Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia.
Li Jianfeng,Dai Yuting,Wu Liang,Zhang Ming,Ouyang Wen,Huang Jinyan,Chen Saijuan
Frontiers of medicine
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by genetic alterations with high heterogeneity. Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology. Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes, such as DUX4 rearrangements, MEF2D rearrangements, ZNF384/ZNF362 rearrangements, NUTM1 rearrangements, BCL2/MYC and/or BCL6 rearrangements, ETV6-RUNX1-like gene expression, PAX5alt (diverse PAX5 alterations, including rearrangements, intragenic amplifications, or mutations), and hotspot mutations PAX5 (p.Pro80Arg) with biallelic PAX5 alterations, IKZF1 (p.Asn159Tyr), and ZEB2 (p.His1038Arg). These molecular subtypes could be classified by gene expression patterns with RNA-seq technology. Refined molecular classification greatly improved the treatment strategy. Multiagent therapy regimens, including target inhibitors (e.g., imatinib), immunomodulators, monoclonal antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy, are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management. We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.
MEF2D-BCL9 Fusion Gene Is Associated With High-Risk Acute B-Cell Precursor Lymphoblastic Leukemia in Adolescents.
Suzuki Kyogo,Okuno Yusuke,Kawashima Nozomu,Muramatsu Hideki,Okuno Tatsuya,Wang Xinan,Kataoka Shinsuke,Sekiya Yuko,Hamada Motoharu,Murakami Norihiro,Kojima Daiei,Narita Kotaro,Narita Atsushi,Sakaguchi Hirotoshi,Sakaguchi Kimiyoshi,Yoshida Nao,Nishio Nobuhiro,Hama Asahito,Takahashi Yoshiyuki,Kudo Kazuko,Kato Koji,Kojima Seiji
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
PURPOSE:Acute lymphoblastic leukemia (ALL) makes up a significant proportion of all pediatric cancers, and relapsed ALL is a leading cause of cancer-associated deaths in children. Identification of risk factors and druggable molecular targets in ALL can lead to a better stratification of treatments and subsequent improvement in prognosis. PATIENTS AND METHODS:We enrolled 59 children with relapsed or primary refractory ALL who were treated in our institutions. We primarily performed RNA sequencing (RNA-seq) using patients' leukemic cells to comprehensively detect gene fusions and analyze gene expression profiles. On the basis of results obtained by RNA-seq, we performed genetic validation, functional analysis, and in vitro drug sensitivity testing using patients' samples and an exogenous expression model. RESULTS:We identified a total of 26 gene fusions in 22 patients by RNA-seq. Among these, 19 were nonrandom gene fusions already described in ALL, and four of the remaining seven involved identical combination of MEF2D and BCL9. All MEF2D-BCL9-positive patients had B-cell precursor immunophenotype and were characterized as being older in age, being resistant to chemotherapy, having very early relapse, and having leukemic blasts that mimic morphologically mature B-cell leukemia with markedly high expression of HDAC9. Exogenous expression of MEF2D-BCL9 in a B-cell precursor ALL cell line promoted cell growth, increased HDAC9 expression, and induced resistance to dexamethasone. Using a primary culture of leukemic blasts from a patient, we identified several molecular targeted drugs that conferred inhibitory effects in vitro. CONCLUSION:A novel MEF2D-BCL9 fusion we identified characterizes a novel subset of pediatric ALL, predicts poor prognosis, and may be a candidate for novel molecular targeting.
Clinical and molecular characteristics of fusion-positive B-cell precursor acute lymphoblastic leukemia in childhood, including a novel translocation resulting in gene fusion.
