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Kusano S, Ueno-Yokohata H, Hori M, Ishibashi T, Fujimura J, Shimizu T, Ohki K, Kiyokawa N. TCF3::ZNF384 induces steroid resistance in B-cell precursor acute lymphoblastic leukemia cells. Pediatr Int 2025; 67:e70078. [PMID: 40391410 DOI: 10.1111/ped.70078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 12/26/2024] [Accepted: 02/25/2025] [Indexed: 05/21/2025]
Abstract
BACKGROUND ZNF384 rearrangements (ZNF384-r) are associated with distinct subgroups of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and the mixed phenotype of acute leukemia. Types of BCP-ALL with ZNF384-r exhibit common immunophenotypic characteristics, whereas their clinical features are not uniform and TCF3::ZNF384-positive patients show a significantly poorer steroid response and higher frequency of relapse, while EP300::ZNF384-positive patients exhibit a favorable response to conventional chemotherapy. Therefore, we aimed to investigate the differences in biological effects between these two ZNF384-r molecules. METHOD We transduced BCP-ALL cell lines with both TCF3::ZNF384 and EP300::ZNF384 by retrovirus-mediated gene transduction, and examined the biological effects. RESULTS Flow cytometric analysis and RT-qPCR revealed down-regulation of CD10 in BCP-ALL cells after transduction with both TCF3::ZNF384 and EP300::ZNF384. The annexin-V binding apoptosis assay indicated that TCF3::ZNF384-, but not EP300::ZNF384-, expressing cells exhibited increased resistance to dexamethasone-induced apoptosis. By means of an oligonucleotide microarray and RT-qPCR, we observed that the transduction of TCF3::ZNF384, but not EP300::ZNF384, leads to significant enhancement of cyclin D2 (CCND2) gene expression in BCP-ALL cells, but no growth advantage was observed. CONCLUSION Our data suggest that the acquisition of dexamethasone resistance in BCP-ALL cell lines is an effect of TCF3::ZNF384 protein distinct from EP300::ZNF384. Other than the common functions of ZNF384-r that contribute to the development of leukemia with a lineage-ambiguous phenotype, TCF3::ZNF384 may exhibit a fusion partner-dependent function distinct from EP300::ZNF384 and participate in the formation of characteristic clinical features of TCF3::ZNF384-expressing ALL patients.
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Affiliation(s)
- Shinpei Kusano
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Hitomi Ueno-Yokohata
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
| | - Momoka Hori
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | - Takeshi Ishibashi
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Junya Fujimura
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
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Wang X, Deng D, Yan Y, Cai M, Liu X, Luo A, Liu S, Zhang X, Jiang H, Liu X. Genetic variants in m5C modification core genes are associated with the risk of Chinese pediatric acute lymphoblastic leukemia: A five-center case-control study. Front Oncol 2023; 12:1082525. [PMID: 36698387 PMCID: PMC9868168 DOI: 10.3389/fonc.2022.1082525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Objective To explore the functions of the polymorphisms in 5-methylcytosine (m5C) modification-related coding genes on the susceptibility of pediatric acute lymphoblastic leukemia (ALL). Methods Case-control study and multinomial logistic regression analysis were performed to construct models to evaluate the susceptibility of pediatric ALL. The relationship between five functional SNPs in m5C modification-coding genes and pediatric ALL risk was analyzed. Genotyping of 808 cases and 1,340 healthy samples from South China was identified using a TaqMan assay; odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the relationship between the five selected SNPs and pediatric ALL susceptibility. Results Among the five analyzed SNPs, NOL1 rs3764909 and NSUN4 rs10252 variants significantly increased the susceptibility of pediatric ALL, while NSUN3 rs7653521, NSUN5 rs1880948, and NSUN6 rs3740102 variants were not associated with the risk of ALL. Stratification analyses demonstrated that NOL1 rs3764909 C>A exhibited a significant association with increased pediatric ALL risk in subgroups of common B ALL, pre-B ALL, T-cell ALL, low and middle risk, other gene fusion types, non-gene fusion, hypodiploid, normal diploid, primitive lymphocytes in marrow < 5% on week 12, and minimal residual disease (MRD) <0.01% on week 12 after induced therapy; NSUN4 rs10252 G>A was related to increased risk of ALL children in subgroups of age ≥ 120 months, normal white blood cell (WBC) number, middle risk, non-gene fusion, MRD ≥ 0.01 on days 15-19, and primitive lymphocytes in marrow < 5% on day 33 after induced therapy. Compared with the reference haplotype CAGTA, children who harbored haplotypes CCGTG and ACATA were remarkably related to increased ALL susceptibility. rs3764909 and rs10252 varieties of alleles were not associated with MRD levels after the selected chemotherapeutics. Conclusions In conclusion, NOL1 rs3764909 and NSUN4 rs10252 variants were enhanced by pediatric ALL risk and were suggested to be potential biomarkers for pediatric ALL.
