Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems
Prokopec, S. D., Houlahan, K. E., Sun, R. X., Watson, J. D., Yao, C. Q., Lee, J., P’ng, C., Pang, R., Wu, A. H., Chong, L. C., Smith, A. B., Harding, N. J., Moffat, I. D., Lindén, J., Lensu, S., Okey, A. B., Pohjanvirta, R., & Boutros, P. C. (2017). Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems. BMC Genomics, 18, Article 78. https://doi.org/10.1186/s12864-016-3446-z
Published in
BMC GenomicsAuthors
Date
2017Copyright
© The Author(s). 2017
This article is distributed under the terms of the Creative Commons Attribution 4.0
International License.
Background
2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute lethality. The severity of toxicity is highly dependent on the aryl hydrocarbon receptor (AHR). Binding of TCDD to the AHR leads to changes in transcription of numerous genes. Studies evaluating the transcriptional changes brought on by TCDD may provide valuable insight into the role of the AHR in human health and disease. We therefore compiled a collection of transcriptomic datasets that can be used to aid the scientific community in better understanding the transcriptional effects of ligand-activated AHR.
Results
Specifically, we have created a datasets package – TCDD.Transcriptomics – for the R statistical environment, consisting of 63 unique experiments comprising 377 samples, including various combinations of 3 species (human derived cell lines, mouse and rat), 4 tissue types (liver, kidney, white adipose tissue and hypothalamus) and a wide range of TCDD exposure times and doses. These datasets have been fully standardized using consistent preprocessing and annotation packages (available as of September 14, 2015). To demonstrate the utility of this R package, a subset of “AHR-core” genes were evaluated across the included datasets. Ahrr, Nqo1 and members of the Cyp family were significantly induced following exposure to TCDD across the studies as expected while Aldh3a1 was induced specifically in rat liver. Inmt was altered only in liver tissue and primarily by rat-AHR.
Conclusions
Analysis of the “AHR-core” genes demonstrates a continued need for studies surrounding the impact of AHR-activity on the transcriptome; genes believed to be consistently regulated by ligand-activated AHR show surprisingly little overlap across species and tissues. Until now, a comprehensive assessment of the transcriptome across these studies was challenging due to differences in array platforms, processing methods and annotation versions. We believe that this package, which is freely available for download (http://labs.oicr.on.ca/boutros-lab/tcdd-transcriptomics) will prove to be a highly beneficial resource to the scientific community evaluating the effects of TCDD exposure as well as the variety of functions of the AHR.
...
Publisher
BioMed CentralISSN Search the Publication Forum
1471-2164Keywords
Publication in research information system
https://converis.jyu.fi/converis/portal/detail/Publication/26482461
Metadata
Show full item recordCollections
- Liikuntatieteiden tiedekunta [3120]
License
Except where otherwise noted, this item's license is described as © The Author(s). 2017
This article is distributed under the terms of the Creative Commons Attribution 4.0
International License.
Related items
Showing items with similar title or keywords.
-
Transcriptional profiling of rat hypothalamus response to 2,3,7,8-tetrachlorodibenzo-ρ-dioxin
Houlahan, Kathleen E.; Prokopec, Stephenie D.; Moffat, Ivy D.; Lindén, Jere; Lensu, Sanna; Okey, Allan B.; Pohjanvirta, Raimo; Boutros, Paul C. (Elsevier; German Toxicology Society, 2015)In some mammals, halogenated aromatic hydrocarbon (HAH) exposure causes wasting syndrome, defined as significant weight loss associated with lethal outcomes. The most potent HAH in causing wasting is 2,3,7,8-tetrachlorod ... -
Transcriptomic variability in population responses of Atlantic cod to temperature
