Introduction
Adult T cell leukemia/lymphoma (ATL) is a rare mature T cell malignancy induced by human T-cell leukemia virus type-1 (HTLV-1). The prognosis is poor, especially in aggressive subtypes ...with a median overall survival (OS) of less than one year despite intensive treatment. Indolent forms also carry a relatively adverse outcome with a median OS of 36 and 56 months for chronic and smoldering types respectively, mainly due to a clonal evolution towards an aggressive subtype. Thus, the identification of indolent patients at high risk for progression to advanced disease remains a major challenge in the management of ATL patients.
Patients and Methods
We have performed an integrated genomic analysis of a retrospective cohort of 61 ATL patients originating from Africa and the Caribbean area. This was achieved by targeted deep sequencing (TDS), SNP array analysis, RNA sequencing and high throughput sequencing (HTS) based mapping of proviral integration sites. In order to explore the potential contribution of the temporal acquisition of driver mutations to progression, we analyzed 15 patients with longitudinal samples, who either relapsed after achieving complete remission or progressed from an indolent to an aggressive subtype.
Results
Sixty-one ATL patients were analyzed at diagnosis. Fifteen had an indolent (smoldering or chronic) subtype and 48 had an aggressive (39 acute and 9 lymphoma) subtype. A total of 248 somatic mutations in 48 genes were identified. The most commonly mutated genes were CCR4 (n=23, 38 %), PLCG1 (n=17, 28%), PRKCB (n=13, 21%), CARD11 (n=13, 21%), TBL1XR1 (n=11, 18%), TP53 (n=11, 18%), FAS (n=10, 16%), GATA3 (n=10, 16%), NOTCH1 (n=9, 15%), CSNK2B (n=9, 15%) , STAT3 (n=8, 13%), RHOA (n=7, 12%) and VAV1 (n=7, 12%). Genomic mutations were clustered in four main pathways. Forty-four (72%) patients harbored mutations affecting the TCR/NF-KB pathway (CD28, PLCG1, CARD11, PRKCB, CBLB, IRF4, CSNK1A1, FYN, RHOA, VAV1). Twenty-eight (46%) harbored mutations affecting the T-cell trafficking pathway (CCR4, CCR7, GP183). Eighteen (29%) showed mutations affecting genes involved in immune escape (FAS, HLA-B, B2M, CD58). Sixteen (26%) showed mutations in genes involved in cell-cycle regulation (TP53, POT1 and RB1). In addition, 31 (50%) showed mutations in genes involved in regulation of transcription and/or epigenetic and 13 (21%) in the JAK/STAT signaling pathway.
The mean number of mutations per sample at diagnosis was higher in aggressive subtypes than in indolent forms: 4.761 (IC95%=4.049-5.472) versus 1.800 (IC95%=0.9071-2.693). This difference was mainly due to a higher number of genetic alterations located in the TCR/NF-κB pathway: 39/46 (85%) patients showed at least one activating mutation in the TCR/NF-κB pathway in the aggressive group compared to 5/15 (33%) in the indolent group (p=0.003).
The analysis of longitudinal samples from patients who relapsed after a remission period showed two different patterns: (i) relapse with an identical malignant clone in terms of proviral integration but with additional somatic alterations mainly in two main pathways (immune escape and TCR/NF-KB pathway) and (ii) relapse with a clone switch and systematic damaging somatic mutations in the TP53 locus.
The analysis of longitudinal samples with a deep sequencing approach from patients who progressed from an indolent to an aggressive subtype revealed a subgroup of indolent forms that carried activating mutations in the TCR/κB pathway clustered in four genes (CARD11, PRKCB, PLCG1 and VAV1), not only at a clonal but also at a subclonal level, subsequently increasing to clonal level upon progression. Moreover, the presence of such mutations either at a clonal or at a subclonal level was associated with a shorter progression time to aggressive subtype compared to other indolent forms (median 18.2 months versus not reached; p=0.0005).
Conclusion
This study defines the genomic landscape of ATL in an Afro-Caribbean population, which is comparable to that of ATL in the Japanese population. Furthermore, the longitudinal study revealed a new indolent ATL subgroup based on a specific oncogenic architecture associated with a shorter progression time. Our findings may be useful for clinicians to identify patients with an indolent subtype at high risk for progression to an aggressive subtype.
No relevant conflicts of interest to declare.
Mutations in TET2, encoding one of the TET members responsible for the conversion of DNA cytosine methylation to hydroxymethylation (5-hmc), have been recently described in Human T-lymphotropic virus ...type 1-associated adult T-cell leukemia/lymphoma (ATLL). However, neither the amount of genomic 5-hmc in ATLL tumor cells nor TET2 expression has been studied yet. In this study, we analyzed these two parameters as well as the mutational status of TET2 in ATLL patients. By employing a direct in situ approach, we documented that tumor T cells infiltrating lymph nodes exhibit low level of 5-hmc compared to residual normal T cells. Furthermore, this 5-hmc defect was more pronounced in tumor T cells from acute patients than from chronic ones and correlated with reduced expression of TET2 protein. TET2 variations were found in 14 patients (20%), including 13 with aggressive forms. Strikingly, 9 of the 14 patients showed the same variation (SNP rs72963007), whose frequency in ATLL patients was significantly higher than that of an ethnically matched control population (13% vs. 5%). However, no reduction of 5-hmc was found in PBMC from individuals possessing the variant rs72963007 TET2 allele, as compared to wild-type individuals. In contrast, a robust correlation was observed between 5-hmc and the levels of TET2 mRNA. Finally, loss of 5-hmc and TET2 downregulation both correlated with poor survival. These findings demonstrate that ATLL progression coincides with loss of genomic 5-hmc and indicate that downregulation of TET2, rather than TET2 mutations, is the key mechanism involved in 5-hmc modulation during ATLL progression.
Mutations in
, encoding one of the TET members responsible for the conversion of DNA cytosine methylation to hydroxymethylation (5-hmc), have been recently described in Human T-lymphotropic virus ...type 1-associated adult T-cell leukemia/lymphoma (ATLL). However, neither the amount of genomic 5-hmc in ATLL tumor cells nor TET2 expression has been studied yet. In this study, we analyzed these two parameters as well as the mutational status of
in ATLL patients. By employing a direct
approach, we documented that tumor T cells infiltrating lymph nodes exhibit low level of 5-hmc compared to residual normal T cells. Furthermore, this 5-hmc defect was more pronounced in tumor T cells from acute patients than from chronic ones and correlated with reduced expression of TET2 protein.
variations were found in 14 patients (20%), including 13 with aggressive forms. Strikingly, 9 of the 14 patients showed the same variation (SNP rs72963007), whose frequency in ATLL patients was significantly higher than that of an ethnically matched control population (13% vs. 5%). However, no reduction of 5-hmc was found in PBMC from individuals possessing the variant rs72963007
allele, as compared to wild-type individuals. In contrast, a robust correlation was observed between 5-hmc and the levels of
mRNA. Finally, loss of 5-hmc and TET2 downregulation both correlated with poor survival. These findings demonstrate that ATLL progression coincides with loss of genomic 5-hmc and indicate that downregulation of
, rather than
mutations, is the key mechanism involved in 5-hmc modulation during ATLL progression.
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