Genomic analysis of mycosis fungoides and Sèzary syndrome identifies recurrent alterations in TNFR22015-08-10 00:01:34
NATURE GENETICS; 10 August 2015: DOI:10.1038/ng.3370
Alexander Ungewickell, Aparna Bhaduri, Eon Rios, Jason Reuter, Carolyn S Lee, Angela Mah, Ashley Zehnder, Robert Ohgami, Shashikant Kulkarni, Randall Armstrong, Wen-Kai Weng, Dita Gratzinger, Mahkam Tavallaee, Alain Rook, Michael Snyder, Youn Kim & Paul A Khavari
Mycosis fungoides and Sèzary syndrome comprise the majority of cutaneous T cell lymphomas (CTCLs), disorders notable for their clinical heterogeneity that can present in skin or peripheral blood. Effective treatment options for CTCL are limited, and the genetic basis of these T cell lymphomas remains incompletely characterized1. Here we report recurrent point mutations and genomic gains of TNFRSF1B, encoding the tumor necrosis factor receptor TNFR2, in 18% of patients with mycosis fungoides and Sèzary syndrome. Expression of the recurrent TNFR2 Thr377Ile mutant in T cells leads to enhanced non-canonical NF-kB signaling that is sensitive to the proteasome inhibitor bortezomib. Using an integrative genomic approach, we additionally discovered a recurrent CTLA4-CD28 fusion, as well as mutations in downstream signaling mediators of these receptors.
We performed whole-exome sequencing on 11 mycosis fungoides and Sèzary syndrome samples each paired with a normal sample to identify somatic genetic alterations associated with these malignancies. A total of 494 genes were selected for deep targeted resequencing, which included genes mutated in the exome data set, genes previously implicated in the pathogenesis of T cell malignancies and related pathway members. A total of 91 individual samples and cell lines were sequenced at an average coverage of ~700×, of which 73 were included in our mycosis fungoides and Sèzary syndrome paired analysis with normal samples The mutational spectrum of mycosis fungoides and Sèzary syndrome is heterogeneous, with the tumor-suppressor genes MLL3 (also known as KMT2C; 26%) and TP53 (13%) being the two most frequently mutated genes. Furthermore, we found gain-of-function mutations in KRAS and PLCG1 that have previously been reported in mycosis fungoides and Sèzary syndrome. The most frequent recurrent point mutation in our data set occurred at codon 377 of TNFRSF1B (5%; 4/73), encoding tumor necrosis factor receptor 2 (TNFR2), resulting in a recurrent TNFR2 Thr377Ile mutant. TNFR2 is a receptor that regulates key T cell signaling pathways and has not previously been implicated in cancer
We noted that many somatic alterations involved pathways related to TNFR2 and non-canonical nuclear factor (NF)kB signaling, primarily regulating T cell survival and proliferation, including the TNFR2 pathway itself, as well as the T cell receptor (TCR) and CD28 pathways. This finding is consistent with previous transcriptome sequencing indicating differential expression of genes in the TCR signaling pathway between Sèzary syndrome cells and autologous polyclonal CD4+ T cells5. In addition to alterations in TNFR2, we found mutations in phosphoinositide 3-kinase (PI3K)-related genes involved in TCR-CD28 signaling and mutations in NF-kB pathway genes, including a subset in the canonical NF-kB signaling pathway, that control transcriptional programs downstream of key T cell signaling pathways.
Structural variations frequently characterize malignancies of lymphoid origin, and we therefore used FACTERA to detect chromosomal structural variations in mycosis fungoides and Sèzary syndrome samples. This analysis identified structural variation events (excluding copy number gains) in pathways related to T cell survival and proliferation in 11% of patients with mycosis fungoides or Sèzary syndrome. Interestingly, the structural variants were largely mutually exclusive with the TNFR2 alterations (Fisher’s exact test, P = 0.0005). The structural variants included NF-kB2 gene truncations in 5% (4/73) of cases with the deletion of a region whose loss is known to generate a truncated p100 protein with predicted proteasome-independent NF-kB2 nuclear localization7, as well as a deletion involving TRAF3 that would also be expected to increase non-canonical NF-kB signaling. We also identified a translocation altering the TP63 gene recently reported to be rearranged in T cell lymphomas, two translocations predicted to disrupt the CD274 gene, encoding PD-L1, which normally inhibits T cell activation via PD1 binding, and a translocation predicted to delete the pro-apoptotic TNFRSF10A receptor.
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