Diffuse Intrinsic Pontine Glioma (DIPG) is categorised as a grade IV paediatric glioma, which arises in the ventral pons region of infants as young as 3 years of age with peak incidences observed between 6 to 9 years. Current treatments, including radiotherapy and chemotherapy, only alleviate symptoms but do not cure the disease. Therefore, alternate approaches such as targeted immunotherapy to combat DIPG are critically needed. This study employs a dual pronged approach of combining proteomics along with immunopeptidomics to identify therapeutic targets. By incorporating healthy brain tissue and comparing these with DIPG cell lines this study identified several targets which can be developed into immunotherapeutics.
Native HLA class I complexes were purified by immunoaffinity purification from 6 DIPG cell lines along with bottoms up proteomics and samples were acquired using liquid chromatography and tandem mass spectrometry (LC-MS/MS).
A total of 21,281 HLA class I peptides restricted to 22 HLA alleles were identified including prominent Caucasian allotypes. Of note, we identified 1,096 cancer testis antigens (CTA) and oncogenic peptides originating from proteins such as MAGE, PRAME and TP53. Moreover, using proteomics we identified 6,947 proteins in healthy brain tissue (n=3) and DIPG cell lines (n=5). When compared to healthy brain we found enrichment of 2,514 proteins specifically in DIPG cell lines that included proteins involved in gene silencing and regulation. The study also explored surface proteins of DIPG cells using cell surface protein atlas, identifying 217 proteins of interest belonging to integrin family of proteins and cluster of differentiation (CD) markers.
By adopting a dual pronged approach, this novel study for the first time reports the HLA class I peptides that can be incorporated into T cell-based vaccines, as well as several surface proteins candidates as targets for bispecific antibodies or CAR T cells.