Prof. Olivier Michielin

MD-PhD, Assistant Professor at the Medical Faculty, University of Lausanne, Group leader at the Swiss Institute of Bioinformatics and the Ludwig Institute for Cancer Research, Lausanne Branch

Prof. Olivier Michielin obtained a diploma of Physics in 1991 at the EPFL and an MD from the University of Lausanne in 1997. He pursued his PhD training under the supervision of Jean-Charles Cerottini (LICR) and Martin Karplus (Harvard and Strasbourg Universities). He was appointed Group Leader of the Swiss Institute of Bioinformatics in 2002 and became an Assistant Professor and Privat Docent at the Medical Faculty of Lausanne in 2004 and 2005, respectively. In parallel, he has trained as a medical oncologist and obtained his board certification in 2007 at the Multidisciplinary Oncology Center (CePO) of Lausanne where he is currently in charge of the melanoma clinic. Prof. Olivier Michielin is mainly focused on translational oncology, developing new molecularly defined therapeutic approaches based on original in silico techniques developed in his laboratory.

Swiss Institute of Bioinformatics
Molecular Modeling Group

Quartier UNIL-Sorge
Bâtiment Génopode
CH-1015 Lausanne

Switzerland

Tel: +41 21 692 40 53

Fax: +41 21 692 40 65

Email:

Rational optimization of TCR for adoptive cell transfer immunotherapy

The recognition by the T Cell Receptor (TCR) of tumor associated peptides (p) presented in the context of Class I Major Histocompatibility Complexes (MHC) is the basis of tumor immunity. This event has been used to design several therapeutic approaches like peptide based immunotherapy or adoptive cell transfer. In the former, tumor associated peptides are injected subcutaneously, together with an adjuvant to enhance the natural immune response. Several clinical trials based on this principle are ongoing in Lausanne (see project of Prof. D. Speiser) and elsewhere with promising preliminary results. In the later, the immune response is short cut and effector T cells are injected after optional in vitro expansion. Again, clinical trials are ongoing where tumor specific T cells are selected and reinjected after an expansion and a lymphoablative conditioning of the patient. Very promising results have been obtained with this approach with high response rates in metastatic melanoma patients.

Figure 1: Strategy towards adoptive cell transfer with genetically modified T cells. 1) Extractions of T cells from the patient. 2) Transfection of an rationally optimized TCR in those cells using a viral vector. 3) Optional expansion. 4) Lymphodepletion of the patient. 5) Reinfusion of the modified T cells to the patient.

It has been hypothesized that the apparent lack of efficacy of the naturally occurring TCR sequences that compose the immune repertoire against tumors might be related to their low affinities for tumor antigens, in part as the result of negative selection during thymic maturation. For this reason, it seems particularly attractive to rationally design new TCR sequences with increased affinity for selected tumor antigens. Such optimized sequences can be used in a context of adoptive transfer of genetically modified T cells. The aim of this project is to propose methods for the design of rationally optimized TCR sequences as well as their evaluation for potential adoptive cell transfer approaches. Two tumor antigens are being worked out, NY-ESO-1 and Melan-A.

Identification of key residues:

Figure 2: Example of mutation, TCR Vb Ala51 to Glu. Ala51 is colored in grey and Glu51 in transparent magenta. This mutation resulted in a markedly increased TCR binding.

Using free energy simulations, it is now possible to compute the binding contribution of each residue that composes the interface between two interacting proteins. Residues having a small or an unfavorable contribution are good candidates for mutagenesis. The effect of the mutation is confirmed in silico by running the simulation with the mutated protein. Several free energy simulations techniques are being used like thermodynamic integration or molecular mechanics generalized Born surface area (MMGBSA). We recently adapted and validated these methods to the TCR-p-MHC system.

Validation of proposed modifications:

Interesting TCR mutation candidates can be validated in vitro using soluble molecules. A rapid transient expression system based on HEK 293 cells is used to produce proteins truncated before the transmembrane region. Screening of these mutations is performed using standard ELISA assays. The most interesting mutants are subsequently expressed in bacteria and refolded in vitro. Their affinity and kinetic parameters can be determined precisely using Biacore experiments and can be compared directly to the predictions of the in silico calculations. Finally, TCR modifications with improved affinities are tested for their effect on T cell function using lentivirus vectors for transfection, see project of Dr. N. Ruffer.

Preliminary results:

So far, around 30 mutants have been proposed by the in silico approach and validated with ELISA and Biacore. Around 50% of them were shown to improve the affinity of the TCR. Most interestingly, the in silico approach allowed to select mutations that are compatible with each others. Based on these results, double and triple mutants have been produced with even better affinities. At the molecular level, the KD of the wild type TCR was improved more than 20 fold. At the cellular level, the best rationally design TCR sequence have been shown to improve all aspect of T cell function: TCR signaling, expansion upon antigenic challenge, and, most importantly, tumor cell killing.

