Anaplastic lymphoma kinase fusions as a target for TCR-directed cellular therapies

Chromosomal rearrangement derived gene fusions with the catalytic domain of anaplastic lymphoma kinase (ALK) drive oncogenesis in several cancers, including in ~5% of non-small-cell lung cancers (NSCLCs). While ALK tyrosine kinase inhibitors (TKIs) have revolutionized the treatment of these patients the majority will develop resistance; novel treatments are required. We hypothesize that the ALK kinase domain may be a suitable target for directed immunotherapy. Full length ALK is normally expressed during fetal development but becomes highly restricted in adults, and anti-ALK immune responses are readily detected in other ALK-fusion+ cancers, correlating with good prognosis. Using peptide pool expansions and T cell activation assays, we have detected numerous anti-ALK T cell responses from normal donors and ALK+ NSCLC patients. These donors express a variety of HLA alleles, and some donors display reactivity to multiple pools spanning the kinase domain, suggestive of common T cell responses to multiple ALK epitopes. Leveraging a high-throughput microfluidic technique to clone and functionally express natively-paired T cell receptor (TCR) genes from these ALK-reactive T cell populations, we are screening for both the exact antigenic peptides and the HLA restrictions of these epitopes. TCRs thus isolated will then be tested against a panel of ALK+/− patient derived and cancer cell lines using in vitro and in vivo models, to assess potential utility in cytotoxic TCR-directed immunotherapies. These patient derived models include those with acquired TKI resistance: by comparing these mutational hotspots with putative epitope sites we expect to find TCRs capable of killing ALK+ cancer cells irrespective of prior treatment.