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Identification of Genes Related to Fat Deposition as Candidates for ER Stress Based on Combined RNA-ATAC Sequencing Analysis

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24 abr 2025

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Abdolahi A., Vahabzadeh Z., Izadpanah E., Moloudi M.R. (2022). Vaspin attenuates steatosis-induced fibrosis via GRP78 receptor by targeting AMPK signaling pathway. J. Physiol. Biochem., 78: 185–197.Search in Google Scholar

Ai X., Xiang L., Huang Z., Zhou S., Zhang S., Zhang T., Jiang T. (2018). Overexpression of PIK3R1 promotes hepatocellular carcinoma progression. Biol. Res., 51: 1–10.Search in Google Scholar

Apostolou A., Shen Y., Liang Y., Luo J., Fang S. (2008). Armet, a UPR-upregulated protein, inhibits cell proliferation and ER stress-induced cell death. Exp. Cell Res., 314: 2454–2467.Search in Google Scholar

Bösl M.R., Takaku K., Oshima M., Nishimura S., Taketo M.M. (1997). Early embryonic lethality caused by targeted disruption of the mouse selenocysteine tRNA gene (Trsp). Proc. Natl. Acad. Sci. USA, 94: 5531–5534.Search in Google Scholar

Buenrostro J.D., Wu B., Chang H.Y., Greenleaf W.J. (2015). ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol., 109: 21.29.1.Search in Google Scholar

Capelle C.M., Zeng N., Danileviciute E., Rodrigues S.F., Ollert M., Balling R., He F.Q. (2021). Identification of VIMP as a gene inhibiting cytokine production in human CD4+ effector T cells. iScience, 24: 102289.Search in Google Scholar

Chhetri G., Liang Y., Shao J., Han D., Yang Y., Hou C., Wang P., Tao X., Shen Y., Jiang T., Feng L., Shen Y. (2020). Role of mesencephalic astrocyte-derived neurotrophic factor in alcohol-induced liver injury. Oxid. Med. Cell. Longev., 2020: 9034864.Search in Google Scholar

Chrobociński K., Witarski W., Piórkowska K., (2022). A method of hepatocytes segmentation in microscopic images of trypan blue stained cellular suspension. Proc. Science and Information Conference, 2022, pp. 214–224.Search in Google Scholar

Curran J.E., Jowett J.B.M., Elliott K.S., Gao Y., Gluschenko K., Wang J., Azim D.M.A., Cai G., Mahaney M.C., Comuzzie A.G., Dyer T.D., Walder K.R., Zimmet P., MacCluer J.W., Collier G.R., Kissebah A.H., Blangero J. (2005). Genetic variation in selenoprotein S influences inflammatory response. Nat. Genet., 37: 1234–1241.Search in Google Scholar

Dudek J., Benedix J., Cappel S., Greiner M., Jalal C., Müller L., Zimmermann R. (2009). Functions and pathologies of BiP and its interaction partners. Cell. Mol. Life Sci., 66: 1556–1569.Search in Google Scholar

Fernandes-da-Silva A., Miranda C.S., Santana-Oliveira D.A., Oliveira-Cordeiro B., Rangel-Azevedo C., Silva-Veiga F.M., Martins F.F., Souza-Mello V. (2021). Endoplasmic reticulum stress as the basis of obesity and metabolic diseases: focus on adipose tissue, liver, and pancreas. Europ. J. Nutr., 60: 2949–2960.Search in Google Scholar

Fruman D.A., Mauvais-Jarvis F., Pollard D.A., Yballe C.M., Brazil D., Bronson R.T., Kahn C.R., Cantley L.C. (2000). Hypoglycaemia, liver necrosis and perinatal death in mice lacking all isoforms of phosphoinositide 3-kinase p85 alpha. Nat. Genet., 26: 379–382.Search in Google Scholar

Gao Y., Feng H.C., Walder K., Bolton K., Sunderland T., Bishara N., Quick M., Kantham L., Collier G.R. (2004). Regulation of the selenoprotein SelS by glucose deprivation and endoplasmic reticulum stress – SelS is a novel glucose-regulated protein. FEBS Lett., 563: 185–190.Search in Google Scholar

Iurlaro R., Muñoz-Pinedo C. (2016). Cell death induced by endoplasmic reticulum stress. FEBS J., 283: 2640–2652.Search in Google Scholar

