Department of Toxicogenomics

2014

  1. 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. 2014 Dec 12. pii: btu827. [Epub ahead of print] PubMed PMID: 25505093.
  2. 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. 2014 Nov 25. doi: 10.1002/jat.3079. [Epub ahead of print] PubMed PMID: 25424538.
  3. Grinberg M, Stöber RM, Edlund K, Rempel E, Godoy P, Reif R, Widera A, Madjar K, Schmidt-Heck W, Marchan R, Sachinidis A, Spitkovsky D, Hescheler J, Carmo H, Arbo MD, van de Water B, Wink S, Vinken M, Rogiers V, Escher S, Hardy B, Mitic D, Myatt G, Waldmann T, Mardinoglu A, Damm G, Seehofer D, Nüssler A, Weiss TS, Oberemm A, Lampen A, Schaap MM, Luijten M, van Steeg H, Thasler WE, Kleinjans JC, Stierum RH, Leist M, Rahnenführer J, Hengstler JG. Toxicogenomics directory of chemically exposed human hepatocytes. Arch Toxicol. 2014 Dec;88(12):2261-87. doi: 10.1007/s00204-014-1400-x. Epub 2014 Nov 16. PubMed PMID: 25399406.
  4. 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. 2014 Nov 7:1-6. [Epub ahead of print] PubMed PMID: 25377948.
  5. 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. 2014 Nov 5:1-15. [Epub ahead of print] PubMed PMID: 25372701.
  6. 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. 2014 Oct 29. pii: kfu232. [Epub ahead of print] PubMed PMID: 25359176.
  7. van den Beucken T, Koch E, Chu K, Rupaimoole R, Prickaerts P, Adriaens M, Voncken JW, Harris AL, Buffa FM, Haider S, Starmans MH, Yao CQ, Ivan M, Ivan C, Pecot CV, Boutros PC, Sood AK, Koritzinsky M, Wouters BG. Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER. Nat Commun. 2014 Oct 29;5:5203. doi: 10.1038/ncomms6203. PubMed PMID: 25351418;
  8. Rupaimoole R, Wu SY, Pradeep S, Ivan C, Pecot CV, Gharpure KM, Nagaraja AS, Armaiz-Pena GN, McGuire M, Zand B, Dalton HJ, Filant J, Miller JB, Lu C, Sadaoui NC, Mangala LS, Taylor M, van den Beucken T, Koch E, Rodriguez-Aguayo C, Huang L, Bar-Eli M, Wouters BG, Radovich M, Ivan M, Calin GA, Zhang W, Lopez-Berestein G, Sood AK. Hypoxia-mediated downregulation of miRNA biogenesis promotes  tumour progression. Nat Commun. 2014 Oct 29;5:5202. doi: 10.1038/ncomms6202. PubMed PMID: 25351346; PubMed Central PMCID: PMC4215647.
  9. Eurlings IM, Reynaert NL, van den Beucken T, Gosker HR, de Theije CC, Verhamme FM, Bracke KR, Wouters EF, Dentener MA. Cigarette smoke extract induces a phenotypic shift in epithelial cells; involvement of HIF1α in mesenchymal transition. PLoS One. 2014 Oct 16;9(10):e107757. doi: 10.1371/journal.pone.0107757. eCollection 2014. PubMed PMID: 25329389; PubMed Central PMCID: PMC4199572.
  10. Hendrickx DM, Boyles RR, Kleinjans JC, Dearry A. Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA. Arch Toxicol. 2014 Dec;88(12):2323-32. doi: 10.1007/s00204-014-1387-3. Epub 2014 Oct 19. PubMed PMID: 25326818; PubMed Central PMCID: PMC4247478.
  11. Kaneko Y, Tajiri N, Staples M, Reyes S, Lozano D, Sanberg PR, Freeman TB, van  Loveren H, Kim SU, Borlongan CV. Bone Marrow-Derived Stem Cell Therapy for Metastatic Brain Cancers. Cell Transplant. 2014 Oct 10. [Epub ahead of print] PubMed PMID: 25310691.
  12. Vande Loock K, Botsivali M, Zangogianni M, Anderson D, Baumgartner A, Fthenou E, Chatzi L, Marcos R, Agramunt S, Namork E, Granum B, Knudsen LE, Nielssen JK, Meltzer HM, Haugen M,  Kyrtopoulos SA, Decordier I, Plas G, Roelants M, Merlo F, Kleinjans J, Kogevinas M, Kirsch-Volders M. The effect of dietary estimates calculated using food frequency questionnaires on micronuclei formation in European pregnant women: a NewGeneris study. Mutagenesis. 2014 Nov;29(6):393-400. doi: 10.1093/mutage/geu052. Epub 2014 Oct 8. PubMed PMID: 25296962.
