Jeroen Bakkers

Jeroen Bakkers received his PhD in 2000 from Leiden University, The Netherlands. During this time he was introduced in the zebrafish system and used it to study the role of glycosyltransferases during early vertebrate development. He continued his work on zebrafish development as a postdoc in the lab of Matthias Hammerschmidt at the Max-Planck Institute for Immunobiology in Freiburg, Germany. Here he started his work on Bmp and Wnt signaling during zebrafish gastrulation and isolated p63 (a member of the p53 tumor suppressor family) as a direct target of Bmp signalling. In 2003 he was appointed at the Hubrecht Institute initially as a junior staff member and in 2008 as a senior staff member and initiated here his work on heart development using zebrafish. In 2008 he was awarded a VIDI career grant from the Dutch science organization NWO and in 2015 he was appointed as Professor of Molecular Cardiogenetics at the UMC Utrecht.

Other activities:

  • Professor at Utrecht University
  • Chairman at the Dutch Society of Developmental Biology

j.bakkers(at)hubrecht.eu  Send Mail

Team membersBakkers

Jeroen Bakkers

Group Leader
j.bakkers@hubrecht.eu

Yeszamin Onderwater

Technician
y.onderwater@hubrecht.eu

Phong Nguyen

Postdoc
p.nguyen@hubrecht.eu

Sarah Kamel

PhD Student
s.kamel@hubrecht.eu

Dennis de Bakker

PhD student
d.bakker@hubrecht.eu

Melanie Laarman

PhD student
m.laarman@hubrecht.eu

Sven Willekers

PhD student
s.willekers@hubrecht.eu

Lotte Koopman

PhD student
l.koopman@hubrecht.eu

Fabian Kruse

PhD student
f.kruse@hubrecht.eu

Silja Burkhard

PhD student
s.burkhard@hubrecht.eu

Laurence Garric

Postdoc
l.garric@hubrecht.eu

Federico Tessadori

Postdoc
f.tessadori@hubrecht.eu

Sonja Chocron

Technician
s.chocron@hubrecht.eu

Show more

Show more

More information

_2RW8992_BW

In Februari 2015 Jeroen Bakkers has been appointed professor in Molecular Cardiogenetics at the University Medical Center. His inauguration took place Februari 3, 2016 in the Utrecht University Hall.

_2RW8789

2016-01-05_news-item_pic3

Unlike humans, zebrafish are able to completely repair their heart after injury, for example a myocardial infarction-like event. But how is the fish able to regenerate this injury and, more specifically, what are the initial factors are that push heart muscle cells to start dividing again in order to replace the lost tissue.

To address this question, we developed a new method in the Bakkers group called tomo-seq. Applied to the regenerating heart, it allows us to obtain whole-genome expression data coupled with spatial resolution. This means, that we are able to find out which genes are expressed in which region along the axis injury area – borderzone – uninjured/remote myocardium. To achieve this, the injured heart is sectioned across one axis and every single section is barcoded before RNA-sequencing. This allows tracing back transcripts to the section (and thus position in the tissue) from which they originated in order to identify genes that are upregulated in a specific region of the tissue.

Focusing on the borderzone, which is known to house the majority of proliferating heart muscle cells, we found that bone morphogenetic protein (BMP) signalling is upregulated. BMP signaling has not been described to be involved in fish heart regeneration so far, and further experiments showed that knock-down of BMP resulted in fewer proliferating heart muscle cells. On the other hand, when BMP signalling was experimentally upregulated, more heart muscle cells started to divide, in turn increasing the regenerative potential.

In summary, we showed that spatially restricted gene expression can be identified with the tomo-seq method and that this can lead to the discovery of novel pathways involved in driving the regenerative process, like BMP signalling. Once we fully understand how regeneration occurs in the fish heart, we might be able to extrapolate these findings to humans in order to treat heart disease.Paper_FKruse

Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration, Kruse, F*, Wu, C-C*,…Bakkers, J., Developmental Cell, 2016.      *these authors contributed equally

Scientists are uncovering how our bodies — and everything within them — tell right from left.