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Affiliation(s)
- Xueliang Wang
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Decheng Deng
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Yaping Yan
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Mansi Cai
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaodan Liu
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Ailing Luo
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Shanshan Liu
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaohong Zhang
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Hua Jiang
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaoping Liu
- Department of Hematology/Oncology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
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Wang Z, Zhang C, Warden CD, Liu Z, Yuan YC, Guo C, Wang C, Wang J, Wu X, Ermel R, Vonderfecht SL, Wang X, Brown C, Forman S, Yang Y, James You M, Chen W. Loss of SIRT1 inhibits hematopoietic stem cell aging and age-dependent mixed phenotype acute leukemia. Commun Biol 2022; 5:396. [PMID: 35484199 PMCID: PMC9051098 DOI: 10.1038/s42003-022-03340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 04/05/2022] [Indexed: 01/07/2023] Open
Abstract
Aging of hematopoietic stem cells (HSCs) is linked to various blood disorders and malignancies. SIRT1 has been implicated in healthy aging, but its role in HSC aging is poorly understood. Surprisingly, we found that Sirt1 knockout improved the maintenance of quiescence of aging HSCs and their functionality as well as mouse survival in serial bone marrow transplantation (BMT) recipients. The majority of secondary and tertiary BMT recipients of aging wild type donor cells developed B/myeloid mixed phenotype acute leukemia (MPAL), which was markedly inhibited by Sirt1 knockout. SIRT1 inhibition also reduced the growth and survival of human B/myeloid MPAL cells. Sirt1 knockout suppressed global gene activation in old HSCs, prominently the genes regulating protein synthesis and oxidative metabolism, which may involve multiple downstream transcriptional factors. Our results demonstrate an unexpected role of SIRT1 in promoting HSC aging and age-dependent MPAL and suggest SIRT1 may be a new therapeutic target for modulating functions of aging HSCs and treatment of MPAL.
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Affiliation(s)
- Zhiqiang Wang
- grid.410425.60000 0004 0421 8357Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA ,grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Chunxiao Zhang
- grid.410425.60000 0004 0421 8357Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Charles David Warden
- grid.410425.60000 0004 0421 8357Integrative Genomics Core, Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Zheng Liu
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Yate-Ching Yuan
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Chao Guo
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Charles Wang
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA ,grid.43582.380000 0000 9852 649XPresent Address: Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350 USA
| | - Jinhui Wang
- grid.410425.60000 0004 0421 8357Integrative Genomics Core, Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Xiwei Wu
- grid.410425.60000 0004 0421 8357Integrative Genomics Core, Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Richard Ermel
- grid.410425.60000 0004 0421 8357Center for Comparative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | | | - Xiuli Wang
- grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Christine Brown
- grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Stephen Forman
- grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Yaling Yang
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - M. James You
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - WenYong Chen
- grid.410425.60000 0004 0421 8357Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
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Yan Z, Zhou Y, Yang Y, Zeng C, Li P, Tian H, Tang X, Zhang G. Zinc finger protein 384 enhances colorectal cancer metastasis by upregulating MMP2. Oncol Rep 2022; 47:49. [PMID: 35029289 PMCID: PMC8771166 DOI: 10.3892/or.2022.8260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022] Open
Abstract
Zinc finger proteins (ZNFs) serve key roles in tumor formation and progression; however, the functions and underlying mechanisms of dysregulated ZNF384 in colorectal cancer (CRC) are yet to be fully elucidated. Therefore, the present study initially aimed to investigate the expression levels of ZNF384 in CRC samples. Moreover, lentiviral ZNF384 overexpression and ZNF384 knockdown models were established in CRC cells. Transwell, wound healing and in vivo tail vein metastasis assays were carried out to evaluate the effects of ZNF384 on CRC cell metastasis. Furthermore, reverse transcription-quantitative PCR, western blotting, serial deletion, site-directed mutagenesis, dual-luciferase reporter and chromatin immunoprecipitation assays were conducted to investigate the potential underlying mechanisms. The results of the present study demonstrated that ZNF384 expression was markedly increased in CRC samples and this was associated with a poor prognosis. Notably, ZNF384 overexpression increased the levels of CRC cell invasion and migration, whereas ZNF384 knockdown inhibited CRC development. Moreover, the results of the present study demonstrated that ZNF384 mediated the expression of MMP2. MMP2 knockdown inhibited ZNF384-mediated CRC cell invasion and migration, whereas MMP2 overexpression ameliorated ZNF384 knockdown-induced inhibition of CRC progression. In addition, the results of the present study demonstrated that hypoxia-inducible factor 1α (HIF-1α) had the ability to bind to the ZNF384 promoter, thereby initiating ZNF384 expression. In human-derived CRC samples, the expression levels of ZNF384 were positively correlated with both MMP2 and HIF-1α expression. Collectively, these findings highlighted that ZNF384 may act as a prognostic marker and regulator of CRC metastasis.
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Affiliation(s)
- Zaihua Yan
- Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Yu Zhou
- Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Yang Yang
- Department of Dermatology, Xining First People's Hospital, Xining, Qinghai 810000, P.R. China
| | - Chongpu Zeng
- Department of General Surgery, Wangcang County People's Hospital, Guangyuan, Sichuan 628200, P.R. China
| | - Peidong Li
- Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Hongpeng Tian
- Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Xuegui Tang
- Anorectal Department of Integrated Traditional Chinese and Western Medicine, The Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
| | - Guangjun Zhang
- Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P.R. China
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Montefiori LE, Mullighan CG. Redefining the biological basis of lineage-ambiguous leukemia through genomics: BCL11B deregulation in acute leukemias of ambiguous lineage. Best Pract Res Clin Haematol 2021; 34:101329. [PMID: 34865701 DOI: 10.1016/j.beha.2021.101329] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Acute leukemias of ambiguous lineage (ALAL), including mixed phenotype acute leukemia (MPAL) and related entities such as early T-cell precursor acute leukemia (ETP-ALL), remain diagnostic and clinical challenges due to limited understanding of pathogenesis, reliance of immunophenotyping to classify disease, and the lack of a rational approach to guide selection of appropriate therapy. Recent studies utilizing genomic sequencing and complementary approaches have provided key insights that are changing the way in which such leukemias are classified, and potentially, treated. Several recurrent genomic alterations define leukemias that straddle immunophenotypic entities, such as ZNF384-rearranged childhood B-ALL and B/myeloid MPAL, and BCL11B-rearranged T/myeloid MPAL, ETP-ALL and AML. In contrast, some cases of MPAL represent canonical ALL/AML entities exhibiting lineage aberrancy. For many cases of ALAL, experimental approaches indicate lineage aberrancy arises from acquisition of a founding genetic alteration into a hematopoietic stem or progenitor cell. Determination of optimal therapeutic approach requires genomic characterization of uniformly treated ALAL patients in prospective studies, but several approaches, including kinase inhibitors and BH3 mimetics may be efficacious in subsets of ALAL.
