Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel

Abstract

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

Frequent Mutations in Natural Killer/T Cell Lymphoma

“…In addition, mutations have been reported in hematologic malignancies such as acute myeloid leukemia (AML) [89], myelodysplastic syndromes [90], and NKTCL [18,71]. In NKTCL, as detected by NGS, the reported frequency of this mutation among the Japanese population is 32% (eight of 25 cases) [18], which is higher than that reported in the Korean population, specifically 20.6% (seven of 34 cases) [66] and 25% (one of five cases) [19]. BCOR alterations tend to emerge more frequently in malignancies associated with EBV infections and often occur in the form of loss-of-function mutations in exon 4 (Fig.…”

“…Seven mutations were revealed in 105 cases (6.7%) among a Chinese population [11]. In Korea, the frequency was found to be higher, with specific incidences of six in 34 (17.6%) [66] and four in five (80%) [19]. Both nonsense and missense mutations were identified, but little is known about their functional roles in NKTCL.…”

“…The majority of these mutations were identified as nonsense mutations, frameshiftinducing insertions, and deletions that cause truncated proteins lacking part or all of the C-terminal domain [77,81,82]. This type of alteration leads to an abnormally short, non-functional histone methyltransferase that has lost its function as a tumor suppressor [19]. Missense mutations impairing MLL2 methyltransferase activity were also identified.…”

“…This method can detect mutant DNA in as little as 3% of the total gene copies in a PCR mixture [17]. Recently, TP53 mutations in NKTCL were also studied by NGS, but the frequencies were relatively lower at 13.3% (14 of 105 cases) among the Chinese population [11], and 16% (four of 25) and 20% (one of five) in Japanese and Korean cohorts [18,19], respectively. There is thus an apparent discrepancy in reported frequencies between the two methods.…”

EBV-negative aggressive NK-cell leukemia/lymphoma: a clinical and pathological study from a single institution

“…Prior studies investigating mutational landscape of EBV-associated extranodal NK/T-cell lymphomas have reported recurrent mutations in genes involved in JAK-STAT pathway(STAT3, JAK3) and chromatin modification (MLL2, BCOR) as well as tumor suppressor genes (TP53, FAS). [29][30][31][32] Among these, the mutations leading to activation of the JAK-STAT pathway are shown to play a significant role in pathogenesis of these neoplasms. 29,33 Genetic alteration in EBV-negative NK/T-cell lymphoma is unclear.…”