Identification of Lncrna-Mrna Networks in Hepg2 Cells upon ATP7B Knockout and Copper Accumulation
-
Yan Yan
,
Yin Xu
,
Lin Chen
,
Yongzhu Han
,
Renmin Yang
,
Wenbin Hu
Abstract
Background: Hepatolenticular degeneration (HLD) is an inherited disorder caused by the mutation in the adenosine triphosphatase copper transporting β gene (ATP7B). W aimed to explore the genetic changes in HLD using bioinformatics analysis.
Methods: The study was conducted in Nepal, in 2019. The GSE107323 dataset was downloaded and the differentially expressed lncRNAs (DElncRNAs) as well as differentially expressed genes (DEGs) induced by ATP7B knockout (KO) and copper toxicity were clustered using Mfuzz clustering analysis. LncRNAs and genes with high coexpression (correlation coefficient > 0.9) and pathways involving the DEGs were used to construct the lncRNA-gene-pathway network.
Results: ATP7B KO and ATP7B KO + copper induced 51 overlapping DEGs and 687 overlapping DElncRNAs, respectively. Mfuzz analysis identified four clusters, including two clusters of consistently upregulated and downregulated DEGs/DElncRNAs. The lncRNA-gene-pathway network consisted of 13 DElncRNAs, 10 DEGs, and two pathways, including “hsa04630: Jak-STAT signaling pathway” and “hsa04920: Adipocytokine signaling pathway”. Eight downregulated genes, including erythropoietin (EPO), insulin receptor substrate 1 (IRS1), and PPARG coactivator 1 alpha (PPARGC1A), and two upregulated genes (cardiotrophin-like cytokine factor 1 and cyclin D3) were involved in the two pathways. These genes were targeted by multiple lncRNAs, including PCAT6 and MALAT1.
Conclusion: Collectively, the differentially expressed lncRNA-mRNA axes play crucial roles in HLD pathogenesis through mediating cell proliferation and inflammation. Moreover, the EPO, IRS1, or PPARGC1A genes were potent therapeutic targets for HLD.
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13. Tsang T, Posimo JM, Gudiel AA, Cicchini M, Feldser DM, Brady DC (2020). Cop-per is an essential regulator of the au-tophagic kinases ULK1/2 to drive lung adenocarcinoma. Nat Cell Biol, 22: 412-424.
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18. Verdier F, Chrétien S, Billat C, Gisselbrecht S, Lacombe C, Mayeux P (1997). Eryth-ropoietin induces the tyrosine phosphor-ylation of insulin receptor substrate-2 an alternate pathway for erythropoietin-induced phosphatidylinositol 3-kinase ac-tivation. J Biol Chem, 272: 26173-26178.
19. Ma S, Chen J, Chen C, et al (2018). Eryth-ropoietin rescues memory impairment in a rat model of chronic cerebral hy-poperfusion via the EPO-R/JAK2/STAT5/PI3K/Akt/GSK-3β pathway. Mol Neurobiol, 55: 3290-3299.
20. Ling C, Del Guerra S, Lupi R, et al (2008). Epigenetic regulation of PPARGC1A in human type 2 diabetic islets and effect on insulin secretion. Diabetologia, 51: 615-622.
21. Franks PW, Christophi CA, Jablonski KA, et al (2014). Common variation at PPARGC1A/B and change in body composition and metabolic traits follow-ing preventive interventions: the Diabetes Prevention Program. Diabetologia, 57: 485-490.
22. Lin J, Handschin C, Spiegelman BM (2005). Metabolic control through the PGC-1 family of transcription coactivators. Cell Metab, 1: 361-370.
23. Pradhan AD, Manson JE, Rifai N, Buring JE, Ridker PM (2001). C-reactive protein, interleukin 6, and risk of developing type 2 diabetes mellitus. JAMA, 286: 327-334.
24. Fontecha‐Barriuso M, Martín‐Sánchez D, Martinez‐Moreno JM, et al (2019). PGC‐1α deficiency causes spontaneous kidney inflammation and increases the severity of nephrotoxic AKI. J Pathol, 249: 65-78.
25. Sheldon RA, Windsor C, Lee BS, Cabeza OA, Ferriero DM (2017). Erythropoietin treatment exacerbates moderate injury af-ter hypoxia-ischemia in neonatal superox-ide dismutase transgenic mice. Develop Neurosci, 39: 228-237.
26. Zhang X, Dong S (2019). Protective effects of erythropoietin towards acute lung inju-ries in rats with sepsis and its related mechanisms. Ann Clin Lab Sci, 49: 257-264.
27. Steelman L, Pohnert S, Shelton J, Franklin R, Bertrand F, McCubrey J (2004). JAK/STAT, Raf/MEK/ERK, PI3K/Akt and BCR-ABL in cell cycle progression and leukemogenesis. Leukemia, 18: 189-218.