Towards clinical trials:

Engineered T cells with improved functionalities are ideal candidates to be used in an adoptive cell transfer strategy. In preparation for this, a clinical trial (ITA-02) has been started at the Centre Pluridisciplinaire d’Oncologie (CePO) in order to evaluate the best lymphodepleting regimen to be given in combination with a standard, peptide based, vaccination. Experiences gained in this preliminary trial will help us design a full adoptive cell transfer trial. We are currently working on developing GMP strategies to bring the rationally modified T cells to the clinic.

List of publications

Published papers with peer reviews

Prior, J. O., Montemurro, M., Orcurto, M. V., Michielin, O., Luthi, F., Benhattar, J., Guillou, L., Elsig, V., Stupp, R., Delaloye, A. B. & Leyvraz, S. Early prediction of response to sunitinib after imatinib failure by 18F-fluorodeoxyglucose positron emission tomography in patients with gastrointestinal stromal tumor. J Clin Oncol 27, 439-445 (2009)

Grosdidier, A., Zoete, V. & Michielin, O. Blind docking of 260 protein-ligand complexes with EADock 2.0. J Comput Chem (2009)

Rohrig, U. F., Grosdidier, A., Zoete, V. & Michielin, O. Docking to heme proteins. J Comput Chem (2009)

Schupbach, T., Zoete, V., Tsakam-Sotche, B. & Michielin, O. Fourier transform convolution integrals applied to generalized Born molecular volume. J Comput Chem (2009)

Zoete, V., Grosdidier, A. & Michielin, O. Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med (2009)

Michielin, O., Rufer, N., Romero, P., Laurent, J., Cerottini, J. P., Gugisberg, D., Leyvraz, S. & Speiser, D. [New developments in cancer immunotherapy]. Rev Med Suisse 4, 1248-1251 (2008)

Cuendet, M. A. & Michielin, O. Protein-Protein Interaction Investigated by Steered Molecular Dynamics: the TCR-pMHC Complex. Biophys J 95, 3575-3590 (2008)

Derre, L., Bruyninx, M., Baumgaertner, P., Ferber, M., Schmid, D., Leimgruber, A., Zoete, V., Romero, P., Michielin, O., Speiser, D. E. & Rufer, N. Distinct sets of alphabeta TCRs confer similar recognition of tumor antigen NY-ESO-1157-165 by interacting with its central Met/Trp residues. Proc Natl Acad Sci U S A 105, 15010-15015 (2008)

Capendeguy, O., Iwaszkiewicz, J., Michielin, O. & Horisberger, J. D. The fourth extracellular loop of the alpha subunit of Na,K-ATPase. Functional evidence for close proximity with the second extracellular loop. J Biol Chem 283, 27850-27858 (2008)

Chodanowski, P., Grosdidier, A., Feytmans, E. & Michielin, O. Local alignment refinement using structural assessment. PLoS ONE 3, e2645 (2008)

Voelter, V., Rufer, N., Reynard, S., Greub, G., Brookes, R., Guillaume, P., Grosjean, F., Fagerberg, T., Michielin, O., Rowland-Jones, S., Pinilla, C., Leyvraz, S., Romero, P. & Appay, V. Characterization of Melan-A reactive memory CD8+ T cells in a healthy donor. Int Immunol 20, 1087-1096 (2008)

Rochat, B., Zoete, V., Grosdidier, A., von Grunigen, S., Marulla, M. and Michielin, O. In vitro Biotransformation of Imatinib by the Tumor Expressed CYP1A1 and CYP1B1. Biopharm. Drug Dispos. 29(2):103-18 (2008)

Zhang, K.L., Mangeat, B., Ortiz, M., Zoete, V., Trono, D., Telenti, A., and Michielin, O. Model structure of human APOBEC3G. PLoS ONE 2, e378 (2007)

Butticaz, C., Michielin, O., Wyniger, J., Telenti, A., and Rothenberger, S. Silencing of both beta-TrCP1 and HOS (beta-TrCP2) is required to suppress human immunodeficiency virus type 1 Vpu-mediated CD4 down-modulation. Journal of virology 81, 1502-1505 (2007)

Derre, L., Ferber, M., Touvrey, C., Devevre, E., Zoete, V., Leimgruber, A., Romero, P., Michielin, O., Levy, F., and Speiser, D.E. A Novel Population of Human Melanoma-Specific CD8 T Cells Recognizes Melan-AMART-1 Immunodominant Nonapeptide but Not the Corresponding Decapeptide. J Immunol 179, 7635-7645 (2007)

Feige, J. N., Gelman, L., Rossi, D., Zoete, V., Metivier, R., Tudor, C., Anghel, S. I., Grosdidier, A., Lathion, C., Engelborghs, Y., Michielin, O., Wahli, W. & Desvergne, B. The endocrine disruptor monoethyl-hexyl-phthalate is a selective peroxisome proliferator-activated receptor gamma modulator that promotes adipogenesis. J Biol Chem 282, 19152-19166 (2007)