Read the whole article here:

How Life Turns Asymmetric

Research

Bakkers: Cardiac Development and Genetics

Wide ranges of cardiac diseases are caused by genetic alterations, which affect normal cardiac development or function. The Bakkers' lab uses the zebrafish model to identify genes and mechanisms that regulate normal heart development, function and regeneration. In addition to better understand the genetics of cardiac diseases we study the effects of patient specific genetic variations in zebrafish. The projects in the lab use a wide range of approaches including reverse- and forward genetics, cell biology, mathematics and bioinformatics.

Read research

Key publications

All publications can be found on research gate.

Wu, C.-C., Kruse, F., Vasudevarao, M. D., Junker, J. P., Zebrowski, D. C., Fischer, K., Bakkers, J. Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration. Dev. Cell, 36(1), 36–49. doi:10.1016/j.devcel.2015.12.010

Tessadori, F., Noël, E.S., Rens, E.G., Magliozzi, R., Evers-van Gogh, I.J.A., Guardavaccaro, D., Merks, R.M.H. and Bakkers, J. Nodal signalling range is regulated by proprotein convertase-mediated secretion. Dev. Cell, doi:10.1016/j.devcel.2014.12.014

Junker, J.P.*, Noël, E.S*., Guryev, V., Peterson, K.A., Shah, G., Huisken, J., McMahon, A.P., Berezikov, E., Bakkers, J*. and van Oudenaarden, A.* (2014) Genome-wide RNA tomography in the zebrafish embryo. Cell159(3): 662-675

Chetaille, P.*, Côté, j.*, Burkhard, S.*, Houde, C., Preuss, C., Piché, J.,Gosset, N., Leclerc, S., Wünnemann, F., Cameron, M., Castilloux, J., Thibeault, M., Gagnon, C., Galli, A., Tuck, A., Hickson, G., Amine, N., Boufaied, I., Lemyre, E.,Santa Barbara, P., Faure, S., Jonzon, A., Dietz, H., Gallo-McFarlane, E., Benson, W., Zhan, S.H., Shen, Y., Jomphe, M., Jones, S.J.M., Bakkers, J., and Andelfinger, G.(2014) A human dysrhythmia syndrome affecting heart and gut is associated with mutations in SGOL1.Nat. Genet.46(11):1245-1249

Noël ES, Verhoeven M, Lagendijk AK, Tessadori F, Smith K, Choorapoikayil S, den Hertog J and Bakkers J. (2013) A Nodal-independent and tissue-intrinsic mechanism controls heart-looping chirality. Nat. Commun4:2754

Mugoni, V., Postel, R., Catanzaro, V., De Luca, E., Turco, E., Digilio, G., Silengo, Murphy, M.P., Medana, C., L., Stainier, D.Y.R., Bakkers, J. and Santoro, M.M. (2013) Ubiad1 Is an Antioxidant Enzyme that Regulates eNOS Activity by CoQ10 Synthesis. Cell 152; 504-518

All publications

A zebrafish Loss-of-Function Model for Human CFAP53 Mutations Reveals its Specific Role in Laterality Organ Function
2016

Emily SNoël, Tarek SMomenah, KhalidAl-Dagriri, AbdulrahmanAl-Suwaid, SafarAl-Shahrani, HuiJiang, SvenWillekers, Yara YOostveen, SonjaChocron, Alex VPostma, Zahurul ABhuiyan, JeroenBakkers

Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2
2016

BilgeSan, Naomi DChrispijn, NadineWittkopp, Simon Jvan Heeringen, Anne KLagendijk, MarcoAben, JeroenBakkers, René FKetting, Leonie MKamminga

Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity
2016

Dragana JJosifova, Glen RMonroe, FedericoTessadori, Estherde Graaff, Bertvan der Zwaag, Sarju GMehta, MagdalenaHarakalova, Karen JDuran, Sanne M CSavelberg, Isaäc JNijman, HeinzJungbluth, Casper CHoogenraad, JeroenBakkers, Nine VKnoers, Helen VFirth, Philip LBeales, Gijsvan Haaften, Mieke Mvan Haelst, DDD Study

Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration
2016

Chi-ChungWu, FabianKruse, Mohankrishna DalvoyVasudevarao, Jan PhilippJunker, David CZebrowski, KristinFischer, Emily SNoël, DominicGrün, EugeneBerezikov, Felix BEngel, Alexandervan Oudenaarden, GilbertWeidinger, JeroenBakkers

GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability
2016

Elisabeth MLodder, PasquelenaDe Nittis, Charlotte DKoopman, WojciechWiszniewski, Carolina FischingerMoura de Souza, NajimLahrouchi, NicolasGuex, ValerioNapolioni, FedericoTessadori, LeanderBeekman, Eline ANannenberg, LamiaeBoualla, Nico ABlom, Wimde Graaff, M.Kamermans, DarioCocciadiferro, NatasciaMalerba, BarbaraMandriani, Zeynep Hande CobanAkdemir, Richard JFish, Mohammad KEldomery, IlhamRatbi, Arthur A MWilde, Teunde Boer, William FSimonds, MargueriteNeerman-Arbez, V ReidSutton, FernandoKok, James RLupski, AlexandreReymond, Connie RBezzina, JeroenBakkers, GiuseppeMerla

Tomo-seq
2016

FKruse, J PJunker, Avan Oudenaarden, JBakkers

Rare novel variants in the ZIC3 gene cause X-linked heterotaxy
2016

Aimee D CPaulussen, AnjaSteyls, JoVanoevelen, Florence Hjvan Tienen, Ingrid P CKrapels, Godelieve RfClaes, SonjaChocron, CroolVelter, Gita MTan-Sindhunata, CatarinaLundin, IreneValenzuela, BalintNagy, IbenBache, Lisa LethMaroun, KristiinaAvela, Han GBrunner, Hubert J MSmeets, JeroenBakkers, Arthurvan den Wijngaard

αE-catenin-dependent mechanotransduction is essential for proper convergent extension in zebrafish
2016

Mitchell K LHan, EstebanHoijman, EmilyNöel, LaurenceGarric, JeroenBakkers, Johande Rooij

GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability
2016

Elisabeth MLodder, PasquelenaDe Nittis, Charlotte DKoopman, WojciechWiszniewski, Carolina FischingerMoura de Souza, NajimLahrouchi, NicolasGuex, ValerioNapolioni, FedericoTessadori, LeanderBeekman, Eline ANannenberg, LamiaeBoualla, Nico ABlom, Wimde Graaff, MaartenKamermans, DarioCocciadiferro, NatasciaMalerba, BarbaraMandriani, Zeynep HandeCoban Akdemir, Richard JFish, Mohammad KEldomery, IlhamRatbi, Arthur A MWilde, Teunde Boer, William FSimonds, MargueriteNeerman-Arbez, V ReidSutton, FernandoKok, James RLupski, AlexandreReymond, Connie RBezzina, JeroenBakkers, GiuseppeMerla

Nodal signaling range is regulated by proprotein convertase-mediated maturation
2015

FedericoTessadori, Emily SNoël, Elisabeth GRens, RobertoMagliozzi, Inkie J AEvers-van Gogh, DanieleGuardavaccaro, Roeland M HMerks, JeroenBakkers

Animal and in silico models for the study of sarcomeric cardiomyopathies
2015

Dirk JDuncker, JeroenBakkers, Bianca JBrundel, JeffRobbins, Jil CTardiff, LucieCarrier

GLUT12 deficiency during early development results in heart failure and a diabetic phenotype in zebrafish
2015

