Detection Of Recurrent/Persistent Disease By T-Cell Receptor Repertoire Profiling In Patients With Mature T-Cell Neoplasm

Identification of recurrent or persistent disease in T-cell neoplasms is important for individualized patient care. While patients with T-cell lineage lymphomas and leukemias are a small subset of all lymphoma and leukemia patients, the incidence of refractory disease in these patients can be higher than patients with B-cell lineage neoplasms. We recently developed a method to sequence the diversity of the TCR CDR3 rearrangements (Blood. 2009; 114(19): 4099-107) that exploits the capacity of high-throughput sequencing (HTS) to document the diverse repertoire of TCRB CDR3 chains simultaneously. These assays can describe both the breadth of T-cell repertoire and quantify individual clones. For example, we have shown in that T-cell clones as rare as 1:100,000 total T cells can be accurately quantified (Journal of Immunological Methods 2012;375:14-9). This technology thus provides a potential opportunity to track the presence and frequency of clones in the context of an evolving, adaptive immune system, during the course of ongoing therapy.

While our recent study demonstrated the first application of high-throughput sequencing to the evaluation of minimal residual disease in precursor acute T lymphoblastic leukemias (Sci. Transl. Med. 4(134):134ra63. 2012), we focus here on mature T-cell neoplasms to demonstrate the broad potential of this technology to contribute to the post-therapeutic monitoring of T cell neoplasia. We amplified the TCRB repertoire of 35 index samples to identify high-frequency TCRB rearrangements. Clones were classified as neoplastic if occurring at a proportion greater than 7 standard deviations above the mean frequency of the most abundant rearranged TCRB in control samples of either blood, bone marrow, or lymphoid tissues. Samples that lacked a detectable TCRB clone were excluded. For each patient, at least one subsequent follow-up sample was available. For these 59 samples, we sequenced the TCRB repertoire to screen for the corresponding index clone. We find that for most samples, high-throughput sequencing concurs with currently available, routine clinical measures of disease, such as clinical flow cytometry or PCR-based evaluation of TCRG rearrangement. High-throughput sequencing of TCRB was concordant in 46 samples with identification of the index clones and in 7 additional samples without the identification of the index clones. However, 5 of 59 samples were only positive for recurrent disease based on HTS only, and 1 of the 59 samples was only positive for recurrent disease based on current diagnostic technology but not HTS.

We find that for most samples, high-throughput sequencing concurs with currently available, routine clinical measures of disease, such as clinical flow cytometry or PCR-based evaluation of TCRG rearrangement and T-cell repertoire analysis may be useful for clinical laboratory evaluation of patients with T-cell neoplasms.