Jang S., Lee C.H. Choi K.M., Lee J., Choi J.W., Kim K.A., Park C.M. (2011). Correlation of fatty liver and abdominal fat distribution using a simple fat computed tomography protocol. World J. Gastroenterol., 17: 3335–3341.Search in Google Scholar

Ji N., Xiang L., Zhou B., Lu Y., Zhang M. (2023). Hepatic gene expression profiles during fed–fasted–refed state in mice. Front. Genet., 14: 1145769.Search in Google Scholar

Kampinga H.H., Craig E.A. (2010). The HSP70 chaperone machinery: J proteins as drivers of functional specificity. Nat. Rev. Mol. Cell Biol., 11: 579–592.Search in Google Scholar

Kim Y.J., Kim H.J., Chung K.Y., Choi I., Kim S.H. (2014). Transcriptional activation of PIK3R1 by PPARγ in adipocytes. Mol. Biol. Rep., 41: 5267–5272.Search in Google Scholar

Kuwabara K., Matsumoto M., Ikeda J., Hori O., Ogawa S., Maeda Y., Kitagawa K., Imuta N., Kinoshita T., Stern D.M., Yanagi H., Kamada T. (1996). Purification and characterization of a novel stress protein, the 150-kDa oxygen-regulated protein (ORP150), from cultured rat astrocytes and its expression in ischemic mouse brain. J. Biol. Chem., 271: 5025–5032.Search in Google Scholar

Lee A.H., Scapa E.F., Cohen D.E., Glimcher L.H. (2008). Regulation of hepatic lipogenesis by the transcription factor XBP1. Science, 320: 1492–1496.Search in Google Scholar

Lee J., Sun C., Zhou Y., Lee J., Gokalp D., Herrema H., Park S.W. Davis R.J., Ozcan U. (2011). p38 MAPK-mediated regulation of Xbp1s is crucial for glucose homeostasis. Nat. Med., 17: 1251–1260.Search in Google Scholar

Lee J.H., Kwon J.H., Jeon Y.H., Ko K.Y., Lee S.R., Kim I.Y. (2014). Pro178 and Pro183 of selenoprotein S are essential residues for interaction with p97(VCP) during endoplasmic reticulum-associated degradation. J. Biol. Chem., 289: 13758–13768.Search in Google Scholar

Lee J.H., Park K.J., Jang J.K., Jeon Y.H., Ko K.Y., Kwon J.H., Lee S.R., Kim I.Y. (2015). Selenoprotein S-dependent selenoprotein K binding to p97(VCP) protein is essential for endoplasmic reticulum-associated degradation. J. Biol. Chem., 290: 29941–29952.Search in Google Scholar

Lin Y., Yang Z., Xu A., Dong P., Huang Y., Liu H., Li F., Wang H., Xu Q., Wang Y., Sun D., Zou Y., Zou X., Wang Yu, Zhang D., Liu H., Wu X., Zhang M., Fu Y., Cai Z., Liu C., Wu S. (2015). PIK3R1 negatively regulates the epithelial-mesenchymal transition and stem-like phenotype of renal cancer cells through the AKT/ GSK3β/CTNNB1 signaling pathway. Sci. Rep., 5: 8997.Search in Google Scholar

Lindholm P., Peränen J., Andressoo J.O., Kalkkinen N., Kokaia Z., Lindvall O., Timmusk T., Saarma M. (2008). MANF is widely expressed in mammalian tissues and differently regulated after ischemic and epileptic insults in rodent brain. Mol. Cell. Neurosci., 39: 356–371.Search in Google Scholar

Liu X., Green R.M. (2019). Endoplasmic reticulum stress and liver diseases. Liver Res., 3: 55–64.Search in Google Scholar

Liu J., Wu Z., Han D., Wei C., Liang Y., Jiang T., Chen L., Sha M., Cao Y., Huang F., Geng X., Yu J., Shen Yujun Wang H., Feng L., Wang D., Fang S., Wang S., Shen Y. (2020). Mesencephalic astrocyte-derived neurotrophic factor inhibits liver cancer through small ubiquitin-related modifier (SUMO)ylation-related suppression of NF-κB/Snail signaling pathway and epithelial-mesenchymal transition. Hepatology, 71: 1262–1278.Search in Google Scholar

