Structural and functional characterization of the ICOS/ICOSL immune complex

Project Information

SI

Grant agreement ID: 790012

DOI

10.3030/790012

Project closed

EC signature date 15 February 2018

Start date 1 August 2018

End date 31 December 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 224 683,20

EU contribution

€ 224 683,20

Coordinated by

UNIVERSIDAD DEL PAIS VASCO/ EUSKAL HERRIKO UNIBERTSITATEA
Spain

Periodic Reporting for period 2 - SI (Structural and functional characterization of the ICOS/ICOSL immune complex)

Reporting period: 2020-08-01 to 2021-07-31

Summary of the context and overall objectives of the project

The work described in the proposal and now published in Nature Communications describes a breakthrough in the structural characterization of the T cell co-receptor inducible co-stimulator (ICOS) and its ligand ICOS-L. Therefore, it represents a significant advance for understanding the molecular events involved in promoting T cell activation and affinity maturation of B cells. and offers yet unexplored opportunities to modulate germinal centers and consequently, the strength of humoral responses in vaccine research and immunotherapy. This work has been also presented in the 29th annual Buffalo-Hamilton-Toronto (BHT) crystallography-CryoEM symposium through an oral communication and at a virtual lecture at the University of Tokyo. Due to the acquired knowledge in antibody engineering during this project, I have joined the efforts to fight COVID19 through the development of potent and broad antibody-like particles against SARS-CoV-2 (published in Nature Communications). Due to the therapeutic potential of this technology, I then applied this strategy to target HIV, arguably the most challenging virus due to its high genetic diversity (published in PNAS). In addition, I have set up serological detection methods to analyze SARS-CoV-2 induced immune response that led to two important collaborations that culminated in two scientific publications (Sci. Adv. and Sci. Rep.).

