Department of Toxicogenomics

2016

  1. Hendrickx DM, Souza T, Jennen DG, Kleinjans JC. DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Arch Toxicol. 2016 Dec 28. Doi :10.1007/s00204-016-1922-5. PubMed PMID: 28032149.
  2. Wolters JE, van Herwijnen MH, Theunissen DH, Jennen DG, Van den Hof WF, de Kok TM, Schaap FG, van Breda SG, Kleinjans JC. Integrative "-Omics" Analysis in Primary Human Hepatocytes Unravels Persistent Mechanisms of Cyclosporine A-Induced Cholestasis. Chem Res Toxicol. 2016 Dec 19;29(12):2164-2174. PubMed PMID: 27989131.
  3. Castagné R, Kelly-Irving M, Campanella G, Guida F, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Kleinjans J, de Kok T, Kyrtopoulos SA, Lang T, Stringhini  S, Vermeulen R, Vineis P, Delpierre C, Chadeau-Hyam M. Biological marks of early-life socioeconomic experience is detected in the adult inflammatory transcriptome. Sci Rep. 2016 Dec 9;6:38705. doi: 10.1038/srep38705. PubMed PMID: 27934951; PubMed Central PMCID: PMC5146729.
  4. Adriaens ME, Prickaerts P, Chan-Seng-Yue M, van den Beucken T, Dahlmans VE, Eijssen LM, Beck T, Wouters BG, Voncken JW, Evelo CT. Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia. Epigenetics Chromatin. 2016 Nov 1;9:48. eCollection 2016. PubMed PMID: 27822313; PubMed Central PMCID: PMC5090954.
  5. Proquin H, Rodríguez-Ibarra C, Moonen CG, Urrutia Ortega IM, Briedé JJ, de Kok TM, van Loveren H, Chirino YI. Titanium dioxide food additive (E171) induces ROS formation and genotoxicity: contribution of micro and nano-sized fractions.Mutagenesis. 2017 Jan;32(1):139-149. doi: 10.1093/mutage/gew051. PubMed PMID: 27789654.
  6. Souza TM, Rieswijk L, Beucken TV, Kleinjans J, Jennen D. Persistent transcriptional responses show the involvement of feed-forward control in a repeated dose toxicity study. Toxicology. 2017 Jan 15;375:58-63. doi:10.1016/j.tox.2016.10.009. PubMed PMID: 27765683.
  7. Vrijens K, Winckelmans E, Tsamou M, Baeyens W, De Boever P, Jennen D, de Kok TM, Den Hond E, Lefebvre W, Plusquin M, Reynders H, Schoeters G, Van Larebeke N, Vanpoucke C, Kleinjans J, Nawrot TS. Sex-Specific Associations between Particulate Matter Exposure and Gene Expression in Independent Discovery and Validation Cohorts of Middle-Aged Men and Women. Environ Health Perspect. 2017 Apr;125(4):660-669. doi: 10.1289/EHP370. PubMed PMID: 27740511; PubMed Central PMCID: PMC5381989.
  8. Mannaerts D, Faes E, Gielis J, Briedé J, Cos P, Van Craenenbroeck E, Gyselaers W, Cornette J, Spaanderman M, Jacquemyn Y. A3. Oxidative stress in maternal serum as endothelial dysfunction marker in preeclampsia, an electron paramagnetic resonance (EPR) pilot study. J Matern Fetal Neonatal Med. 2016 Aug;29(sup2):3. PubMed PMID: 27680784.
  9. O'Callaghan-Gordo C, Kogevinas M, Pedersen M, Fthenou E, Espinosa A, Tsiapa X, Chalkiadaki G, Daraki V, Dermitzaki E, Decordier I, Farmer PB, Georgiadis P, Georgiou V, Kyrtopoulos SA, Merlo DF, Romaguera D, Roumeliotaki T, Sarri K, Törnqvist M, Loock KV, von Stedingk H, Kleinjans J, Kirsch-Volders M, Chatzi L. Maternal diet during pregnancy and micronuclei frequency in peripheral blood T lymphocytes in mothers and newborns (Rhea cohort, Crete). Eur J Nutr. 2016 Sep 21. PubMed PMID: 27655526.
  10. Lenz M, Roumans NJ, Vink RG, van Baak MA, Mariman EC, Arts IC, de Kok TM, Ertaylan G. Estimating real cell size distribution from cross-section microscopy imaging. Bioinformatics. 2016 Sep 1;32(17):i396-i404. doi:10.1093/ bioinformatics/btw431. PubMed PMID: 27587655.
