Targeting the repertoire of mutated peptides in cancer by specific T-cell receptors

In cancer, DNA mutations give rise to altered proteins/peptide sequences, so-called neo-antigens. Such altered proteins can be "seen" by the immune system as foreign, similarly to foreign proteins/peptides from bacteria and viruses. The overall aim of this project is to understand the rules that dictate immune responses to proteins/peptides that arise from DNA mutations. There is now strong evidence that immunotherapy can be effective when conventional treatment fails, and that T cells play a major role in the anti-tumor effect. The key component in tumor recognition is the T-cell receptor. However, there is currently very limited information about 1) which proteins and mutations the T cells can recognize and respond to, and 2) if clinical responses require immune responses to multiple mutated targets, or if responses to one or a few would suffice. Such information is essential to improve immunotherapeutic strategies. The current project aims at identifying neo-antigenic repertoires in different cancer types and at cloning and characterizing T-cell receptors that recognize these neo-antigens. To this end, we have developed and established new technologies to i) identify molecular targets in tumor cells that are recognized by cytotoxic T cells, ii) isolate the T cells responding to these targets, iii) clone their T-cell receptors, and iv) engineer patient T cells to express the cloned T-cell receptors. We have now demonstrated that we can use these technologies to generate T cells from healthy donors that specifically recognize neo-antigens from melanoma patients. Moreover, we have shown that T-cell receptors isolated from these T cells can mediate killing of patient tumor cells after genetic insertion into peripheral blood T cells. The results were published in Science, and resulted in considerable nationwide and international attention from media. We further optimized the technology, and the results were in 2019 published in Nature Protocols. The method was utilized for generation of a T-cell receptor that recognizes a mutation that is shared by patients with myeloid leukemia. This T-cell receptors mediates efficient killing of leukemia cells from patients harbouring the mutation. In 2019, we characterized the T cell receptor in detail by identifying which amino acids in the targeted peptide that are required for recognition. Mapping of the T cell receptor reactivity demonstrated a high degree of specificity for the mutated cancer cells. Moreover, we showed that patient leukemia stem cells containing the mutation were killed.In 2020 we performed extensive studies in different leukemia models in immunodeficient mice. Leukemia from patients was transplanted to mie, that after engraftment were treated with human T cells expressing the therapeutic T cell receptor. The efficacy was high, as the bone marrow of the mice was cleared of leukemia in a short time. Moreover, we have demonstrated that the leukemia stem cells were killed by the gene modified T cells in the mice. Finally, we have characterized guidelines for which mutations that are presented on HLA molecules by use of mass spectrometry. In 2020 we demonstrated that mistakes made during protein synthesis by starving cancer cells (translational mistakes) can represent a new category of neoantigens that T cells can recognize and respond to. The results suggest that this type of neoantigens can be utilized as new and promising targets of cancer immunotherapy in the future. The study, performed as a collaborative project initiated by two groups at the Netherlands Cancer Institute and the Weizman Institute in Israel, was published in Nature in December 2020.

Vi har utviklet en ny metode for samtidig identifikasjon av neoantigener og terapeutiske T-cellereseptorer som gjenkjenner disse, ved å benytte T celler fra friske blodgivere i et nytt konsept. Dette ble publisert i Science i 2016 og i Nature Protocols i 2019. Videre har vi identifisert en terapeutisk T-cellereseptor som gjenkjenner en frekvent mutasjon i akutt leukemi og vist lovende resultater ved behandling av mus (med human leukemi). Endelig har vi vist at en ny kategori neoantigener som oppstår når kreftceller begår feil i proteinsyntesen, kan benyttes som mål for immunterapi (Nature i 2021). Resultatene fra prosjektet kan danne direkte grunnlag for ny kreftbehandling. Videre kan metodene som er utviklet danne grunnlag for oppdagelsen av nye mål og medikamenter til bruk ved immunterapi av kreft. Endelig har prosjektet ført til nytt internasjonalt samarbeid med toppforskningsmiljøer ved Karolinska Institutet, the Netherlands Cancer Institute og Weizman Institute i Israel.

The overall aim of this project is to understand immune responses to mutations in cancer and use this information to genetically engineer immune cells to eradicate cancer. There is now strong evidence that immunotherapy can be effective when conventional treatment fails. This is exemplified by results from our recent in-house vaccine trial in follicular lymphoma patients. Clinical responses were strongly correlated with systemic anti-tumor T-cell responses. There is increasing evidence that the elements recognized by clinically efficacious anti-tumor T cells are altered peptide sequences encoded by mutated genes, so-called neo-antigens. The key component in tumor recognition is the T-cell receptor. However, there is currently very limited information about 1) which proteins and mutations the T cells can recognize and respond to, and 2) if clinical responses require immune responses to multiple mutated targets, or if responses to one or a few would suffice. Such information is essential to improve immunotherapeutic strategies. Here, we seek funding for four work packages aimed at identifying neo-antigenic repertoires in lymphoma and melanoma and at cloning and characterizing T-cell receptors that recognize these neo-antigens. To this end, we have developed and established new technologies to i) identify molecular targets in tumor cells that are recognized by CD8+ cytotoxic T cells, ii) isolate the T cells responding to these targets, iii) clone their T-cell receptors, and iv) engineer patient T cells to express the cloned T-cell receptors. These technologies will be used in two strategies to develop molecularly defined immunotherapy for lymphoma and melanoma. The research is expected to form basis for clinical trials where patients will receive genetically modified T cells capable of killing cancer cells.