Transcriptomic and epigenomic effects of insoluble particles on J774 macrophages

References

• Chen S, Yang J, Wei Y, et al. Epigenetic regulation of macrophages: from homeostasis maintenance to host defense. Cell Mol Immunol. 2020;17(1):36–49. PMC6952359.
   Google Scholar
• Marr AK, MacIsaac JL, Jiang R, et al. Leishmania donovani infection causes distinct epigenetic DNA methylation changes in host macrophages. PLoS Pathog. 2014;10(10):e1004419. PMC4192605.
   Google Scholar
• Kawasaki H. A mechanistic review of particle overload by titanium dioxide. Inhal Toxicol. 2017;29(12–14):530–540. PMID: 29458306.
   Google Scholar
• Warheit DB, Overby LH, George G, et al. Pulmonary macrophages are attracted to inhaled particles through complement activation. Exp Lung Res. 1988;14(1):51–66. PMID: 2830106.
   Google Scholar
• Gilberti RM, Knecht DA. Macrophages phagocytose nonopsonized silica particles using a unique microtubule-dependent pathway. Mol Biol Cell. 2015;26(3):518–529. PMC4310742.
   Google Scholar
• Mandarino A, Gregory DJ, McGuire CC, et al. The effect of talc particles on phagocytes in co-culture with ovarian cancer cells. Environ Res. 2020;180:108676. PMID: 31785414.
   Google Scholar
• Berge W, Mundt K, Luu H, et al. Genital use of talc and risk of ovarian cancer: a meta-analysis. Eur J Cancer Prev. 2018 May;27(3):248–257. PMID: 28079603.
   Google Scholar
• Fedulov AV, Leme A, Yang Z, et al. Pulmonary exposure to particles during pregnancy causes increased neonatal asthma susceptibility. Am J Respir Cell Mol Biol. 2008;38(1):57–67. PMC2176127.
   Google Scholar
• Zhang Y, Mikhaylova L, Kobzik L, et al. Estrogen-mediated impairment of macrophageal uptake of environmental TiO2 particles to explain inflammatory effect of TiO2 on airways during pregnancy. J Immunotoxicol. 2015;12(1):81–91. PMID: 24825546.
   Google Scholar
• Ralph P, Prichard J, Cohn M. Reticulum cell sarcoma: an effector cell in antibody-dependent cell- mediated immunity. J Immunol. 1975;114:898–905. PMID: 1089721.
   Google Scholar
• Ralph P, Nakoinz I. Phagocytosis and cytolysis by a macrophage tumour and its cloned cell line. Nature. 1975;257:393–394. PMID: 1101071.
   Google Scholar
• Józefowski S, Arredouani M, Sulahian T, et al. Disparate regulation and function of the class A scavenger receptors SR-AI/II and MARCO. J Immunol. 2005;175(12):8032–8041. PMID: 16339540.
   Google Scholar
• Hayashi T, Yamada K, Esaki T, et al. Physiological concentrations of 17beta-estradiol inhibit the synthesis of nitric oxide synthase in macrophages via a receptor-mediated system. J Cardiovasc Pharmacol. 1998;31(2):292–298. PMID: 9475272.
   Google Scholar
• Meer A, Gnirke A, Bell GW, et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005;33(18):5868–5877. PMC1258174.
   Google Scholar
• Gu H, Smith ZD, Bock C, et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc. 2011;6(4):468–481. PMID: 21412275.
   Google Scholar
• Fouse SD, Nagarajan RO, Costello JF. Genome-scale DNA methylation analysis. Epigenomics. 2010;2(1):105–117. PMC2907108.
   Google Scholar
• Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, et al. Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. J Vis Exp. 2015;96:e52246. PMC4354670
   Google Scholar
• Mejías Rivera L, Fedulov AV The effect of talc on J774 cells. Gene expression omnibus (GEO) database entry. Record# GSE135238.
   Google Scholar
• Andrews S FastQC: a quality control tool for high throughput sequence data. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
   Google Scholar
• Krueger F. Trim galore. Available from: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore.
   Google Scholar
• Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–1572. PMC3102221.
   Google Scholar
• Chen Y, Pal B, Visvader JE, et al. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Res. 2017;6(2055):PMC5747346.
   Google Scholar
• Emi T, Mejias-Rivera L, Wallace J, et al. Epigenomic effect of talc particles on macrophages. Gene Expression Omnibus (GEO) database entry. Record# GSE150322.