28. Fuke H, Shiraki K, Sugimoto K, et al (2007). Jak inhibitor induces S phase cell-cycle ar-rest and augments TRAIL-induced apop-tosis in human hepatocellular carcinoma cells. Biochem Biophy Res Commun, 363: 738-744.
29. Sims NA (2015). Cardiotrophin-like cytokine factor 1 (CLCF1) and neuropoietin (NP) signalling and their roles in development, adulthood, cancer and degenerative dis-orders. Cytokine Growth Factor Rev, 26: 517-522.
30. Su W, Guo C, Wang L, et al (2019). LncRNA MIR22HG abrogation inhibits proliferation and induces apoptosis in esophageal adenocarcinoma cells via acti-vation of the STAT3/c-Myc/FAK signal-ing. Aging (Albany NY), 11: 4587.
31. Gao J, Dai C, Yu X, Yin XB, Zhou F (2020). Long noncoding RNA LINC00324 exerts protumorigenic ef-fects on liver cancer stem cells by upregu-lating fas ligand via PU box binding pro-tein. FASEB J, 34: 5800-5817.
32. Zhang Y, Zhang H, Zhang Z, et al (2019). LncRNA MALAT1 cessation antagoniz-es hypoxia/reoxygenation injury in hepatocytes by inhibiting apoptosis and inflammation via the HMGB1-TLR4 axis. Mol Immunol, 112: 22-29.
33. Li C, Chang L, Chen Z, Liu Z, Wang Y, Ye Q (2017). The role of lncRNA MALAT1 in the regulation of hepatocyte prolifera-tion during liver regeneration. International J Mol Med, 39: 347-356.
2. Nishimuta M, Masui K, Yamamoto T, et al (2018). Copper deposition in oligoden-droglial cells in an autopsied case of hepatolenticular degeneration. Neuropathol-ogy, 38(3): 321-328.
3. Ovchinnikov A, Shprakh V (2016). Hepatolenticular degeneration: diagnostic difficulties (practical experience). Acta Bio-medica Scientifica, 1: 198-201.
4. Bandmann O, Weiss KH, Kaler SG (2015). Wilson's disease and other neurological copper disorders. Lancet Neurol, 14: 103-113.
5. Yang K, Deng Z, Wang J, Jiang L (2017). Clinical analysis of hepatolenticular de-generation in 38 children. J Clin Pediatr, 35: 733-736.
6. Polishchuk EV, Merolla A, Lichtmannegger J, et al (2019). Activation of autophagy, observed in liver tissues from patients with Wilson disease and from ATP7B-deficient animals, protects hepatocytes from copper-induced apoptosis. Gastroen-terology, 156: 1173-1189. e1175.
7. Wu F, Wang J, Pu C, Qiao L, Jiang C (2015). Wilson’s disease: a comprehensive review of the molecular mechanisms. Int J Mol Sci, 16: 6419-6431.
8. Robinson MD, McCarthy DJ, Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of dig-ital gene expression data. Bioinformatics, 26(1): 139-140.
9. Kumar L, Futschik ME (2007). Mfuzz: a software package for soft clustering of microarray data. Bioinformation, 2(1): 5-7.
10. Bao R, Huang L, Andrade J, et al (2014). Re-view of current methods, applications, and data management for the bioinfor-matics analysis of whole exome sequenc-ing. Cancer Inform, 13: CIN. S13779.
11. Tang B, Pan Z, Yin K, Khateeb A (2019). Recent advances of deep learning in bio-informatics and computational biology. Front Genet, 10: 214.
12. Yang F, Liao J, Pei R, et al (2018). Autopha-gy attenuates copper-induced mitochon-drial dysfunction by regulating oxidative stress in chicken hepatocytes. Chemosphere, 204: 36-43.
13. Tsang T, Posimo JM, Gudiel AA, Cicchini M, Feldser DM, Brady DC (2020). Cop-per is an essential regulator of the au-tophagic kinases ULK1/2 to drive lung adenocarcinoma. Nat Cell Biol, 22: 412-424.
14. Singbrant S, Russell MR, Jovic T, et al (2011). Erythropoietin couples erythro-poiesis, B-lymphopoiesis, and bone ho-meostasis within the bone marrow mi-croenvironment. Blood, 117: 5631-5642.
15. Frýdlová J, Rychtarčíková Z, Gurieva I, Vo-kurka M, Truksa J, Krijt J (2017). Effect of erythropoietin administration on pro-teins participating in iron homeostasis in Tmprss6-mutated mask mice. PLoS One, 2: e0186844.
16. Aliosmanoglu I, Kapan M, Gul M, et al (2013). Effects of Erythropoietin on the Serum and Liver Tissue Levels of Cop-per and Zinc in Rats with Obstructive Jaundice. J Med Biochem, 32: 47-51.
