Department of Toxicogenomics

2015

  1. Gibb H, Devleesschauwer B, Bolger PM, Wu F, Ezendam J, Cliff J, Zeilmaker M, Verger P, Pitt J, Baines J, Adegoke G, Afshari R, Liu Y, Bokkers B, van Loveren H, Mengelers M, Brandon E, Havelaar AH, Bellinger D. World Health Organization estimates of the global and regional disease burden of four foodborne chemical toxins, 2010: a data synthesis. F1000Res. 2015 Dec 3;4:1393. doi: 10.12688/f1000research.7340.1. eCollection 2015. PubMed PMID: 26918123; PubMed Central PMCID: PMC4755404.
  2. Doedée AM, Kannegieter N, Öztürk K, van Loveren H, Janssen R, Buisman AM. Higher numbers of memory B-cells and Th2-cytokine skewing in high responders to hepatitis B vaccination. Vaccine. 2015 Dec 22. pii: S0264-410X(15)01799-5. doi: 10.1016/j.vaccine.2015.12.027. [Epub ahead of  print] PubMed PMID: 26721327.
  3. Askenase PW, Bryniarski K, Paliwal V, Redegeld F, Groot Kormelink T, Kerfoot S, Hutchinson AT, van Loveren H, Campos R, Itakura A, Majewska-Szczepanik M, Yamamoto N, Nazimek K, Szczepanik M, Ptak W. A subset of AID-dependent B-1a cells initiates hypersensitivity and pneumococcal pneumonia resistance. Ann N Y AcadSci. 2015 Dec;1362(1):200-14. doi: 10.1111/nyas.12975. PubMed PMID: 26662721; PubMed Central PMCID: PMC4681304.
  4. Dik S, Pennings JL, van Loveren H, Ezendam J. Development of an in vitro test to identify respiratory sensitizers in bronchial epithelial cells using gene expression profiling. Toxicol In Vitro. 2015 Dec 25;30(1 Pt B):274-80. doi:10.1016/j.tiv.2015.10.010. Epub 2015 Oct 28. PubMed PMID: 26518187.
  5. Krauskopf J, Verheijen M, Kleinjans JC, de Kok TM, Caiment F. Development and regulatory application of microRNA biomarkers. Biomark Med. 2015;9(11):1137-51. doi: 10.2217/bmm.15.50. Epub 2015 Oct 26. PubMed PMID: 26502281.
  6. O'Callaghan-Gordo C, Fthenou E, Pedersen M, Espinosa A, Chatzi L, Beelen R, Chalkiadaki G, Decordier I, Hoek G, Merlo DF, Nieuwenhuijsen M, Roumeliotaki T, Vafeiadi M, Vande Loock K, Kleinjans J, Stephanou E, Kirsch-Volders M, Kogevinas M. Outdoor air pollution exposures and micronuclei frequencies in lymphocytes from pregnant women and newborns in Crete, Greece (Rhea cohort). Environ Res. 2015 Nov;143(Pt A):170-6. doi: 10.1016/j.envres.2015.10.011. Epub 2015 Oct 21. PubMed PMID: 26496153.
  7. Cavill R, Jennen D, Kleinjans J, Briedé JJ. Transcriptomic and metabolomics data integration. Brief Bioinform. 2015 Oct 14. pii: bbv090. [Epub ahead of print] PubMed PMID: 26467821.