Ohki Kentaro,Kiyokawa Nobutaka,Saito Yuya,Hirabayashi Shinsuke,Nakabayashi Kazuhiko,Ichikawa Hitoshi,Momozawa Yukihide,Okamura Kohji,Yoshimi Ai,Ogata-Kawata Hiroko,Sakamoto Hiromi,Kato Motohiro,Fukushima Keitaro,Hasegawa Daisuke,Fukushima Hiroko,Imai Masako,Kajiwara Ryosuke,Koike Takashi,Komori Isao,Matsui Atsushi,Mori Makiko,Moriwaki Koichi,Noguchi Yasushi,Park Myoung-Ja,Ueda Takahiro,Yamamoto Shohei,Matsuda Koichi,Yoshida Teruhiko,Matsumoto Kenji,Hata Kenichiro,Kubo Michiaki,Matsubara Yoichi,Takahashi Hiroyuki,Fukushima Takashi,Hayashi Yasuhide,Koh Katsuyoshi,Manabe Atsushi,Ohara Akira,
Fusion genes involving have recently been identified in precursor B-cell acute lymphoblastic leukemia, mutually exclusive of the common risk stratifying genetic abnormalities, although their true incidence and associated clinical characteristics remain unknown. We identified 16 cases of acute lymphoblastic leukemia and 1 of lymphoma harboring fusions, including (n=10), (n=6), and one novel fusion. The incidence of fusions overall was 2.4% among consecutive precursor B-cell acute lymphoblastic leukemia patients enrolled onto a single clinical trial. They frequently showed a cytoplasmic μ chain-positive pre-B immunophenotype, and often expressed an aberrant CD5 antigen. Besides up- and down-regulation of and , elevated expression was also a characteristic feature of fusion-positive patients. Mutations of , recurrent in T-cell acute lymphoblastic leukemia, also showed an unexpectedly high frequency (50%) in these patients. fusion-positive patients were older (median age 9 years) with elevated WBC counts (median: 27,300/ml) at presentation and, as a result, were mostly classified as NCI high risk. Although they responded well to steroid treatment, fusion-positive patients showed a significantly worse outcome, with 53.3% relapse and subsequent death. Stem cell transplantation was ineffective as salvage therapy. Interestingly, relapse was frequently associated with the presence of gene deletions. Our observations indicate that fusions comprise a distinct subgroup of precursor B-cell acute lymphoblastic leukemia with a characteristic immunophenotype and gene expression signature, associated with distinct clinical features.
MEF2D-BCL9 B-Lymphoblastic Leukemia Blast Morphology Does Not Always Mimic Mature B-Cell Leukemia.
Baek Hee Jo,Choi Yoon Jung,Kim Bo Ram,Lee Jun Hyung,Shin Myung-Geun,Kook Hoon
Journal of pediatric hematology/oncology
MEF2D (myocyte enhancer factor 2D)-rearranged acute lymphoblastic leukemia (ALL) has recently been documented by transcriptome sequencing in B-cell precursor ALL. It is associated with older age of onset (median: 14 y), and characterized by very early relapse and poorer outcomes than other B-cell precursor ALL groups. According to report by Suzuki and colleagues, all 4 cases of MEF2D-BCL9-fusion ALL among 59 children with relapsed or primary refractory ALL had leukemic blasts morphologically mimicking mature B-cell leukemia cells. However, we display morphologically different blast populations in 2 patients with MEF2D-BCL9-rearranged ALL. Mature B-cell leukemia-like morphology would aid the detection of MEF2D-BCL9 fusion, but not all cases might have typical morphology.
Transcription factor MEF2D is required for the maintenance of MLL-rearranged acute myeloid leukemia.
Acute myeloid leukemia (AML) with MLL-rearrangement (MLL-r) comprises ∼10% of all AML cases and portends poor outcomes. Much remains uncovered on how MLL-r AML drives leukemia development while preventing cells from normal myeloid differentiation. Here, we identified that transcription factor MEF2D is a super-enhancer-associated, highly expressed gene in MLL-r AML. Knockout of MEF2D profoundly impaired leukemia growth, induced myeloid differentiation, and delayed oncogenic progression in vivo. Mechanistically, MEF2D loss led to robust activation of a CEBPE-centered myeloid differentiation program in AML cells. Chromatin profiling revealed that MEF2D binds to and suppresses the chromatin accessibility of CEBPE cis-regulatory regions. In human acute leukemia samples, MEF2D expression showed a strong negative correlation with the expression of CEBPE. Depletion of CEBPE partially rescued the cell growth defect and myeloid cell differentiation induced by the loss of MEF2D. Lastly, we show that MEF2D is positively regulated by HOXA9, and downregulation of MEF2D is an important mechanism for DOT1L inhibitor-induced antileukemia effects. Collectively, our findings suggest that MEF2D plays a critical role in human MLL-r AML and uncover the MEF2D-CEBPE axis as a crucial transcriptional mechanism regulating leukemia cell self-renewal and differentiation block.
