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VU Research Portal

US28 nanobodies

De Groof, T.W.M.

2020

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citation for published version (APA)

De Groof, T. W. M. (2020). US28 nanobodies: a “VUN” example of targeting viral GPCRs.

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Curriculum Vitae

Timo De Groof was born on December 15th_{,1992 in Sint-Niklaas, Belgium. In 2010, he}

finished secondary school where he obtained the degree Sports-Science from the Onze-Lieve-Vrouw-Presentatie school in Sint-Niklaas. That same year, Timo started his bachelor studies Biochemistry and Biotechnology at Ghent University. After obtaining his bachelor degree, Timo proceeded with his Master studies Biochemistry and Biotechnology where he specialized in Biomedical Biotechnology and Biochemistry and Structural Biology. During his final year of studies, he performed research in the biopharmaceutical company Argen x under the supervision of Dr. Christophe Blanchetot (Argen x) and Prof. Dr. Nico Callewaert (UGent). There he focused on the identification and characterization of llama-derived antibodies for the treatment of asthma.

In 2015, Timo obtained his master degree cum laude and proceeded with his PhD at the VU University Amsterdam in the Molecular Pharmacology group under the supervision of Prof. Dr. Martine Smit. During his PhD, he aided in the establishment of the VU Nanobody platform for the development of nanobodies targeting G protein-coupled receptors in collaboration with Dr. Raimond Heukers. He used this platform to develop multiple nanobodies targeting the viral chemokine receptor US28. During his PhD, Timo focused on different applications of these nanobodies ranging from therapeutic applications to fundamental research which resulted in multiple awards, invited talks and two patent applications. As part of a collaboration, Timo also performed research as a visiting scientist in the group of Prof. Dr. John Sinclair at Cambridge University.

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Personal information

Name: Timo De Groof

Adress: Ottergemsesteenweg 121, 9000 Ghent, Belgium Email: timo.de.groof@vub.be

Nationality: Belgian

Place, date of birth: Sint-Niklaas, 15 December 1992

Education and scientific career Vrije Universiteit Brussel

Sep 2019-… Postdoctoral scientist at the In Vivo Molecular Imaging (ICMI)

group under supervision of Prof. Dr. Nick Devoogdt

Research topic: Non-invasive imaging of immune cells using nanobodies (Immune image project)

VU University Amsterdam

Sep 2015- Aug 2019 PhD student at the Molecular Pharmacology group under

supervision of Prof. Dr. Martine Smit

Dissertation: US28 nanobodies: A ”VUN” example of targeting viral GPCRs

University of Cambridge

May 2019 Visiting scientist in the lab of Prof. Dr. John Sinclair

Research topic: Targeting HCMV latency using US28-targeting nanobodies

Ghent University

2013-2015 Master in Biochemistry and Biotechnology

Major: Biomedical Biotechnology

Minor: Biochemistry and Structural Biology Graduated Cum Laude

Master dissertation: Identification and characterization of therapeutic antibodies in asthma at Argen x

Academic promotor: Prof. Dr. Nico Callewaert Industrial promotor: Dr. Christophe Blanchetot

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Additional courses

Introduction to CYAN flow cytometry

VU University Amsterdam

Course on tutoring students

Article 9: Laboratory animal science (FELASA C)

Utrecht University

Course on working with radioactivity

Awards and scholarships BioVU travel grant

Awarded a travel grant of 500 euro to subsidize short term visit to group of Prof. Dr. John Sinclair (University of Cambridge) by BioVU (Cambridge, May 2019)

Mini-Herpesworkshop travel grant

Selected for a travel grant of 250 euro based on the submitted abstract for the Mini-Herpesworkshop (Hamburg, October 2018)

BioVU travel grant

Awarded a travel grant of 500 euro to attend the international Herpesworkshop by BioVU (Vancouver, July 2018)

AIMMS annual meeting PhD oral presentation competition 2018

Winner of the PhD oral competition between 7 selected PhD students from the Amsterdam institute of Molecules, Medicines and Systems (AIMMS) (Amsterdam, April 2018)

FIGON DMD Medicinal Chemistry PhD poster prize award 2017

Winner of the PhD poster prize award in the category “Medicinal Chemistry” handed out by the Koninklijke Nederlandse Chemische Vereniging (KNCV) during the FIGON DMD congress (Ede, October 2017)

AIMMS annual meeting poster prize award 2016

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Oral presentations

Mini-Herpes Workshop 2018 (Hamburg, DE)

Title: Nanobodies targeting and modulating the oncogenic viral GPCR US28

Pfizer PhD student competition at FIGON DMD 2018 (Ede, NL)

IHW 2018 satellite workshop on betaherpesviruses (Vancouver, CA)

Title: Nanobodies targeting HCMV-encoded receptor US28 as modulators of US28 function and means to eradicate US28-expressing cells.