Publications:
1. Edurne Rujas; Hong Ciu; Taylor Sicard; Anthony Semesi; Jean-Philippe Julien. Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies. Nat. Commun.11 - 5066, 2020.
2. Edurne Rujas, Hong Cui, Jonathan Burnie, Clare Burn Aschner, Tiantian Zhao, Sara Insausti, Krithika Muthuraman, Anthony Semesi, Jasper Ophel, Jose Luis Nieva, Michael S. Seaman, Christina Guzzo, Bebhinn Treanor, Jean-Philippe Julien. Engineering pan-HIV-1 neutralization breadth and outstanding potency by multi-specific antibody avidity. PNAS, In Press. 2021.
3. Edurne Rujas*, Daniel P. Leaman, Sara Insausti, Pablo Carravilla, Miguel Garc a-Porras, Eneko Largo, Izaskun Morillo, Rub n S nchez-Eugenia, Lei Zhang, Hong Cui, Ibon Iloro, F lix Elortza, Jean-Philippe Julien, Christian Eggeling, Michael B. Zwick, Jose M. M. Caaveiro*, Jos  L*. Nieva. Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile. iScience. 24 - 9, 2021.
*Corresponding author
4. Moustafa T. Mabrouk, Kevin Chiem, Edurne Rujas, Wei-Chiao Huang, Dushyant Jahagirdar, Breandan Quinn, Meera Surendran Nair, Ruth H Nissly, Victoria S. Cavener, Nina R. Boyle, Ty A. Sornberger, Suresh V. Kuchipudi, Joaquin Ortega, Jean-Philippe Julien, Luis Martinez-Sobrido, Jonathan Lovell. Lyophilized, Thermostable Spike or RBD Immunogenic Liposomes Induce Protective Immunity Against SARS-CoV-2 in Mice. Sci. Adv. 7 (49), 2021.
5. Michael G. Sugiyama, Haotian Cui, Dar’ya S. Redka, Mehran Karimzadeh, Edurne Rujas, Hassaan Maan, Sikander Hayat, Kyle Cheung, Rahul Misra, Joseph B. McPhee, Russell D. Viirre, Andrew Haller, Roberto J. Botelho, Raffi Karshafian, Sarah A. Sabatinos, Gregory D. Fairn, Seyed Ali Madani Tonekaboni, Andreas Windemuth, Jean-Philippe Julien, Vijay Shahani, Stephen S. MacKinnon, Bo Wang, Costin N. Antonescu. Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. Sci Rep. 11(1) 23315, 2021.
6. Edurne Rujas, Iga Kucharska, Yong Zi Tan, Samir Benlekbir, Hong Cui, Tiantian Zhao, Gregory A. Wasney, Patrick Budylowski, Furkan Guvenc, Jocelyn C. Newton, Taylor Sicard, Anthony Semesi, Krithika Muthuraman, Amy Nouanesengsy, Clare Burn Aschner, Katherine Prieto, Stephanie A. Bueler, Sawsan Youssef, Sindy Liao-Chan, Jacob Glanville, Natasha Christie-Holmes, Samira Mubareka, Scott D. Gray-Owen, John L. Rubinstein, Bebhinn Treanor, Jean-Philippe Julien. Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers. Nat. Commun. 12 - 3661, 2021.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the last two years I have been able to solve the first crystal structure of the co-complex between human ICOS and its ligand ICOS-L at 3.3 Å resolution. The crystal structure revealed similarities and differences with other receptor/ligand pairs within this family. Specifically, it shows that ICOS adopts a predicted overall Ig-fold structure similar to CTLA-4 and CD28 and that like them, it has a central cis-trans-cis PPP motif flanked by aromatic residues to engage its cognate ligand. However, ICOS has an unusually long strand C’ that protrudes from the surface of the ectodomain that is involved in the formation of a second set of interactions with its ligand. This second set of interactions, not yet observed in any of the previously solved CD28/B7 family complexes, results in a distinct receptor binding orientation of the ICOS/ICOS-L complex compared to CTLA-4/B7-1 and PD-1/PD-L1. A notable feature uncovered by the ICOS/ICOS-L co-complex structure is the presence of ICOS N-linked glycan N110 at the binding interface. The N110Q mutation removing this N-linked glycan resulted in a 4.3-fold improvement in binding affinity of ICOS to ICOS-L. Hence, this finding contribute further evidence of post-translation modifications, and particularly glycobiology in modulating binding thresholds, in this case relevant for T cell activation.
The number of antibodies targeting the ICOS/ICOS-L complex entering clinical trials is rapidly increasing but no information on their mode of action at the molecular level have been reported to date. Hence, I have also solved the crystal structure of two clinically relevant antibodies named STIM003 and prezalumab in complex with ICOS and ICOS-L, respectively. The crystallographic studies revealed that these antibodies mimic the physiological interaction of ICOS and ICOS-L with remarkable similarity. Accordingly, the structural data provides insights into the mechanism of action of prezalumab suggesting that its antagonistic effect is likely due to a combination of outcompeting ICOS for binding to ICOS-L and steric hindrances that block receptor ligand clustering at the membrane surface.
A detailed analysis of the antibody binding interfaces identified eight single nucleotide variations (SNVs) in ICOS (S76P, G70R, N73Y, K78N, F114V, P116S, P116H and P117A) and two in ICOS-L (Y51C and Y65H) that could impact antibody binding and hence their therapeutic outcome.
In addition, I developed a protein-based antibody multimerization strategy to increase antibody avidity. This approach transformed antibodies targeting the RBD of SARS-CoV-2 into potent neutralizers with an average of 1000-fold higher potency than the parental IgGs. The “plug-and-play” format of this technology allows to alter specificities by easily swapping antibody sequences and hence it was also used to rapidly transform the broadly acting HIV antibodies into potent neutralizers.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

These structural data in combination with functional studies on the ICOS/ICOSL immune complex will lead to an improved understanding of human adaptive immunity and will have direct downstream implications for the development of novel therapies in human health.
In addition, the potent and broadly-active antiviral antibody-like molecules against SARS-CoV-2 and HIV will directly contribute to lasting medical countermeasures developed against COVID-19 and AIDS.

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