Resource: A compendium of HLA types and expression in pediatric cancer models

TL;DR

This study creates a detailed immunogenomic resource for pediatric cancers, including HLA typing and neoantigen predictions to support immunotherapy development.

Contribution

The novel contribution is a comprehensive, publicly accessible dataset profiling HLA types and immune-related features in over 200 pediatric cancer models.

Findings

High-resolution HLA typing and neoantigen prediction were inferred across multiple pediatric tumor types.

Immune escape mechanisms like HLA gene loss of heterozygosity and allele-specific expression loss were explored.

The dataset provides insights into antigen processing and presentation pathways in pediatric cancers.

Abstract

Cancer immunotherapy has revolutionized treatment by leveraging the immune system to recognize and destroy tumor cells, offering a promising, less toxic option for pediatric patients. A key component of this response is antigen presentation, which depends on accurate human leukocyte antigen (HLA) typing and expression. However, immune-focused resources for pediatric cancers remain limited. In this study, we present a comprehensive immunogenomic resource covering 231 cancer cell lines and 56 tumor-associated fibroblast cell lines from the Childhood Cancer Model Atlas (CCMA). We inferred high-resolution HLA types, predicted neoantigens arising from somatic single nucleotide variants, gene fusions, and splicing isoforms across multiple tumor types, and quantified HLA expression levels. We also explored immune escape mechanisms, including loss of heterozygosity and allele-specific expression loss of HLA genes. This publicly accessible dataset provides critical insight into the immune landscape of pediatric cancers and serves as a foundational tool for immunotherapy development.

•HLA types profiled across 200+ pediatric cancer cell line models•Neoantigen candidates predicted by mutations, fusions, and splicing events•Transcriptional landscape of antigen processing and presentation pathways•Resource enables immunogenomic discovery in pediatric cancer research

HLA types profiled across 200+ pediatric cancer cell line models

Neoantigen candidates predicted by mutations, fusions, and splicing events

Transcriptional landscape of antigen processing and presentation pathways

Resource enables immunogenomic discovery in pediatric cancer research

Molecular biology; Immunology; Cancer

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