Bart Deplancke Explained

Bart Deplancke
Birth Date:21 August 1975
Nationality:Belgian
Alma Mater:Ghent University
University of Illinois at Urbana-Champaign
Workplaces:École Polytechnique Fédérale de Lausanne
Harvard Medical School
UMass Chan Medical School

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]

Career

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. 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

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.[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

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

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]

External links

Notes and References

  1. Web site: Bart Deplancke's lab at EPFL. 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. en. 17. 10. 1310–1312. 10.1096/fj.02-0883fje. free . 12738807. 14505067. 1530-6860.
  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. en. 76. 5. 1117–1125. 10.1093/ajcn/76.5.1117. 12399288. 0002-9165. free.
  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. en. 73. 6. 1131S–1141S. 10.1093/ajcn/73.6.1131S. 11393191. 0002-9165. free.
  5. Deplancke. Bart. Dupuy. Denis. Vidal. Marc. Walhout. Albertha J. M.. 2004-10-15. A Gateway-Compatible Yeast One-Hybrid System. Genome Research. en. 14. 10b. 2093–2101. 10.1101/gr.2445504. 1088-9051. 15489331. 528925.
  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. en. 125. 6. 1193–1205. 10.1016/j.cell.2006.04.038. 16777607. 6485745. 0092-8674. free.
  7. Marx. Vivien. 2017-03-01. Bart Deplancke. Nature Methods. en. 14. 3. 211. 10.1038/nmeth.4188. 45038650. 1548-7105. free.
  8. Web site: Flegel. Sylvie. Deplancke Bart. 2020-09-02. www.sib.swiss. en-gb.
  9. Web site: Speakers – NRRN. 2020-09-02. nuclearreceptorresearchnetwork.org.
  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. Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. eLife. 3. e03346. 10.7554/eLife.03346. 25163748. 4359378. 2050-084X . free .
  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. en. 10. 1. 1809. 10.1038/s41467-019-09803-9. 31000713. 6472429. 2019NatCo..10.1809C . 2041-1723.
  12. 2012-05-11. Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO. Molecular Cell. en. 46. 3. 335–350. 10.1016/j.molcel.2012.03.017. 1097-2765. Raghav. Sunil K.. Waszak. Sebastian M.. Krier. Irina. Gubelmann. Carine. Isakova. Alina. Mikkelsen. Tarjei S.. Deplancke. Bart. 22521691. free.
  13. Web site: Dovey. Dana. 21 June 2018. Scientists Might Have Figured out How to Stop People from Getting Fat. 2 September 2020. Newsweek.
  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. en. 559. 7712. 103–108. 10.1038/s41586-018-0226-8. 29925944. 2018Natur.559..103S . 49348518. 1476-4687.
  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. 10.1126/science.1242463. 1095-9203. 5502466. 24136355. 2013Sci...342..744K .
  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. en. 162. 5. 1039–1050. 10.1016/j.cell.2015.08.001. 0092-8674. 26300124. 16537629. free.
  17. 2016-07-28. The Genetics of Transcription Factor DNA Binding Variation. Cell. en. 166. 3. 538–554. 10.1016/j.cell.2016.07.012. 0092-8674. Deplancke. Bart. Alpern. Daniel. Gardeux. Vincent. 27471964. 8237138. free.
  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. en. 24. 7. 1193–1208. 10.1101/gr.171546.113. 1088-9051. 24714809. 4079974.
  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. en. 1. 12. 1226–1242. 10.1038/s42255-019-0147-3. 32694676. 209162535. 2522-5812.
  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. en. 6. 1. 7829. 10.1038/ncomms8829. 26213329. 4525169. 2015NatCo...6.7829B . 2041-1723.
  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. 10.1186/s13059-019-1912-z. 1474-760X. 6966807. 31948474 . free .
  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. 10.1186/s13059-019-1918-6. 1474-760X. 6966827. 31948480 . free .
  23. Web site: Agilent Completes Acquisition of Genohm. 2021-02-23. www.agilent.com.
  24. Web site: Bart Deplancke (Supervisor). 2021-02-23. ENHPATHY. en-GB.
  25. Hitchcock. Imogen. 2021-01-19. Mapping Out the Future of Drug Discovery via Gene Expression Analysis. en.
  26. Web site: Alithea Genomics SA. 2021-02-23. www.venturekick.ch. en.
  27. June 2005. Awards and Kudos at ASNS. Nutrition Today. 40. 98.
  28. Web site: SNSF Research Council: six new members elected - SNF. 2020-09-02. www.snf.ch.

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