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Bart Deplancke

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Bart Deplancke (born 21 August 1975) is a Belgian bio-engineer and researcher. He is a full professor at École Polytechnique Fédérale de Lausanne, where he leads the laboratory of systems biology and genetics.[1]

Bart Deplancke
Deplancke in 2017
Born (1975-08-21) August 21, 1975 (age 49)
NationalityBelgian
Academic background
Alma materGhent University
University of Illinois at Urbana-Champaign
Academic work
InstitutionsÉcole Polytechnique Fédérale de Lausanne
Harvard Medical School
UMass Chan Medical School
Websitedeplanckelab.epfl.ch

Career

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Deplancke studied biochemical engineering at Ghent University and graduated with a Master of Science in 1998. In 2002, he obtained a PhD in immunobiology from the University of Illinois at Urbana-Champaign for his studies on intestinal host-microbe interactions and innate immunity.[2][3][4] He then pursued postdoctoral studies in the laboratories of Marc Vidal (Harvard Medical School) and Marian Walhout (University of Massachusetts), where he developed a high-throughput protein-DNA interaction screening approach and worked on elucidating metazoan genetic regulatory networks.[5][6] In 2007, he established his own lab at École Polytechnique Fédérale de Lausanne, where he was successively promoted to associate professor in 2014, and to full professor in 2020. He is currently vice-dean for innovation there.[1] He is a cofounder of the Junior European Drosophila Investigators (JEDI) scientific network.[7] Since 2013, Deplancke is a group leader at the Swiss Institute of Bioinformatics.[8]

Research

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The laboratory of Bart Deplancke develops microfluidics, high-throughput sequencing, and single cell genomics tools to study the origin, diversity and functions of stromal cells in adipose tissues as well as to better understand how genomic variations may affect molecular and organismal diversity, with a specific focus on metabolic phenotypes.[1][9] In particular, Deplancke uses adipogenesis as a model system to better understand the regulatory networks driving cellular differentiation, focusing on the role of transcription factors[10][11] and transcriptional co-regulators.[12]

Using single cell transcriptomics, Deplancke's team discovered the previously unknown adipogenesis-regulatory cells (Aregs), which are endowed with the ability to suppress adipogenesis, a finding that may have important implications for the treatment of chronic metabolic disorders such as obesity or type 2 diabetes.[13][14] Deplancke's lab has also contributed to the understanding that non-coding genetic variants have broader impact on molecular and organismal diversity than previously expected, thus introducing the concept of variable chromatin modules (VCMs).[15][16][17]

Together with the laboratory of Trudy Mackay, Deplancke and colleagues characterized the Drosophila Genetic Reference Panel, with the aim to improve the robustness of genotype to phenotype relationship studies,[18][19] allowing elucidation of important genetic principles underlying variation in gut immunocompetence.[20][21][22]

Innovation

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In 2011, Deplancke co-founded Genohm, a company delivering software (big data management) products and services for pharmaceutical and R&D laboratories, which was acquired by Agilent in May 2018.[23][24]

In 2020, he co-founded Alithea Genomics, a company specializing in making high-throughput transcriptomics highly affordable for academic projects, biobank functionalization, and drug screening platforms.[25][26]

Distinctions

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In 2005, Deplancke received the Peter Reeds Young Investigator Award from the American Society for Nutritional Sciences for his work on the impact of genetic factors in response to bacterial infections.[27]

In 2017, he was elected to the National Research Council of the Swiss National Science Foundation.[28]