  8. Kato N, Loh M, Takeuchi F, Verweij N, Wang X, Zhang W, Kelly TN, Saleheen D, Lehne B, Mateo Leach I, Drong AW, Abbott J, Wahl S, Tan ST, Scott WR, Campanella G, Chadeau-Hyam M, Afzal U, Ahluwalia TS, Bonder MJ, Chen P, Dehghan A, Edwards TL, Esko T, Go MJ, Harris SE, Hartiala J, Kasela S, Kasturiratne A, Khor CC, Kleber ME, Li H, Mok ZY, Nakatochi M, Sapari NS, Saxena R, Stewart AF, Stolk L, Tabara Y, Teh AL, Wu Y, Wu JY, Zhang Y, Aits I, Da Silva Couto Alves A, Das S, Dorajoo R, Hopewell JC, Kim YK, Koivula RW, Luan J, Lyytikäinen LP, Nguyen QN, Pereira MA, Postmus I, Raitakari OT, Bryan MS, Scott RA, Sorice R, Tragante V, Traglia M, White J, Yamamoto K, Zhang Y, Adair LS, Ahmed A, Akiyama K, Asif R, Aung T, Barroso I, Bjonnes A, Braun TR, Cai H, Chang LC, Chen CH, Cheng CY, Chong YS, Collins R, Courtney R, Davies G, Delgado G, Do LD, Doevendans PA, Gansevoort RT, Gao YT, Grammer TB, Grarup N, Grewal J, Gu D, Wander GS, Hartikainen AL, Hazen SL, He J, Heng CK, Hixson JE, Hofman A, Hsu C, Huang W, Husemoen LL, Hwang JY, Ichihara S, Igase M, Isono M, Justesen JM, Katsuya T, Kibriya MG, Kim YJ, Kishimoto M, Koh WP, Kohara K, Kumari M, Kwek K, Lee NR, Lee J, Liao J, Lieb W, Liewald DC, Matsubara T, Matsushita Y, Meitinger T, Mihailov E, Milani L, Mills R, Mononen N, Müller-Nurasyid M, Nabika T, Nakashima E, Ng HK, Nikus K, Nutile T, Ohkubo T, Ohnaka K, Parish S, Paternoster L, Peng H, Peters A, Pham ST, Pinidiyapathirage MJ, Rahman M, Rakugi H, Rolandsson O, Rozario MA, Ruggiero D, Sala CF, Sarju R, Shimokawa K, Snieder H, Sparsø T, Spiering W, Starr JM, Stott DJ, Stram DO, Sugiyama T, Szymczak S, Tang WH, Tong L, Trompet S, Turjanmaa V, Ueshima H, Uitterlinden AG, Umemura S, Vaarasmaki M, van Dam RM, van Gilst WH, van Veldhuisen DJ, Viikari JS, Waldenberger M, Wang Y, Wang A, Wilson R, Wong TY, Xiang YB, Yamaguchi S, Ye X, Young RD, Young TL, Yuan JM, Zhou X, Asselbergs FW, Ciullo M, Clarke R, Deloukas P, Franke A, Franks PW, Franks S, Friedlander Y, Gross MD, Guo Z, Hansen T, Jarvelin MR, Jørgensen T, Jukema JW, Kähönen M, Kajio H, Kivimaki M, Lee JY, Lehtimäki T, Linneberg A, Miki T, Pedersen O, Samani NJ, Sørensen TI, Takayanagi R, Toniolo D; BIOS-consortium; CARDIo GRAMplusCD; LifeLines Cohort Study; InterAct Consortium, Ahsan H, Allayee H, Chen YT, Danesh J, Deary IJ, Franco OH, Franke L, Heijman BT, Holbrook JD, Isaacs A, Kim BJ, Lin X, Liu J, März W, Metspalu A, Mohlke KL, Sanghera DK, Shu XO, van Meurs JB, Vithana E, Wickremasinghe AR, Wijmenga C, Wolffenbuttel BH, Yokota M, Zheng W, Zhu D, Vineis P, Kyrtopoulos SA, Kleinjans JC, McCarthy MI, Soong R, Gieger C, Scott J, Teo YY, He J, Elliott P, Tai ES, van der Harst P, Kooner JS, Chambers JC. Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet. 2015 Nov;47(11):1282-93. doi: 10.1038/ng.3405. Epub 2015 Sep 21. PubMed PMID: 26390057; PubMed Central PMCID: PMC4719169.
  9. Jennen DG, van Leeuwen DM, Hendrickx DM, Gottschalk RW, van Delft JH, Kleinjans JC. Bayesian Network Inference Enables Unbiased Phenotypic Anchoring of Transcriptomic Responses to Cigarette Smoke in Humans. Chem Res Toxicol. 2015 Oct 19;28(10):1936-48. doi: 10.1021/acs.chemrestox.5b00145. Epub 2015 Sep 17. PubMed PMID: 26360787.
