{
  "abstract": "Background The global cancer burden continues to escalate, with 20 million new cases reported in 2024. Breast cancer remains the most prevalent, accounting for 2.3 million cases. 1 Despite advances such as CDK4/6 inhibitors in combination with endocrine therapy for hormone receptor-positive (HR+) breast cancer, therapeutic resistance frequently emerges.2 To address this challenge and uncover novel immunotherapeutic strategies, we investigated the neoantigenic landscape of RNA fusion events, focusing on chimeric transcripts in CDK4/6 resistant patient derived xenograft (PDX) models.Methods Comprehensive RNA sequencing data from 985 PDX models covering 27 cancer types were obtained and analyzed from models established by XenoSTART. In the ST940C model originating from an ER+/HER2+ breast cancer patient with acquired CDK4/6 inhibitor resistance, 2 we identified a highly expressed in frame ESR1-PRKN fusion involving exons 1–8 of ESR1 and exons 4–12 of PRKN. Fusion transcript validation was performed by PCR and Sanger sequencing. Fusion-spanning 9–11-mer peptides were evaluated for HLA class I binding using NetMHCpan 4.1, MixMHCpred 3.0, and BigMHC. HLA typing via OptiType revealed high-affinity binding to HLA-A*01:01. Top-ranked peptides were tested for immunogenicity via IFN-γ ELISpot and flow cytometry using HLA-matched PBMCs. T cell responses were further characterized through 10x Genomics single-cell 5′ RNA sequencing and TCR profiling following peptide stimulation of CD8+ and CD4+ T cells.Results Six peptides CLKSIILLNSA, SAGRSIYNSFY, LNSAGRSIY, NSAGRSIY, ILLNSAGRSIY, and NSAGRSIYNSF elicited robust HLA-A*01:01-specific responses. Single-cell analysis revealed clonal expansion of cytotoxic CD8 + T cells in response to these neoepitopes. Independently, XenoSTART confirmed that ST940C retained ER and HER2 expression, exhibited resistance to fulvestrant, and remained sensitive to CDK4/6 inhibition in vivo.Conclusions These findings establish ESR1-PRKN as a clinically relevant fusion generating immunogenic neoantigens and highlight its potential as a target for personalized peptide and mRNA vaccine strategies in therapy-resistant breast cancer.Acknowledgements \\UH Sequencing core for sequencing and XenoSTART for the PDX modelsReferences World Health Organization. Global cancer burden growing, amidst mounting need for services. Geneva: World Health Organization; 2024 Feb 1,Hernandez T, Kneifel D, Simonson A, Flores J, Quick S, Cabang A, Ulmer A, Papadopoulos K, Lang A, Rodriguez G, Beeram M, Rasco D, Patnaik A, Ulmer S, Wick M. Establishment and characterization of luminal A breast XPDX models from patients with acquired resistance to CDK 4/6 inhibitors. Cancer Res. 2022;82:P5–01.",
  "authors": [
    {
      "affiliations": [
        "University of Houston, Houston, TX, USA"
      ],
      "name": "Aaranyah Kandasamy"
    },
    {
      "affiliations": [
        "University of Houston, Houston, TX, USA"
      ],
      "name": "Preethi H Gunaratne"
    },
    {
      "affiliations": [
        "University of Houston, Houston, TX, USA"
      ],
      "name": "Shiyanth Thevasagayampillai"
    },
    {
      "affiliations": [
        "University of Houston, Houston, TX, USA"
      ],
      "name": "Dilshan Adhikari"
    }
  ],
  "title": "931 Discovery of immunogenic neopeptides from actionable RNA fusion ESR1-PRKN for developing cancer vaccines",
  "uid": "92259e88-511a-5ef1-8dc3-22e259de25f7"
}