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Affiliation(s)
- Lindsey E Montefiori
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Lin N, Yan X, Cai D, Wang L. Leukemia With TCF3-ZNF384 Rearrangement as a Distinct Subtype of Disease With Distinct Treatments: Perspectives From A Case Report and Literature Review. Front Oncol 2021; 11:709036. [PMID: 34395283 PMCID: PMC8357369 DOI: 10.3389/fonc.2021.709036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background ZNF384 rearrangements are found in 5-10% of B-cell acute lymphoblastic leukemia (B-ALL) and 48% of B cell/myeloid mixed phenotype acute leukemia (B/M MPAL). ZNF384-rearranged B-ALL is prone to lineage conversion after chemotherapy. TCF3 is the second most common rearrangement partner of ZNF384 in B-ALL (27.5%) and the most common partner in B/M MPAL (53.3%). TCF3-ZNF384 fusion is related to a poor steroid response and a high frequency of relapse. It is mostly reported in children and adolescents but rarely seen in adults. Patients and Methods Here, we report a rare case of adult common B-ALL with TCF3-ZNF384 fusion in which the patient relapsed after one cycle of consolidation chemotherapy. Relapsed leukemia cells from the bone marrow were cultured for 72 hours ex vivo, and a panel of 156 kinds of cytotoxic drugs, targeted therapy drugs, combination chemotherapy drugs, etc., was used for sensitivity screening. The literature on TCF3-ZNF384 fusion was reviewed, and reported cases with TCF3-ZNF384 fusion were summarized. Clinical characteristics were compared between B-ALL and MPAL with TCF3-ZNF384 fusion. Results The relapsed lymphoblasts showed moderate sensitivity to both acute myelocytic leukemia (AML) - and acute lymphoblastic leukemia (ALL)-directed combination chemotherapy schemes, as well as to multiple targeted therapeutic drugs. The hyper-CVAD (B) scheme showed synergistic effects with multiple targeted compounds and had the highest sensitivity. The patient chose the hyper-CVAD (B) scheme combined with sorafenib and achieved complete remission (CR), then consolidated with myeloid-directed homoharringtonine+cytarabine+daunorubicin (HAD) scheme and gained molecular CR. By reviewing the literature, we found that both the genomic landscapes and gene expression profiles of ZNF384-rearranged B-ALL and MPAL are similar and that both diseases have lineage plasticity. The gene expression profile in TCF3-ZNF384-positive patients shows enrichment of hematopoietic stem cell features. No significant differences in clinical characteristics were found between TCF3-ZNF384-positive ALL and MPAL. Conclusion TCF3-ZNF384-positive leukemia may be a distinct subtype of leukemia regardless of immunophenotype. Considering the frequent lineage switches and sensitivity to both ALL- and AML-directed schemes, a uniform strategy directed at both lymphoid and myeloid lineages or at hematopoietic stem cells may be better for TCF3-ZNF384-positive leukemia. Small molecule targeted therapies may be promising treatment options and deserve further investigation.
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Affiliation(s)
- Na Lin
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaojing Yan
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Dali Cai
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Lei Wang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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Qin YZ, Jiang Q, Xu LP, Wang Y, Jiang H, Dao FT, Chen WM, Zhao XS, Liu YR, Zhang XH, Liu KY, Huang XJ. The Prognostic Significance of ZNF384 Fusions in Adult Ph-Negative B-Cell Precursor Acute Lymphoblastic Leukemia: A Comprehensive Cohort Study From a Single Chinese Center. Front Oncol 2021; 11:632532. [PMID: 33816270 PMCID: PMC8010301 DOI: 10.3389/fonc.2021.632532] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/21/2021] [Indexed: 11/23/2022] Open
Abstract
Novel recurrent fusion gene types such as zinc finger protein 384 (ZNF384) fusions have been identified in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with the application of next-generation sequencing technologies. However, the comprehensive large-scale clinical cohort study for clarifying their prognostic significance remains scarce to date. A total of 242 consecutive adult Ph-negative BCP-ALL patients treated in our institute were retrospectively screened ZNF384 fusions at diagnosis by multiplex real time quantitative PCR. ZNF384 fusions were identified in 47 patients (19.4%) and all belonged to B-other ALL (having no high hyperdiploid karyotype, BCR-ABL1, TCF3-PBX1, ETV6-RUNX1, or MLL rearrangement). In the whole cohort, patients with ZNF384 fusions had significantly higher 3-year relapse-free-survival (RFS) and tended to have a higher 3-year overall survival (OS) than those with no ZNF384 fusions (80.1% vs. 52.5%, P = 0.013; 67.6% vs. 54.0%, P = 0.10). For patients receiving chemotherapy alone and received allogeneic-hematologic stem cell transplantation (allo-HSCT) were censored at the time of transplantation, patients with ZNF384 fusions had both similar RFS and similar OS to B-other ALL patients with no ZNF384 fusions (RFS: P =0.94 and 0.30; OS: P =0.94 and 0.51). For patients receiving transplantation, those with ZNF384 fusions had significantly higher 3-year RFS than B-other ALL patients with no ZNF384 fusions and their OS were similar (P = 0.022 and 0.24). Only two of 31 patients with ZNF384 fusions and receiving allo-HSCT relapsed, individually occurred 66.8 and 69.8 months after transplantation. Therefore, ZNF384 fusion is common in adult BCP-ALL, which may define a new group from BCP-ALL containing no classical fusion transcript with better prognosis through receiving allo-HSCT.