AIMMS annual meeting PhD oral presentation competition 2018 (Amsterdam, NL)

IHW 2017 satellite workshop on interventions (Ghent, BE)

Title: Identification and Characterization of HCMV-Encoded US28-Targeting nanobodies

Student Supervision Bachelor internships

Fatima Bikhezar

Topic: Characterization of US28 nanobodies April 2016-June 2016

Nick Bergkamp

Shaima Ayubi

Fatih Aydin

Topic: Characterization of nanobody-loaded extracellular vesicles November 2016-January 2017

Steven Eleonora

Topic: Characterization of US28-targeting intrabodies VUN103 and Nb7 April 2017-June 2017

Abdullahi Elmi

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Natesh Sewnath

Topic: Investigation of effect of linker flexibility on nanobody functionality April 2018-June 2018

Levy Matricon

Topic: Investigation of effect of linker lengths on nanobody functionality April 2018-June 2018

Master internships

Danielle Bianchi

Topic: Identification of nanobodies binding to the viral GPCRs US28 and UL33 March 2016-December 2016

Truc Giap

Topic: Characterization of the US28 intrabody VUN103 April 2017-January 2018

Vincent Blum

Topic: Investigation of functionality of US28 nanobodies using Bio ID2 February 2018-June 2018

Noa Rosenberg

Topic: Patenting of US28 nanobodies January 2019-June 2019

Master literature thesis

Cherie Kemmel

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Publications and patents

Publications

1. Heukers, R., Fan, T., de Wit, R.H., van Senten, J.R., De Groof, T.W.M., Bebelman, M.P., Lagerweij, T., Vieira, J., de Munnik, S.M., Smits-de Vries, L., van Offenbeek, J., Rahbar, A., van Hoorick, D., Söderberg-Naucler, C., Würdinger, T., Leurs, R., Siderius, M.H., Vischer, H.F. and Smit, M.J. (2018). The constitutive activity of the virally encoded chemokine receptor US28 accelerates glioblastoma growth. Oncogene. 37, 4110-4121

2. De Groof, T.W.M., Bobkov, V., Heukers, R. and Smit, M.J. (2019). Nanobodies:

new avenues for imaging, stabilizing and modulating GPCRs. Molecular and Cellular Endocrinology. 484, 15-24

3. Heukers, R., De Groof, T.W.M., Smit, M.J. (2019) Nanobodies detecting and modulating GPCRs outside in and inside out. Current Opinion in Cell Biology. 57, 115-122

4. De Groof, T.W.M. ‡_{, Mashayekhi, V.} ‡_{, Fan, T., Bergkamp, N.D., Sastre Torano J., van}

Senten, J.R., Heukers, R., Smit, M.J.†_{and Oliveira, S.}†_{(2019). Nanobody-targeted}

photodynamic therapy selectively kills viral GPCR-expressing glioblastoma cells. Molecular Pharmaceutics. 16, 3145-3156

5. Bobkov, V., Zarca, A., Arimont, M., De Groof, T.W.M., van der Woning, B., de Haard, H. and Smit, M.J. (2019). Antibodies targeting chemokine receptors CXCR4 and ACKR3. Molecular Pharmacology. 96(5), 753-764

6. De Groof, T.W.M., Heukers, R., Bergkamp, N.D., Giap, T., Bebelman, M.P.,

Goeij-de Haas R., Piersma, S., Jimenez, C.R., Garcia, K.C., Ploegh, H.L. SiGoeij-derius M.H. and Smit, M.J. Selective targeting of ligand-dependent and -independent signaling by conformation-specific anti-GPCR intrabodies. (Manuscript submitted).

7. De Groof, T.W.M. ‡_{, Elder, E.G.} ‡_{, Heukers, R., Lim, E., Sinclair, J.H.}†_{and Smit, M.J.}†

Targeting the latent human cytomegalovirus reservoir with virus specific nanobodies (Manuscript submitted).

8. Fan, T., De Groof T.W.M., van Senten, J.R., Rahbar, A., Söderberg-Naucler, C., Siderius M.H. and Smit, M.J. (Manuscript in preparation). The HCMV-encoded chemokine receptor US28 regulates PD-L1 via the Hippo pathway in glioblastoma.

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Patents

1. De Groof, T.W.M. 2018. Inverse agonistic anti-US28 antibodies. EP18155119.3. Filed February 2018. Patent Pending

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Acknowledgments

Here we are, at the end (or most likely the start for most of you) of this thesis. Although my name is on this thesis, I can’t take full credit for this work and there are a lot of people to thank who supported me on a scientific and non-scientific level.

