Genetic Features of AML with MLL-Rearrangement and NPM1 Mutation: An Interim-Analysis of HM-Screen-Japan 01
Authors: Chi SungGi , Hosono Naoko , Yamauchi Takahiro , Fukushima Kentaro , Shibayama Hirohiko , Katagiri Seiichiro , Gotoh Akihiko , Okabe Motohito , Morishita Takanobu , Yanada Masamitsu , Yamamoto Kazuhito , Fujishima Naohito , Takahashi Naoto , Ogasawara Reiki , Kondo Takeshi , Utsu Yoshikazu , Aotsuka Nobuyuki , Kamoda Yoshimasa , Usuki Kensuke , Takemura Kanenari , Nagata Yasuyuki , Ono Takaaki , Kobayashi Tsutomu , Kuroda Junya , Horiguchi Hiroto , Iyama Satoshi , Fukuhara Suguru , Izutsu Koji , Nakamura Makoto , Togitani Kazuto , Kojima Kensuke , Yamamoto Kaoru , Nakamura Yukinori , Yoshimitsu Makoto , Ishitsuka Kenji , Miyamoto Kenichi , Minami Yosuke 
Published: February 2021

Background: Acute myeloid leukemias with KMT2A (formerly known as MLL-1) fusion genes (MLL-AML) and those with NPM1 mutations (NPM1-AML) are distinct subtypes as defined by the WHO classification. Although they have different clinical features and prognostic impact , recent studies suggest that the MLL1 co-factor, menin, plays a key role in maintaining self-renewal of immature leukemic cells by upregulating transcription of HOXA and MEIS (Gundry et al.). New targeted strategies for these AML subtypes are expected as preliminary data suggest that menin-MLL1 inhibition may inhibit malignancy. In addition to classical chromosomal analysis and prefixed fusion gene screening, next-generation sequencing (NGS) should help in identifying the precise prevalence of these alterations and understanding the relationship with other pathological mutations. We launched the HM-SCREEN-JAPAN01 study (UMIN000035233) in which gene alterations are analyzed by FoundationOne Heme® in patients with AML who are relapsed/refractory to, or ineligible for standard therapies. Aiming for 200 registrations, recruitment has reached approximately 100. The interim results are described here.
Methods: HM-SCREEN-JAPAN01 is an observational study and conducted by 17 participating institutions. The eligibility criteria are as follows: 1) histological diagnosis of AML must be made by bone marrow testing; 2) one of the following conditions must be fulfilled: i) a patient with newly diagnosed AML and is ineligible for standard treatment, or ii) a patient with AML who has relapsed or is refractory to prior therapy; 3) sufficient amount of bone marrow sample must be available; 4) age at registration must be 20 or more; and 5) written informed consent must be taken. All samples were analyzed by FoundationOne Heme®.
Results:Nine patients (9.9%) with MLL-AML and seventeen patients (18.7%) with NPM1-AML were found among 91 available cases (either one found in 28.6%). No patients demonstrated MLL-rearrangement and NPM1-mutation simultaneously. Median age of patients with MLL-AML (42-68 y) was a decade less than that of patients with NPM1-AML (55-74 y), and the majority of cases had a clinical relapse or were refractory to prior therapies. Translocations involving chromosome 11q23.3 (e.g. t(9;11)(p21.3;q23.3)) were found in 5 of 8 patients (62.5%) with MLL-AML (data not available due to insufficient cell count in one case) and no chromosomal abnormalities were detected in 10 of 16 patients (62.5%) with NPM1-AML (chromosomal analysis was not performed in one case). In patients with MLL-AML (see Figure), FLT3 mutations were found in 3 of 9 cases (33.3%), all of which were point mutations within the tyrosine kinase domain (FLT3-TKD). PTPN11 mutations were also found simultaneously in these three cases. Co-existing NRAS and TP53 mutations with high allele-frequency (32-50%) were also seen in two different cases. A targetable mutation of IDH2 was seen in one patient (11.1%) who had an FLT3 mutation with low allele-frequency (2%). In patients with NPM1-AML (see Figure), allele-frequency of mutated NPM1 ranged from 10 to 44%. Relatively common co-existing mutations were TET2 (7 of 17; 41.2%), DNMT3A (9 of 17; 52.9%), and FLT3 (9 of 17; 52.9%). Unlike in MLL-AML patients, all FLT3 alterations were internal tandem duplication (FLT-ITD) with one case of dual FLT3-ITD and -TKD mutation. IDH1 and IDH2 mutations were found in two (11.8%) and four (23.5%) separate cases, respectively. A rare fusion gene ETV6-NTRK3 (one of primary targets of NTRK inhibitors) was detected in one patient (5.9%) who had IDH1 mutation with moderate allele-frequency (17%).
