# Personalized medicine in triple-negative breast cancer: combining neoantigen vaccination and genomic profiling in a patient undergoing neoadjuvant chemotherapy

## TL;DR

A triple-negative breast cancer patient received personalized neoantigen vaccination and genomic profiling during chemotherapy, showing immune responses and actionable mutations.

## Contribution

This case study explores the integration of neoantigen vaccines and genomic profiling in TNBC during neoadjuvant chemotherapy.

## Key findings

- Neoantigens elicited IFN-γ responses in PBMCs before vaccination, indicating pre-existing immunity.
- Post-vaccination, increased IFN-γ secretion and T-cell activation markers were observed.
- A germline ATM variant and somatic mutations in TP53, NF1, and PIK3CA were identified with clinical relevance.

## Abstract

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with the poorest prognosis among all breast cancer subtypes. The limited effectiveness of first-line treatments, such as systemic neoadjuvant chemotherapy (NAC) and surgery, underscores the urgent need for alternative therapeutic strategies. Next-generation sequencing (NGS) has revolutionized precision oncology by enabling the identification of tumor-specific neoantigens for personalized vaccines and the profiling of actionable mutations for targeted treatments. However, the application of these approaches in TNBC, particularly in the context of NAC, remains largely unexplored.

We present a case study of a TNBC patient treated with NAC combined with dendritic cells (DCs) pulsed with a personalized tumor neoantigen vaccine. Whole-exome sequencing (WES) of germline and tumor tissue, along with tumor RNA sequencing (RNA-Seq), was performed to identify potential neoantigens. Candidate neoantigens were selected for vaccine development and evaluated for immunogenicity in peripheral blood mononuclear cells (PBMCs) through IFN-γ secretion assays, flow cytometric analysis of activation markers (CD69 and CD154) on CD4+ and CD8+ T cells, and T-cell receptor (TCR) CDR3 repertoire profiling after peptide stimulation. Germline and somatic variants were analyzed to assess hereditary risk and actionable mutations, respectively.

Selected neoantigens elicited IFN-γ responses in PBMCs prior to vaccination, indicating pre-existing immunity. Post-vaccination, enhanced immunogenicity was demonstrated by increased IFN-γ secretion, upregulation of activation markers CD69 and CD154 on CD8+ and CD4+ T cells, and polyclonal expansion of TCR CDR3 clones. Notably, an immune response against a non-vaccine neoantigen was observed following immunization, suggesting possible epitope spreading; however, responses detected in pre-vaccination samples preclude attributing this effect exclusively to vaccination. Germline WES identified a splice-altering pathogenic variant in ATM (c.2250G>A, p.Lys750=), confirming hereditary cancer predisposition. Somatic mutation analysis revealed alterations in TP53 (p.Gly199Ter), NF1 (p.Phe1593SerfsTer31), and PIK3CA (p.Glu542Lys), all supported by OncoKB level-1 evidence.

This case highlights the potential of integrating precision oncology for TNBC patients undergoing NAC by identifying inherited cancer risks, detecting actionable mutations, and developing personalized neoantigen-based immunotherapies. The observation of immune responses to both vaccine and non-vaccine neoantigens raises the possibility of epitope spreading, though this finding requires cautious interpretation due to pre-existing immune responses. As a single-patient case study, these results remain preliminary and must be validated in larger cohorts.