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Affiliation(s)
- Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Qian Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Lan-Ping Xu
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Yu Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Hao Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Feng-Ting Dao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Xiao-Su Zhao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Yan-Rong Liu
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Xiao-Hui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Kai-Yan Liu
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
| | - Xiao-Jun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, National Clinical Research Center for Hematologic Disease, Beijing, China
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Gao YY, Ling ZY, Zhu YR, Shi C, Wang Y, Zhang XY, Zhang ZQ, Jiang Q, Chen MB, Yang S, Cao C. The histone acetyltransferase HBO1 functions as a novel oncogenic gene in osteosarcoma. Am J Cancer Res 2021; 11:4599-4615. [PMID: 33754016 PMCID: PMC7978299 DOI: 10.7150/thno.55655] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/06/2021] [Indexed: 02/06/2023] Open
Abstract
HBO1 (KAT7 or MYST2) is a histone acetyltransferase that acetylates H3 and H4 histones. Methods: HBO1 expression was tested in human OS tissues and cells. Genetic strategies, including shRNA, CRISPR/Cas9 and overexpression constructs, were applied to exogenously alter HBO1 expression in OS cells. The HBO1 inhibitor WM-3835 was utilized to block HBO1 activation. Results:HBO1 mRNA and protein expression is significantly elevated in OS tissues and cells. In established (MG63/U2OS lines) and primary human OS cells, shRNA-mediated HBO1 silencing and CRISPR/Cas9-induced HBO1 knockout were able to potently inhibit cell viability, growth, proliferation, as well as cell migration and invasion. Significant increase of apoptosis was detected in HBO1-silenced/knockout OS cells. Conversely, ectopic HBO1 overexpression promoted OS cell proliferation and migration. We identified ZNF384 (zinc finger protein 384) as a potential transcription factor of HBO1. Increased binding between ZNF384 and HBO1 promoter was detected in OS cell and tissues, whereas ZNF384 silencing via shRNA downregulated HBO1 and produced significant anti-OS cell activity. In vivo, intratumoral injection of HBO1 shRNA lentivirus silenced HBO1 and inhibited OS xenograft growth in mice. Furthermore, growth of HBO1-knockout OS xenografts was significantly slower than the control xenografts. WM-3835, a novel and high-specific small molecule HBO1 inhibitor, was able to potently suppressed OS cell proliferation and migration, and led to apoptosis activation. Furthermore, intraperitoneal injection of a single dose of WM-3835 potently inhibited OS xenograft growth in SCID mice. Conclusion: HBO1 overexpression promotes OS cell growth in vitro and in vivo.
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10
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Detection of EP300-ZNF384 fusion in patients with acute lymphoblastic leukemia using RNA fusion gene panel sequencing. Ann Hematol 2020; 99:2611-2617. [PMID: 32980888 PMCID: PMC7536166 DOI: 10.1007/s00277-020-04251-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
EP300-ZNF384 fusion is a rare recurrent cytogenetic abnormality associated with B cell acute lymphoblastic leukemia (B-ALL), which was rarely studied in Chinese patient cohort. Here, we used a customized RNA fusion gene panel to investigate gene fusions in 56 selected acute leukemia patients without conventional genetic abnormalities. Two EP300-ZNF384 fusion forms were detected in ten cases, which were in-frame fusions of EP300 exon 6 fused with exon 3 or 2 of ZNF384. The fusions led to the lack of most functional domains of EP300. We firstly reported EP300-ZNF384 fusion in a mixed-phenotype acute leukemia (MPAL) patient whose CD33 and CD13 were negative. The rest nine B-ALL patients with EP300-ZNF384 fusion expressed CD33 and/or CD13. Fifty-six percent of B-ALL patients (5/9) with EP300-ZNF384 fusion were positive with CD10. After the diagnosis of EP300-ZNF384 fusion, 70% of the patients achieved remission after chemotherapy. Our observations indicated that EP300-ZNF384 fusion consists of a distinct subgroup of B-ALL with a characteristic immunophenotype. These patients are sensitive to current chemotherapy regimen and have an excellent outcome.
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11
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Russell-Hallinan A, Watson CJ, O'Dwyer D, Grieve DJ, O'Neill KM. Epigenetic Regulation of Endothelial Cell Function by Nucleic Acid Methylation in Cardiac Homeostasis and Disease. Cardiovasc Drugs Ther 2020; 35:1025-1044. [PMID: 32748033 PMCID: PMC8452583 DOI: 10.1007/s10557-020-07019-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pathological remodelling of the myocardium, including inflammation, fibrosis and hypertrophy, in response to acute or chronic injury is central in the development and progression of heart failure (HF). While both resident and infiltrating cardiac cells are implicated in these pathophysiological processes, recent evidence has suggested that endothelial cells (ECs) may be the principal cell type responsible for orchestrating pathological changes in the failing heart. Epigenetic modification of nucleic acids, including DNA, and more recently RNA, by methylation is essential for physiological development due to their critical regulation of cellular gene expression. As accumulating evidence has highlighted altered patterns of DNA and RNA methylation in HF at both the global and individual gene levels, much effort has been directed towards defining the precise role of such cell-specific epigenetic changes in the context of HF. Considering the increasingly apparent crucial role that ECs play in cardiac homeostasis and disease, this article will specifically focus on nucleic acid methylation (both DNA and RNA) in the failing heart, emphasising the key influence of these epigenetic mechanisms in governing EC function. This review summarises current understanding of DNA and RNA methylation alterations in HF, along with their specific role in regulating EC function in response to stress (e.g. hyperglycaemia, hypoxia). Improved appreciation of this important research area will aid in further implicating dysfunctional ECs in HF pathogenesis, whilst informing development of EC-targeted strategies and advancing potential translation of epigenetic-based therapies for specific targeting of pathological cardiac remodelling in HF.