Alves, P. M., Viatte, S., Fagerberg, T., Michielin, O., Bricard, G., Bouzourene, H., Vuilleumier, H., Kruger, T., Givel, J. C., Levy, F., Speiser, D. E., Cerottini, J. C. & Romero, P. Immunogenicity of the carcinoembryonic antigen derived peptide 694 in HLA-A2 healthy donors and colorectal carcinoma patients. Cancer Immunol Immunother 56, 1795-1805 (2007)

Stupp, R., Pica, A., Mirimanoff, R. O. & Michielin, O. A practical guide for the management of gliomas. Bull Cancer 94, 817-822 (2007)

Michielin, O. Application of molecular modeling to new therapeutic cancer approaches. Bull Cancer 94, 763-768 (2007)

Zoete, V. and Michielin, O. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA. Application to the TCR-p-MHC complex. Proteins. 67(4):1026-47 (2007)

Grosdidier, A., Zoete, V., Michielin, O. EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins. 67(4):1010-25 (2007)

Zoete, V., Grosdidier, A., Michielin, O. Peroxisome proliferator-activated receptor structures: Ligand specificity, molecular switch and interactions with regulators. Biochim Biophys Acta. 1771(8):915-25 (2007)

Michalik, L., Zoete, V., Krey, G., Grosdidier, A., Gelman, L., Chodanowski, P., Feige, J.N., Desvergne, B., Wahli, W., Michielin, O. Combined simulation and mutagenesis analyses reveal the involvement of key residues for peroxisome proliferator-activated receptor alpha helix 12 dynamic behavior. J Biol Chem. 282(13):9666-77 (2007)

Aublin, A., Ciofani, M., Willkomm, N., Hamrouni, A., Szymczak-Workman, A., Takahashi, T., Sandjeu, Y., Guillaume, P., Vignali, D., Michielin, O., Zúñiga-Pflücker, J.C. and Maryanski, J. A natural structural variant of the mouse TCR b-chain displays intrinsic receptor function and antigen specificity, J Immunol. 177(12):8587-94 (2006)

Capendeguy, O., Chodanowski, P., Michielin, O. & Horisberger, J. D. Access of extracellular cations to their binding sites in Na,K-ATPase: role of the second extracellular loop of the alpha subunit. J Gen Physiol 127, 341-352 (2006)

Yip, L., Zoete, V., Scheib, H. and Michielin, O. Structural assessment of single amino acid mutations: application to TP53 function, Hum Mutat, 27(9):926-37 (2006)

Colombetti, S., Fagerberg, T., Baumgartner, P., Chapatte, L., Speiser, D.E., Rufer, N., Michielin, O., Lévy, F., Impact of orthologous melan-A peptide immunizations on the anti-self melan-A/HLA-A2 T cell cross-reactivity, J Immunol., 176(11):6560-7 (2006)

Fagerberg, T., Cerottini, J.C., Michielin, O., Structural Prediction of Peptides Bound to MHC Class I, Journal of Molecular Biology, 356(2):521-46 (2006)

Suarez, M., Haenni, M., Canarelli, S., Fisch, F., Chodanowski, P., Servis, C., Michielin, O., Freitag, R., Moreillon, P., Mermod, N., Structure-function characterization and optimization of a plant-derived antibacterial peptide, Antimicrob Agents Chemother, 49(9):3847-57 (2005)

De Los Rios, P., Cecconi, F., Pretre, A., Dietler, G., Michielin, O., Piazza, F., Juanico, B., Functional dynamics of PDZ binding domains: a normal-mode analysis, Biophys J.,89(1):14-21. Epub (2005) full article [pdf]

Cebecauer, M., Guillaume, P., Mark, S., Michielin, O., Boucheron, N., Bezard, M., Meyer, B.H., Segura, J.M., Vogel, H., Luescher, I.F., CD8+ cytotoxic T lymphocyte activation by soluble major histocompatibility complex-peptide dimers. J Biol Chem.;280(25):23820-8 (2005)

Reviews

Zoete, V., Grosdidier, A. & Michielin, O. Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med (2009)

Zoete, V., Grosdidier, A. & Michielin, O. Peroxisome proliferator-activated receptor structures: ligand specificity, molecular switch and interactions with regulators. Biochim Biophys Acta 1771, 915-925 (2007)

Michielin, O., Blanchet, J.S., Fagerberg, T., Valmori, D., Rubio-Godoy, V., Speiser, D.E., Ayyoub, M., Alves, P., Luescher, I., Gairin, J.E., Cerottini. J.C., Romero, P., Tinkering with nature: the tale of optimizing peptide based cancer vaccines. Cancer Treat Res. 2005;123:267-91 (2005)

Filges, I., Zaman, K., Michielin, O., Vulliemoz, D., Perey, L., Stupp, R., Present chemoprevention and future vision, Rev Med Suisse;1(20):1343-6, 1349. French, (2005)

National Center of Competence in Research - NCCR Molecular Oncology