RT Journal Article
SR Electronic
T1 ImmunoMap: A Bioinformatics Tool for T-cell Repertoire Analysis
JF Cancer Immunology Research
JO Cancer Immunol Res
FD American Association for Cancer Research
SP 151
OP 162
DO 10.1158/2326-6066.CIR-17-0114
VO 6
IS 2
A1 Sidhom, John-William
A1 Bessell, Catherine A.
A1 Havel, Jonathan J.
A1 Kosmides, Alyssa
A1 Chan, Timothy A.
A1 Schneck, Jonathan P.
YR 2018
UL http://cancerimmunolres.aacrjournals.org/content/6/2/151.abstract
AB Despite a dramatic increase in T-cell receptor (TCR) sequencing, few approaches biologically parse the data in a fashion that both helps yield new information about immune responses and may guide immunotherapeutic interventions. To address this issue, we developed a method, ImmunoMap, that utilizes a sequence analysis approach inspired by phylogenetics to examine TCR repertoire relatedness. ImmunoMap analysis of the CD8 T-cell response to self-antigen (Kb-TRP2) or to a model foreign antigen (Kb-SIY) in naïve and tumor-bearing B6 mice showed differences in the T-cell repertoire of self- versus foreign antigen-specific responses, potentially reflecting immune pressure by the tumor, and also detected lymphoid organ–specific differences in TCR repertoires. When ImmunoMap was used to analyze clinical trial data of tumor-infiltrating lymphocytes from patients being treated with anti–PD-1, ImmunoMap, but not standard TCR sequence analyses, revealed a clinically predicative signature in pre- and posttherapy samples. Cancer Immunol Res; 6(2); 151–62. ©2017 AACR.