  13. Dik S, Ezendam J, Cunningham AR, Carrasquer CA, van Loveren H, Rorije E. Evaluation of in silico models for the identification of respiratory sensitizers. Toxicol Sci. 2014 Dec;142(2):385-94. doi: 10.1093/toxsci/kfu188. Epub 2014 Sep 19. PubMed PMID: 25239631.
  14. 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.
  15. Braakhuis HM, Gosens I, Krystek P, Boere J, Cassee FR, Fokkens P, Post J, van Loveren H, Park M. Particle size dependent deposition and pulmonary inflammation after short-term inhalation of silver nanoparticles. Part Fibre Toxicol. 2014 Sep 17;11(1):49. [Epub ahead of print] PubMed PMID: 25227272.
  16. 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. 2014 Sep 17. [Epub ahead of print] PubMed PMID: 25224403.
  17. 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. 2014 Sep 9. [Epub ahead of print] PubMed PMID: 25199682.
  18. Pronk TE, van der Veen JW, Vandebriel RJ, van Loveren H, de Vink EP, Pennings JL. Comparison of the molecular topologies of stress-activated transcription factors HSF1, AP-1, NRF2, and NF-κB in their induction kinetics of HMOX1. Biosystems. 2014 Oct;124:75-85. doi: 10.1016/j.biosystems.2014.09.005. Epub 2014 Sep 6. PubMed PMID: 25199502.
  19. Gedye CA, Hussain A, Paterson J, Smrke A, Saini H, Sirskyj D, Pereira K, Lobo N, Stewart J, Go C, Ho J, Medrano M, Hyatt E, Yuan J, Lauriault S, Kondratyev M, van den Beucken T, Jewett M, Dirks P, Guidos CJ, Danska J, Wang J, Wouters B, Neel B, Rottapel R, Ailles LE. Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity. PLoS One. 2014 Aug 29;9(8):e105602. doi: 10.1371/journal.pone.0105602. eCollection 2014. PubMed PMID: 25170899; PubMed Central PMCID: PMC4149490.
  20. 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. PubMed PMID: 25164923.
  21. Huijskens MJ, Walczak M, Koller N, Briedé JJ, Senden-Gijsbers BL, Schnijderberg MC, Bos GM, Germeraad WT. Technical Advance: Ascorbic acid induces development of double-positive T cells from human hematopoietic stem cells in the absence of stromal cells. J Leukoc Biol. 2014 Dec;96(6):1165-75. doi: 10.1189/jlb.1TA0214-121RR. Epub 2014 Aug 25. PubMed PMID: 25157026. 
  22. Dragsted LO, Alexander J, Amdam G, Bryan N, Chen D, Haug A, Karlsson AH, de Kok T, Kulseng BE, Martin RJ Jr, Milkowski A, Pajari AM, Pickowa J, Rudi K, Sødring MS, Oostindjer M, Egelandsdal B. Letter to the editor: Colorectal cancer risk and association with red meat--is it inconsistent? Answer to the letter by Corpet, De Smet and Demeyer. Meat Sci. 2014 Dec;98(4):792-4. doi: 10.1016/j.meatsci.2014.07.032. Epub 2014 Aug 6. PubMed PMID: 25150631. 
  23. Van den Hof WF, Van Summeren A, Lommen A, Coonen ML, Brauers K, van Herwijnen M, Wodzig WK, Kleinjans JC. Integrative cross-omics analysis in primary mouse hepatocytes unravels mechanisms of cyclosporin A-induced hepatotoxicity. Toxicology. 2014 Oct 3;324:18-26. doi: 10.1016/j.tox.2014.06.003. Epub 2014 Jul 15. PubMed PMID: 25047351.
  24. van der Veen JW, Soeteman-Hernández LG, Ezendam J, Stierum R, Kuper FC, van Loveren H. Anchoring molecular mechanisms to the adverse outcome pathway for skin sensitization: Analysis of existing data. Crit Rev Toxicol. 2014 Aug;44(7):590-9. doi: 10.3109/10408444.2014.925425. Epub 2014 Jul 7. PubMed PMID: 25000333.