Oomen, Rebekah; Knutsen, Halvor; Moland Olsen, Esben; Jentoft, Sissel; Stenseth, Nils Christian; Hutchings, Jeffrey (Open Science Centre, University of Jyväskylä, 2018)Temperature has profound effects on ectotherm physiology, impacting metabolic and developmental rates, aerobic scope, and inducing cellular stress responses. The resulting phenotypic and fitness consequences ultimately ... -
Role of angiogenesis in skeletal muscle transcriptomic responses to endurance training
Koho, Saara (2022)Liikunta aiheuttaa muutoksia luurankolihaksen supistuvissa, rakenteellisissa ja aineenvaihdunnallisissa ominaisuuksissa, mikä saa aikaan useita terveyshyötyjä. Nämä muutokset tapahtuvat useiden tilapäisten säätelymekanismien, ... -
Preparing for Winter: The Transcriptomic Response Associated with Different Day Lengths in Drosophila montana
Parker, Darren; Ritchie, Michael G.; Kankare, Maaria (Genetics Society of America, 2016)At northern latitudes, the most robust cue for assessing the onset of winter is the shortening of day lengths. Many species use day length as a cue to increase their cold tolerance and/or enter into diapause, but little ... -
The Psychological Science Accelerator’s COVID-19 rapid-response dataset
Buchanan, Erin M.; Lewis, Savannah C.; Paris, Bastien; Forscher, Patrick S.; Pavlacic, Jeffrey M.; Beshears, Julie E.; Drexler, Shira Meir; Gourdon-Kanhukamwe, Amélie; Mallik, Peter R; Silan, Miguel Alejandro A.; Miller, Jeremy K.; IJzerman, Hans; Moshontz, Hannah; Beaudry, Jennifer L.; Suchow, Jordan W.; Chartier, Christopher R.; Coles, Nicholas A.; Sharifian, MohammadHasan; Todsen, Anna Louise; Levitan, Carmel A.; Azevedo, Flávio; Legate, Nicole; Heller, Blake; Rothman, Alexander J.; Dorison, Charles A.; Gill, Brian P.; Wang, Ke; Rees, Vaughan W.; Gibbs, Nancy; Goldenberg, Amit; Thi Nguyen, Thuy-vy; Gross, James J.; Kaminski, Gwenaêl; von Bastian, Claudia C.; Paruzel-Czachura, Mariola; Mosannenzadeh, Farnaz; Azouaghe, Soufian; Bran, Alexandre; Ruiz-Fernandez, Susana; Santos, Anabela Caetano; Reggev, Niv; Zickfeld, Janis H.; Akkas, Handan; Pantazi, Myrto; Ropovik, Ivan; Korbmacher, Max; Arriaga, Patrícia; Gjoneska, Biljana; Warmelink, Lara; Alves, Sara G.; de Holanda Coelho, Gabriel Lins; Stieger, Stefan; Schei, Vidar; Hanel, Paul H. P.; Szaszi, Barnabas; Fedotov, Maksim; Antfolk, Jan; Marcu, Gabriela-Mariana; Schrötter, Jana; Kunst, Jonas R.; Geiger, Sandra J.; Adetula, Adeyemi; Kocalar, Halil Emre; Kielińska, Julita; Kačmár, Pavol; Bokkour, Ahmed; Galindo-Caballero, Oscar J.; Djamai, Ikhlas; Pöntinen, Sara Johanna; AGESIN, Bamikole Emmanuel; Jernsäther, Teodor; Urooj, Anum; Rachev, Nikolay R.; Koptjevskaja-Tamm, Maria; Kurfalı, Murathan; Pit, Ilse L.; Li, Ranran; Çoksan, Sami; Dubrov, Dmitrii; Paltrow, Tamar Elise; Baník, Gabriel; Korobova, Tatiana; Studzinska, Anna; Jiang, Xiaoming; Aruta, John Jamir Benzon R.; Vintr, Jáchym; Chiu, Faith; Kaliska, Lada; Berkessel, Jana B.; Tümer, Murat; Morales-Izquierdo, Sara; Chuan-Peng, Hu; Vezirian, Kevin; Rosa, Anna Dalla; Bialobrzeska, Olga; Vasilev, Martin R.; Beitner, Julia; Kácha, Ondřej; Žuro, Barbara; Westerlund, Minja; Nedelcheva-Datsova, Mina; Findor, Andrej; Krupić, Dajana; Kowal, Marta; Askelund, Adrian Dahl; Pourafshari, Razieh; Đorđević, Jasna Milošević; Schmidt, Nadya-Daniela; Baklanova, Ekaterina; Szala, Anna; Zakharov, Ilya; Vranka, Marek A.; Ihaya, Keiko; Grano, Caterina; Cellini, Nicola; Białek, Michał; Anton-Boicuk, Lisa; Dalgar, Ilker; Adıgüzel, Arca; Verharen, Jeroen P. H.; Maturan, Princess Lovella G.; Kassianos, Angelos P.; Oliveira, Raquel; Čadek, Martin; Adoric, Vera Cubela; Özdoğru, Asil Ali; Sverdrup, Therese E.; Aczel, Balazs; Zambrano, Danilo; Ahmed, Afroja; Tamnes, Christian K.; Yamada, Yuki; Volz, Leonhard; Sunami, Naoyuki; Suter, Lilian; Vieira, Luc; Groyecka-Bernard, Agata; Kamburidis, Julia Arhondis; Reips, Ulf-Dietrich; Harutyunyan, Mikayel; Adetula, Gabriel