Conclusion: MLL-rearrangements and NPM1-mutations were found in approximately a quarter of the 91 AML patient (mostly relapsed or refractory) bone marrow samples analyzed. These alterations appeared to be mutually exclusive. FLT3 alterations were seen in a third of the MLL-AML cases and half of the NPM1-AML cases, seemingly more frequent than that previously reported. Interestingly, FLT3-TKDs were dominant in MLL-AML cases, whereas NPM1-AML cases carried FLT3-ITD. IDH1 and IDH2 mutations commonly co-existed in both groups. This HM-SCREEN-Japan01 study is now recruiting patients, and a further understanding of genomic distribution and correlation is expected.
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Disclosures
Yamauchi: Otsuka:Research Funding;Astellas:Research Funding;Daiichi Sankyo:Research Funding;Chugai:Honoraria;Pfizer:Honoraria, Research Funding;Abbie:Research Funding;Solasia Pharma:Research Funding;Ono Pharmaceutical:Honoraria.Shibayama:AstraZeneca:Honoraria, Membership on an entity's Board of Directors or advisory committees;Sanofi:Honoraria;Pfizer:Honoraria;Fujimoto:Honoraria;Janssen:Honoraria, Research Funding;Teijin:Research Funding;Novartis:Honoraria, Research Funding;Takeda:Honoraria, Research Funding;Nippon Shinyaku:Honoraria, Research Funding;Daiichi Sankyo:Honoraria;Chugai:Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding;Sumitomo Dainippon:Honoraria, Research Funding;Merck Sharp & Dohme:Research Funding;Shionogi:Research Funding;Astellas:Research Funding;Taiho:Research Funding;Otsuka:Honoraria;Bristol-Myers Squibb:Honoraria;Celgene:Membership on an entity's Board of Directors or advisory committees, Research Funding;Eisai:Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding;AbbVie:Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding;Kyowa Kirin:Honoraria;Ono:Honoraria, Research Funding;Mundi Pharma:Honoraria.Yamamoto:Stemline Therapeutics:Consultancy;Meiji Seika Pharma:Consultancy, Honoraria;MSD:Consultancy, Honoraria, Research Funding;Chugai:Consultancy, Honoraria, Research Funding;Eisai:Consultancy, Honoraria, Research Funding;Daiichi Sankyo:Consultancy;IQIVA/HUYA:Honoraria;HUYA:Consultancy;IQIVA/Incyte:Research Funding;Mundipharma:Consultancy, Honoraria, Research Funding;Kyowa Kirin:Honoraria;Mochida:Honoraria;Gilead Sciences:Research Funding;Solasia Pharma:Research Funding;Nippon Shinyaku:Honoraria, Research Funding;Novartis:Honoraria, Research Funding;Ono:Consultancy, Honoraria, Research Funding;Aichi Cancer Center:Current Employment;AbbVie:Consultancy, Honoraria, Research Funding;Astra-Zeneca:Consultancy, Research Funding;Bayer:Research Funding;Bristol-Myers Squibb:Honoraria;Celgene:Consultancy, Honoraria, Research Funding;Zenyaku:Research Funding;Takeda:Consultancy, Honoraria, Research Funding;Yakult:Research Funding;SymBio:Research Funding;Pfizer:Honoraria;Otsuka:Consultancy, Honoraria, Research Funding;Sanofi:Honoraria;Sumitomo Dainippon:Honoraria;Janssen:Honoraria.Fujishima:Pfizer:Speakers Bureau.Takahashi:Pfizer Japan Inc.:Honoraria, Research Funding;Novartis Pharma KK:Honoraria, Research Funding;Bristol-Myers Squibb Company:Honoraria.Usuki:Alexion:Speakers Bureau;Pfizer:Research Funding;Nippon Boehringer Ingelheim:Research