Molecular Characterization Of Adult T-Cell Leukemia/Lymphoma

Adult T-cell leukemia/lymphoma (ATL) is an aggressive form of peripheral T-cell lymphoma (PTCL), which is etiologically associated with human T-lymphotropic virus type I (HTLV-1) infection during early infancy. Although HTLV-1 can effectively immortalize T-cells, there is a long latency period of ∼50 years prior to the onset of ATL, suggesting that HTLV-1 infection alone may not be sufficient for the development of ATL, but additional acquired genetic hits that occur in immortalized T-cells during the later life are essential for its pathogenesis. However, little has been known about those genetic hits that are involved in the pathogenesis of ATL.

The purpose of this study is to understand the genetic basis of ATL, 32 cases with different ATL subtypes, including acute (N=15), chronic (N=6), lymphoma (N=10), smoldering (N=1) types were analyzed by whole exome sequencing as well as copy number analysis. With a mean coverage of 119, 94% of the target sequences were analyzed at more than 20 depth on average. A total of 2,862 somatic changes were detected in 32 cases with a true positive rate of 99% (329 of the 334 tested were confirmed by PCR-based deep sequencing). These consisted of 2,512 missense mutations, 174 nonsense mutations, 65 splice-site mutations, and 111 indels. The mutation rate of 89 (44-227) per sample was significantly higher than that in acute myeloid leukemia (7.3–13), myelodysplastic syndromes (9.2) and chronic lymphocytic leukemia (11.5). Recurrent mutations were observed in 350 genes, of which 192 were considered to be significantly mutated (q < 0.05) compared to background mutation rates (1.79 mutations per megabase).

To investigate significantly mutated pathways, each pathway registered in the Kyoto Encyclopedia of Genes and Genomes, BioCarta, Reactome, Sigma-Aldrich and Signaling Transduction KE was tested on the basis of the background mutation rate observed in whole-exome sequencing data, which revealed a number of significantly mutated functional pathways, including pathways involeved in T cell receptor signaling, leukocyte trans-endothelial migration, VEGF and WNT signalings and other signaling pathways.

Genes for epigenetic regulations were also among the frequent targets of gene mutations. We performed targeted deep sequencing of TET2, IDH1/2 and DNMT3A in 182 ATL cases. In total, 19 TET2 mutations were identified in 16 cases (8.7%). Different subtypes of ATL were almost evenly affected with 9 out of 67 acute, 3 out of 42 chronic and 4 out of 56 lymphoma types having TET2 mutations. Less frequent mutations of IDH2 and DNMT3A (both 1%) were also identified. Our findings on genetic alterations provide a novel insight into the pathogenesis of ATL.