Agboola; Allred, Tara Bulut; Barzykowski, Krystian; Antazo, Benedict G; Zsido, Andras N.; Šakan, Dušana Dušan; Cyrus-Lai, Wilson; Ahlgren, Lina Pernilla; Hruška, Matej; Vega, Diego; Manunta, Efisio; Mokady, Aviv; Capizzi, Mariagrazia; Martončik, Marcel; Say, Nicolas; Filip, Katarzyna; Vilar, Roosevelt; Staniaszek, Karolina; Vdovic, Milica; Adamkovic, Matus; Johannes, Niklas; Hajdu, Nandor; Cohen, Noga; Overkott, Clara; Krupić, Dino; Hubena, Barbora; Nilsonne, Gustav; Mioni, Giovanna; Solorzano, Claudio Singh; Ishii, Tatsunori; Chen, Zhang; Kushnir, Elizaveta; Karaarslan, Cemre; Ribeiro, Rafael R.; Khaoudi, Ahmed; Kossowska, Małgorzata; Bavolar, Jozef; Hoyer, Karlijn; Roczniewska, Marta; Karababa, Alper; Becker, Maja; Monteiro, Renan P.; Kunisato, Yoshihiko; Metin-Orta, Irem; Adamus ,Sylwia; Kozma, Luca; Czarnek, Gabriela; Domurat, Artur; Štrukelj, Eva; Alvarez, Daniela Serrato; Parzuchowski, Michal; Massoni, Sébastien; Czamanski-Cohen, Johanna; Pronizius, Ekaterina; Muchembled, Fany; van Schie, Kevin; Saçaklı, Aslı; Hristova, Evgeniya; Kuzminska, Anna O.; Charyate, Abdelilah; Bijlstra, Gijsbert; Afhami, Reza; Majeed, Nadyanna M.; Musser, Erica D.; Sirota, Miroslav; Ross, Robert M.; Yeung, Siu Kit; Papadatou-Pastou, Marietta; Foroni, Francesco; Almeida, Inês A. T.; Grigoryev, Dmitry; Lewis, David M. G.; Holford, Dawn L.; Janssen, Steve M. J.; Tatachari, Srinivasan; Batres, Carlota; Olofsson, Jonas K.; Daches, Shimrit; Belaus, Anabel; Pfuhl, Gerit; Corral-Frias, Nadia Sarai; Sousa, Daniela; Röer, Jan Philipp; Isager, Peder Mortvedt; Godbersen, Hendrik; Walczak, Radoslaw B.; Van Doren, Natalia; Ren, Dongning; Gill, Tripat; Voracek, Martin; DeBruine, Lisa M.; Anne, Michele; Očovaj, Sanja Batić; Thomas, Andrew G.; Arvanitis, Alexios; Ostermann, Thomas; Wolfe, Kelly; Arinze, Nwadiogo Chisom; Bundt, Carsten; Lamm, Claus; Calin-Jageman, Robert J; Davis, William E.; Karekla, Maria; Zorjan, Saša; Jaremka, Lisa M.; Uttley, Jim; Hricova, Monika; Koehn, Monica A; Kiselnikova, Natalia; Bai, Hui; Krafnick, Anthony J.; Balci, Busra Bahar; Ballantyne, Tonia; Lins, Samuel; Vally, Zahir; Esteban-Serna, Celia; Schmidt, Kathleen; Macapagal, Paulo Manuel L.; Szwed, Paulina; Zdybek, Przemysław Marcin; Moreau, David; Collins, W. Matthew; Joy-Gaba, Jennifer A.; Vilares, Iris; Tran, Ulrich S.; Boudesseul, Jordane; Albayrak-Aydemir, Nihan; Dixson, Barnaby James Wyld; Perillo, Jennifer T; Ferreira, Ana; Westgate, Erin C.; Aberson, Christopher L.; Arinze, Azuka Ikechukwu; Jaeger, Bastian; Butt, Muhammad Mussaffa; Silva, Jaime R.; Storage, Daniel Shafik; Janak, Allison P; Jiménez-Leal, William; Soto, Jose A.; Sorokowska, Agnieszka; McCarthy, Randy; Tullett, Alexa M; Frias-Armenta, Martha; Ribeiro, Matheus Fernando Felix; Hartanto, Andree; Forbes, Paul A. G.; Willis, Megan L.; del Carmen, Tejada R María; Torres, Adriana Julieth Olaya; Stephen, Ian D; Vaidis, David C.; de la Rosa-Gómez, Anabel; Yu, Karen; Sutherland, Clare A. M.; Manavalan, Mathi; Behzadnia, Behzad; Urban, Jan; Baskin, Ernest; McFall, Joseph P.; Ogbonnaya, Chisom Esther; Fu, Cynthia H. Y.; Rahal, Rima-Maria; Ndukaihe, Izuchukwu L. G.; Hostler, Thomas J.; Kappes, Heather Barry; Sorokowski, Piotr; Khosla, Meetu; Lazarevic, Ljiljana B.; Eudave, Luis; Vilsmeier, Johannes K.; Luis, Elkin O.; Muda, Rafał; Agadullina, Elena; Cárcamo, Rodrigo A.; Reeck, Crystal; Anjum, Gulnaz; Venegas, Mónica Camila Toro; Misiak, Michal; Ryan, Richard M.; Nock, Nora L.; Travaglino, Giovanni A.; Mensink, Michael C.; Feldman, Gilad; Wichman, Aaron L.; Chou, Weilun; Ziano, Ignazio; Seehuus, Martin; Chopik, William J.; Kung, Franki Y. H.; Carpentier, Joelle; Vaughn, Leigh Ann; Du, Hongfei; Xiao, Qinyu; Lima, Tiago J. S.; Noone, Chris; Onie, Sandersan; Verbruggen, Frederick; Radtke, Theda; Primbs, Maximilian A. (Nature Publishing Group, 2023)In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing ...