Next-Generation Sequencing Suggests Complex, Heterogeneous Pathogenesis In Peripheral T-Cell Lymphoma Unspecified

Peripheral T-cell lymphoma (PTCL) makes up about 12 percent of non-Hodgkin lymphoma, comprising 18 diseases that are poorly understood and carry a generally worse prognosis than B-lymphomas. PTCL not otherwise specified (PTCL-NOS), a diagnosis of exclusion, is most common, making up 25-30 percent. Gene-expression studies suggest a heterogeneous origin of this diagnosis, with overlap to other PTCL types, but the genetic factors underlying its pathogenesis are undefined. Current therapy for PTCL-NOS is empiric and ultimately ineffective for most patients. Identification of specific therapeutic targets is therefore a high priority. We have sought better understanding of pathogenesis through next-generation sequencing of PTCL-NOS tumor DNA. Whole-exome sequencing revealed candidate genes but low availability of fresh-frozen samples limited our ability to draw conclusions by this method alone. We therefore sequenced the coding regions of 237 candidate genes in a collection formalin-fixed paraffin-embedded samples. We used Nimblegen Sequence Capture for PCR amplification of exons and Illumina hiSeq for raw sequence generation. Results were aligned to hg19 and compared to dbSNP and the 1,000 genomes data to exclude germline variants. Analysis, including comparison to the COSMIC database of cancer-specific mutations, revealed high-confidence mutations affecting more than 60 known cancer-related genes in 25 PTCL-NOS cases. Recurrent mutations pointed to frequent activation of three key signaling pathways: NF-kB (TNFAIP3), WNT/B-Catenin (APC, CHD8, CELSR2), and NOTCH (NOTCH1, FBXW7). Recurrent deregulation of epigenetic processes was indicated by mutations in genes affecting histone acetylation (EP300, CREBBP), histone methylation (MLL2, KDM6A), and DNA methylation (TET2, DNMT3A). In addition, components of core tumor suppressor pathways showed evidence of frequent inactivation (TP53, ATM, RB1, CUL9, PRKDC). In all, 22 of 25 cases had mutations in at least one of these 17 recurrently mutated genes. Multiple additional candidate disease mechanisms also were suggested by lower-confidence mutations but require confirmation studies, which are under way. In sum, analysis of the coding region of PTCL-NOS tumor DNA suggests a complex and heterogeneous pathogenesis, in line with gene-expression profiling. This work provides an opportunity to better sub-classify entities within the diagnosis of PTCL-NOS and identify specific therapeutic targets and their associated biomarkers.