Funding;Mundipharma:Research Funding;Astellas-Amgen-Biopharma:Research Funding;Nippon shinyaku:Research Funding, Speakers Bureau;Eisai:Speakers Bureau;MSD:Speakers Bureau;Takeda:Speakers Bureau;PharmaEssentia:Speakers Bureau;Yakult:Speakers Bureau;Symbio:Research Funding, Speakers Bureau;Daiichi Sankyo:Research Funding, Speakers Bureau;Sumitomo Dainippon:Research Funding;Otsuka:Research Funding, Speakers Bureau;Novartis:Research Funding, Speakers Bureau;Brisol-Myers Squibb:Research Funding, Speakers Bureau;Kyowa Kirin:Research Funding, Speakers Bureau;Ono:Research Funding, Speakers Bureau;Janssen:Research Funding;Celgene:Research Funding, Speakers Bureau;Takeda:Research Funding;Astellas:Research Funding, Speakers Bureau;Abbvie:Research Funding;Gilead:Research Funding.Ono:Celgene:Honoraria, Research Funding;Kyowa Kirin Co., Ltd.:Honoraria, Research Funding;Chugai Pharmaceutical Co., Ltd.:Honoraria, Research Funding;Novartis Pharma KK:Honoraria;Mundipharma K.K.:Honoraria;TAIHO PHARMACEUTICAL CO., LTD.:Research Funding;Eisai Co., Ltd.:Honoraria;Otsuka Pharmaceutical Co., Ltd.:Honoraria;Astellas Pharma Inc.:Honoraria;Bristol-Myers Squibb Company:Honoraria;Pfizer Japan Inc.:Honoraria;Takeda Pharmaceutical Company Limited.:Honoraria;ONO PHARMACEUTICAL CO., LTD.:Honoraria, Research Funding;DAIICHI SANKYO COMPANY, LIMITED.:Honoraria;Janssen Pharmaceutical K.K:Honoraria.Kuroda:Daiichi Sankyo:Honoraria, Research Funding;Pfizer:Honoraria, Research Funding;Sysmex:Research Funding;Janssen Pharmaceutical K.K:Consultancy;Eisai:Honoraria, Research Funding;Sanofi:Consultancy, Honoraria, Research Funding;Kyowa Kirin:Honoraria, Research Funding;Otsuka Pharmaceutical:Honoraria, Research Funding;Ono Pharmaceutical:Honoraria, Research Funding;Abbvie:Consultancy, Honoraria;MSD:Research Funding;Celgene:Consultancy, Honoraria, Research Funding;Dainippon Sumitomo Pharma:Honoraria, Research Funding;Chugai Pharmaceutical:Honoraria, Research Funding;Takeda:Honoraria, Research Funding;Bristol-MyersSquibb:Consultancy, Honoraria, Research Funding;Astellas Pharma:Honoraria, Research Funding;Fujimoto Pharmaceutical:Honoraria, Research Funding;Taiho Pharmaceutical:Research Funding;Asahi Kasei:Research Funding;Shionogi:Research Funding;Nippon Shinyaku:Honoraria, Research Funding.Ishitsuka:Celgene:Other: Personal Fees;Kyowa Hakko Kirin:Other: Personal fees, Research Funding;BMS:Other: Personal fees;Chugai Pharmaceutical:Other: Personal fees, Research Funding;Takeda:Other: Personal fees, Research Funding;mundiharma:Other: Personal fees;Taiho Pharmaceuticals:Other: Personal fees, Research Funding;Janssen Pharmaceuticals:Other: Personal fees;Novartis:Other: Personal fees;Pfizer:Other: Personal fees;Astellas Pharma:Other, Research Funding;Genzyme:Other;Sumitomo Dainippon Pharma:Other, Research Funding;Eisai:Other, Research Funding;Mochida:Other, Research Funding;Shire:Other;Otsuka Pharmaceutical:Other;Ono Pharmaceutical:Other, Research Funding;Teijin Pharma:Research Funding;MSD:Research Funding;Asahi kasei:Research Funding;Eli Lilly:Research Funding;Daiichi Sankyo:Other;Huya Japan:Other.Minami:Bristol-Myers Squibb Company:Honoraria;Novartis Pharma KK:Honoraria;Pfizer Japan Inc.:Honoraria;Takeda:Honoraria.