VanesaJiménez-Amilburu, SusanneJong-Raadsen, JeroenBakkers, Herman PSpaink, RubénMarín-Juez

Glypican4 promotes cardiac specification and differentiation by attenuating canonical Wnt and Bmp signaling
2015

InaStrate, FedericoTessadori, JeroenBakkers

Recurrent Mutations in the Basic Domain of TWIST2 Cause Ablepharon Macrostomia and Barber-Say Syndromes
2015

ShannonMarchegiani, TaylorDavis, FedericoTessadori, Gijsvan Haaften, FrancescoBrancati, AlexanderHoischen, HaigenHuang, EliseValkanas, BarbaraPusey, DennySchanze, HankaVenselaar, Anneke TVulto-van Silfhout, Lynne AWolfe, Cynthia JTifft, Patricia MZerfas, GiovannaZambruno, ArianaKariminejad, FarahnazSabbagh-Kermani, JaniceLee, Maria GTsokos, Chyi-Chia RLee, VictorFerraz, Eduarda Morganada Silva, Cathy AStevens, NathalieRoche, OliverBartsch, PeterFarndon, EvaBermejo-Sanchez, Brian PBrooks, ValerieMaduro, BrunoDallapiccola, Feliciano JRamos, Hon-Yin BrianChung, CédricLe Caignec, FabianaMartins, Witold KJacyk, LauraMazzanti, Han GBrunner, JeroenBakkers, ShuoLin, May Christine VMalicdan, Cornelius FBoerkoel, William AGahl, Bert B Ade Vries, Mieke Mvan Haelst, MartinZenker, Thomas CMarkello

Developmental Alterations in Heart Biomechanics and Skeletal Muscle Function in Desmin Mutants Suggest an Early Pathological Root for Desminopathies
2015

CarolineRamspacher, EmilySteed, FrancescoBoselli, RitaFerreira, NathalieFaggianelli, StéphaneRoth, CoralieSpiegelhalter, NadiaMessaddeq, LeTrinh, MichaelLiebling, NikhilChacko, FedericoTessadori, JeroenBakkers, JocelynLaporte, KarimHnia, JulienVermot

Noonan and LEOPARD syndrome Shp2 variants induce heart displacement defects in zebrafish
2014

MonicaBonetti, JeroenPaardekooper Overman, FedericoTessadori, EmilyNoël, JeroenBakkers, Jeroenden Hertog

Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm
2014

PhilippeChetaille, ChristophPreuss, SiljaBurkhard, Jean-MarcCôté, ChristineHoude, JulieCastilloux, JessicaPiché, NatachaGosset, SéverineLeclerc, FlorianWünnemann, MaryseThibeault, CarmenGagnon, AntonellaGalli, ElizabethTuck, Gilles RHickson, NourEl Amine, InesBoufaied, EmmanuelleLemyre, Pascalde Santa Barbara, SandrineFaure, AndersJonzon, MichelCameron, Harry CDietz, ElenaGallo-McFarlane, D WoodrowBenson, ClaudiaMoreau, DamianLabuda, Shing HZhan, YaoqingShen, MichèleJomphe, Steven J MJones, JeroenBakkers, GregorAndelfinger, FORGE Canada Consortium

Genome-wide RNA Tomography in the zebrafish embryo
2014

Jan PhilippJunker, Emily SNoël, VictorGuryev, Kevin APeterson, GopiShah, JanHuisken, Andrew PMcMahon, EugeneBerezikov, JeroenBakkers, Alexandervan Oudenaarden

On the robustness of germ cell migration and microRNA-mediated regulation of chemokine signaling
2013

M.Goudarzi, I.Strate, A.Paksa, A.K.Lagendijk, J.Bakkers, E.Raz

Hyaluronan: a critical regulator of endothelial-to-mesenchymal transition during cardiac valve formation
2013

A.K.Lagendijk, A.Szabo, R.M.Merks, J.Bakkers