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Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Denis O'Dwyer
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - David J Grieve
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Karla M O'Neill
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.
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12
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Rowsey RA, Smoley SA, Williamson CM, Vasmatzis G, Smadbeck JB, Ning Y, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Characterization of TCF3 rearrangements in pediatric B-lymphoblastic leukemia/lymphoma by mate-pair sequencing (MPseq) identifies complex genomic rearrangements and a novel TCF3/TEF gene fusion. Blood Cancer J 2019; 9:81. [PMID: 31575852 PMCID: PMC6773761 DOI: 10.1038/s41408-019-0239-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022] Open
Abstract
The TCF3/PBX1 gene fusion is a recurrent genetic abnormality in pediatric B-lymphoblastic leukemia/lymphoma (B-ALL/LBL). While dual-color, dual-fusion fluorescence in situ hybridization (D-FISH) probes can detect TCF3/PBX1 fusions, further characterization of atypical TCF3 FISH patterns as indicated by additional or diminished TCF3 signals is currently limited. Herein we describe the use of a next-generation sequencing assay, mate-pair sequencing (MPseq), to characterize typical and cryptic TCF3/PBX1 fusions and to identify TCF3 translocation partners based on results obtained from our laboratory-developed TCF3/PBX1 D-FISH probe set. MPseq was performed on 21 cases of pediatric B-ALL/LBL with either TCF3/PBX1 fusion, or no TCF3/PBX1 fusion but with additional or diminished TCF3 signals obtained by our PBX1/TCF3 D-FISH probe set. In addition, MPseq was performed on one pediatric B-ALL/LBL case with an apparently normal karyotype and abnormal TCF3 break-apart probe results. Of 22 specimens successfully evaluated by MPseq, 13 cases (59%) demonstrated TCF3/PBX1 fusion, including three cases with previously undescribed insertional rearrangements. The remaining nine cases (41%) harbored various TCF3 partners, including six cases with TCF3/ZNF384, and one case each with TCF3/HLF, TCF3/FLI1 and TCF3/TEF. Our results illustrate the power of MPseq to characterize TCF3 rearrangements with increased precision and accuracy over traditional cytogenetic methodologies.
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Affiliation(s)
- Ross A Rowsey
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Cynthia M Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Mayo Clinic, Rochester, MN, USA
| | - Yi Ning
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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13
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Yamamoto H, Hayakawa F, Yasuda T, Odaira K, Minamikawa Y, Tange N, Hirano D, Kojima Y, Morishita T, Tsuzuki S, Naoe T, Kiyoi H. ZNF384-fusion proteins have high affinity for the transcriptional coactivator EP300 and aberrant transcriptional activities. FEBS Lett 2019; 593:2151-2161. [PMID: 31234226 DOI: 10.1002/1873-3468.13506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/07/2022]
Abstract
Zinc-finger protein 384 (ZNF384) fusion (Z-fusion) genes have recently been identified as recurrent fusion genes in B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) and have been detected in 7-17% of Philadelphia chromosome-negative BCP-ALL cases. We selected SALL4 and ID2 as potential Z-fusion-specific transcriptional targets that might lead to the differentiation disorder of Z-fusion-positive ALL. The introduction of EP300-ZNF384 and SYNRG-ZNF384 induced the expression of these genes. Z-fusion proteins exhibited stronger transcriptional activities on the promoter or enhancer region of these genes than Wild-Z. Furthermore, GST pull-down assay revealed that Z-fusion proteins associated more strongly with EP300 than Wild-Z. Coexpression of EP300 specifically enhanced the transcriptional activities of Z-fusion proteins. We propose the increased EP300 binding of Z-fusion proteins as a mechanism for their increased transcriptional activities.
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Affiliation(s)
- Hideyuki Yamamoto
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Fumihiko Hayakawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan.,Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Japan
| | - Takahiko Yasuda
- Clinical Research Center, Nagoya Medical Center, National Hospital Organization, Nagoya, Japan
| | - Koya Odaira
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Japan
| | - Yuka Minamikawa
- Department of Analytical Neurobiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Naoyuki Tange
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Daiki Hirano
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Yuki Kojima
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Takanobu Morishita
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
| | - Shinobu Tsuzuki
- Department of Biochemistry, School of Medicine, Aichi Medical University, Japan
| | - Tomoki Naoe
- Nagoya Medical Center, National Hospital Organization, Nagoya, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Japan
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14
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Overexpression of zinc finger protein 384 (ZNF 384), a poor prognostic predictor, promotes cell growth by upregulating the expression of Cyclin D1 in Hepatocellular carcinoma. Cell Death Dis 2019; 10:444. [PMID: 31168049 PMCID: PMC6551341 DOI: 10.1038/s41419-019-1681-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous, multigene-driven malignant tumor. ZNF384 is an overexpressed gene with a high frequency of alteration in HCC, but research on the function of ZNF384 in HCC is lacking. In this study, the expression level of ZNF384 in HCC was analyzed through immunohistochemical (IHC) staining, Western blot analysis and qRT-PCR. We also generated ZNF384 knockdown and knockout HCC cell lines using short hairpin RNA (shRNA) and CRISPR/Cas9 systems. MTS, colony formation, and 5-ethynyl-20-deoxyuridine (EdU) assays; flow cytometry; and a xenograft mouse model were used to evaluate the effects of ZNF384 on cell proliferation. Western blot analysis, a dual luciferase reporter assay and a ChIP assay were performed to explore the potential mechanism. We found that overexpression of ZNF384 in HCC and elevated expression of ZNF384 in HCC tissues was significantly correlated with tumor recurrence (P = 0.0097). Kaplan-Meier survival analysis revealed that high expression levels of ZNF384 were correlated with poor overall survival (P = 0.0386). Downregulation of ZNF384 expression suppressed HCC cell proliferation by inhibiting the expression of Cyclin D1. These findings suggest that ZNF384 tends to act as an oncogene in the development of HCC. ZNF384 promotes the proliferation of HCC cells by directly upregulating the expression of Cyclin D1 and might serve as a prognostic predictive factor for HCC patients.