  10. Kleinjans J, Botsivali M, Kogevinas M, Merlo DF; NewGeneris consortium. Fetal exposure to dietary carcinogens and risk of childhood cancer: what the NewGeneris project tells us. BMJ. 2015 Aug 28;351:h4501. doi: 10.1136/bmj.h4501. PubMed PMID: 26320143.
  11. Shao J, Stout I, Volger OL, Hendriksen PJ, van Loveren H, Peijnenburg AA. Inhibition of CXCL12-mediated chemotaxis of Jurkat cells by direct immunotoxicants. Arch Toxicol. 2015 Aug 28. [Epub ahead of print] PubMed PMID: 26314263.
  12. Krauskopf J, Espín-Pérez A, Kleinjans JC, de Kok TM. Global MicroRNA Analysis in Primary Hepatocyte Cultures. Methods Mol Biol. 2015;1250:241-50. doi: 10.1007/978-1-4939-2074-7_17. PubMed PMID: 26272147.
  13. Souza T, Jennen D, van Delft J, van Herwijnen M, Kyrtoupolos S, Kleinjans J. New insights into BaP-induced toxicity: role of major metabolites in transcriptomics and contribution to hepatocarcinogenesis. Arch Toxicol. 2015 Aug 4. [Epub ahead of print] PubMed PMID: 26238291.
  14. Espín-Pérez A, de Kok TM, Jennen DG, Hendrickx DM, De Coster S, Schoeters G, Baeyens W, van Larebeke N, Kleinjans JC. Distinct genotype-dependent differences in transcriptome responses in humans exposed to environmental carcinogens. Carcinogenesis. 2015 Oct;36(10):1154-61. doi: 10.1093/carcin/bgv111. Epub 2015 Aug 1. PubMed PMID: 26233959.
  15. Deferme L, Wolters J, Claessen S, Briedé J, Kleinjans J. Oxidative Stress Mechanisms Do Not Discriminate between Genotoxic and Nongenotoxic Liver Carcinogens. Chem Res Toxicol. 2015 Aug 17;28(8):1636-46. doi: 10.1021/acs.chemrestox.5b00222. Epub 2015 Aug 4. PubMed PMID: 26198647.
  16. Jiang J, Wolters JE, van Breda SG, Kleinjans JC, de Kok TM. Development of novel tools for the in vitro investigation of drug-induced liver injury. Expert Opin Drug Metab Toxicol. 2015;11(10):1523-37. doi: 10.1517/17425255.2015.1065814. Epub 2015 Jul 9. PubMed PMID: 26155718.
  17. Wijnands KA, Meesters DM, van Barneveld KW, Visschers RG, Briedé JJ, Vandendriessche B, van Eijk HM, Bessems BA, van den Hoven N, von Wintersdorff CJ, Brouckaert P, Bouvy ND, Lamers WH, Cauwels A, Poeze M. Citrulline Supplementation Improves Organ Perfusion and Arginine Availability under Conditions with Enhanced Arginase Activity. Nutrients. 2015 Jun 29;7(7):5217-38. doi: 10.3390/nu7075217. PubMed PMID: 26132994; PubMed Central PMCID: PMC4516994.
  18. Jetten MJ, Ruiz-Aracama A, Coonen ML, Claessen SM, van Herwijnen MH, Lommen A, van Delft JH, Peijnenburg AA, Kleinjans JC. Interindividual variation in gene expression responses and metabolite formation in acetaminophen-exposed primary human hepatocytes. Arch Toxicol. 2015 Jun 24. [Epub ahead of print] PubMed PMID: 26104854.
  19. Rieswijk L, Brauers KJ, Coonen ML, van Breda SG, Jennen DG, Kleinjans JC. Evaluating microRNA profiles reveals discriminative responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes. Mutagenesis. 2015 Nov;30(6):771-84. doi: 10.1093/mutage/gev036. Epub 2015 May 14. PubMed PMID: 25976910.