Of course, I need to start with thanking Martine and Marco as my promotors. Martine, thank you for hiring the “small Belgian person” 4-5 years ago and giving me the chance to come to Amsterdam and do my PhD in your lab. As a supervisor, you gave me a lot of freedom to pursue different projects and interests which undoubtedly is a big reason why I look back fondly on the last four years. Our “brainstorm” sessions with Raimond, always ending up with a white board written full with new ideas, were fun and kept me motivated and inspired during my PhD. Your supervision helped me grow as a scientist and thanks for pushing me to pursue a postdoc position. I also would like to thank you for letting me go to Cambridge which was a nice extra experience to these four years. I wish you all the best with the lab and all the future projects.

Marco, also a big thanks to you. Although you weren’t involved in all the different projects, you were always interested in discussing these projects. You (and Jan Paul) got me interested in the Bio ID2 approach which finally ended up in this last chapter and can hopefully be used as a starting point for new research. Besides talking science, it was also very pleasant to discuss some music with you and to get to know some new artists to listen to.

The one person who I cannot forget is of course Raimond (aka Heukie, Heukie Beukie, Dr. Who-Cares, Herr Dr. Heukers,…). I think it is fair to say that we were quite the dynamic duo and that this thesis would not exist in the way it is now without you. I’ve learned a lot from you on a scientific level and it was nice to have a partner-in-crime to discuss results or to ask your opinion when I had new (some crazy) ideas. Besides talking science, we could talk about pretty much everything and I can say that you’ve become a close friend over the last four years.

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Besides collaborations, there are of course my (daily) colleagues to thank who made those four years quite the adventure. From Friday (afternoon) drinks to playing football, watching a lot of football matches in the pubs, concerts, VR gaming and so many other experiences. I’ve started with all of you as colleagues but I left with a group of new friends. Thank you Daniel, Aurelien, Hendrik, Maarten, Reggie, Tian, Jan Paul, Nick, Jelle, Jeffrey, Bert, Vladimir, Elsa, Maurice, Alex, Payman, Tiffany, Noortje, Irfan, Dan, Sabrina R, Sabrina dM, Tamara, Henry, Lisa and of course all the MolTox people. I am looking forward to all the other upcoming PhD defenses which I will use as a good excuse to come back to Amsterdam and have a beer with you. Good luck and to quote Steve Perry from Journey: Don’t stop believin’ (in your PhD)! Next to the “old” colleagues, also thank you to my new colleagues from ICMI, CMIM and Camel-IDS for the warm welcome in the new labs. Some other unsung heroes are the students that did their internship with me. To Fatima, Nick, Shaima, Steven, Abdullahi, Levy, Natesh, Fatih, Danielle, Truc, Vincent and Noa: all your different projects helped me out and has led to some papers or ideas that can be found in these chapters. Finally there are still some people to thank from Argen x. Christophe and Marie, thank you for the supervision during my master thesis at Argen x. Both your supervision has led to me learning all the techniques and scientific attitude that have proven to be the basis for my PhD and now postdoc position. Also thank you to Hans for putting me in contact with the VU which helped me finding this PhD position.

And finally we arrive at the friends and family section. Two big groups in the friends department stand out who made my PhD more bearable. Too many names to sum up but I know you all know who I mean when I say thank you to “Sint-Niklaas pottendarm Ambiance” and “L-Dopa”! Thanks for all the fun trips, weekends and evenings where I could forgot about the “science stuff” for a while and big thanks for making the trip to Amsterdam for my defense.

Het bedanken van de familie zal ik in het Nederlands doen. Mama, Papa, in de eerste plaats moet ik jullie bedanken om al die jaren me te ondersteunen zowel tijdens mijn studies als mijn tijd in Amsterdam. Zonder jullie was dit allemaal niet mogelijk en dat zal ik nooit vergeten! Ook de rest van de familie moet ik bedanken voor alle morele steun over de jaren heen: Caro, Laurens, Oma, Opa, Bomma (en Bompa), Evelyn, Greet, Gino, Karel en Eline. En dan rest me alleen nog de laatste persoon te bedanken die mogelijks het meest “geleden” heeft onder mijn beslissing om mijn PhD in Amsterdam te doen: Hanne. Bedankt om me in deze beslissing te steunen in de afgelopen 4 jaar. Ik weet dat het niet altijd makkelijk was afgelopen jaren waren maar dit heeft zeker ook mooie avonturen opgeleverd (zie Canada!). We hebben vaak naar elkaar frustraties en geklaag geluisterd in de afgelopen 4 jaar maar hier staan we dan na vandaag beide als doctor! Laat dit de start zijn van iets mooi en laten we eerst eens beginnen met wat welverdiende vakantie te boeken!

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