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15
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Advances in B-cell Precursor Acute Lymphoblastic Leukemia Genomics. Hemasphere 2018; 2:e53. [PMID: 31723781 PMCID: PMC6746003 DOI: 10.1097/hs9.0000000000000053] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/13/2018] [Accepted: 04/20/2018] [Indexed: 01/07/2023] Open
Abstract
In childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), cytogenetic abnormalities remain important diagnostic and prognostic tools. A number of well-established abnormalities are routinely used in risk stratification for treatment. These include high hyperdiploidy and ETV6-RUNX1 fusion, classified as good risk, while Philadelphia chromosome (Ph) positive ALL and rearrangements of the KMT2A (MLL) gene define poor risk. A poor risk subgroup of intrachromosomal amplification of chromosome 21 (iAMP21-ALL) has been described, in which intensification of therapy has greatly improved outcome. Until recently, no consistent molecular features were defined in around 30% of BCP-ALL (known as B-other-ALL). Recent studies are classifying them into distinct subgroups, some with clear potential for novel therapeutic approaches. For example, in 1 poor risk subtype, known as Ph-like/BCR-ABL1-like ALL, approximately 10% have rearrangements of ABL-class tyrosine kinases: including ABL1, ABL2, PDGFRB, PDGFRA, and CSF1R. Notably, they show a poor response to standard chemotherapy, while they respond to treatment with tyrosine kinase inhibitors, such as imatinib. In other Ph-like-ALL patients, deregulation of the cytokine receptor, CRLF2, and JAK2 rearrangements lead to activation of the JAK-STAT signaling pathway, implicating a specific role for JAK inhibitors in their treatment. Other novel subgroups within B-other-ALL are defined by the IGH-DUX4 translocation, related to deletions of the ERG gene and a good outcome, while fusions involving ZNF384, MEF2D, and intragenic PAX5 amplification (PAX5AMP) are linked to a poor outcome. Continued genetic screening will eventually lead to complete genomic classification of BCP-ALL and define more molecular targets for less toxic therapies.
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16
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RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun 2018; 9:1163. [PMID: 29563491 PMCID: PMC5862959 DOI: 10.1038/s41467-018-03513-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 01/26/2018] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
The roles of RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) in lineage-associated chromatin organization and drug response/resistance are unclear. Here we demonstrate that the RCMTs, namely NSUN3 and DNMT2, directly bind hnRNPK, a conserved RNA-binding protein. hnRNPK interacts with the lineage-determining transcription factors (TFs), GATA1 and SPI1/PU.1, and with CDK9/P-TEFb to recruit RNA-polymerase-II at nascent RNA, leading to formation of 5-Azacitidine (5-AZA)-sensitive chromatin structure. In contrast, NSUN1 binds BRD4 and RNA-polymerase-II to form an active chromatin structure that is insensitive to 5-AZA, but hypersensitive to the BRD4 inhibitor JQ1 and to the downregulation of NSUN1 by siRNAs. Both 5-AZA-resistant leukaemia cell lines and clinically 5-AZA-resistant myelodysplastic syndrome and acute myeloid leukaemia specimens have a significant increase in RNA:m5C and NSUN1-/BRD4-associated active chromatin. This study reveals novel RNA:m5C/RCMT-mediated chromatin structures that modulate 5-AZA response/resistance in leukaemia cells, and hence provides a new insight into treatment of leukaemia. Resistance to chemotherapy is a serious issue that can be influenced by RNA epigenetics and chromatin structure. Here, the authors show in leukaemia cells that RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) mediate chromatin structures that can modulate 5-Azacitidine response and resistance.
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17
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New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia. Blood 2017; 130:1395-1401. [PMID: 28778863 DOI: 10.1182/blood-2017-05-742643] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/27/2017] [Indexed: 12/22/2022] Open
Abstract
Until recently, 20% to 30% of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) could not be classified into any of the established molecular subtypes. Recent molecular studies of such cases have, however, further clarified their mutational spectrum and identified new oncogenic subtypes consisting of cases with DUX4 rearrangements, ETV6-RUNX1-like gene expression, MEF2D rearrangements, and ZNF384 rearrangements. In this review, we describe these new subtypes, which account for up to 50% of previously unclassified pediatric BCP-ALL cases.
