Tempo-seq Publications

2023

Murphy, C., Naderlinger, E., Mater, A., et al. Comparison of Human Recombinant Protein Coatings and Fibroblast-ECM to Matrigel for Induced Pluripotent Stem Cell Culture and Renal Podocyte Differentiation. ALTEX 40 (2023). https://doi.org/10.14573/altex.2112204

2022

Liu, Q., van der Stel, W., van der Noord, V.E., et al. Hypoxia Triggers TAZ Phosphorylation in Basal A Triple Negative Breast Cancer Cells. International Journal of Molecular Sciences, Volume 23 (2022). https://doi.org/10.3390/ijms231710119

Everett, L.J., Mav, D., Phadke, D.P., et al. Impact of aligner, normalization method, and sequencing depth on TempO-seq accuracy. Bioinformatics and Biology Insights, Volume 16 (2022). https://doi.org/10.1177/11779322221095216

Cannizzo, M.D., Wood, C.E., Hester, S.D. et al. Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action. Toxicology Reports, Volume 9 (2022). https://doi.org/10.1016/j.toxrep.2022.04.012

Ghosh, S., De Smedt, J., Tricot, T. et al. HiPSC-Derived Hepatocyte-like Cells Can Be Used as a Model for Transcriptomics-Based Study of Chemical Toxicity. Toxics 10, 1 (2022). https://doi.org/10.3390/toxics10010001

Black, M.B., Stern, A., Efremenko, A. et al. Biological system considerations for application of toxicogenomics in next-generation risk assessment and predictive toxicology. Toxicology in Vitro, Volume 80 (2022). https://doi.org/10.1016/j.tiv.2022.105311

Conley, J. M., Lambright, C. S., Evans, N. et al. Developmental toxicity of Nafion byproduct 2 (NBP2) in the Sprague-Dawley rat with comparisons to hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX) and perfluorooctane sulfonate (PFOS). Environmental International, Volume 160 (2022). https://doi.org/10.1016/j.envint.2021.107056

Vrijenhoek, N. G., Wehr, M. M., Kunnen, S.J. et al. Application of High-Throughput Transcriptomics for Mechanism-Based Biological Read-Across of Short-Chain Carboxylic Acid Analogues of Valproic Acid. ALTEX - Alternatives to animal experimentation (2022). https://doi.org/10.14573/altex.2107261

Nunes, C. Singh, P. Mazidi, Z. et al. An in vitro strategy using multiple human induced pluripotent stem cell-derived models to assess the toxicity of chemicals: A case study on paraquat. Toxicology in Vitro, Volume 81 (2022). https://doi.org/10.1016/j.tiv.2022.105333

2021

Bubak, A.N., Mescher, T., Mariani, M., et al. Targeted RNA sequencing of formalin-fixed, paraffin-embedded temporal arteries from giant cell arteritis cases reveals viral signatures. Neurology Neuroimmunology & Neuroinflamation 8 (2021). https://doi.org/10.1212/NXI.0000000000001078

Harrill, J.A., Everett, L.J., Haggard, D.E., et al. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. Toxicological Sciences, Volume 181, Issue 1 (2021). https://doi.org/10.1093/toxsci/kfab009

Cho, E., Rowan-Carroll, A., Williams, A., et al. Development and Validation of the TGx-HDACi Transcriptomic Biomarker to Detect Histone Inhibitors in Human TK6 Cells. Archives of Toxicology 95 (2021) 10.1007/s00204-021-03014-2

Rowan-Carroll, A., Reardon, A, Leingartner, K. et al. High-Throughput Transcriptomic Analysis of Human Primary Hepatocyte Spheroids Exposed to Per- and Polyfluoroalkyl Substances as a Platform for Relative Potency Characterization. Toxicological Sciences, Volume 181, Issue 2 (2021). https://doi.org/10.1093/toxsci/kfab039

Wellens, S., Dehouck, L., Chandrasekaran, V. et al. Evaluation of a human iPSC-derived BBB model for repeated dose toxicity testing with cyclosporine A as model compound. Toxicology in Vitro, Volume 73 (2021). https://doi.org/10.1016/j.tiv.2021.105112

Matteo, G., Hoyeck, M.P., Blair, H.L., et al. Prolonged Low-Dose Exposure Impairs Metabolic Adaptability to High-Fat Diet Feeding in Female but Not Male Mice. Endocrinology, Volume 162 (2021). https://doi.org/10.1210/endocr/bqab050

Buick, J.K., Williams, A., Meier, M.J., et al. A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip and the TGx-DDI Transcriptomic Biomarker in Human HepaRG Cell Cultures. Frontiers in Public Health, Volume 9 (2021). https://doi.org/10.3389/fpubh.2021.694834