Liu X., Henkel A.S., LeCuyer B.E., Schipma M.J., Anderson K.A., Green R.M. (2015). Hepatocyte X-box binding protein 1 deficiency increases liver injury in mice fed a high-fat/sugar diet. Am. J. Physiol. Gastrointest. Liver Physiol., 309: G965–G974.Search in Google Scholar

Love M.I., Huber W., Anders S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15: 550.Search in Google Scholar

Malhi H., Kaufman R.J. (2011). Endoplasmic reticulum stress in liver disease. J. Hepatol., 54: 795–809.Search in Google Scholar

Milani P., Escalante-Chong R., Shelley B.C., Patel-Murray N.L., Xin X., Adam M., Mandefro B., Sareen D., Svendsen C.N., Fraenkel E. (2016). Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells. Sci. Rep., 61: 1–10.Search in Google Scholar

Mizobuchi N., Hoseki J., Kubota H., Toyokuni S., Nozaki J.I., Naitoh M., Koizumi A., Nagata K. (2007). ARMET is a soluble ER protein induced by the unfolded protein response via ERSE-II element. Cell Struct. Funct., 32: 41–50.Search in Google Scholar

Park S.W., Zhou Y., Lee J., Lu A., Sun C., Chung J., Ueki K., Ozcan U. (2010). The regulatory subunits of PI3K, p85α and p85β, interact with XBP-1 and increase its nuclear translocation. Nat. Med., 16: 429–437.Search in Google Scholar

Piórkowska K., Żukowski K., Ropka-Molik K., Tyra M. (2022). New long-non coding RNAs related to fat deposition based on pig model. Ann. Anim. Sci., 22: 1211–1224.Search in Google Scholar

Pitts M.W., Hoffmann P.R. (2018). Endoplasmic reticulum-resident selenoproteins as regulators of calcium signaling and homeostasis. Cell Calcium, 70: 76–86.Search in Google Scholar

Rao S., Oyang L., Liang J., Yi P., Han Y., Luo X., Xia L., Lin J., Tan S., Hu J., Wang H., Tang L., Pan Q., Tang Y., Zhou Y., Liao Q. (2021). Biological function of HYOU1 in tumors and other diseases. Onco. Targets. Ther., 14: 1727–1735.Search in Google Scholar

Rehati A., Abuduaini B., Liang Z., Chen D., He F. (2023). Identification of heat shock protein family A member 5 (HSPA5) targets involved in nonalcoholic fatty liver disease. Genes Immun., 24: 124–129.Search in Google Scholar

Ropka-Molik K., Pawlina-Tyszko K., Żukowski K., Tyra M., Derebecka N., Wesoły J., Szmatoła T., Piórkowska K. (2020). Identification of molecular mechanisms related to pig fatness at the transcriptome and miRNAome levels. Genes (Basel)., 11: 600.Search in Google Scholar

Rueli R.H.L.H., Torres D.J., Dewing A.S.T., Kiyohara A.C., Barayuga S.M., Bellinger M.T., Uyehara-Lock J.H., White L.R., Moreira P.I., Berry M.J., Perry G., Bellinger F.P. (2017). Selenoprotein S reduces endoplasmic reticulum stress-induced phosphorylation of tau: potential role in selenate mitigation of tau pathology. J. Alzheimers. Dis., 55: 749–762.Search in Google Scholar

Sanson M., Ingueneau C., Vindis C., Thiers J.C., Glock Y., Rousseau H., Sawa Y., Bando Y., Mallat Z., Salvayre R., Nègre-Salvayre A. (2008). Oxygen-regulated protein-150 prevents calcium homeostasis deregulation and apoptosis induced by oxidized LDL in vascular cells. Cell Death Differ., 15: 1255–1265.Search in Google Scholar

Savell J.W., Cross H.R. (1988). The role of fat in the palatability of beef, pork, and lamb. Committee on Technological Options to Improve the Nutritional Attributes of Animal Products. National Academies Press (US).Search in Google Scholar

Schulze A., Standera S., Buerger E., Kikkert M., Van Voorden S., Wiertz E., Koning F., Kloetzel P.M., Seeger M. (2005). The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway. J. Mol. Biol., 354: 1021–1027.Search in Google Scholar

Schweizer U., Fradejas-Villar N. (2016). Why 21? The significance of selenoproteins for human health revealed by inborn errors of metabolism. FASEB J., 30: 3669–3681.Search in Google Scholar

