Genomic Profiling of T-Cell Neoplasms Reveals Frequent and Mutations With Clonal Evasion From Targeted Therapies.

Greenplate A, Wang K, Tripathi RM, Palma N, Ali SM, Stephens PJ, Miller VA, Shyr Y, Guo Y, Reddy NM, Kozhaya L, Unutmaz D, Chen X, Irish JM, Davé UP
JCO Precis Oncol. 2018 2018

PMID: 30079384

Purpose - The promise of precision oncology is that identification of genomic alterations will direct the rational use of molecularly targeted therapy. This approach is particularly applicable to neoplasms that are resistant to standard cytotoxic chemotherapy, like T-cell leukemias and lymphomas. In this study, we tested the feasibility of targeted next-generation sequencing in profiles of diverse T-cell neoplasms and focused on the therapeutic utility of targeting activated JAK1 and JAK3 in an index case.

Patients and Methods - Using Foundation One and Foundation One Heme assays, we performed genomic profiling on 91 consecutive T-cell neoplasms for alterations in 405 genes. The samples were sequenced to high uniform coverage with an Illumina HiSeq and averaged a coverage depth of greater than 500× for DNA and more than 8M total pairs for RNA. An index case of T-cell prolymphocytic leukemia (T-PLL), which was analyzed by targeted next-generation sequencing, is presented. T-PLL cells were analyzed by RNA-seq, in vitro drug testing, mass cytometry, and phospho-flow.

Results - One third of the samples had genomic aberrations in the JAK-STAT pathway, most often composed of and gain-of-function mutations. We present an index case of a patient with T-PLL with a clonal V658F mutation that responded to ruxolitinib therapy. After relapse developed, an expanded clone that harbored mutant M511I and downregulation of the phosphatase, CD45, was identified. We demonstrate that the missense mutations were activating, caused pathway hyperactivation, and conferred cytokine hypersensitivity.

Conclusion - These results underscore the utility of profiling occurrences of resistance to standard regimens and support JAK enzymes as rational therapeutic targets for T-cell leukemias and lymphomas.

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