  20. Jiang J, Briedé JJ, Jennen DG, Kleinjans JC, de Kok TM. Response to cytochrome P450-derived versus mitochondrial oxidant stress in acetaminophen hepatotoxicity. Toxicol Lett. 2015 Jun 15;235(3):218-9. doi: 10.1016/j.toxlet.2015.04.003. Epub 2015 Apr 17. PubMed PMID: 25895633.
  21. Tonk EC, Verhoef A, Gremmer ER, van Loveren H, Piersma AH. Developmental immunotoxicity testing of 4-methyl anisole. Regul Toxicol Pharmacol. 2015 Jul;72(2):379-85. doi: 10.1016/j.yrtph.2015.04.003. Epub 2015 Apr 14. PubMed PMID: 25882306.
  22. Coonen MLj, Theunissen DH, Kleinjans JC, Jennen DG. MagiCMicroRna: a web implementation of AgiMicroRna using shiny. Source Code Biol Med. 2015 Mar 26;10:4. doi: 10.1186/s13029-015-0035-5. eCollection 2015. PubMed PMID: 25838840; PubMed Central PMCID: PMC4383057.
  23. Nymark P, Wijshoff P, Cavill R, van Herwijnen M, Coonen ML, Claessen S, Catalán J, Norppa H, Kleinjans JC, Briedé JJ. Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells. Nanotoxicology. 2015;9(5):624-35. doi: 10.3109/17435390.2015.1017022. Epub 2015 Apr 1. PubMed PMID: 25831214.
  24. Pennings JL, Jennen DG, Nygaard UC, Namork E, Haug LS, van Loveren H, Granum B. Cord blood gene expression supports that prenatal exposure to perfluoroalkyl substances causes depressed immune functionality in early childhood. J Immunotoxicol. 2016 Mar;13(2):173-80. doi: 10.3109/1547691X.2015.1029147. Epub 2015 Mar 27. PubMed PMID: 25812627.
  25. Deferme L, Briedé JJ, Claessen SM, Cavill R, Kleinjans JC. Cell line-specific oxidative stress in cellular toxicity: A toxicogenomics-based comparison between liver and colon cell models. Toxicol In Vitro. 2015 Aug;29(5):845-55. doi:10.1016/j.tiv.2015.03.007. Epub 2015 Mar 21. PubMed PMID: 25800948.
  26. Schaaf MB, Jutten B, Keulers TG, Savelkouls KG, Peeters HJ, van den Beucken T, van Schooten FJ, Godschalk RW, Vooijs M, Rouschop KM. Canonical autophagy does not contribute to cellular radioresistance. Radiother Oncol. 2015 Mar;114(3):406-12. doi: 10.1016/j.radonc.2015.02.019. Epub 2015 Mar 13. PubMed PMID: 25779723.
  27. Henatsch D, Wesseling F, Briedé JJ, Stokroos RJ. Treatment of chronically infected open mastoid cavities with medical honey: a randomized controlled trial. Otol Neurotol. 2015 Jun;36(5):782-7. doi: 10.1097/MAO.0000000000000728. PubMed PMID: 25730446.
  28. Shao J, Stout I, Hendriksen PJ, van Loveren H, Peijnenburg AA, Volger OL. Protein phosphorylation profiling identifies potential mechanisms for direct immunotoxicity. J Immunotoxicol. 2016;13(1):97-107. doi: 10.3109/1547691X.2015.1016635. Epub 2015 Sep 4. PubMed PMID: 25715851.
  29. van Breda SG, Wilms LC, Gaj S, Jennen DG, Briedé JJ, Kleinjans JC, de Kok TM. The exposome concept in a human nutrigenomics study: evaluating the impact of exposure to a complex mixture of phytochemicals using transcriptomics signatures. Mutagenesis. 2015 Nov;30(6):723-31. doi: 10.1093/mutage/gev008. Epub 2015 Feb 22. PubMed PMID: 25711498.