   Google Scholar
• Gimenez JLG, Carbonell NE, Mateo CR, et al. Epigenetics as the driving force in long-term immunosuppression. J Clin Epigenet. 2016;2:2.
   Google Scholar
• Gordon S. Phagocytosis: an immunobiologic process. Immunity. 2016;44(3):463–475. PMID: 26982354.
   Google Scholar
• Baan R, Straif K, Grosse Y, et al.; WHO International Agency for Research on Cancer Monograph Working Group. Carcinogenicity of carbon black, titanium dioxide, and talc. Lancet Oncol. 2006 Apr;7(4):295–296. No abstract available. Erratum in: Lancet Oncol. 2006 May;7(5):365.PMID: 16598890. doi:https://doi.org/10.1016/S1470-2045(06)70651-9.
   Google Scholar
• Cramer DW, Vitonis AF, Terry KL, et al. The association between talc use and ovarian cancer: a retrospective case-control study in two US states. Epidemiology. 2016 May;27(3):334–346. PMC4820665.
   Google Scholar
• Langseth H, Hankinson SE, Siemiatycki J, et al. Perineal use of talc and risk of ovarian cancer. J Epidemiol Community Health. 2008 Apr;62(4):358–360. PMID: 18339830.
   Google Scholar
• Cramer DW, Welch WR, Berkowitz RS, et al. Presence of talc in pelvic lymph nodes of a woman with ovarian cancer and long-term genital exposure to cosmetic talc. Obstet Gynecol. 2007;110(2 Pt 2):498–501.
   Google Scholar
• Titanium dioxide in food — should you be concerned? Available from: https://www.healthline.com/nutrition/titanium-dioxide-in-food#uses
   Google Scholar
• Titanium dioxide. Available from: https://www.chemicalsafetyfacts.org/titanium-dioxide/
   Google Scholar
• Nogueira CM, de Azevedo WM, Dagli ML, et al. Titanium dioxide induced inflammation in the small intestine. World J Gastroenterol. 2012;18(34):4729–4735. PMC3442211.
   Google Scholar
• IARC monographs on the evaluation of carcinogenic risks to humans. Vol. 93. Lyon, France: Carbon Black, Titanium Dioxide, and Talc; 2010. Available from: https://www.ncbi.nlm.nih.gov/books/NBK326521/
   Google Scholar
• Titanium Dioxide (TiO2). by Eileen D. Kuempel and Avima Ruder. Citation for most recent IARC review. IARC Monograph 93 (in press). TR42-4. Available from: https://monographs.iarc.fr/wp-content/uploads/2018/06/TR42-4.pdf.
   Google Scholar
• Kim BG, Lee PH, Lee SH, et al. Effect of TiO₂ nanoparticles on inflammasome-mediated airway inflammation and responsiveness. Allergy Asthma Immunol Res. 2017;9(3):257–264. PMC5352577.
   Google Scholar
• Refaat T, West D, El Achy S, et al. Distribution of iron oxide core-titanium dioxide shell nanoparticles in VX2 tumor bearing rabbits introduced by two different delivery modalities. Nanomaterials (Basel). 2016;6(8):143. PMC5224625.
   Google Scholar
• Sandoval-Sierra JV, Salgado García FI, Brooks JH, et al. Effect of short-term prescription opioids on DNA methylation of the OPRM1 promoter. Clin Epigenetics. 2020;12(1):76. PMC7268244.
   Google Scholar
• Byun HM, Nordio F, Coull BA, et al. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PLoS One. 2012;7(6):e39220. PMC3379987.
   Google Scholar
• Hartley I, Elkhoury FF, Heon Shin J, et al. Long-lasting changes in DNA methylation following short-term hypoxic exposure in primary hippocampal neuronal cultures. PLoS One. 2013;8(10):e77859. PMC3808424.
   Google Scholar
• Ferrari L, Carugno M, Bollati V. Particulate matter exposure shapes DNA methylation through the lifespan. Clin Epigenetics. 2019;11(1):129. PMC6717322.
   Google Scholar
• Gregory DJ, Kobzik L, Yang Z, et al. Transgenerational transmission of asthma risk after exposure to environmental particles during pregnancy. Am J Physiol Lung Cell Mol Physiol. 2017;313(2):L395–L405. PMC5582941.
   Google Scholar
• Pacis A, Mailhot-Léonard F, Tailleux L, et al. Gene activation precedes DNA demethylation in response to infection in human dendritic cells. Proc Natl Acad Sci U S A. 2019;116(14):6938–6943. PMC6452747.
   Google Scholar