  11. Vineis P, Chadeau-Hyam M, Gmuender H, Gulliver J, Herceg Z, Kleinjans J, Kogevinas M, Kyrtopoulos S, Nieuwenhuijsen M, Phillips DH, Probst-Hensch N, Scalbert A, Vermeulen R, Wild CP; EXPOsOMICS Consortium.. The exposome in practice: Design of the EXPOsOMICS project. Int J Hyg Environ Health. 2017 Mar;220(2 Pt A):142-151. doi: 10.1016/j.ijheh.2016.08.001. PubMed PMID: 27576363.
  12. Deferme L, Wolters JE, Claessen SM, Theunissen DH, van den Beucken T, Wagner JR, van Breda SG, Kleinjans JC, Briedé JJ. Dynamic Interplay between the Transcriptome and Methylome in Response to Oxidative and Alkylating Stress. Chem Res Toxicol. 2016 Sep 19;29(9):1428-38. doi: 10.1021/ acs.chemrestox.6b00090. PubMed PMID: 27509014.
  13. Dik S, Rorije E, Schwillens P, van Loveren H, Ezendam J. Can the Direct Peptide Reactivity Assay Be Used for the Identification of Respiratory Sensitization Potential of Chemicals? Toxicol Sci. 2016 Oct;153(2):361-71. doi: 10.1093/toxsci/kfw130. PubMed PMID: 27473337.
  14. O'Callaghan-Gordo C, Kogevinas M, Fthenou E, Pedersen M, Espinosa A, Chalkiadaki G, Daraki V, Dermitzaki E, Decordier I, Georgiou V, Merlo DF, Roumeliotaki T, Vande Loock K, Kleinjans J, Kirsch-Volders M, Chatzi L. Vitamin D insufficient levels during pregnancy and micronuclei frequency in peripheral blood T lymphocytes mothers and newborns (Rhea cohort, Crete). Clin Nutr. 2016 Jun 27. pii: S0261-5614(16) 30150-9. doi: 10.1016/j.clnu.2016.06.016. PubMed PMID: 27396287.
  15. Giannakou C, Park MV, de Jong WH, van Loveren H, Vandebriel RJ, Geertsma RE. A comparison of immunotoxic effects of nanomedicinal products with regulatory immunotoxicity testing requirements. Int J Nanomedicine. 2016 Jun 22;11:2935-52. doi: 10.2147/IJN.S102385. eCollection 2016. Review. PubMed PMID: 27382281; PubMed Central PMCID: PMC4922791.
  16. Hessel EV, Ezendam J, van Broekhuizen FA, Hakkert B, DeWitt J, Granum B, Guzylack L, Lawrence BP, Penninks A, Rooney AA, Piersma AH, van Loveren H. Assessment of recent developmental immunotoxicity studies with bisphenol A in the context of the 2015 EFSA t-TDI. Reprod Toxicol. 2016 Oct;65:448-456. doi: 10.1016/j.reprotox.2016.06.020. PubMed PMID: 27352639.
  17. Rieswijk L, Brauers KJ, Coonen ML, Jennen DG, van Breda SG, Kleinjans JC. Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity. Mutagenesis. 2016 Sep;31(5):603-15. doi: 10.1093/mutage/gew027. PubMed PMID: 27338304.
  18. Hebels DG, Rasche A, Herwig R, van Westen GJ, Jennen DG, Kleinjans JC. A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure. Methods Mol Biol. 2016;1425:339-59. doi: 10.1007/978-1-4939-3609-0_15. PubMed PMID: 27311473.
  19. Hung Y, de Kok TM, Verbeke W. Consumer attitude and purchase intention towards processed meat products with natural compounds and a reduced level of nitrite. Meat Sci. 2016 Nov;121:119-26. doi: 10.1016/j.meatsci.2016.06.002. PubMed PMID: 27310600.
  20. Rieswijk L, Claessen SM, Bekers O, van Herwijnen M, Theunissen DH, Jennen DG, de Kok TM, Kleinjans JC, van Breda SG. Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma. Toxicology. 2016 Mar 28;350-352:31-9. doi: 10.1016/ j.tox.2016.05.002. Epub 2016 May 3. PubMed PMID: 27153756.
  21. Fernando RN, Chaudhari U, Escher SE, Hengstler JG, Hescheler J, Jennings P, Keun HC, Kleinjans JC, Kolde R, Kollipara L, Kopp-Schneider A, Limonciel A, Nemade H, Nguemo F, Peterson H, Prieto P, Rodrigues RM, Sachinidis A, Schäfer C, Sickmann A, Spitkovsky D, Stöber R, van Breda SG, van de Water B, Vivier M, Zahedi RP, Vinken M, Rogiers V. "Watching the Detectives" report of the general assembly of the EU project DETECTIVE Brussels, 24-25 November 2015. Arch Toxicol. 2016 Jun;90(6):1529-39. doi: 10.1007/s00204-016-1719-6. Epub 2016 Apr 29. PubMed PMID: 27129694.
