Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer.

ABSTRACT:

Introduction

We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer.

Method

We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot).

Results

We uncovered 20 novel fusion transc

SUBMITTER: Mistretta B 

PROVIDER: S-EPMC10512078 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature