Abstract 6736: Suppression of antigen presentation is a hallmark of pediatric rhabdomyosarcoma
Authors: Milewski David , Tian Meijie , Kim Yong , Wei Jun , Khan Javed 
Published: April 2023

Background: Rhabdomyosarcoma (RMS) is the most common soft tissue tumor in children and young adults, accounting for approximately 350-400 new cases annually in the US. These tumors are diagnosed based on their expression of skeletal muscle lineage markers. Clinical trials testing conventional immunotherapies such as cancer vaccines or immune checkpoint blockade (ICB) therapy have found no activity in RMS, although the root causes of failure are largely unexplored. A recent study by our group found that RMS tumors have a lack of immune infiltrate, consistent with previous reports. However, we made an unexpected observation that RMS tumors had a near absence of antigen processing and presentation (APP) gene expression, a key requisite for anti-tumor CD8+ T lymphocytes. In this study, we investigate the root causes of the lack of APP in RMS and evaluate implications for immunotherapy.

Methods: Publicly available DNA sequencing datasets were used to evaluate APP gene mutations in RMS tumor samples. RNAseq from reporter iPSC cell lines demarcating specific stages of skeletal muscle differentiation were used to evaluate APP gene expression during myogenesis. Surface MHC class I expression was evaluated using flow cytometry against a panel of pediatric sarcoma cell lines. RMS PDX and cell line APP protein levels were measured by western blot. Stimulation of APP in RMS cell lines was tested using IFNγ or sub-cytotoxic doses of different epigenetic therapeutics (DNMTi, HDACi, EZH2i) before analyzing surface MHC class I expression by flow cytometry.

Results: RNAseq analysis of the differentiation states across the normal human skeletal muscle lineage revealed a myoblastic cell state which transiently downregulates the APP pathway. RNA expression of HLA-A,B,C genes were lower in RMS than any other pediatric extracranial solid tumor histology studied. RMS cell lines and PDX models also displayed low APP pathway gene expression by western blot and flow cytometry, with FOXO1 fusion positive RMS having a near absence of expression. RMS tumor exome sequencing data from RMS patients showed a lack of enrichment of APP gene mutations. Instead, we found that APP could be induced in nearly all samples tested using IFNγ or epigenetic stimulation with Decitabine, Entinostat, or Tazemetostat.

Conclusions: We uncovered a previously unappreciated lack of antigen presentation in RMS which phenocopies myoblasts in normal skeletal muscle development. The downregulation of MHC class I antigen presentation is not due to APP pathway mutations but rather a partially reversible downregulation mirroring this specific stage of normal skeletal muscle development. Our findings suggest that pharmacological reversal of the APP pathway downregulation may enhance immunotherapies targeting MHC class I antigens in RMS.

Citation Format: David Milewski, Meijie Tian, Yong Kim, Jun Wei, Javed Khan. Suppression of antigen presentation is a hallmark of pediatric rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6736.