Jurgen R. Haanstra / Managing Director AIMMS, Lecturer and researcher

Current research projects

1. Together with bachelor and master students, I try to understand how the integration of metabolism and signalling is altered in liver cancer cells compared to the healthy liver.
2. Together with bachelor and master students, I have several computational and experimental projects on energy metabolism in parasites (see also list of students below)

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Invited talks

Talk at the ‘Computational hub fall meeting‘ on Nov 1, 2016, in Leiden, The Netherlands. Title: Attacking blood-borne parasites with mathematics

Talk at the Cancer Centre Amsterdam (CCA) Bioinformatics meeting on May 12, 1017 in Amsterdam, the Netherlands. Title: Metabolism in disease: target the system!

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Background and previous projects

Jurgen Haanstra studied Biomedical Sciences at Utrecht University, with one internship on the impact of stress on food-intake regulating neuropeptides and another on the downstream effects of MAP kinase signalling. He graduated in 2002 and started as a PhD student at VU University in the lab of Dr. Barbara Bakker and Prof. dr. Hans Westerhoff on network-based drug design against glycolysis in the tropical parasite Trypanosoma brucei. In this project he combined mathematical modelling and wet lab experimentation. During this time, he spend 6 months in Heidelberg to study the control and regulation of trypanosome gene expression.

After his PhD, Haanstra was a post-doctoral researcher in the Hematology department of the Erasmus MC in Rotterdam, where he focussed on elucidating the molecular mechanism of leukemogenesis after bone marrow failure. In 2011, he returned to trypanosomes and again combined mathematical modelling with wet lab experiments. He divided his time between his post-doc position at the UMCG Groningen and his position as a guest researcher in the department of Molecular Cell Physiology at VU University Amsterdam and worked on redox metabolism of T. brucei and differential-based drug design. In the latter part of his work he aimed to find drug targets within metabolism that, when targeted, affect the parasite more than the mammalian host. Three times he has hosted the AIMMS-sponsored annual microsymposium on ‘Parasite/Trypanosmatid Metabolism, Drug Design and Glycosomes’ at the VU.