References

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  1. ^ a b c "Bart Deplancke's lab at EPFL". Retrieved 2 September 2020.
  2. ^ Deplancke, Bart; Gaskins, H. Rex (2003). "Hydrogen sulfide induces serum-independent cell cycle entry in nontransformed rat intestinal epithelial cells". The FASEB Journal. 17 (10): 1310–1312. doi:10.1096/fj.02-0883fje. ISSN 1530-6860. PMID 12738807. S2CID 14505067.
  3. ^ Deplancke, Bart; Vidal, Olivier; Ganessunker, Deshanie; Donovan, Sharon M.; Mackie, Roderick I.; Gaskins, H. Rex (2002-11-01). "Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition". The American Journal of Clinical Nutrition. 76 (5): 1117–1125. doi:10.1093/ajcn/76.5.1117. ISSN 0002-9165. PMID 12399288.
  4. ^ Deplancke, Bart; Gaskins, H. Rex (2001-06-01). "Microbial modulation of innate defense: goblet cells and the intestinal mucus layer". The American Journal of Clinical Nutrition. 73 (6): 1131S–1141S. doi:10.1093/ajcn/73.6.1131S. ISSN 0002-9165. PMID 11393191.
  5. ^ Deplancke, Bart; Dupuy, Denis; Vidal, Marc; Walhout, Albertha J. M. (2004-10-15). "A Gateway-Compatible Yeast One-Hybrid System". Genome Research. 14 (10b): 2093–2101. doi:10.1101/gr.2445504. ISSN 1088-9051. PMC 528925. PMID 15489331.
  6. ^ Deplancke, Bart; Mukhopadhyay, Arnab; Ao, Wanyuan; Elewa, Ahmed M.; Grove, Christian A.; Martinez, Natalia J.; Sequerra, Reynaldo; Doucette-Stamm, Lynn; Reece-Hoyes, John S.; Hope, Ian A.; Tissenbaum, Heidi A. (2006-06-13). "A Gene-Centered C. elegans Protein-DNA Interaction Network". Cell. 125 (6): 1193–1205. doi:10.1016/j.cell.2006.04.038. ISSN 0092-8674. PMID 16777607. S2CID 6485745.
  7. ^ Marx, Vivien (2017-03-01). "Bart Deplancke". Nature Methods. 14 (3): 211. doi:10.1038/nmeth.4188. ISSN 1548-7105. S2CID 45038650.
  8. ^ Flegel, Sylvie. "Deplancke Bart". www.sib.swiss. Retrieved 2020-09-02.
  9. ^ "Speakers – NRRN". nuclearreceptorresearchnetwork.org. Retrieved 2020-09-02.
  10. ^ Gubelmann, Carine; Schwalie, Petra C; Raghav, Sunil K; Röder, Eva; Delessa, Tenagne; Kiehlmann, Elke; Waszak, Sebastian M; Corsinotti, Andrea; Udin, Gilles; Holcombe, Wiebke; Rudofsky, Gottfried (2014-08-27). Tontonoz, Peter (ed.). "Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network". eLife. 3: e03346. doi:10.7554/eLife.03346. ISSN 2050-084X. PMC 4359378. PMID 25163748.
  11. ^ Chen, Wanze; Schwalie, Petra C.; Pankevich, Eugenia V.; Gubelmann, Carine; Raghav, Sunil K.; Dainese, Riccardo; Cassano, Marco; Imbeault, Michael; Jang, Suk Min; Russeil, Julie; Delessa, Tenagne (2019-04-18). "ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer". Nature Communications. 10 (1): 1809. Bibcode:2019NatCo..10.1809C. doi:10.1038/s41467-019-09803-9. ISSN 2041-1723. PMC 6472429. PMID 31000713.
  12. ^ Raghav, Sunil K.; Waszak, Sebastian M.; Krier, Irina; Gubelmann, Carine; Isakova, Alina; Mikkelsen, Tarjei S.; Deplancke, Bart (2012-05-11). "Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO". Molecular Cell. 46 (3): 335–350. doi:10.1016/j.molcel.2012.03.017. ISSN 1097-2765. PMID 22521691.
  13. ^ Dovey, Dana (21 June 2018). "Scientists Might Have Figured out How to Stop People from Getting Fat". Newsweek. Retrieved 2 September 2020.
  14. ^ Schwalie, Petra C.; Dong, Hua; Zachara, Magda; Russeil, Julie; Alpern, Daniel; Akchiche, Nassila; Caprara, Christian; Sun, Wenfei; Schlaudraff, Kai-Uwe; Soldati, Gianni; Wolfrum, Christian (July 2018). "A stromal cell population that inhibits adipogenesis in mammalian fat depots". Nature. 559 (7712): 103–108. Bibcode:2018Natur.559..103S. doi:10.1038/s41586-018-0226-8. ISSN 1476-4687. PMID 29925944. S2CID 49348518.
