with Dr. Catherine J. Wu, Professor of Medicine at Dana-Farber Cancer Institute
Presenting at the virtual TIDES: Oligonucleotide and Peptide Therapeutics conference in September 2020, Dr. Catherine J. Wu from the Dana-Farber Cancer Institute Boston, MA, showed how effective anti-tumour immunity in humans has been associated with the presence of T-cells directed at cancer neoantigens, a class of HLA-bound peptides that arise from tumour-specific mutations. These are highly immunogenic, because they are not present in normal tissues; and therefore, bypass central thymic tolerance.
Although neoantigens were long-envisioned as optimal targets for an anti-tumour immune response, their systematic discovery and evaluation only became feasible with the recent availability of massively parallel sequencing for detection of all coding mutations within tumours, and of machine learning approaches to reliably predict those mutated peptides with high-affinity binding of autologous human leukocyte antigen (HLA) molecules.
Vaccination with neoantigens can both expand pre-existing neoantigen-specific T-cell populations and induce a broader repertoire of new T-cell specificities in cancer patients, tipping the intra-tumoral balance in favour of enhanced tumour control. Dr. Catherine J. Wu studies demonstrated the feasibility, safety, and immunogenicity of a vaccine that targets up to 20 predicted personal tumour neoantigens (Melanoma Neovax anti-PD1). Vaccine-induced polyfunctional CD4+ and CD8+ T cells targeted unique neoantigens used across patients; with these T cells discriminating mutated from wild-type antigens, and in some cases directly recognizing autologous tumour.
More recently, Dr. Catherine J. Wu lab researchers went back to these previously treated patients and grasped how persistent these memory T cell responses are, by seeing a continuous response 5-7-years later, with a second-wave of immune response that shows epitope spreading from the initial epitope.
The question now is if doctors and researchers can better predict the antigen presentation given the ambiguity that arises from the co-expression of multiple HLA alleles. With that in mind, Dr. Wu’s lab used cell lines expressing a single HLA allele, optimizing immune-purifications, and developing an application-specific spectral search algorithm, identifying thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of subdominant binding motifs and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression.
Next, with the help of mass spectrometry the profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines were identified; together with canonical peptide motifs per HLA allele, unique and shared binding sub-motifs across alleles, and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, Dr. Wu’s lab developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumour cell lines.
Another important question in Dr. Wu’s lab is whether they can find new classes of targets in splice variants, gene fusions, or unannotated open reading frames that are translated; and, whether they can render the tumours more immunogenic. Also, by trying to understand how cell states are involved in natural disease progression, Dr. Wu’s lab was able to realize how CD8+ cells are terminally exhausted in metastatic disease of renal cell carcinoma; and, their interaction with tumour macrophages can actually return a prognostic value.
Find out more about the 2020 TIDES: Oligonucleotide and Peptide Therapeutics virtual event in our full overview here.