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Publications 

1. Nilsson, A, Haanstra, JR, Engqvist, M, Gerding, A, Bakker, BM, Klingmüller, U et al.. Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. Proc. Natl. Acad. Sci. U.S.A. 2020;117 (19):10294-10304. doi: 10.1073/pnas.1919250117. PubMed PMID:32341162 PubMed Central PMC7229649.
2. Nilsson, A, Haanstra, JR, Teusink, B, Nielsen, J. Metabolite Depletion Affects Flux Profiling of Cell Lines. Trends Biochem. Sci. 2018;43 (6):395-397. doi: 10.1016/j.tibs.2018.03.009. PubMed PMID:29656822 .
3. Bosdriesz, E, Wortel, MT, Haanstra, JR, Wagner, MJ, de la Torre Cortés, P, Teusink, B et al.. Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux. Sci Rep. 2018;8 (1):5576. doi: 10.1038/s41598-018-23528-7. PubMed PMID:29615663 PubMed Central PMC5883050.
4. Haanstra, JR, Gerding, A, Dolga, AM, Sorgdrager, FJH, Buist-Homan, M, du Toit, F et al.. Targeting pathogen metabolism without collateral damage to the host. Sci Rep. 2017;7 :40406. doi: 10.1038/srep40406. PubMed PMID:28084422 PubMed Central PMC5234033.
5. Antwi, EB, Haanstra, JR, Ramasamy, G, Jensen, B, Droll, D, Rojas, F et al.. Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression. BMC Genomics. 2016;17 :306. doi: 10.1186/s12864-016-2624-3. PubMed PMID:27118143 PubMed Central PMC4845500.
6. Haanstra, JR, Bakker, BM. Drug target identification through systems biology. Drug Discov Today Technol. 2015;15 :17-22. doi: 10.1016/j.ddtec.2015.06.002. PubMed PMID:26464086 .
7. Haanstra, JR, González-Marcano, EB, Gualdrón-López, M, Michels, PA. Biogenesis, maintenance and dynamics of glycosomes in trypanosomatid parasites. Biochim. Biophys. Acta. 2016;1863 (5):1038-48. doi: 10.1016/j.bbamcr.2015.09.015. PubMed PMID:26384872 .
8. Alemdehy, MF, Haanstra, JR, de Looper, HW, van Strien, PM, Verhagen-Oldenampsen, J, Caljouw, Y et al.. ICL-induced miR139-3p and miR199a-3p have opposite roles in hematopoietic cell expansion and leukemic transformation. Blood. 2015;125 (25):3937-48. doi: 10.1182/blood-2014-11-612507. PubMed PMID:25778535 .
9. Haanstra, JR, Bakker, BM, Michels, PA. In or out? On the tightness of glycosomal compartmentalization of metabolites and enzymes in Trypanosoma brucei. Mol. Biochem. Parasitol. 2014;198 (1):18-28. doi: 10.1016/j.molbiopara.2014.11.004. PubMed PMID:25476771 .
10. Szöör, B, Haanstra, JR, Gualdrón-López, M, Michels, PA. Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids. Curr. Opin. Microbiol. 2014;22 :79-87. doi: 10.1016/j.mib.2014.09.006. PubMed PMID:25460800 .
11. Fadda, A, Ryten, M, Droll, D, Rojas, F, Färber, V, Haanstra, JR et al.. Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Mol. Microbiol. 2014;94 (2):307-26. doi: 10.1111/mmi.12764. PubMed PMID:25145465 PubMed Central PMC4285177.
12. Achcar, F, Fadda, A, Haanstra, JR, Kerkhoven, EJ, Kim, DH, Leroux, AE et al.. The silicon trypanosome: a test case of iterative model extension in systems biology. Adv. Microb. Physiol. 2014;64 :115-43. doi: 10.1016/B978-0-12-800143-1.00003-8. PubMed PMID:24797926 PubMed Central PMC4773886.
13. Leroux, AE, Haanstra, JR, Bakker, BM, Krauth-Siegel, RL. Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling. J. Biol. Chem. 2013;288 (33):23751-64. doi: 10.1074/jbc.M113.483289. PubMed PMID:23814051 PubMed Central PMC3745322.
14. Pieretti, S, Haanstra, JR, Mazet, M, Perozzo, R, Bergamini, C, Prati, F et al.. Naphthoquinone derivatives exert their antitrypanosomal activity via a multi-target mechanism. PLoS Negl Trop Dis. 2013;7 (1):e2012. doi: 10.1371/journal.pntd.0002012. PubMed PMID:23350008 PubMed Central PMC3547856.
15. Verhagen-Oldenampsen, JH, Haanstra, JR, van Strien, PM, Valkhof, M, Touw, IP, von Lindern, M et al.. Loss of ercc1 results in a time- and dose-dependent reduction of proliferating early hematopoietic progenitors. Anemia. 2012;2012 :783068. doi: 10.1155/2012/783068. PubMed PMID:22701168 PubMed Central PMC3371671.
16. Haanstra, JR, van Tuijl, A, van Dam, J, van Winden, W, Tielens, AG, van Hellemond, JJ et al.. Proliferating bloodstream-form Trypanosoma brucei use a negligible part of consumed glucose for anabolic processes. Int. J. Parasitol. 2012;42 (7):667-73. doi: 10.1016/j.ijpara.2012.04.009. PubMed PMID:22580731 .
17. Bindels, EM, Havermans, M, Lugthart, S, Erpelinck, C, Wocjtowicz, E, Krivtsov, AV et al.. EVI1 is critical for the pathogenesis of a subset of MLL-AF9-rearranged AMLs. Blood. 2012;119 (24):5838-49. doi: 10.1182/blood-2011-11-393827. PubMed PMID:22553314 PubMed Central PMC3382941.
18. Beekman, R, Valkhof, MG, Sanders, MA, van Strien, PM, Haanstra, JR, Broeders, L et al.. Sequential gain of mutations in severe congenital neutropenia progressing to acute myeloid leukemia. Blood. 2012;119 (22):5071-7. doi: 10.1182/blood-2012-01-406116. PubMed PMID:22371884 .
19. Haanstra, JR, Kerkhoven, EJ, van Tuijl, A, Blits, M, Wurst, M, van Nuland, R et al.. A domino effect in drug action: from metabolic assault towards parasite differentiation. Mol. Microbiol. 2011;79 (1):94-108. doi: 10.1111/j.1365-2958.2010.07435.x. PubMed PMID:21166896 .
20. Wölfler, A, Danen-van Oorschot, AA, Haanstra, JR, Valkhof, M, Bodner, C, Vroegindeweij, E et al.. Lineage-instructive function of C/EBPα in multipotent hematopoietic cells and early thymic progenitors. Blood. 2010;116 (20):4116-25. doi: 10.1182/blood-2010-03-275404. PubMed PMID:20807890 .

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Supervision of students

If you are interested in an internship look at our Internships page for the available openings and contact me.