  30. Jiang J, Briedé JJ, Jennen DG, Van Summeren A, Saritas-Brauers K, Schaart G, Kleinjans JC, de Kok TM. Increased mitochondrial ROS formation by acetaminophen in human hepatic cells is associated with gene expression changes suggesting disruption of the mitochondrial electron transport chain. Toxicol Lett. 2015 Apr 16;234(2):139-50. doi: 10.1016/j.toxlet.2015.02.012. Epub 2015 Feb 19. PubMed PMID: 25704631.
  31. Braakhuis HM, Cassee FR, Fokkens PH, de la Fonteyne LJ, Oomen AG, Krystek P, de Jong WH, van Loveren H, Park MV. Identification of the appropriate dose metric for pulmonary inflammation of silver nanoparticles in an inhalation toxicity study. Nanotoxicology. 2016 Feb;10(1):63-73. doi: 10.3109/17435390.2015.1012184. Epub 2015 Feb 23. PubMed PMID: 25704116.
  32. Hendrickx DM, Jennen DG, Briedé JJ, Cavill R, de Kok TM, Kleinjans JC. Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study. Bioinformatics. 2015 Jul 1;31(13):2115-22. doi: 10.1093/bioinformatics/btv108. Epub 2015 Feb 19. PubMed PMID: 25701576.
  33. Caiment F, Gaj S, Claessen S, Kleinjans J. High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity. Nucleic Acids Res. 2015 Mar 11;43(5):2525-34. doi: 10.1093/nar/gkv115. Epub 2015 Feb 17. PubMed PMID: 25690898; PubMed Central PMCID: PMC4357716.
  34. Pedersen M, Mendez MA, Schoket B, Godschalk RW, Espinosa A, Landström A, Villanueva CM, Merlo DF, Fthenou E, Gracia-Lavedan E, van Schooten FJ, Hoek G, Brunborg G, Meltzer HM, Alexander J, Nielsen JK, Sunyer J, Wright J, Kovács K, de Hoogh K, Gutzkow KB, Hardie LJ, Chatzi L, Knudsen LE, Anna L, Ketzel M, Haugen M, Botsivali M, Nieuwenhuijsen MJ, Cirach M, Toledano MB, Smith RB, Fleming S, Agramunt S, Kyrtopoulos SA, Lukács V, Kleinjans JC, Segerbäck D, Kogevinas M. Environmental, dietary, maternal, and fetal predictors of bulky DNA adducts in cord blood: a European mother-child study (NewGeneris). Environ Health Perspect.2015 Apr;123(4):374-80. doi: 10.1289/ehp.1408613. Epub 2015 Jan 27. Erratum in: Environ Health Perspect. 2016 Jan 1;124(1):A12. PubMed PMID: 25626179; PubMed Central PMCID: PMC4383575.
  35. Gielis JF, Boulet GA, Briedé JJ, Horemans T, Debergh T, Kussé M, Cos P, Van Schil PE. Longitudinal quantification of radical bursts during pulmonary ischaemia and reperfusion. Eur J Cardiothorac Surg. 2015 Oct;48(4):622-9. doi: 10.1093/ejcts/ezu518. Epub 2015 Jan 5. PubMed PMID: 25564212.
  36. Van den Hof WF, Ruiz-Aracama A, Van Summeren A, Jennen DG, Gaj S, Coonen ML, Brauers K, Wodzig WK, van Delft JH, Kleinjans JC. Integrating multiple omics to unravel mechanisms of Cyclosporin A induced hepatotoxicity in vitro. Toxicol In Vitro. 2015 Apr;29(3):489-501. doi: 10.1016/j.tiv.2014.12.016. Epub 2015 Jan 3. PubMed PMID: 25562108.
  37. Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JC. diXa: a data infrastructure for chemical safety assessment. Bioinformatics. 2015 May 1;31(9):1505-7. doi: 10.1093/ bioinformatics/btu827. Epub 2014 Dec 12. PubMed PMID: 25505093; PubMed Central PMCID: PMC4410652.
