Abstract P2-04-02: Recognition of autologous neoantigens by tumor infiltrating lymphocytes derived from breast cancer metastases
Authors: Goff SL , Zacharakis N , Assadipour Y , Prickett T , Gartner J , Somerville R , Black MA , Xu H , Chinnasamy H , Kriley I , Lu L , Statler M , Wunderlich J , Robbins PF , Rosenberg SA , Feldman SA 
Published: March 2017

Abstract
Background & Translational Relevance: Adoptive transfer of tumor infiltrating lymphocytes (TIL) can effect long-term durable regression in patients with metastatic melanoma but has not been widely tested in common epithelial cancers. When examining the TIL of successfully treated patients with melanoma, a heterogeneous T cell population can be identified with reactivity against melanoma differentiation antigens, cancer germline antigens, and personalized non-synonymous somatic mutations. Common epithelial cancers, including breast cancer, express far fewer somatic mutations than melanoma, however, a patient with metastatic cholangiocarcinoma was treated with autologous CD4+ TIL enriched for neoantigen specificity and has experienced an ongoing partial response (&gt;2 years). It is known that the presence of TIL on pathologic examination of triple-negative breast cancers is a positive prognostic marker for disease-free survival and overall survival. The identification of enriched populations of neoantigen-specific TIL could form the basis for personalized cell therapy for patients with metastatic breast cancer. This pilot study investigates the ability to grow TIL from breast cancer metastases, to identify personalized non-synonymous somatic mutations and potential neoantigens, and to adoptively transfer TIL into patients with breast cancer.
Methods: Eligible patients were evaluated and treated under IRB-approved protocols for tissue procurement, genomic testing, and adoptive cell transfer. Portions of resected tumors were placed in culture under standard TIL conditions. DNA was extracted from tumor and matched normal peripheral blood samples for whole exome sequencing (WES). Non-synonymous somatic mutations were identified and tested for potential immunogenicity.
Results: Nine patients have undergone surgical resection in this ongoing pilot study, and TIL was successfully grown from the tumors of all patients. All were primarily CD3+ (median 79%) with a small population of natural killer cells. Of the CD3+ cells, 7 of 9 patients had a predominantly CD4+ population (median CD4:CD8 ratio 2.2, range 0.4-5.8). With the exception of a single patient with inflammatory breast cancer, tumor purity allowed for WES of the tumors of eight patients, and non-synonymous somatic mutations were identified as potential neoantigens (median 96.5, range 71-148). Autologous T cell reactivity has been identified against tumor-specific mutations in 4 of 6 patients studied. The TIL of one patient demonstrated in vitro reactivity to a mutated form of RBPJ, a DNA-binding protein involved in Notch1 signaling. In addition, specimens obtained from this patient at autopsy contained the specific RBPJ mutation (RBPJ c.A611T) in every sampled tumor (n=16). Other patient-specific neoantigens identified by autologous reactivity include SLC3A2, KIAA0368, and a mutated TCRBV domain.
Conclusions: Tumor-infiltrating lymphocytes derived from metastatic breast cancer can react to tumor-specific non-synonymous somatic mutations in vitro. TIL grown from breast cancers are predominantly CD4+ and can form the basis of an adoptive cell transfer experimental approach to patients with metastatic breast cancer.
Citation Format: Goff SL, Zacharakis N, Assadipour Y, Prickett T, Gartner J, Somerville R, Black MA, Xu H, Chinnasamy H, Kriley I, Lu L, Statler M, Wunderlich J, Robbins PF, Rosenberg SA, Feldman SA. Recognition of autologous neoantigens by tumor infiltrating lymphocytes derived from breast cancer metastases [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-04-02.