From www.bloodjournal.org by guest on October 10, 2018. For personal use only. Regular Article LYMPHOID NEOPLASIA North American ATLL has a distinct mutational and transcriptional profile and responds to epigenetic therapies Urvi A. Shah,1-3 Elaine Y. Chung,2 Orsi Giricz,3 Kith Pradhan,3 Keisuke Kataoka,4 Shanisha Gordon-Mitchell,3 Tushar D. Bhagat,3 Yun Mai,2 Yongqiang Wei,2,5 Elise Ishida,2 Gaurav S. Choudhary,3 Ancy Joseph,6 Ronald Rice,7 Nadege Gitego,3 Crystall Parrish,3 Matthias Bartenstein,3 Swati Goel,1 Ioannis Mantzaris,1 Aditi Shastri,1,3 Olga Derman,1 Adam Binder,1 Kira Gritsman,1,2 Noah Kornblum,1 Ira Braunschweig,1 Chirag Bhagat,8 Jeff Hall,8 Armin Graber,8 Lee Ratner,6 Yanhua Wang,9 Seishi Ogawa,4 Amit Verma,1,3 B. Hilda Ye,2 and Murali Janakiram1 1Department of Oncology, Montefiore Medical Center, Bronx, NY; 2Department of Cell Biology and 3Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY; 4Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; 5Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China; 6Division of Oncology, Washington University School of Medicine, St Louis, MO; 7Department of Pathology, Phelps Hospital, Northwell Health, Sleepy Hollow, NY; 8Genoptix, Carlsbad, CA; and 9Department of Pathology, Montefiore Medical Center, Bronx, NY KEY POINTS 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 l North American ATLL has a distinct genomic Caribbean descent and are characterized by high rates of chemo-refractory disease and landscape with a worse prognosis compared with Japanese ATLL. To determine genomic differences be- high frequency of tween these 2 cohorts, we performed targeted exon sequencing on 30 North American prognostic epigenetic ATLL patients and compared the results with the Japanese ATLL cases. Although the mutations, including EP300 mutations. frequency of TP53 mutations was comparable, the mutation frequency in epigenetic and histone modifying genes (57%) was significantly higher, whereas the mutation frequency l ATLL samples with in JAK/STAT and T-cell receptor/NF-kB pathway genes was significantly lower. The most mutated EP300 have compromised p53 common type of epigenetic mutation is that affecting EP300 (20%). As a category, epi- function and are genetic mutations were associated with adverse prognosis. Dissimilarities with the selectively sensitive to Japanese cases were also revealed by RNA sequencing analysis of 9 primary patient decitabine treatment. 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 im- portantly, 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. (Blood. 2018;132(14):1507-1518) Introduction of Caribbean/American ATLL (n 5 53), the median overall sur- vival (OS) was only 6.9 months,3,6 similar to other reported North Adult T-cell leukemia lymphoma (ATLL) is a rare aggressive T-cell American studies.2,7 The outcomes in Japanese cohorts of ATLL neoplasm, which is caused by a retrovirus (human T-cell lym- are more favorable, with median survival times for acute, lym- photropic virus [HTLV]-1), and carries a dismal prognosis. HTLV-1 phomatous, chronic, and smoldering subtypes of 8.3, 10.6, has low sequence variability, enabling its sequence to be used 31.5, and 55.0 months, respectively.8 The percentage of pa- as a molecular tool to follow migrations. The most common tients with aggressive subtypes (acute and lymphomatous) in the subtype of HTLV-1 is the cosmopolitan subtype A, which is American cohorts is ;91%,2,3,7 compared with 78% in the Japa- endemic to Japan, the Caribbean, Central and South America, nese population.8 Thus, despite a younger age at diagnosis, north and west Africa, and parts of the Middle East.1 Conse- NorthAmericanATLLpatientsappeartopresentwithsig- quently, ATLL is diagnosed most frequently in the Japanese and nificantly more aggressive subtypes of the disease than their Caribbean populations2,3 but is likely underreported in Africa, Japanese counterparts. The majority of research on this disease Latin America,4 and the Middle East.5 is from Japan, where it is endemic, and most preclinical models used in published ATLL studies are Japanese-derived cell lines Despite similar viral subtypes, the prognosis of ATLL is worse in and xenografts. It is not known whether North American ATLL is the Caribbean and American populations than in the Japanese genotypically distinct from the Japanese cases and whether such population. In our retrospective analysis