  38. Schmeits PC, Shao J, van der Krieken DA, Volger OL, van Loveren H, Peijnenburg AA, Hendriksen PJ. Successful validation of genomic biomarkers for human immunotoxicity in Jurkat T cells in vitro. J Appl Toxicol. 2015 Jul;35(7):831-41. doi: 10.1002/jat.3079. Epub 2014 Nov 25. PubMed PMID: 25424538.
  39. van der Veen JW, Paskel RF, Smits NA, Hodemaekers H, van Loveren H, Ezendam J. The involvement of the Toll-like receptor signaling and Nrf2-Keap1 pathways in the in vitro regulation of IL-8 and HMOX1 for skin sensitization. J Immunotoxicol. 2016;13(1):1-6. doi: 10.3109/1547691X.2014.975897. Epub 2015 Sep 4. PubMed PMID: 25377948.
  40. Hessel EV, Tonk EC, Bos PM, van Loveren H, Piersma AH. Developmental immunotoxicity of chemicals in rodents and its possible regulatory impact. Crit Rev Toxicol. 2015 Jan;45(1):68-82. doi: 10.3109/10408444.2014.959163. Epub 2014 Nov 5. Review. PubMed PMID: 25372701.
  41. Krauskopf J, Caiment F, Claessen SM, Johnson KJ, Warner RL, Schomaker SJ, Burt DA, Aubrecht J, Kleinjans JC. Application of high-throughput sequencing to circulating microRNAs reveals novel biomarkers for drug-induced liver injury. Toxicol Sci. 2015 Feb;143(2):268-76. doi: 10.1093/toxsci/kfu232. Epub 2014 Oct 29. PubMed PMID: 25359176.
  42. van der Veen JW, Hodemaekers H, Reus AA, Maas WJ, van Loveren H, Ezendam J. Human relevance of an in vitro gene signature in HaCaT for skin sensitization. Toxicol In Vitro. 2015 Feb;29(1):81-4. doi: 10.1016/j.tiv.2014.08.010. Epub 2014 Sep 16. PubMed PMID: 25236440.
  43. Schmeits PC, Schaap MM, Luijten M, van Someren E, Boorsma A, van Loveren H, Peijnenburg AA, Hendriksen PJ. Detection of the mechanism of immunotoxicity of cyclosporine A in murine in vitro and in vivo models. Arch Toxicol. 2015 Dec;89(12):2325-37. doi: 10.1007/s00204-014-1365-9. Epub 2014 Sep 17. PubMed PMID: 25224403.
  44. van Breda SG, Claessen SM, Lo K, van Herwijnen M, Brauers KJ, Lisanti S, Theunissen DH, Jennen DG, Gaj S, de Kok TM, Kleinjans JC. Epigenetic mechanisms underlying arsenic-associated lung carcinogenesis. Arch Toxicol. 2015 Nov;89(11):1959-69. doi: 10.1007/s00204-014-1351-2. Epub 2014 Sep 9. PubMed PMID: 25199682.
  45. Habermeyer M, Roth A, Guth S, Diel P, Engel KH, Epe B, Fürst P, Heinz V, Humpf HU, Joost HG, Knorr D, de Kok T, Kulling S, Lampen A, Marko D, Rechkemmer G, Rietjens I, Stadler RH, Vieths S, Vogel R, Steinberg P, Eisenbrand G. Nitrate and nitrite in the diet: how to assess their benefit and risk for human health. Mol Nutr Food Res. 2015 Jan;59(1):106-28. doi: 10.1002/mnfr.201400286. Epub 2014 Oct 14. Review. PubMed PMID: 25164923.
  46. Katika MR, Hendriksen PJ, van Loveren H, A C M Peijnenburg A. Characterization of the modes of action of deoxynivalenol (DON) in the human Jurkat T-cell line. J Immunotoxicol. 2015 Jul-Sep;12(3):206-16. doi: 10.3109/1547691X.2014.925995. Epub 2014 Jul 2. PubMed PMID: 24988111.