  22. Urrutia-Ortega IM, Garduño-Balderas LG, Delgado-Buenrostro NL, Freyre-Fonseca V, Flores-Flores JO, González-Robles A, Pedraza-Chaverri J, Hernández-Pando R, Rodríguez-Sosa M, León-Cabrera S, Terrazas LI, van Loveren H, Chirino YI. Food-grade titanium dioxide exposure exacerbates tumor formation in colitis associated cancer model. Food Chem Toxicol. 2016 Jul;93:20-31. doi: 10.1016/j.fct.2016.04.014. Epub 2016 Apr 23. PubMed PMID: 27117919.
  23. Hardt C, Beber ME, Rasche A, Kamburov A, Hebels DG, Kleinjans JC, Herwig R. ToxDB: pathway-level interpretation of drug-treatment data. Database (Oxford). 2016 Apr 13;2016. pii: baw052. doi: 10.1093/database/baw052. Print 2016. PubMed PMID: 27074805; PubMed Central PMCID: PMC4830474.
  24. van Bree BW, Lenaers E, Nabben M, Briedé JJ, Jörgensen JA, Schaart G, Schrauwen P, Hoeks J, Hesselink MK. A genistein-enriched diet neither improves skeletal muscle oxidative capacity nor prevents the transition towards advanced insulin resistance in ZDF rats. Sci Rep. 2016 Mar 14;6:22854. doi: 10.1038/srep22854. PubMed PMID: 26973284; PubMed Central PMCID: PMC4789602.
  25. Panth KM, van den Beucken T, Biemans R, Lieuwes NG, Weber M, Losen M, Yaromina A, Dubois LJ, Lambin P. In vivo optical imaging of MMP2 immuno protein antibody: tumor uptake is associated with MMP2 activity. Sci Rep. 2016 Feb 29;6:22198. doi: 10.1038/srep22198. PubMed PMID: 26923459; PubMed Central PMCID: PMC4770595.
  26. Georgiadis P, Hebels DG, Valavanis I, Liampa I, Bergdahl IA, Johansson A, Palli D, Chadeau-Hyam M, Chatziioannou A, Jennen DG, Krauskopf J, Jetten MJ, Kleinjans JC, Vineis P, Kyrtopoulos SA; EnviroGenomarkers consortium.. Omics for prediction of environmental health effects: Blood leukocyte-based cross-omic profiling reliably predicts diseases associated with tobacco smoking. Sci Rep. 2016 Feb 3;6:20544. doi: 10.1038/srep20544. PubMed PMID: 26837704; PubMed Central PMCID: PMC4738297.
  27. Braakhuis HM, Giannakou C, Peijnenburg WJ, Vermeulen J, van Loveren H, Park MV. Simple in vitro models can predict pulmonary toxicity of silver nanoparticles. Nanotoxicology. 2016 Aug;10(6):770-9. doi: 10.3109/17435390.2015.1127443. Epub 2016 Jan 26. PubMed PMID: 26809698.
  28. 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. 2016 Apr 27;34(19):2281-9. doi: 10.1016/j.vaccine.2015.12.027. Epub 2015 Dec 22. PubMed PMID: 26721327.
  29. 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. Erratum: "Environmental, Dietary, Maternal, and Fetal Predictors of Bulky DNA Adducts in Cord Blood: A European Mother-Child Study (NewGeneris)". Environ Health Perspect. 2016 Jan; 124(1):A12. doi: 10.1289/ehp.124-A12. PubMed PMID: 26720407; PubMed Central PMCID: PMC4710585.
  30. Cavill R, Jennen D, Kleinjans J, Briedé JJ. Transcriptomic and metabolomic data integration. Brief Bioinform. 2016 Sep;17(5):891-901. doi: 10.1093/bib/bbv090. PubMed PMID: 26467821.
  31. 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. 2016 Jul;90(7):1685-94. doi: 10.1007/s00204-015-1585-7. PubMed PMID: 26314263.
  32. 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. 2016 Jun;90(6):1449-58. doi: 10.1007/s00204-015-1572-z. PubMed PMID: 26238291; PubMed Central PMCID: PMC4873527.
  33. 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. 2016 May;90(5):1103-15. doi: 10.1007/s00204-015-1545-2. PubMed PMID: 26104854; PubMed Central PMCID: PMC4830893.
  34. 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;13(2):173-80. doi: 10.3109/1547691X. 2015.1029147. PubMed PMID: 25812627.
  35. 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.PubMed PMID: 25715851.
  36. 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;10(1):63-73. doi: 10.3109/17435390. 2015.1012184. PubMed PMID: 25704116. 
  37. 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. PubMed PMID: 25377948.