17. Higuchi T, Matsukawa Y, Okada K, et al (2006). Correction of copper deficiency improves erythropoietin unresponsive-ness in hemodialysis patients with ane-mia. Int Med, 45(5): 271-273.
18. Verdier F, Chrétien S, Billat C, Gisselbrecht S, Lacombe C, Mayeux P (1997). Eryth-ropoietin induces the tyrosine phosphor-ylation of insulin receptor substrate-2 an alternate pathway for erythropoietin-induced phosphatidylinositol 3-kinase ac-tivation. J Biol Chem, 272: 26173-26178.
19. Ma S, Chen J, Chen C, et al (2018). Eryth-ropoietin rescues memory impairment in a rat model of chronic cerebral hy-poperfusion via the EPO-R/JAK2/STAT5/PI3K/Akt/GSK-3β pathway. Mol Neurobiol, 55: 3290-3299.
20. Ling C, Del Guerra S, Lupi R, et al (2008). Epigenetic regulation of PPARGC1A in human type 2 diabetic islets and effect on insulin secretion. Diabetologia, 51: 615-622.
21. Franks PW, Christophi CA, Jablonski KA, et al (2014). Common variation at PPARGC1A/B and change in body composition and metabolic traits follow-ing preventive interventions: the Diabetes Prevention Program. Diabetologia, 57: 485-490.
22. Lin J, Handschin C, Spiegelman BM (2005). Metabolic control through the PGC-1 family of transcription coactivators. Cell Metab, 1: 361-370.
23. Pradhan AD, Manson JE, Rifai N, Buring JE, Ridker PM (2001). C-reactive protein, interleukin 6, and risk of developing type 2 diabetes mellitus. JAMA, 286: 327-334.
24. Fontecha‐Barriuso M, Martín‐Sánchez D, Martinez‐Moreno JM, et al (2019). PGC‐1α deficiency causes spontaneous kidney inflammation and increases the severity of nephrotoxic AKI. J Pathol, 249: 65-78.
25. Sheldon RA, Windsor C, Lee BS, Cabeza OA, Ferriero DM (2017). Erythropoietin treatment exacerbates moderate injury af-ter hypoxia-ischemia in neonatal superox-ide dismutase transgenic mice. Develop Neurosci, 39: 228-237.
26. Zhang X, Dong S (2019). Protective effects of erythropoietin towards acute lung inju-ries in rats with sepsis and its related mechanisms. Ann Clin Lab Sci, 49: 257-264.
27. Steelman L, Pohnert S, Shelton J, Franklin R, Bertrand F, McCubrey J (2004). JAK/STAT, Raf/MEK/ERK, PI3K/Akt and BCR-ABL in cell cycle progression and leukemogenesis. Leukemia, 18: 189-218.
28. Fuke H, Shiraki K, Sugimoto K, et al (2007). Jak inhibitor induces S phase cell-cycle ar-rest and augments TRAIL-induced apop-tosis in human hepatocellular carcinoma cells. Biochem Biophy Res Commun, 363: 738-744.
29. Sims NA (2015). Cardiotrophin-like cytokine factor 1 (CLCF1) and neuropoietin (NP) signalling and their roles in development, adulthood, cancer and degenerative dis-orders. Cytokine Growth Factor Rev, 26: 517-522.
30. Su W, Guo C, Wang L, et al (2019). LncRNA MIR22HG abrogation inhibits proliferation and induces apoptosis in esophageal adenocarcinoma cells via acti-vation of the STAT3/c-Myc/FAK signal-ing. Aging (Albany NY), 11: 4587.
31. Gao J, Dai C, Yu X, Yin XB, Zhou F (2020). Long noncoding RNA LINC00324 exerts protumorigenic ef-fects on liver cancer stem cells by upregu-lating fas ligand via PU box binding pro-tein. FASEB J, 34: 5800-5817.
32. Zhang Y, Zhang H, Zhang Z, et al (2019). LncRNA MALAT1 cessation antagoniz-es hypoxia/reoxygenation injury in hepatocytes by inhibiting apoptosis and inflammation via the HMGB1-TLR4 axis. Mol Immunol, 112: 22-29.
33. Li C, Chang L, Chen Z, Liu Z, Wang Y, Ye Q (2017). The role of lncRNA MALAT1 in the regulation of hepatocyte prolifera-tion during liver regeneration. International J Mol Med, 39: 347-356.
| Files | ||
| Issue | Vol 52 No 5 (2023) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijph.v52i5.12720 | |
| Keywords | ||
| Hepatolenticular degeneration Adenosine triphosphatase copper transporting β Bioinformatics analysis Copper accumulation | ||
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How to Cite
1.
Yan Y, Xu Y, Chen L, Han Y, Yang R, Hu W. Identification of Lncrna-Mrna Networks in Hepg2 Cells upon ATP7B Knockout and Copper Accumulation. Iran J Public Health. 2023;52(5):1019-1030.