  15. ^ Kilpinen, Helena; Waszak, Sebastian M.; Gschwind, Andreas R.; Raghav, Sunil K.; Witwicki, Robert M.; Orioli, Andrea; Migliavacca, Eugenia; Wiederkehr, Michaël; Gutierrez-Arcelus, Maria; Panousis, Nikolaos I.; Yurovsky, Alisa (2013-11-08). "Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription". Science. 342 (6159): 744–747. Bibcode:2013Sci...342..744K. doi:10.1126/science.1242463. ISSN 1095-9203. PMC 5502466. PMID 24136355.
  16. ^ Waszak, Sebastian M.; Delaneau, Olivier; Gschwind, Andreas R.; Kilpinen, Helena; Raghav, Sunil K.; Witwicki, Robert M.; Orioli, Andrea; Wiederkehr, Michael; Panousis, Nikolaos I.; Yurovsky, Alisa; Romano-Palumbo, Luciana (2015-08-27). "Population Variation and Genetic Control of Modular Chromatin Architecture in Humans". Cell. 162 (5): 1039–1050. doi:10.1016/j.cell.2015.08.001. ISSN 0092-8674. PMID 26300124. S2CID 16537629.
  17. ^ Deplancke, Bart; Alpern, Daniel; Gardeux, Vincent (2016-07-28). "The Genetics of Transcription Factor DNA Binding Variation". Cell. 166 (3): 538–554. doi:10.1016/j.cell.2016.07.012. ISSN 0092-8674. PMID 27471964. S2CID 8237138.
  18. ^ Huang, Wen; Massouras, Andreas; Inoue, Yutaka; Peiffer, Jason; Ràmia, Miquel; Tarone, Aaron M.; Turlapati, Lavanya; Zichner, Thomas; Zhu, Dianhui; Lyman, Richard F.; Magwire, Michael M. (2014-07-01). "Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines". Genome Research. 24 (7): 1193–1208. doi:10.1101/gr.171546.113. ISSN 1088-9051. PMC 4079974. PMID 24714809.
  19. ^ Bevers, Roel P. J.; Litovchenko, Maria; Kapopoulou, Adamandia; Braman, Virginie S.; Robinson, Matthew R.; Auwerx, Johan; Hollis, Brian; Deplancke, Bart (December 2019). "Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel". Nature Metabolism. 1 (12): 1226–1242. doi:10.1038/s42255-019-0147-3. ISSN 2522-5812. PMID 32694676. S2CID 209162535.
  20. ^ Bou Sleiman, Maroun S.; Osman, Dani; Massouras, Andreas; Hoffmann, Ary A.; Lemaitre, Bruno; Deplancke, Bart (2015-07-27). "Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence". Nature Communications. 6 (1): 7829. Bibcode:2015NatCo...6.7829B. doi:10.1038/ncomms8829. ISSN 2041-1723. PMC 4525169. PMID 26213329.
  21. ^ Frochaux, Michael V.; Bou Sleiman, Maroun; Gardeux, Vincent; Dainese, Riccardo; Hollis, Brian; Litovchenko, Maria; Braman, Virginie S.; Andreani, Tommaso; Osman, Dani; Deplancke, Bart (2020-01-17). "cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel". Genome Biology. 21 (1): 6. doi:10.1186/s13059-019-1912-z. ISSN 1474-760X. PMC 6966807. PMID 31948474.
  22. ^ Bou Sleiman, Maroun; Frochaux, Michael Vincent; Andreani, Tommaso; Osman, Dani; Guigo, Roderic; Deplancke, Bart (2020-01-17). "Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes". Genome Biology. 21 (1): 4. doi:10.1186/s13059-019-1918-6. ISSN 1474-760X. PMC 6966827. PMID 31948480.
  23. ^ "Agilent Completes Acquisition of Genohm". www.agilent.com. Retrieved 2021-02-23.
  24. ^ "Bart Deplancke (Supervisor)". ENHPATHY. Retrieved 2021-02-23.
  25. ^ Hitchcock, Imogen (2021-01-19). "Mapping Out the Future of Drug Discovery via Gene Expression Analysis". {{cite journal}}: Cite journal requires |journal= (help)
  26. ^ "Alithea Genomics SA". www.venturekick.ch. Retrieved 2021-02-23.
  27. ^ "Awards and Kudos at ASNS" (PDF). Nutrition Today. 40: 98. June 2005.
  28. ^ "SNSF Research Council: six new members elected - SNF". www.snf.ch. Retrieved 2020-09-02.
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