  25. 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. 2014 Jul 2:1-11. [Epub ahead of print] PubMed PMID: 24988111. 
  26. Jetten MJ, Claessen SM, Dejong CH, Lahoz A, Castell JV, van Delft JH, Kleinjans JC. Interindividual variation in response to xenobiotic exposure established in precision-cut human liver slices. Toxicology. 2014 Sep 2;323:61-9. doi: 10.1016/j.tox.2014.06.007. Epub 2014 Jun 17. PubMed PMID: 24949552. 
  27. Doedée AM, Boland GJ, Pennings JL, de Klerk A, Berbers GA, van der Klis FR, de Melker HE, van Loveren H, Janssen R. Effects of prophylactic and therapeutic paracetamol treatment during vaccination on hepatitis B antibody levels in adults: two open-label, randomized controlled trials. PLoS One. 2014 Jun 4;9(6):e98175. doi: 10.1371/journal.pone.0098175. eCollection 2014. PubMed PMID: 24897504; PubMed Central PMCID: PMC4045752.
  28. Vandebriel RJ, Tonk EC, de la Fonteyne-Blankestijn LJ, Gremmer ER, Verharen HW, van der Ven LT, van Loveren H, de Jong WH. Immunotoxicity of silver nanoparticles in an intravenous 28-day repeated-dose toxicity study in rats. Part Fibre Toxicol. 2014 May 7;11:21. doi: 10.1186/1743-8977-11-21. PubMed PMID: 24885556; PubMed Central PMCID: PMC4052812.
  29. van der Veen JW, Rorije E, Emter R, Natsch A, van Loveren H, Ezendam J. Evaluating the performance of integrated approaches for hazard identification of skin sensitizing chemicals. Regul Toxicol Pharmacol. 2014 Aug;69(3):371-9. doi: 10.1016/j.yrtph.2014.04.018. Epub 2014 May 9. PubMed PMID: 24813372.
  30. Oostindjer M, Alexander J, Amdam GV, Andersen G, Bryan NS, Chen D, Corpet DE, De Smet S, Dragsted LO, Haug A, Karlsson AH, Kleter G, de Kok TM, Kulseng B, Milkowski AL, Martin RJ, Pajari AM, Paulsen JE, Pickova J, Rudi K, Sødring M, Weed DL, Egelandsdal B. The role of red and processed meat in colorectal cancer development: a perspective. Meat Sci. 2014 Aug;97(4):583-96. doi: 10.1016/j.meatsci.2014.02.011. Epub 2014 Feb 24. PubMed PMID: 24769880.
  31. Hebels DG, van Herwijnen MH, Brauers KJ, de Kok TM, Chalkiadaki G, Kyrtopoulos SA, Kleinjans JC. Elimination of heparin interference during microarray processing of fresh and biobank-archived blood samples. Environ Mol Mutagen. 2014 Jul;55(6):482-91. doi: 10.1002/em.21869. Epub 2014 Apr 17. PubMed PMID: 24740823.
  32. Papadopoulou E, Kogevinas M, Botsivali M, Pedersen M, Besselink H, Mendez MA, Fleming S, Hardie LJ, Knudsen LE, Wright J, Agramunt S, Sunyer J, Granum B, Gutzkow KB, Brunborg G, Alexander J, Meltzer HM, Brantsæter AL, Sarri K, Chatzi L, Merlo DF, Kleinjans JC, Haugen M. Maternal diet, prenatal exposure to dioxin-like compounds and birth outcomes in a European prospective mother-child study (NewGeneris). Sci Total Environ. 2014 Jun 15;484:121-8. doi: 10.1016/j.scitotenv.2014.03.047. Epub 2014 Mar 30. PubMed PMID: 24691212.
  33. Kleinjans J, van Ravenzwaay B. Epigenetics and chemical safety - concluding remarks. Mutat Res Genet Toxicol Environ Mutagen. 2014 Apr;764-765:72-3. doi: 10.1016/j.mrgentox.2014.03.003. Epub 2014 Mar 24. PubMed PMID: 24674849.
  34. Miller T, Lau T, Vasan R, Danner C, Youssef AS, van Loveren H, Agazzi S. Reporting success rates in the treatment of vestibular schwannomas: are we accounting for the natural history? J Clin Neurosci. 2014 Jun;21(6):914-8. doi: 10.1016/j.jocn.2013.11.029. Epub 2014 Mar 18. Review. PubMed PMID: 24656737.