Lee, F., Shah, I., Soong, Y.T., et al. Reproducibility and robustness of high-throughput S1500+ transcriptomics on primary rat hepatocytes for chemical-induced hepatotoxicity assessment. Current Research in Toxicology 2 (2021). https://doi.org/10.1016/j.crtox.2021.07.003

Fransen, L.F.H., Leonard, M.O. CD34+ derived macrophage and dendritic cells display differential responses to paraquat. Toxicology in Vitro, Volume 75 (2021). https://doi.org/10.1016/j.tiv.2021.105198

Singh, P., Chandrasekaran, V., Hardy, B., et al. Temporal transcriptomic alterations of cadmium exposed human iPSC-derived renal proximal tubule-like cells. Toxicology in Vitro, Volume 76 (2021). https://doi.org/10.1016/j.tiv.2021.105229

2020

He, J., McLaughlin, R.P., van der Beek, L., et al. Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple-negative breast cancer progression. Oncogene 39 (2020). https://doi.org/10.1038/s41388-020-1279-3

Turnbull, A.K., Selli, C., Martinez-Perez, C. et al. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches. BMC Bioinformatics 21, 30 (2020). https://doi.org/10.1186/s12859-020-3365-5

Yang, H., Niemeijer, M., van de Water, B., Beltman, J.B. ATF6 is a critical determinant of CHOP dynamics during the unfolded protein response. iSCIENCE 23, 2 (2020). https:// doi.org/10.1016/j.isci.2020.100860.

Piras, I.S., Bleul, C., Schrauwen, I., et al. Transcriptional profiling of multiple system atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease. Acta Neuropathologica Communications 8, 76 (2020). https://doi.org/10.1186/s40478-020-00950-5

Baltazar, M.T., Cable, S., Carmichael, P.L. et al. A next generation risk assessment case study for courmarin in cosmetic products. Toxicological Sciences kfaa048 (2020). https://doi.org/10.1093/toxsci/kfaa048

Verheijen, M., Tong, W., Shi, L. et al. Towards the development of an omics data analysis framework. Toxicology and Pharmacology 112, 106621. https://doi.org/10.1016/j.yrtph.2020.104621 

Bushel, P.R., Ferguson, S.S., Ramaiahgari, S.C. et al. Comparison of Normalisation Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data. Frontiers in Genetics 11, 594 (2020). https://doi.org/10.3389/fgene.2020.00594

van der Wel, T., Hilhorst, R., den Dulk, H. et al. Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis. Nature Communications 11, 3216 (2020). https://doi.org/10.1038/s41467-020-17027-5

Mav, D., Phadke, D.P., Balik-Meisner, M.R. et al. Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study. Bioinformatics and Biology Insights 14 (2020). https://doi.org/10.1177/1177932220952742

Lewis, R.W., Hill III, T., Corton, J.C., A set of six gene expression biomarkers and their thresholds identify rat liver tumorigens in short-term assays. Toxicology, 443 (2020). https://doi.org/10.1016/j.tox.2020.152547

McAllister, M.J., McCall, P., Dickson, A. et al. Androgen receptor phosphorylation at serine 81 and serine 213 in castrate-resistant prostate cancer. Prostate Cancer and Prostatic Diseases (2020) https://doi.org/10.1038/s41391-020-0235-1

2019

Trejo, C.L., Babić, M., Imler, E., Gonzalez, M., Bibikov, S.I., Shepard, P.J., VanSteenhouse, H.C., Yeakley, J.M. and Seligmann, B.E. Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue. PloS one 14, 2 (2019): e0212031. https://doi.org/10.1371/journal.pone.0212031

Ramaiahgari, S.C., Auerbach, S.S., Saddler, et al. The power of resolution: contextualized understanding of biological responses to liver injury chemicals using high-throughput transcriptomics and benchmark concentration modeling. Toxicological Sciences 169, 2 (2019). https://doi.org/10.1093/toxsci/kfz065

Balik-Meisner, M.R., Mav, D., et al. Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. Zebrafish 16, 4 (2019). https://doi.org/10.1089/zeb.2018.1720

Chappell, G.A., Rager, J.E., Wolf, J., et al. Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway. Toxicologic Pathology 47, 7 (2019). https://doi.org/10.1177/0192623319873882

Bischoff, L.J., Kuijper, I.A., Schimming, J.P., et al. A systematic analysis of Nrf2 pathway activation dynamics during repeated xenobiotic exposure. Archives of Toxicology 93, 2 (2019). https://doi.org/10.1007/s00204-018-2353-2

Trejo, C., Imler, E., Babic, M., et al. Whole transcriptome TempO-Seq profiling of focal areas of H&E stained FFPE: Differentiation of normal colon and cancer phenotypes between donors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; Abstract # 5241. Cancer Research 79, 13 (2019). https://doi.org/10.1158/1538-7445.AM2019-5241