Functional, structural, and molecular characterizations of the leukemogenic driver MEF2D-HNRNPUL1 fusion.
Recurrent MEF2D fusions with poor prognosis have been identified in B-cell precursor ALL (BCP-ALL). The molecular mechanisms underlying the pathogenic function of MEF2D fusions are poorly understood. Here, we show that MEF2D-HNRNPUL1 (MH) knock-in mice developed a progressive disease from impaired B-cell development at the pre-pro-B stage to pre-leukemia over 10 to 12 months. When cooperating with NRASG12D, MH drove an outbreak of BCP-ALL, with a more aggressive phenotype than the NRASG12D-induced leukemia. RNA-sequencing identified key networks involved in disease mechanisms. In chromatin immunoprecipitation-sequencing experiments, MH acquired increased chromatin-binding ability, mostly through MEF2D-responsive element (MRE) motifs in target genes, compared with wild-type MEF2D. Using X-ray crystallography, the MEF2D-MRE complex was characterized in atomic resolution, whereas disrupting the MH-DNA interaction alleviated the aberrant target gene expression and the B-cell differentiation arrest. The C-terminal moiety (HNRNPUL1 part) of MH was proven to contribute to the fusion protein's trans-regulatory activity, cofactor recruitment, and homodimerization. Furthermore, targeting MH-driven transactivation of the HDAC family by using the histone deacetylase inhibitor panobinostat in combination with chemotherapy improved the overall survival of MH/NRASG12D BCP-ALL mice. Altogether, these results not only highlight MH as an important driver in leukemogenesis but also provoke targeted intervention against BCP-ALL with MEF2D fusions.
Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia.
Gu Zhaohui,Churchman Michelle,Roberts Kathryn,Li Yongjin,Liu Yu,Harvey Richard C,McCastlain Kelly,Reshmi Shalini C,Payne-Turner Debbie,Iacobucci Ilaria,Shao Ying,Chen I-Ming,Valentine Marcus,Pei Deqing,Mungall Karen L,Mungall Andrew J,Ma Yussanne,Moore Richard,Marra Marco,Stonerock Eileen,Gastier-Foster Julie M,Devidas Meenakshi,Dai Yunfeng,Wood Brent,Borowitz Michael,Larsen Eric E,Maloney Kelly,Mattano Leonard A,Angiolillo Anne,Salzer Wanda L,Burke Michael J,Gianni Francesca,Spinelli Orietta,Radich Jerald P,Minden Mark D,Moorman Anthony V,Patel Bella,Fielding Adele K,Rowe Jacob M,Luger Selina M,Bhatia Ravi,Aldoss Ibrahim,Forman Stephen J,Kohlschmidt Jessica,Mrózek Krzysztof,Marcucci Guido,Bloomfield Clara D,Stock Wendy,Kornblau Steven,Kantarjian Hagop M,Konopleva Marina,Paietta Elisabeth,Willman Cheryl L,Loh Mignon L,Hunger Stephen P,Mullighan Charles G
Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between MEF2D (myocyte enhancer factor 2D) and five genes (BCL9, CSF1R, DAZAP1, HNRNPUL1 and SS18) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is MEF2D-BCL9. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with MEF2D rearrangements, which include an additional fusion partner, FOXJ2; thus, MEF2D-rearranged cases comprise 5.3% of cases lacking recurring alterations. MEF2D-rearranged ALL is characterized by a distinct immunophenotype, DNA copy number alterations at the rearrangement sites, older diagnosis age and poor outcome. The rearrangements result in enhanced MEF2D transcriptional activity, lymphoid transformation, activation of HDAC9 expression and sensitive to histone deacetylase inhibitor treatment. Thus, MEF2D-rearranged ALL represents a distinct form of high-risk leukaemia, for which new therapeutic approaches should be considered.