  35. ter Burg W, Bouma K, Schakel DJ, Wijnhoven SW, van Engelen J, van Loveren H, Ezendam J. Assessment of the risk of respiratory sensitization from fragrance allergens released by air fresheners. Inhal Toxicol. 2014 Apr;26(5):310-8. doi: 10.3109/08958378.2014.888110. Epub 2014 Mar 18. PubMed PMID: 24640966.
  36. Ramaekers CH, van den Beucken T, Bristow RG, Chiu RK, Durocher D, Wouters BG. RNF8-independent Lys63 poly-ubiquitylation prevents genomic instability in response to replication-associated DNA damage. PLoS One. 2014 Feb 28;9(2):e89997. doi: 10.1371/journal.pone.0089997. eCollection 2014. PubMed PMID: 24587176; PubMed Central PMCID: PMC3938561.
  37. Chadeau-Hyam M, Vermeulen RC, Hebels DG, Castagné R, Campanella G, Portengen L, Kelly RS, Bergdahl IA, Melin B, Hallmans G, Palli D, Krogh V, Tumino R, Sacerdote C, Panico S, de Kok TM, Smith MT, Kleinjans JC, Vineis P, Kyrtopoulos SA; EnviroGenoMarkers project consortium. Prediagnostic transcriptomic markers of Chronic lymphocytic leukemia reveal perturbations 10 years before diagnosis. Ann Oncol. 2014 May;25(5):1065-72. doi: 10.1093/annonc/mdu056. Epub 2014 Feb 20. PubMed PMID: 24558024.
  38. Hebels DG, Jetten MJ, Aerts HJ, Herwig R, Theunissen DH, Gaj S, van Delft JH, Kleinjans JC. Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity. Biomark Med. 2014;8(2):185-200. doi: 10.2217/bmm.13.154. Review. PubMed PMID: 24521014.
  39. Osman AM, van Loveren H. Matrin 3 co-immunoprecipitates with the heat shock proteins glucose-regulated protein 78 (GRP78), GRP75 and glutathione S-transferase π isoform 2 (GSTπ2) in thymoma cells. Biochimie. 2014 Jun;101:208-14. doi: 10.1016/j.biochi.2014.01.015. Epub 2014 Jan 31. PubMed PMID: 24491357.
  40. Vafeiadi M, Agramunt S, Pedersen M, Besselink H, Chatzi L, Fthenou E, Fleming S, Hardie LJ, Wright J, Knudsen LE, Nielsen JK, Sunyer J, Carreras R, Brunborg G, Gutzkow KB, Nygaard UC, Løvik M, Kyrtopoulos SA, Segerbäck D, Merlo DF, Kleinjans JC, Vrijheid M, Kogevinas M; NewGeneris Consortium. In utero exposure to compounds with dioxin-like activity and birth outcomes. Epidemiology. 2014 Mar;25(2):215-24. doi: 10.1097/EDE.0000000000000046. PubMed PMID: 24487205.
  41. van Ravenzwaay B, Kleinjans J, Vrijhof H. Editorial - epigenetics and chemical safety. Mutat Res Genet Toxicol Environ Mutagen. 2014 Apr;764-765:1-2. doi: 10.1016/j.mrgentox.2014.01.008. Epub 2014 Jan 26. PubMed PMID: 24472829.
  42. Nymark P, Jensen KA, Suhonen S, Kembouche Y, Vippola M, Kleinjans J, Catalán J, Norppa H, van Delft J, Briedé JJ. Free radical scavenging and formation by multi-walled carbon nanotubes in cell free conditions and in human bronchial epithelial cells. Part Fibre Toxicol. 2014 Jan 18;11:4. doi: 10.1186/1743-8977-11-4. PubMed PMID: 24438343; PubMed Central PMCID: PMC3933237.
  43. Van den Hof WF, Coonen ML, van Herwijnen M, Brauers K, Wodzig WK, van Delft JH, Kleinjans JC. Classification of hepatotoxicants using HepG2 cells: A proof of principle study. Chem Res Toxicol. 2014 Mar 17;27(3):433-42. doi: 10.1021/tx4004165. Epub 2014 Jan 28. PubMed PMID: 24437676. 
