North American ATLL has a distinct mutational and transcriptional profile and responds to epigenetic therapies

Abstract

Adult T-cell leukemia lymphoma (ATLL) is a rare T cell neoplasm that is endemic in Japanese, Caribbean, and Latin American populations. Most North American ATLL patients are of Caribbean descent and are characterized by high rates of chemo-refractory disease and worse prognosis compared with Japanese ATLL. To determine genomic differences between these 2 cohorts, we performed targeted exon sequencing on 30 North American ATLL patients and compared the results with the Japanese ATLL cases. Although the frequency of TP53 mutations was comparable, the mutation frequency in epigenetic and histone modifying genes (57%) was significantly higher, whereas the mutation frequency in JAK/STAT and T-cell receptor/NF-κB pathway genes was significantly lower. The most common type of epigenetic mutation is that affecting EP300 (20%). As a category, epigenetic mutations were associated with adverse prognosis. Dissimilarities with the Japanese cases were also revealed by RNA sequencing analysis of 9 primary patient samples. ATLL samples with a mutated EP300 gene have decreased total and acetyl p53 protein and a transcriptional signature reminiscent of p53-mutated cancers. Most importantly, decitabine has highly selective single-agent activity in the EP300-mutated ATLL samples, suggesting that decitabine treatment induces a synthetic lethal phenotype in EP300-mutated ATLL cells. In conclusion, we demonstrate that North American ATLL has a distinct genomic landscape that is characterized by frequent epigenetic mutations that are targetable preclinically with DNA methyltransferase inhibitors.

Graphical abstract

Figure 1.

North American ATLL has a distinct mutational landscape. (A) North American ATLL samples (n = 30) and Japanese ATLL cell lines (n = 8) were sequenced by targeted deep next-generation sequencing. Identified mutations are grouped into various functional categories. Corresponding mutations reported in Japanese ATLL are marked in the last row. (B) Location of point mutations in the p53 protein structure. (C) Location of point mutations in the p300 protein structure. Green, blue, and black circles depict missense single nucleotide polymorphisms, splice site single nucleotide polymorphisms, and truncating mutations, respectively. (D) Frequency of mutations in North American and Japanese ATLL. (E) Frequency of epigenetic mutations in North American ATLL and whole-exome sequenced Japanese ATLL cases. *P < .05, North American vs Japanese.

Figure 2.

North American ATLL features a high frequency of epigenetic mutations that are prognostic. (A) OS of North American ATLL patients with epigenetic mutations is worse than those without these mutations. (B) OS of North American ATLL patients with TP53 mutations shows a trend toward worse survival, but it is not statistically significant. (C) EP300 mutations are associated with reduced p300 levels, as well as total and acetylated p53 levels, in primary patient samples. (D) Gene set enrichment analysis revealed enrichment of the P53_DN.V1_UP signature in the 2 EP300-mutated samples (ATL21 and ATL18) compared with 2 EP300 WT samples (ATL29 and ATL30).

Figure 3.

Distinct transcriptomic features are seen in North American ATLL. (A) Unsupervised clustering analysis of RNA-seq profiles of healthy CD4 controls and ATLL samples. (B) Volcano plot shows aberrantly expressed genes in North American ATLL compared with healthy controls. (C) Supervised clustering analysis reveals genes that are aberrantly expressed in North American ATLL. (D) Functional pathways enriched in differentially expressed genes. (E) Unsupervised clustering based on RNA-seq profiles shows transcriptomic differences between Japanese (blue, n = 57) and North American (orange, n = 9) ATLL samples.

Figure 4.

Decitabine has cytotoxic activity in ATLL. Results from cell-viability assays following 5 days of decitabine treatment in Japanese (A) and North American (B) ATLL samples. (C) Summary of decitabine IC₅₀ doses for all samples tested with EP300 and TP53 mutation status. (D-E) Doxorubicin and decitabine combination showed synergistic efficacy in 1 ATLL cell line and 1 North American ATLL culture. (F) Apoptosis measured by Annexin V/propidium iodide staining in decitabine-treated samples. Results shown are representative of 2 (ATL43Tb⁻) and 3 (ATL18) independent experiments. (G) Reduction in total 5-methylcytosine content after 48 hours of decitabine treatment at 0.6 μM was quantified by mass spectrometry. *P < .05. (H) Volcano plot. RNA-seq analysis revealed many re-expressed genes in 4 primary samples (ATL18, ATL21, ATL29, ATL30) following decitabine treatment.