Bachelor (Bsc) and master (Msc) students

Name	Co-supervisor	Project	Bsc/Msc	Year	Period
Josan Yauw		The role of the FBP-activatable LDH in the metabolism of Schistosoma Mansoni	Msc	2015	May - October
Lili Cheng	Marco Siderius	THT1-expressing yeast	Bsc	2015	March - June
Thijs Tinneveld		Liver (cancer) metabolism	Bsc	2015	March - July
Alina Renz	Klaas Krab	Personalized Medicine – Modelling of Tumorigenesis	Bsc	2015	February - June
Jose Gavalda Garcia	Meike Wortel Marijke Wagner	Membrane low affinity transporter increase net substrate uptake in Saccharomyces cerevisiae: an experimental verification	Msc	2015	February - June
Elena Merino Tejero		Quantification of enzyme activity in HepG2 cells in different nutrient conditions	Msc	2015-2016	September 2015 - March 2016
Dimitri Lindijer		Modelling the redox pathway in Trypanosoma brucei	Bsc	2015-2016	August 2015 - April 2016 (50%)
Mariah Kes Eva Mooij	Marijke Wagner	Quantification of glycogen and urea/ammonia production in liver cancer cell lines	Bsc (honours programme 2nd year)	2016	July
Mandy Koomen		The role of Branched-Chain Amino Acids in Metabolism and Proliferation of HepG2 Cells	Bsc	2016	February - June
Nicole Geduld		The carbon balance in liver cancer cells	Bsc	2016-2017	Sept 2016 - Feb 2017
Hakan Cicigul		The dynamics of glycolytic enzyme activities after growth factor stimulation	Guest researcher	2016-2017	Okt 2016 - Feb 2017
Daan van den Akker		Exploration of constraint-based modeling approaches for the identification of hepatocellular carcinoma specific metabolic pathways	Msc (literature thesis UU)	2017	May - Aug
Maurice Vink		The dynamics of glycolytic enzyme activities after growth factor stimulation	Bsc	2017	Feb - June
Gius Kerster	Marco Siderius	The effect of HIV protease inhibitors on Trypanosoma brucei	Bsc	2017	Feb - June
Olivier Martin		The role of the FBP-activatable LDH in the metabolism of Schistosoma Mansoni	Msc	2017	Feb - June
Stefan Westerink		Amino acid metabolism in liver (cancer) cells	Msc	2017	April - Aug
Annabel Dekker		The dynamics of glycolytic enzyme activities after growth factor stimulation	Msc	2017-2018	Sept 2017 - Feb 2018
Joyce IJspelder		Glycolysis as potential target pathway for drugs against Trypanosoma brucei, Trypanosoma cruzi and Leishmania	Msc (literature thesis)	2018	January - July
Glenn Mollevanger		Metabolism of cancer cell lines	HBO/University of Applied Sciences	2018	February - September
Malu Steenwijk	Marijke Wagner	Development of assays to screen for inhibitors of glucose transport in Trypanosoma brucei	Msc	2018	February - June
Thijs van der Heijden		Does Trypanosoma brucei adapt to glucose transport inhibition?	Msc	2019	January - July
Mick de Bree		Kill curves of glucose transport inhibition	Bsc	2019	February - May
Deborah Jekel	Rosanne Hertzberger	Growth and metabolims of Lactopbacillus crispatus	Bsc	2019	February - May
Marlieke Oostdam		Towards a semi-highthrougput test system for glucose transport inhibition	Msc	2019	February - June
Jikke Wijninga		Metabolism of T. brucei in the adipose tissue	Msc (literature thesis)	2019	March - September
Ritesh Panchoe	Rosanne Hertzberger	Glycogen metabolism of vaginal bacterial species	Msc	2019	April - September
Federica Spiga		Oxygen consumption in liver cancer cells	volunteer (1st year bachelor)	2019	August
Claire Ribbers		Enzyme activities in liver cancer cells	Bsc	2019	September-December
Senin Ermesilia		Liver cancer cells: growth, flux and enzyme activities	HBO/University of Applied Sciences	2019/2020	September - June
Ruben Kramer		Eradication of African sleeping sickness by 2030, possible or not?	Bsc (literature thesis	2020	January
Alexander Woudstra	Rosanne Hertzberger	Metabolism of vaginal bacterial species	Msc	2019	November - March
Julia Beets		Bottlenecks in liver cancer glycolysis	Bsc	2020	February - May
Antoon Kouwenhoven	Pranas Grigaitis	Integration of thermodynamics data into large-scale metabolic networks	Bsc	2020	February - May
Maaike Janz		Semi-high throughput assay for glucose transport inhibitors	Msc	2020	March - August
Daniel Centanni		Antitrypanosomal drugs in the context of inborn errors of metabolism	Bsc	2020	April - August
Tom Belleman		The effect of inhibition of glycolytic enzymes in liver cancer cells	Bsc	2020	August - November

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Links

LinkedIn profile Jurgen Haanstra

Google Scholar Jurgen Haanstra

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Contact information

Email: j.r.haanstra[at]vu[dot]nl

Systems Bioinformatics
Vrije Universiteit Amsterdam
room O|2 01W57
De Boelelaan 1108
1081 HZ Amsterdam
Tel: 020-5987193