  44. Hogervorst JG, de Bruijn-Geraets D, Schouten LJ, van Engeland M, de Kok TM, Goldbohm RA, van den Brandt PA, Weijenberg MP. Dietary acrylamide intake and the risk of colorectal cancer with specific mutations in KRAS and APC. Carcinogenesis. 2014 May;35(5):1032-8. doi: 10.1093/carcin/bgu002. Epub 2014 Jan 7. PubMed PMID: 24398672.
  45. Osman AM, van Loveren H. The immunosuppressant tributyltin oxide blocks the mTOR pathway, like rapamycin, albeit by a different mechanism. J Appl Toxicol. 2014 Dec;34(12):1361-7. doi: 10.1002/jat.2966. Epub 2013 Dec 26. PubMed PMID: 24375594.
  46. Shao J, Berger LF, Hendriksen PJ, Peijnenburg AA, van Loveren H, Volger OL. Transcriptome-based functional classifiers for direct immunotoxicity. Arch Toxicol. 2014 Mar;88(3):673-89. doi: 10.1007/s00204-013-1179-1. Epub 2013 Dec 20. PubMed PMID: 24356939.
  47. van Breda SG, Wilms LC, Gaj S, Jennen DG, Briedé JJ, Helsper JP, Kleinjans JC, de Kok TM. Can transcriptomics provide insight into the chemopreventive mechanisms of complex mixtures of phytochemicals in humans? Antioxid Redox Signal. 2014 May 10;20(14):2107-13. doi: 10.1089/ars.2013.5528. Epub 2014 Feb 27. PubMed PMID: 24328558; PubMed Central PMCID: PMC3994912.
  48. De Boever P, Wens B, Forcheh AC, Reynders H, Nelen V, Kleinjans J, Van Larebeke N, Verbeke G, Valkenborg D, Schoeters G. Characterization of the peripheral blood transcriptome in a repeated measures design using a panel of healthy individuals. Genomics. 2014 Jan;103(1):31-9. doi: 10.1016/j.ygeno.2013.11.006. Epub 2013 Dec 7. PubMed PMID: 24321174.
  49. Rieswijk L, Lizarraga D, Brauers KJ, Kleinjans JC, van Delft JH. Characterisation of cisplatin-induced transcriptomics responses in primary mouse hepatocytes, HepG2 cells and mouse embryonic stem cells shows conservation of regulating transcription factor networks. Mutagenesis. 2014 Jan;29(1):17-26. doi: 10.1093/mutage/get055. Epub 2013 Nov 26. PubMed PMID: 24280081.
  50. Merlo DF, Agramunt S, Anna L, Besselink H, Botsivali M, Brady NJ, Ceppi M, Chatzi L, Chen B, Decordier I, Farmer PB, Fleming S, Fontana V, Försti A, Fthenou E, Gallo F, Georgiadis P, Gmuender H, Godschalk RW, Granum B, Hardie LJ, Hemminki K, Hochstenbach K, Knudsen LE, Kogevinas M, Kovács K, Kyrtopoulos SA, Løvik M, Nielsen JK, Nygaard UC, Pedersen M, Rydberg P, Schoket B, Segerbäck D, Singh R, Sunyer J, Törnqvist M, van Loveren H, van Schooten FJ, Vande Loock K, von Stedingk H, Wright J, Kleinjans JC, Kirsch-Volders M, van Delft JH; NewGeneris Consortium. Micronuclei in cord blood lymphocytes and associations with biomarkers of exposure to carcinogens and hormonally active factors, gene polymorphisms, and gene expression: the NewGeneris cohort. Environ Health Perspect. 2014 Feb;122(2):193-200. doi: 10.1289/ehp.1206324. Epub 2013 Nov 18. PubMed PMID: 24252472; PubMed Central PMCID: PMC3914866.
  51. Schmeits PC, Katika MR, Peijnenburg AA, van Loveren H, Hendriksen PJ. DON shares a similar mode of action as the ribotoxic stress inducer anisomycin while TBTO shares ER stress patterns with the ER stress inducer thapsigargin based on comparative gene expression profiling in Jurkat T cells. Toxicol Lett. 2014 Jan 30;224(3):395-406. doi: 10.1016/j.toxlet.2013.11.005. Epub 2013 Nov 15. PubMed PMID: 24247028.
  52. Caiment F, Tsamou M, Jennen D, Kleinjans J. Assessing compound carcinogenicity in vitro using connectivity mapping. Carcinogenesis. 2014 Jan;35(1):201-7. doi: 10.1093/carcin/bgt278. Epub 2013 Aug 12. PubMed PMID: 23940306.