Kilian Schober: Explorations in the T-cell universe

Immunotherapies that focus on T cells have become beacons of hope in cancer medicine. Blocking molecular control sites on T cells using so-called checkpoint inhibitors, for example, is successfully used to treat melanoma or non-small cell lung cancer. CAR-T cell therapies, on the other hand, are proving successful in the treatment of certain forms of blood and lymph gland cancer. “These therapies are a good indicator of how much we already understand about the biology of T cells,” says Kilian Schober. “But they also show how much we still don’t know.” This is because checkpoint inhibitors and CAR-T cells are not yet effective against most types of cancer. It is also unclear why the tumors of many patients prove resistant to checkpoint inhibitors, which are extremely effective in others. In addition, both treatments can lead to violent attacks on healthy body tissue, including a deadly cytokine storm. “We need to understand more thoroughly the incredible diversity of our T cells and their targets.” The optimal starting point for this is to thoroughly analyze the “standard” T cell responses to vaccinations. The findings from these analyses could then possibly be transferred to the development of new cancer therapies. Kilian Schober and his research group at the Institute of Clinical Microbiology, Immunology and Hygiene at Erlangen University Hospital (Director: Christian Bogdan) have set out to achieve this goal.

A largely unresolved question

Like the antibody-producing B cells, T cells originate from the bone marrow and are part of the adaptive immune system, which kicks in a few days after a bacterial or viral infection or a cancer flare-up if the innate immune system was unable to defuse the danger on its own. T cells must undergo rigorous training in order to fulfill their function. They get their name from the location of this training: It begins during embryonic development in the thymus, the organ behind the breastbone, which largely regresses in adulthood. There, each T cell learns to recognize infected cells or tumour cells and distinguish them from healthy ones. If it fails to do this, it is discarded. The fact that a killer T cell, for example, is able to master this task at all is due on the one hand to its sensors, the receptors, and on the other hand to the peptides that all body cells display on their surface like snapshots from their interior in special frames called MHC-I molecules. These peptides are called epitopes and usually comprise around nine amino acids. They are fragments of virus or cancer proteins that the diseased cell has shredded in its proteasome – so-called antigens that are supposed to signal the T cell to destroy them. However, the problem is that every body cell constantly shreds countless of its own proteins that it no longer needs, leaving their fragments to appear as a kind of proof of identity in MHC frames.  Accordingly, every T cell on its patrols through the body mainly encounters self-peptides from healthy cells – and has to recognize the foreign epitope, its antigen, that matches its specific receptor in the midst of this enormous background noise. “Every person has around one hundred million different T cells,” explains Schober. “Each of them has a unique receptor that recognizes a different antigen.” Which antigen a particular T cell receptor recognizes, i.e. its antigen specificity, is unknown in most cases. Across all disease entities, it is a largely “unresolved question as to what T cells actually recognize” – from infections to cancer to autoimmune diseases.

Initiation at the Joslin Diabetes Center

Type 1 diabetes is a common autoimmune disease. An interplay of genetic and environmental factors that is not yet fully understood leads to inflammatory processes in people affected by the disease, which trigger an attack by the immune system on the pancreas. Killer T cells mistake the ß cells’ own peptides, in which insulin is produced, for foreign antigens. This leads them to launch a destructive attack. Kilian Schober found his way into immunology by researching this disease. He had already been fascinated by the scientific principles of medicine during his pre-clinical semesters at the University of Würzburg. After two clinical semesters abroad at St. George’s Medical School in London, he therefore decided to tackle a challenging experimental doctoral thesis. Under the aegis of Stephan Kissler, he investigated the role of the CLEC16A gene in the development of type 1 diabetes. No sooner had he started than Kissler was appointed to the renowned Joslin Diabetes Center at Harvard Medical School in Boston in 2012, where Schober followed him for a year. “That was a revelation for me, it made me realize how much I enjoy research and that I have a talent for it.” Schober completed the experimental work for his dissertation in 2013. After obtaining his license to practice medicine in Würzburg in 2014, he defended his doctorate there in 2016 with the grade summa cum laude.

Two completely new technologies

By this time, he had long since found a research position that best suited his interest in T cells and joined the group of Dirk Busch, a luminary in the field of infection immunology, at the Technical University of Munich (TUM). He spent almost seven years as a postdoctoral researcher in his group, during which time he learned to use two completely new technologies that took research into T cells to a new qualitative level and brought them to a quantitative resolution that he had never dreamed of during his medical studies. We are talking about genome editing with the help of CRISPR-Cas gene scissors and single-cell RNA sequencing (scRNA-seq). Genome editing makes it possible to precisely modify T cells by replacing their natural receptors with any predefined receptors. scRNA-seq makes it possible to comprehensively determine which genes are currently active in a particular T cell and thus also to sequence its characteristic receptor. In Munich, Kilian Schober thus became an accomplished T cell engineer, as evidenced by his habilitation at TUM, still supervised by Dirk Busch, entitled “The T cell receptor – evolution of complex antigen-specific immune responses and genetic engineering for T cell therapy”. A title that is programmatic for the research that Schober has been conducting with his own group in Erlangen for three and a half years. Focusing on test series with human T cells, he wants to understand natural T cell responses in their “incredible combinatorial complexity” on the one hand and contribute to the development of individually optimized cell therapies with precisely engineered T cell receptors on the other – as a clinician scientist, incidentally, who spends a quarter of his time working as a doctor in microbiological diagnostics.

