Cancer vaccines is the frontier of cancer immunotherapy. The greatest challenge in their development is the precise identification of neoantigens, a factor that directly determines clinical efficacy. The current mainstream approach involves using Next-Generation Sequencing (NGS) on patient DNA to identify genetic mutations, followed by software-based prediction of neoantigen peptide sequences. However, this approach faces several limitations that hinder the field's progress.

To address this technical challenge, ProtTech has developed a novel cancer neoantigen discovery technology based on MHC peptidomics. This technology enables De Novo sequencing of neoantigen amino acid sequences, without requiring tumor DNA sequencing data. This approach not only identifies neoantigens derived from both protein-coding and non-coding regions of the human genome but also captures neoantigens originating from aberrant transcription or translation, and originating from various human viral genomes. Additionally, we have developed vector systems for mRNA in vitro production, as well as the enzymes required to manufacture mRNA cancer vaccines (including T7 RNA polymerase, mRNA capping enzymes, and O-methyltransferases).

Compared to NGS-based neoantigen discovery, the MHC peptidomics-based approach offers several significant advantages:

1. Accuracy. This approach relies on the direct sequencing of MHC-bound peptides, so it is possible to achieve 100% accuracy in neoantigen identification. In contrast, DNA sequencing-based methods rely on software to predict neoantigens based on a patient's MHC type. Given the vast diversity of MHC genotypes in the human population—totaling approximately 45,000 variants—software-based prediction often yields low clinical accuracy.

2. Completeness. DNA sequencing approaches infer neoantigen sequences by analyzing mutations in the protein-coding DNA of cancer tissues compared to matched normal cells. However, protein-coding regions account for only 1.5% of the human genome. Many known neoantigens originate from the non-coding regions (which make up 98.5% of the genome) or arise from aberrant transcription or translation products of non-mutated genes (such as cancer-testis antigens). Consequently, DNA sequencing methods may fail to detect a significant number of genuine neoantigens. In contrast, our MHC peptidomics technology platform directly sequences MHC-bound peptides, enabling the accurate identification of neoantigens derived from non-protein-coding regions, products of aberrant transcription or translation, and invading viral genomes.

3. Low cost. Traditional approaches based on next-generation sequencing (NGS) require deep sequencing—repeated hundreds of times—of the entire cancer genome and a matched normal genome (totaling approximately 3.2 billion base pairs in a human genome), followed by extensive analysis and validation. By comparison, our MHC peptidomics-based neoantigen discovery technology requires only the sequencing of roughly 1,000–2,000 short peptides (10–20 amino acids in length) via liquid chromatography-mass spectrometry (LC-MS), resulting in significant savings in both time and R&D costs.

We have established long-standing, in-depth collaborations with Thermo Fisher and several U.S. companies in the field of MHC peptidomics analysis (Ref. 1).

Please contact us if you are interested in ProtTech’s Neoantigen Discovery and Cancer Vaccine Development.

Reference 1: Shih, N.R., Nong, T., Murphey, C. et al. HLA class I peptide polymorphisms contribute to class II DQβ0603:DQα0103 antibody specificity. Nat Commun 15, 609 (2024) [Abstract]