The clinical need for a broad antigen landscape in low TMB tumours
Deep tumour regressions after treatment with checkpoint inhibitor (CPI) antibodies and CAR T-cells have prompted a series of FDA approvals that have begun to change the face of cancer care. Ever since these discoveries, there has been a clear focus on utilising immunotherapies in tumours with a high tumour mutational burden (typical for cancer cells in continuous contact with clear mutagens such as UV and tobacco smoke for melanoma and pulmonary cancers respectively). Nevertheless, the patients carrying lowly mutated malignancies are mostly unresponsive to these standard immunotherapies, and require alternative, more personalised options.
Reversing a cold into a hot tumour
The absence of T-cells in the tumour can be due to the lack of tumour-specific antigens, APC deficit, absence of T-cell priming/activation and impaired trafficking of T-cells to the tumour mass (left panel). Removal of these brakes that malignancies use to immune escape can turn cold tumours into hot tumours (right panel) (adjusted from Bonaventura et al. 2019).
"Personalised cancer vaccination can have an added value to reinforce the activity and therapeutic margin of CPIs by increasing the number of specific effector T-cells or by converting cold tumours into inflamed tumours"
The holy grail of personalised immunotherapy is centred around finding correct neoantigens, i.e. peptides different from the normal peptidome (set of peptides expressed by a normal cell). Hence, they can be used as an identifier for uniquely targeting tumour cells which will evoke minor side effects since cell death will only be induced in cells with these neoantigens on their surface.
Finding immunogenic neoantigens, however, for personalised cancer vaccination in cold tumours is a lot more challenging due to the low mutation frequency where the number of possible mutational peptides expressed in the tumour cells is limited. Overall, limited success has been obtained in clinical studies for these low TMB malignancies. It is thus of great importance to identify as many disparate peptides as possible. Although there are clear indications that the immune system can drive successful tumour eliminations of low TMB tumours (pancreas, MSS CRC, etc...), different and more thorough neoantigen discovery methods are required as postulated by Laumont et al. (2018).
myNEO development of novel neoantigen discovery methods
The myNEO neoantigen prediction platform identifies a broad range of tumour-specific alterations and neoantigens, to be able to select more valuable targets for personalised vaccination strategies, as is highly required for patients with less mutated tumours. Due to extensive academic expertise in Belgium in these low TMB (Tumour Mutational Burden) tumour types, myNEO has incorporated many low TMB datasets and focuses deeply on research and validation efforts as well on these tumour types.
"The myNEO platform focuses on identifying tumour-specific alterations on several distinct levels within a cell. The myNEO focus of variant calling is shifting beyond purely exomic mutational event detection by using patient-specific MS-datasets combined with Whole-Genome Sequencing (WGS), ribosome depleted RNA-Seq and even Ribo-Seq"
During a basic mutational analysis, only the effects of simple genomic events on the antigen repertoire are considered (Single Nucleotide Variants, Insertions/Deletions, Overexpression of certain genomic regions). myNEO performs a deep analysis of comprehensive tumour datasets via proprietary algorithms which allow for the detection of many more valuable targets. The algorithms to detect these tumour-specific alterations and their implications have been built in-house and are explained in more detail under technology.
The importance of this approach was confirmed in 2019 by Löffler, who stressed the relevance of non-exomic tumour antigens in tumours with low tumour mutational burden. Genomic mutations caused on DNA level such as single nucleotide variants, indels, gene fusions, and retrotransposon activity are detected based on comparative analysis of DNA sequencing datasets. RNA sequencing is used to confirm the expression and presence of these alterations. Tumour-specific transcriptomic changes, such as alternative splicing and non-canonical transcription, are also extracted from the RNA sequencing datasets. The addition of ribosome profiling and mass spectrometry screening confirms the detected variation in the previous datasets but also allows detection of new levels of tumour-specific modifications (RNA-editing, alternative ORFs, partial lncRNA translation, peptide phosphorylation, and alternative proteasomal cleavage). Each subsequent dataset thus identifies new alterations while confirming the tumour mutations that were detected in previous analyses.
"myNEO looks further than antigens resulting from simple genomic modifications such as SNVs and indels (which are unique for 99.5% of the patients), taking an extensive set of antigens resulting from non-canonical tumour-specific alterations into account"
The feasibility of even further extending the variant search domain to include more non-canonical variant types such as non-coding RNA mutations, alternative processing (TAP independent pathways, immunoproteasome), alternative start codons and uncanonical ORFs (in introns, 5’UTRs, etc...), among others are currently researched by myNEO as well.
Want to learn more about this?
Vonderheide RH. The Immune Revolution: A Case for Priming, Not Checkpoint. Cancer Cell. 2018 Apr 9;33(4):563-569. Bonaventura P. et al. Cold tumours: a therapeutic challenge for immunotherapy. Front Immunol. 2019 Feb 8.
Laumont, C. M. et al. Noncoding regions are the main source of targetable tumour-specific antigens. Sci. Transl. Med. 10, (2018). Löffler et al. Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome Med, 2019 Apr;11(28)