Abstract 2957: T-cell receptor immunosequencing reveals novel insights into the immune response to human pancreatic cancer
Authors: Seo Yongwoo D. , Jalikis Florencia G. , Jiang Xiuyun , Vignali Marissa , Robins Harlan , Pillarisetty Venu G. 
Published: July 2017

Abstract
Introduction Despite advancements in therapy, pancreatic ductal adenocarcinoma (PDA) remains an aggressive cancer with high mortality. It is characterized by dense inflammation, including many T cells; however, it is unclear whether these T cells signify a true antitumor response. In the setting of disappointing early results of immunotherapy in PDA, we sought to gain a deeper understanding of the tumor-associated T-cell response.
Methods With IRB approval, we obtained archival resected PDA tumors in paraffin-embedded blocks from 54 patients. We performed histopathology to identify blocks containing lymph nodes (LN) and performed T-cell receptor (TCR) immunosequencing on DNA extracted from immediately adjacent tissue. To address possible intratumoral heterogeneity, we analyzed duplicate samples from separate blocks for 10 patients. Productive clonality was defined as 1-Pielou’s evenness for TCR rearrangements encoding a functional protein; TCR fraction was calculated from number of observed templates and the amount of input DNA. Two-tailed t-tests were used to compare subgroups. TCR sequence overlap between each of the 10 pairs of duplicate samples were calculated at the amino acid level.
Results Among samples that did not contain LN, mean TCR fraction was 0.27, and mean clonality was 0.15 (typical peripheral blood mononuclear cell clonality is 0.08). TCR fraction was positively correlated with clonality (R2=0.23, p=0.007), though this correlation was only significant in patients who received neoadjuvant chemotherapy (R2=0.19, p=0.03). TCR fraction was higher in patients with positive nodal status (0.32 vs. 0.23, p=0.02), but lower in patients who received neoadjuvant therapy (0.22 vs. 0.33, p=0.02). There was no survival difference between high or low TCR fraction or clonality. Samples containing LN (not included in previous analyses) had higher TCR fraction (0.49 vs. 0.27, p&lt;0.0001) but lower clonality (0.09 vs. 0.15, p=0.0002); this relationship was maintained regardless of nodal status. Among 10 pairs of duplicate samples, there was 53% mean overlap of TCR amino acid sequences, compared to 0.1% for pairs of unmatched samples (p&lt;0.0001).
Conclusion Here we demonstrate evidence of clonal expansion of T cells in the human PDA microenvironment. Extensive overlap of TCR sequences between two distinct samples for each of 10 pairs analyzed further suggests that the clonal expansion may be specific to tumor antigens. Neoadjuvant therapy may also influence clonal expansion, as only treated patients had a positive correlation between TCR fraction and clonality. Finally, the presence of a lymph node appears to skew TCR sequencing data toward a less clonal but more numerous population. This suggests that the most rigorous analysis of TCRs in a solid tumor microenvironment needs to exclude blocks that contain lymph nodes in order to characterize the true intratumoral population of T cells.
Citation Format: Yongwoo D. Seo, Florencia G. Jalikis, Xiuyun Jiang, Marissa Vignali, Harlan Robins, Venu G. Pillarisetty. T-cell receptor immunosequencing reveals novel insights into the immune response to human pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2957. doi:10.1158/1538-7445.AM2017-2957