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18
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Yaguchi A, Ishibashi T, Terada K, Ueno-Yokohata H, Saito Y, Fujimura J, Shimizu T, Ohki K, Manabe A, Kiyokawa N. EP300-ZNF384 fusion gene product up-regulates GATA3 gene expression and induces hematopoietic stem cell gene expression signature in B-cell precursor acute lymphoblastic leukemia cells. Int J Hematol 2017; 106:269-281. [PMID: 28378055 DOI: 10.1007/s12185-017-2220-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 01/08/2023]
Abstract
ZNF384-related fusion genes are associated with a distinct subgroup of B-cell precursor acute lymphoblastic leukemias in childhood, with a frequency of approximately 3-4%. We previously identified a novel EP300-ZNF384 fusion gene. Patients with the ZNF384-related fusion gene exhibit a hematopoietic stem cell (HSC) gene expression signature and characteristic immunophenotype with negative or low expression of CD10 and aberrant expression of myeloid antigens, such as CD33 and CD13. However, the molecular basis of this pathogenesis remains completely unknown. In the present study, we examined the biological effects of EP300-ZNF384 expression induced by retrovirus-mediated gene transduction in an REH B-cell precursor acute lymphoblastic leukemia cell line, and observed the acquisition of the HSC gene expression signature and an up-regulation of GATA3 gene expression, as assessed by microarray analysis. In contrast, the gene expression profile induced by wild-type ZNF384 in REH cells was significantly different from that by EP300-ZNF384 expression. Together with the results of reporter assays, which revealed the enhancement of GATA3-promoter activity by EP300-ZNF384 expression, these findings suggest that EP300-ZNF384 mediates GATA3 gene expression and may be involved in the acquisition of the HSC gene expression signature and characteristic immunophenotype in B-cell precursor acute lymphoblastic leukemia cells.
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Affiliation(s)
- Akinori Yaguchi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takeshi Ishibashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kazuki Terada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Hitomi Ueno-Yokohata
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Junya Fujimura
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, 9-1 Akashi-cho, Chuo-ku, Tokyo, 104-8560, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
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19
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Abstract
Both B-cell and T-cell acute lymphoblastic leukemia (ALL) exhibit recurrent cytogenetic alterations, many with prognostic implications. This chapter overviews the major recurrent categories of cytogenetic abnormalities associated with ALL, with an emphasis on the detection and characterization of these cases by G-band and FISH analyses.
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20
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Qian M, Zhang H, Kham SKY, Liu S, Jiang C, Zhao X, Lu Y, Goodings C, Lin TN, Zhang R, Moriyama T, Yin Z, Li Z, Quah TC, Ariffin H, Tan AM, Shen S, Bhojwani D, Hu S, Chen S, Zheng H, Pui CH, Yeoh AEJ, Yang JJ. Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP. Genome Res 2016; 27:185-195. [PMID: 27903646 PMCID: PMC5287225 DOI: 10.1101/gr.209163.116] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 11/29/2016] [Indexed: 12/30/2022]
Abstract
Chromosomal translocations are a genomic hallmark of many hematologic malignancies. Often as initiating events, these structural abnormalities result in fusion proteins involving transcription factors important for hematopoietic differentiation and/or signaling molecules regulating cell proliferation and cell cycle. In contrast, epigenetic regulator genes are more frequently targeted by somatic sequence mutations, possibly as secondary events to further potentiate leukemogenesis. Through comprehensive whole-transcriptome sequencing of 231 children with acute lymphoblastic leukemia (ALL), we identified 58 putative functional and predominant fusion genes in 54.1% of patients (n = 125), 31 of which have not been reported previously. In particular, we described a distinct ALL subtype with a characteristic gene expression signature predominantly driven by chromosomal rearrangements of the ZNF384 gene with histone acetyltransferases EP300 and CREBBP. ZNF384-rearranged ALL showed significant up-regulation of CLCF1 and BTLA expression, and ZNF384 fusion proteins consistently showed higher activity to promote transcription of these target genes relative to wild-type ZNF384 in vitro. Ectopic expression of EP300-ZNF384 and CREBBP-ZNF384 fusion altered differentiation of mouse hematopoietic stem and progenitor cells and also potentiated oncogenic transformation in vitro. EP300- and CREBBP-ZNF384 fusions resulted in loss of histone lysine acetyltransferase activity in a dominant-negative fashion, with concomitant global reduction of histone acetylation and increased sensitivity of leukemia cells to histone deacetylase inhibitors. In conclusion, our results indicate that gene fusion is a common class of genomic abnormalities in childhood ALL and that recurrent translocations involving EP300 and CREBBP may cause epigenetic deregulation with potential for therapeutic targeting.
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Affiliation(s)
- Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China, 510120
| | - Shirley Kow-Yin Kham
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599
| | - Shuguang Liu
- Beijing Key Laboratory of Pediatric Hematology Oncology, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, Beijing, China, 100045
| | - Chuang Jiang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China, 200240
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yi Lu
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599
| | - Charnise Goodings
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Ting-Nien Lin
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Ranran Zhang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China, 510120
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Zhaohong Yin
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Zhenhua Li
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599
| | - Thuan Chong Quah
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599.,VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228
| | - Hany Ariffin
- Paediatric Haematology-Oncology Unit, University of Malaya Medical Centre, Kuala Lumpur, Malaysia, 59100
| | - Ah Moy Tan
- KKH-CCF Children's Cancer Centre, Paediatric Haematology & Oncology, KK Women's and Children's Hospital, Singapore, 229899
| | - Shuhong Shen
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China, 200127
| | - Deepa Bhojwani
- Department of Pediatrics, Children's Hospital of Los Angeles, Los Angeles, California 90027, USA
| | - Shaoyan Hu
- Department of Hematology & Oncology, Children's Hospital of Soochow University, Suzhou, China, 215025
| | - Suning Chen
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China, 215006
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, Beijing, China, 100045
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Allen Eng-Juh Yeoh
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599.,VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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21
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Endo A, Tomizawa D, Aoki Y, Morio T, Mizutani S, Takagi M. EWSR1/ELF5 induces acute myeloid leukemia by inhibiting p53/p21 pathway. Cancer Sci 2016; 107:1745-1754. [PMID: 27627705 PMCID: PMC5198945 DOI: 10.1111/cas.13080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 08/26/2016] [Accepted: 09/09/2016] [Indexed: 02/06/2023] Open
Abstract
The Ewing sarcoma breakpoint region 1 (EWSR1) gene is known to fuse with various partner genes to promote the development of the Ewing sarcoma family of tumors and other sarcomas. In contrast, the association of EWSR1 chimeric fusion genes with leukemia has rarely been reported. We identified a novel EWSR1‐associated chimeric fusion gene in a patient with acute myeloid leukemia harboring 46, XY, t (11; 22) (p13; q12) karyotype abnormality. The patient was refractory to intensified chemotherapy including hematopoietic stem cell transplantation. Total RNA paired‐end sequencing identified a novel chimeric fusion gene as EWSR1/ELF5, a member of the E26 transformation‐specific transcription factor family. Transduction of EWSR1/ELF5 to NIH3T3 cells induced transformation by attenuating with the p53/p21‐dependent pathway. The injection of EWSR1/ELF5‐transduced NIH3T3 cells into NSG‐SCID mice systematically induced the development of tumors in vivo. These results revealed the oncogenic potency of EWSR1/ELF5.