of a single-center cohort differences, if present, can be correlated with clinical outcomes. © 2018 by The American Society of Hematology blood® 4 OCTOBER 2018 | VOLUME 132, NUMBER 14 1507 From www.bloodjournal.org by guest on October 10, 2018. For personal use only. A PATHWAY -catenin PI3K/AKT/mTOR signaling B cell receptor signaling Stress response Stress Receptor kinases tyrosine Other Notch signaling Epigenetic and histone modification Transcriptional regulation Cell death Jak/Stat signaling Ras signaling TCR signaling FGFR signaling Cell cycle and DNA maintenance Wnt/ signaling structure Chromatin VHL XPO1 ATLL PATIENTS ATLL AGE GENDER CYTOGENETICS Overall Survival KEAP1 CREBBP PBRM1 TET2 EZH2 MED12 SPEN HIST1H1E IDH1 KRAS HRAS POT1 SETBP1 CDKN2A BRCA1 PALB2 GATA3 TBL1XR1 AR BCL6 TCF3 MYC NOTCH2 CARD11 TNFAIP3 RHOA PLCG2 FGFR3 FGFR1 TSC1 AKT1 MCL1 RIPK1 ERBB3 ALK ERBB2 PDGFRB IGF1R DDR2 RET CD79A SYK SMC3 STAG2 STAT3 PTCH1 SPOP CDH1 FLT1 AXL MAP2K2 MDM4 NTRK1 FAS SUBTYPE TP53 EP300 DNMT3A KMT2A SMARCB1 ASXL1 NRAS BRCA2 PRDM1 GATA2 CEBPA BCOR NKX2-1 KLF2 FAT1 APC DDX3X NOTCH1 FBXW7 TRAF3 FGFR4 FGFR2 AKT2 RICTOR PIK3CD KDR KIT EGFR PDGFRA FLT3 JAK3 STAT5B ITPKB ZYMM3 P2RY8 ZFHX4 MAP3K9 ESR1 ATL 1 83 M 33 ATL 2 59 M 382 ATL 3 30 F 543 ATL 4 66 F 363 ATL 5 74 F 160 ATL 6 53 M88 ATL 7 48 F 225 ATL 8 64 F 215 ATL 9 63 F 739 ATL 10 36 M 52 ATL 11 70 F 451 ATL 12 54 F 23 ATL 13 37 F 17 ATL 14 41 M 771* ATL 15 51 M 312 ATL 16 57 F 2554* ATL 17 36 M 75 ATL 18 67 F 175 ATL 19 65 M 392 ATL 20 74 M 1191* ATL 21 37 F 6345* ATL 22 60 M 126 ATL 23 54 F 503* ATL 24 59 F 176 ATL 25 64 M 73 ATL 26 61 F 102 ATL 27 40 F 351* ATL 28 40 M 322 ATL 29 63 F 192 ATL 30 70 F 153* ATL55T(+) Su9T01 ATL43T(+) ATL43Tb(-) ED40515(+) ED40515(-) ED41214(+) ED41214(-) Japanese ATL 1-30: North American ATLL Patients ATL55T(+) to ED41214(-) are 8 Japanese derived cell lines Japanese: Mutations also seen in Japanese patients Subtype: Acute Lymphomatous Chronic/Smoldering Cytogenetics: Normal Complex Unknown Overall Survival: Number of days from diagnosis to death *: Alive B p53 TAD DNABD TM 0 100 200 300 393 aa C p300 TAZ Z TAZ 1 KIX BD HAT Z 2 IBiD 0 400 800 1200 1600 2000 2414 aa D E 60% 50% 25% 40% 20% 30% 15% Frequency (%) Frequency 20% 10% Frequency (%) Frequency 5% 10% 0% 0% IDH1 IDH2 TP53 TET2 TET2 JAK3 JAK1 EZH2 SPEN POT1 STAT3 EP300 EP300 RHOA ASXL1 GATA3 PBRM1 MED12 KMT2A PIK3CD CARD11 TNFAIP3 TBL1XR1 CDKN2A NOTCH1 DNMT3A DNMT3A HIST1H1E SMARCB1 All epigenetic Mutated genes Mutated genes North American (n=30) Japanese (n=370) North American (n = 30) Japanese (n = 81) Figure 1. North American ATLL has a distinct mutational landscape. (A) North American ATLL samples (n 5 30) and Japanese ATLL cell lines (n 5 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 1508 blood® 4 OCTOBER 2018 | VOLUME 132, NUMBER 14 SHAH et al From www.bloodjournal.org by guest on October 10, 2018. For personal use only. Furthermore, understanding the mutational landscape of North genes is determined through bioinformatic analysis and com- American ATLL is critical in an effort to develop new targeted parison with databases (eg, COSMIC and dbSNP). Quality-control therapies for these patients. metrics included a minimum of 200 ng of genomic DNA and average mean sequencing depth of 5003 coverage to give a limit Epidemiology of ATLL in the United States reflects emigration of detection of 5% for SNVs, 10% for insertions/deletions patterns from endemic areas, especially the Caribbean region, and translocation fusions, gene amplifications $ 6 copies, and and is characterized by an increasing incidence in New York City homozygous gene deletions , 0.3 copies. These mutational data and Miami.9,10 Montefiore Medical Center treats a significant were compared with clinical characteristics and patient out- proportion of ATLL patients in the United States as a result of comes to determine the prognostic impact of particular mutations. the large number of Caribbean immigrants in the Bronx, NY.3,6 Here, we present the mutational and transcriptional landscape of Patient records were queried using Clinical Looking Glass soft- Caribbean ATLL and demonstrate that it is characterized by a distinct ware to identify all cases of HTLV positivity and ATLL by searching mutation pattern that targets epigenetic pathways more frequently pathology and laboratory reports of patients who presented than that reported for Japanese ATLL.