Steensels S., Qiao J., Ersoy B.A. (2020). Transcriptional regulation in non-alcoholic fatty liver disease. Metabolites, 10: 1–34.Search in Google Scholar

Sun Y., Cai R., Wang Y., Zhao R., Qin J., Pang W. (2020). A newly identified lncRNA LncIMF4 controls adipogenesis of porcine intramuscular preadipocyte through attenuating autophagy to inhibit lipolysis. Animals, 10: 926.Search in Google Scholar

Tyra M., Zak G. (2013). Analysis of the possibility of improving the indicators of pork quality through selection with particular consideration of intramuscular fat (IMF) content. Ann. Anim. Sci., 13: 33–44.Search in Google Scholar

Ueki K., Algenstaedt P., Mauvais-Jarvis F., Kahn C.R. (2000). Positive and negative regulation of phosphoinositide 3-kinase-dependent signaling pathways by three different gene products of the p85alpha regulatory subunit. Mol. Cell. Biol., 20: 8035–8046.Search in Google Scholar

Vickers A.E.M., Ulyanov A.V., Fisher R.L. (2018). Progression of repair and injury in human liver slices. Int. J. Mol. Sci., 19: 4130. Wang D.Q., Miao X., Gao J., Zhou Y., Ji F., Cheng X. (2019). The 150-kDa oxygen-regulated protein (ORP150) regulates proteinuria in diabetic nephropathy via mediating VEGF. Exp. Mol. Pathol., 110: 104255.Search in Google Scholar

Wang J., Lee J., Liem D., Ping P. (2017). HSPA5 Gene encoding Hsp70 chaperone BiP in the endoplasmic reticulum. Gene, 618: 14–23. Wang M., Wey S., Zhang Y., Ye R., Lee A.S. (2009). Role of the unfolded protein response regulator GRP78/BiP in development, cancer, and neurological disorders. Antioxid. Redox Signal., 11: 2307–2316.Search in Google Scholar

Wang M., Zhang J., Gong N. (2022). Role of the PI3K/Akt signaling pathway in liver ischemia reperfusion injury: a narrative review. Ann. Palliat. Med., 11: 806–817.Search in Google Scholar

Xiao G., Zhang T., Yu S., Lee S., Calabuig-Navarro V., Yamauchi J., Ringquist S., Dong H.H. (2013). ATF4 protein deficiency protects against high fructose-induced hypertriglyceridemia in mice. J. Biol. Chem., 288: 25350–25361.Search in Google Scholar

Xing K., Wang K., Ao H., Chen S., Tan Z., Wang Y., Xitong Z., Yang T., Zhang F., Liu Y., Ni H., Sheng X., Qi X., Wang X., Guo Y., Wang C. (2019). Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds. Sci. Rep., 9: 1–11.Search in Google Scholar

Yan F., Powell D.R., Curtis D.J., Wong N.C. (2020). From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol., 21: 1–16.Search in Google Scholar

Yang C., Gao Y. (2020). Mesencephalic astrocyte-derived neurotrophic factor: A treatment option for Parkinson’s disease. Front. Biosci., 25: 1718–1731.Search in Google Scholar

Yang W., Shen Y., Chen Y., Chen L., Wang L., Wang H., Xu S., Fang S., Fu Y., Yu Y., Shen Yuxian (2014). Mesencephalic astrocyte-derived neurotrophic factor prevents neuron loss via inhibiting ischemia-induced apoptosis. J. Neurol. Sci., 344: 129–138.Search in Google Scholar

Ye Y., Shibata Y., Yun C., Ron D., Rapoport T.A., Ye Y., Shibata Y., Yun C., Ron D., Rapoport T.A. (2004). A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol. Nature, 429: 841–847.Search in Google Scholar

Yoshiuchi K., Kaneto H., Matsuoka T., Kohno K., Iwawaki T., Nakatani Y., Yamasaki Y., Hori M., Matsuhisa M. (2008). Direct monitoring of in vivo ER stress during the development of insulin resistance with ER stress-activated indicator transgenic mice. Biochem. Biophys. Res. Commun., 366: 545–550.Search in Google Scholar

Zong Z.H., Du Z.X., Zhang H.Y., Li C., An M.X., Li S., Yao H.B., Wang H.Q. (2016). Involvement of Nrf2 in proteasome inhibition-mediated induction of ORP150 in thyroid cancer cells. Oncotarget, 7: 3416–3426.Search in Google Scholar

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