Next generation sequencing of the immune repertoire is a comprehensive immune profiling methodology that allows detailed, sequence-specific insight into the adaptive immune response. While many studies focus solely on the T-cell receptor beta chain, insight into the variable rearrangements of the immune repertoire as a whole through the study of all seven TCR and BCR chains together (i.e., TCR-beta, TCR-alpha, TCR-delta, TCR-gamma, BCR-IgH, and BCR-IgK and IgL) provides a broader view of the immune landscape with potential prognostic value. A major challenge for all-inclusive multiplex PCR development is primer-dimer formation. We have developed a new technique, dimer avoided multiplex PCR (dam-PCR), that effectively avoids dimer formation during PCR and incorporates unique molecular identifiers for direct RNA quantification and error removal. With one sample - either PBMC, FFPE, or tumor tissue - we are able to amplify and obtain sequences of all seven chains in the immune repertoire together. Applying this technique to clinical renal cancer PBMC with treatment, we found that both TCR-alpha and -beta diversity prior to treatment and the expression ratio between B cells and T cells are good predictors of treatment efficacy. Furthermore, differences in treatment protocols can potentially increase BCR-IgH and BCR-IgL expression. Our study suggests that examining multi-chain immune repertoire composition can be valuable for predicting treatment response and evaluating treatment protocols.
Wenjing Pan– iRepertoire Inc.
Mollye Depinet– iRepertoire, inc.
Shang-Gin Wu– Department of Internal Medicine, National Taiwan University Cancer Center, National Taiwan University
Xiaohong Hou– iRepertoire, Inc.
Brittany Brown– iRepertoire, Inc.
Mary Eisenhower– iRepertoire, Inc.
Alexa Fort– iRepertoire, Inc.
Song Li– iRepertoire, Inc.
Miranda Byrne-Steele– iRepertoire, Inc.
Michael Lotze– UPMC Hillman Cancer Center
Jian Han– iRepertoire, Inc.