Identification of immunopeptides (pHLA) as candidate therapeutic targets in chondrosarcoma.

BACKGROUND: Chondrosarcoma (CHS) is the second most common primary malignant bone tumor and remains resistant to conventional therapies, underscoring the need to discover novel therapeutic targets. Cancer/testis antigens (CTAs), a class of tumor-associated proteins, represent attractive antigens for cancer immunotherapies such as adoptive T cell therapy. However, the expression profile of CTAs and their associated targetable immunopeptides presented in the Human Leukocyte Antigen-I context (pHLA) remain unknown in CHS. This study aims to characterize the CTA expression profile according to the tumor immune phenotype and clinical outcomes, and to identify the most relevant pHLA to target in CHS.

METHOD: We analyzed the CTA expression profile in tumors from 63 conventional CHS patients and in healthy tissues using GTEx and HPA databases to identify CHS-associated CTAs. Cox proportional hazards models combined with hierarchical clustering were used to correlate CTA expression with the overall survival of patients. The tumor immune phenotype was estimated based on immune gene expression signatures using a deconvolution method and a Pearson correlation coefficient matrix. The CTA-derived pHLA were characterized using immunopeptidomic profiling based on HLA-I immunoprecipitation and mass spectrometry in grade 2 and 3 CHS models. NetMHC was used to predict the binding affinity of identified pHLA to the HLA-A*02:01 and HLA-A*01:01 alleles.

RESULTS: We identified a poor prognosis CTA signature predominantly associated with a non-inflamed tumor immunophenotype. Immunopeptidomic profiling revealed broad pHLA repertoires, including previously well-characterized CTAs from PRAME, CTAG2 and the MAGE-A family, as well as newly identified candidates with strong predicted HLA-binding affinity from CTAs such as HHIPL2, DBF4, BRIP1, CBX2 and DIAPH3.

CONCLUSION: This study provides the first atlas of pHLA in CHS and suggests specific antigenic targets for TCR-T cell therapies and targeted therapies such as antibody-drug conjugates.