 5′-GAAAAATGGGAATCTTGGGAGC-3′ |
FLNC | NM_001458.5 | 5′-CTGTCCATGTGTCGGAAGCC-3′ | 5′-ACACCTTGAAGTCAGCCACC -3′ |
ITGA2 | NM_002203.4 | 5′-AAATGATATTCTGATGCTGGG-3′ | 5′- CCA GCC TTT TCT AGT AGA GC-3′ |
ITGA6 | NM_000210.4 | 5′-CTT AGG TTT TTC TTT GGA CTC A-3′ | 5′-TCTCTTCAGCAAAACCACGG-3′ |
MATN2 | NM_002380.5 | 5′-AAACGCTGCCGAAGGAAGG -3′ | 5′-TCCTCAGCTAGAACAAATCCG -3′ |
VIM | NM_003380.5 | 5′-ATGGACAGGTTATCAACGAAA-3′ | 5′-AAGTTTGGAAGAGGCAGAGA-3′ |
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Matera, I.; Miglionico, R.; Abruzzese, V.; Marchese, G.; Ventola, G.M.; Castiglione Morelli, M.A.; Bisaccia, F.; Ostuni, A. A Regulator Role for the ATP-Binding Cassette Subfamily C Member 6 Transporter in HepG2 Cells: Effect on the Dynamics of Cell–Cell and Cell–Matrix Interactions. Int. J. Mol. Sci. 2023, 24, 16391. https://doi.org/10.3390/ijms242216391
Matera I, Miglionico R, Abruzzese V, Marchese G, Ventola GM, Castiglione Morelli MA, Bisaccia F, Ostuni A. A Regulator Role for the ATP-Binding Cassette Subfamily C Member 6 Transporter in HepG2 Cells: Effect on the Dynamics of Cell–Cell and Cell–Matrix Interactions. International Journal of Molecular Sciences. 2023; 24(22):16391. https://doi.org/10.3390/ijms242216391
Chicago/Turabian StyleMatera, Ilenia, Rocchina Miglionico, Vittorio Abruzzese, Giovanna Marchese, Giovanna Maria Ventola, Maria Antonietta Castiglione Morelli, Faustino Bisaccia, and Angela Ostuni. 2023. "A Regulator Role for the ATP-Binding Cassette Subfamily C Member 6 Transporter in HepG2 Cells: Effect on the Dynamics of Cell–Cell and Cell–Matrix Interactions" International Journal of Molecular Sciences 24, no. 22: 16391. https://doi.org/10.3390/ijms242216391
APA StyleMatera, I., Miglionico, R., Abruzzese, V., Marchese, G., Ventola, G. M., Castiglione Morelli, M. A., Bisaccia, F., & Ostuni, A. (2023). A Regulator Role for the ATP-Binding Cassette Subfamily C Member 6 Transporter in HepG2 Cells: Effect on the Dynamics of Cell–Cell and Cell–Matrix Interactions. International Journal of Molecular Sciences, 24(22), 16391. https://doi.org/10.3390/ijms242216391