Abstract

Gene fusions, including JAK-family fusions, drive oncogenesis in a subset of cutaneous T-cell lymphoma/lymphoproliferative disorders (CTCL/CLPD). Their detection may aid in the identification of clonal/neoplastic populations. While predicted functional gene fusions are detectable by targeted RNA-sequencing/next-generation-sequencing (NGS), such assays are costly, time-consuming, and not widely available. Fluorescence in situ hybridization (FISH), routinely used in myeloid and solid tumor diagnosis, is faster and less expensive. We hypothesized that JAK2 and/or TYK2 FISH could assist pathologic diagnosis of CTCL/CLPD. We aimed to evaluate the utility of FISH for detecting JAK-family fusions in NGS-positive specimens. Sixteen skin biopsies from 15 CTCL patients with JAK2 or TYK2 fusions by NGS, and concurrent break-apart FISH were identified. Eight had same-lesion flow-cytometry (FC).  Molecular and cytogenetic reports were reviewed for congruence (positive/negative result). Numerical values from FISH and FC were compared. FISH detected rearrangements in 12/16 samples (75%) involving 5-86% cells (median 27%). JAK2 FISH was positive in 6/7 cases (86%) in 8-86% cells (median 56%). TYK2 FISH detected rearrangements in 6/9 cases (67%) in 5-70% cells (median 12%). Two cases with TYK2 fusions but negative FISH correlated to FC acquisition of 17 and 57 cells and no immunophenotypic abnormalities. Four of five FISH+ cases with FC correlates (2 JAK2, 2 TYK2) demonstrated immunophenotypically abnormal cells (19-59%; median 38%). One TYK2 case with 8% FISH+ cells had no abnormal cells by FC.  FISH appears useful to detect JAK-family fusions in CTCL/CLPD. Challenging cases have low percentages of FISH+ cells or low cellularity overall, requiring careful screening.