Imler, E., Nagle, R. and Seligmann, B. Digital Spatial Molecular Profiling evidence from H&E stained FFPE that the tumor microenvironment confers gene expression phenotype specificity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; Abstract # 125. Cancer Research 79, 13 (2019). https://doi.org/10.1158/1538-7445.AM2019-125

Raghunathan, M., Imler, E., Trejo, C., et al. Whole transcriptome dose response profiling enables characterization of efficacy, metabolism, side effects and cytotoxicity in a single comprehensive assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; Abstract # LB-097. Cancer Research 79, 13 (2019). https://doi.org/10.1158/1538-7445.AM2019-LB-097

Turnbull, A.K., Selli, C., Martinez-Perez, C., et al. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium 2018; Abstract # P3-06-17. Cancer Research 79, 4 (2019). https://doi.org/10.1158/1538-7445.SABCS18-P3-06-17

Carleo, A., Terwolbeck, O. and Prasse, A. Transciptomic Profile TGF-β Inhibitor Treatment in BAL Cells from IPF Patients [abstract]. Pneumologie 73, 02, p. A12. https://doi.org/10.1055/s-0039-1678392

2018

Batai, K., Imler, E., Pangilinan, J., et al. Whole-transcriptome sequencing identified gene expression signatures associated with aggressive clear cell renal cell carcinoma. Genes & Cancer 9, 5-6 (2019). https://doi.org/10.18632/genesandcancer.183

Limonciel, A., Ates, G., Carta, G., et al. Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq. Archives of Toxicology 92, 8 (2018). https://doi.org/10.1007/s00204-018-2256-2

Bushel, P.R., Paules, R.S. and Auerbach, S.S. A comparison of the TempO-Seq S1500+ platform to RNA-Seq and microarray using rat liver mode of action samples. Frontiers in Genetics 9 (2018). https://doi.org/10.3389/fgene.2018.00485

Grimm, F.A., Blanchette, A., House, J.S., et al. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX 35, 4 (2018). https://doi.org/10.14573/altex.1805301

Hanke, N.T., Imler, E., Marron, M.T., et al. Characterization of carfilzomib-resistant non-small cell lung cancer cell lines. Journal of Cancer Research and Clinical Oncology 144, 7 (2018). https://doi.org/10.1007/s00432-018-2662-0

Imler, E., Babic, M., Adams, D., et al. Focal gene expression profiling of counterstained FFPE with correlation to morphology using TempO-Seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; Abstract # 2106. Cancer Research 78, 13. https://doi.org/10.1158/1538-7445.AM2018-2106

Judson, R. Rapid toxicity screening of chemicals combining in vitro high-throughput transcriptomics, toxicokinetics and exposure estimates. In Toxicology Letters (Vol. 295, pp. S28-S28). Eurotox (2018).

2017

Yeakley, J.M., Shepard, P.J., Goyena, D.E., et al. A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling. PLoS One 12, 5 (2017). https://doi.org/10.1371/journal.pone.0178302

Rooney, J.P., Ryan, N., Chorley, B.N., et al. From the cover: genomic effects of androstenedione and sex-specific liver cancer susceptibility in mice. Toxicological Sciences 160, 1 (2017). https://doi.org/10.1093/toxsci/kfx153

House, J.S., Grimm, F.A., Jima, et al. A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics. Frontiers in Genetics 8 (2017). https://doi.org/10.3389/fgene.2017.00168

Seligmann, B., Marron, M., Babic, M., et al. Detection of gene expression biomarkers from enriched CTC preparations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; Abstract # 1729. Cancer Research 77, 13 (2017). https://doi.org/10.1158/1538-7445.AM2017-1729

Babic, M., Imler, E., Shepard, P., et al. Changes in gene expression of stromal and epithelial cells during prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; Abstract # 1992. Cancer Research 77, 13 (2017). https://doi.org/10.1158/1538-7445.AM2017-1992

VanSteenhouse, H., Shepard, P., Yeakley, J. et al. Targeted whole transcriptome gene expression profiling for mechanistic toxicology [abstract]. Toxicology Letters 280 (2017). http://dx.doi.org/10.1016/j.toxlet.2017.07.827

2016

Grimm, F.A., Iwata, Y., Sirenko, O., et al. A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives. Green Chemistry 18, 16 (2016). https://doi.org/10.1039/C6GC01147K

Babic, M., Shepard, P., Yeakley, J., et al. Differential expression and mechanistic pathways of prostate cancer identified from FFPE tissue using surrogate or whole transcriptome TempO-Seq targeted gene expression assays [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; Abstract # 1840. Cancer Research 76, 14 (2016). https://doi.org/10.1158/1538-7445.AM2016-1840