Learning from the yellow fever vaccination

He benefits from the fact that the vaccination and travel consultation at the University Hospital Erlangen is carried out at the Institute of Microbiology. Vaccinations are good model systems for studying T cell responses because they provide a clear timeline for the immune response and its interaction between B and T cells, starting on the day of vaccination, which cannot be counted on in the case of infections or tumors that have existed for an unknown period of time. During the pandemic, SARS-CoV2 vaccinations naturally played the main role in this regard. Schober and his group have published highly regarded work on this[i] . However, the best model system is usually set in motion during travel vaccination consultations. It is the vaccination against yellow fever. “One dose of vaccine is probably enough for lifelong protection in immunocompetent people,” says Schober. “This is our blueprint for a successful immune response.” A blueprint that records quite precisely which receptor recognizes which viral epitope and has the advantage of remaining legible for life, because the immune system of the vast majority of vaccinees only sees the antigens of the yellow fever virus once, namely during vaccination. A blueprint whose information about the immune response therefore does not become an illegible palimpsest, as can be the case after several coronavirus vaccinations, for example, especially if it is overlaid by breakthrough infections. A blueprint that Schober has been using since January 2024 as one of the principal investigators of an EU Horizon project to understand immune responses to Zika or West Nile fever. Like yellow or dengue fever, both are caused by flaviviruses and there is currently no vaccine for either. The World Nile fever virus has already arrived in Europe due to climate change.

The dream of tumor-specific T-cell therapies

A sophisticated assay invented by French colleagues gives Schober and his team the opportunity to track exactly how T cells develop in humans after a yellow fever vaccination. “We measure their metabolic activity at single-cell resolution and combine this with short-term treatment with inhibitors of certain signaling pathways.” Schober says that this made it possible to differentiate between almost countless T-cell manifestations, but the crucial question is whether these forms are also associated with a distinct function. If he had to decide on a minimum number after acute infections – or immunization with a live vaccine – then he would only distinguish three T cell types: Naïve T cells, which have never encountered the antigen, immature T cells, which are more stem cell in character and long-lived, and multiply proficient T cells, which have learned to respond effectively to the antigen but also disappear more quickly. Schober can transfer the knowledge of metabolic differences between different T cells to T cell therapies against cancer. “For an existing therapy, the aim is to make the responses and response rates more predictable.” And for the development of new therapies, it is important to know the epitopes and their MHC frameworks through which cancer cells exhibit their inner world. “Because these are the potential target structures for customized T-cell receptors.” However, the landscape of these structures is enormously diverse, both between patients and within a patient. “Our vision is to one day give each tumor patient cocktails of T cells with many different receptors, perhaps even hundreds, to do justice to this diversity.” This would require being able to predict which epitope a defined receptor will recognize. [i]

Avidity as a key concept

To this end, Schober and his team are in the process of building up a library of T cell receptors and validated epitopes. Given the rudimentary nature of the relationships discovered to date, this is a huge amount of hard work. However, there are now technologies that can be used to test the variety of possible epitopes against certain T cell receptors. They are supported by attempts to let AI programs learn on the basis of already known relationships between receptors and epitopes. “These programs, which are being developed by our cooperation partners at the Helmholtz Center in Munich, help us to separate the wheat from the chaff when it comes to the specificity of epitope recognition.” Let’s remember: a doctor’s action, for example, has 100 percent specificity if he or she does not diagnose a disease in anyone who is healthy. Accordingly, a T cell receptor must not bind to one of the large numbers of self-peptides presented by a healthy cell. It must prove its binding strength to epitopes that originate from proteins that are foreign or hostile to the body. And in certain situations, it should combine this with a certain greed (lat. aviditas) to get hold of these epitopes. Binding strength can be illustrated with the image of a hand clasping a fruit that it wants to pick. But may have to let go again when the branch on which it is hanging snaps upwards. Avidity, explains Kilian Schober, is comparable to a sticky hand from which the fruit cannot easily escape. “During my postdoctoral period and now in my group, we have learned to understand the dependence of the T cell response on the avidity of the receptor in depth in many models.”[i] In order for him to achieve his goals, which promise new approaches for the prevention and treatment of infections, autoimmune diseases and cancer, the Aventis Foundation is supporting him with its Life Sciences Bridge Award on his way to a permanent professorship.

Author:  Joachim Pietzsch, Wissenswort

Photos: © Uwe Dettmar

[1] For example, the presentation of the immune responses of a man who was vaccinated 217 times against SARS-CoV-2: K. Kocher*, C. Moosmann*, F. Drost, C. Schülein, P. Irrgang, P. Steininger, J. Zhong, J. Träger, B. Spriewald, C. Bock, D.H. Busch, C: Bogdan, B. Schubert, T.H. Winkler, M. Tenbusch, E. Schuster*, K. Schober*. Adaptive immune responses are larger and functionally preserved in a hypervaccinated individual. Lancet. Infect Dis. 450, 10-12 (2024) ) doi:10.1016/S1473-3099(24)00134-8

[2] F. Drost, E. Dorigatti, A. Straub, P. Hilgendorf, K. I. Wagner, K. Heyer, M. López Montes, B. Bischl, D. H. Busch*, K. Schober*, B. Schubert*, Predicting T cell receptor functionality against mutant epitopes. Cell Genomics, (2024), doi: 10.1016/j.xgen.2024.100634

[3] A. Purcarea*, S. Jarosch*, J. Barton, S. Grassmann, L. Pachmayr, E. D’Ippolito, M. Hammel, A. Hochholzer, K. I. Wagner, J. H. van den Berg, V. R. Buchholz, J. B. A. G. Haanen, D. H. Busch*, K. Schober*, Signatures of recent activation identify a circulating T cell compartment containing tumor-specific antigen receptors with high avidity. Sci. Immunol. 7, eabm2077 (2022)

*Shared first or last authorship