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Affiliation(s)
- Akifumi Endo
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daisuke Tomizawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan.,Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yuki Aoki
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Pediatric Oncology, National Cancer Center, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shuki Mizutani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
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22
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Shago M, Abla O, Hitzler J, Weitzman S, Abdelhaleem M. Frequency and outcome of pediatric acute lymphoblastic leukemia with ZNF384 gene rearrangements including a novel translocation resulting in an ARID1B/ZNF384 gene fusion. Pediatr Blood Cancer 2016; 63:1915-21. [PMID: 27392123 DOI: 10.1002/pbc.26116] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/17/2016] [Accepted: 05/31/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND ZNF384 gene rearrangements with multiple partner genes are recurrent in acute leukemia and are most often associated with a precursor B cell immunophenotype. The overall incidence of this genetic category of leukemia is uncertain. PROCEDURE Patients with ZNF384 gene rearrangements from a cohort of 240 precursor B cell acute lymphoblastic leukemia (ALL) pediatric patients over a 3.5-year time period were characterized with detailed cytogenetic, FISH, genomic, and clinical analyses. RESULTS Seven of the 240 patients were identified to have ZNF384 gene rearrangements including partner genes TCF3 (four patients), EWSR1 (one patient), EP300 (one patient), and the novel gene partner ARID1B (one patient). The translocations were confirmed by FISH analysis and with RNA sequencing for the EP300 and ARID1B partner genes. Genomic microarray analysis showed an average of 2.7 copy number alterations in each case with no evidence of imbalance at the translocation breakpoints. Six of the patients with ZNF384 gene rearrangements had precursor B cell ALL with a CD10- immunophenotype and myeloid-associated antigens. One of the patients also had myeloperoxidase expression and was diagnosed as mixed phenotype B/myeloid acute leukemia. None of the patients have relapsed with event-free survival ranging from 6 years 2 months to 9 years 2 months. CONCLUSIONS This study suggests that the frequency of ZNF384 gene rearrangement in pediatric precursor B cell ALL is approximately 3%. The ARID1B gene, commonly mutated in multiple types of cancer, was identified as an additional ZNF384 gene fusion partner.
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Affiliation(s)
- Mary Shago
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Oussama Abla
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Johann Hitzler
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Sheila Weitzman
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Mohamed Abdelhaleem
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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23
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Mori N, Ohwashi-Miyazaki M, Okada M, Yoshinaga K, Shiseki M, Tanaka J. Translocation (9;12)(q34.1;p13.?3) Resulted in ETV6-ABL1 Fusion in a Patient with Philadelphia Chromosome-Negative Chronic Myelogenous Leukemia. Acta Haematol 2016; 136:240-243. [PMID: 27710957 DOI: 10.1159/000448984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/07/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Naoki Mori
- Department of Hematology, Tokyo Women's Medical University, Tokyo, Japan
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24
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Hirabayashi S, Ohki K, Nakabayashi K, Ichikawa H, Momozawa Y, Okamura K, Yaguchi A, Terada K, Saito Y, Yoshimi A, Ogata-Kawata H, Sakamoto H, Kato M, Fujimura J, Hino M, Kinoshita A, Kakuda H, Kurosawa H, Kato K, Kajiwara R, Moriwaki K, Morimoto T, Nakamura K, Noguchi Y, Osumi T, Sakashita K, Takita J, Yuza Y, Matsuda K, Yoshida T, Matsumoto K, Hata K, Kubo M, Matsubara Y, Fukushima T, Koh K, Manabe A, Ohara A, Kiyokawa N. ZNF384-related fusion genes define a subgroup of childhood B-cell precursor acute lymphoblastic leukemia with a characteristic immunotype. Haematologica 2016; 102:118-129. [PMID: 27634205 DOI: 10.3324/haematol.2016.151035] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/14/2016] [Indexed: 01/19/2023] Open
Abstract
Fusion genes involving ZNF384 have recently been identified in B-cell precursor acute lymphoblastic leukemia, and 7 fusion partners have been reported. We further characterized this type of fusion gene by whole transcriptome sequencing and/or polymerase chain reaction. In addition to previously reported genes, we identified BMP2K as a novel fusion partner for ZNF384 Including the EP300-ZNF384 that we reported recently, the total frequency of ZNF384-related fusion genes was 4.1% in 291 B-cell precursor acute lymphoblastic leukemia patients enrolled in a single clinical trial, and TCF3-ZNF384 was the most recurrent, with a frequency of 2.4%. The characteristic immunophenotype of weak CD10 and aberrant CD13 and/or CD33 expression was revealed to be a common feature of the leukemic cells harboring ZNF384-related fusion genes. The signature gene expression profile in TCF3-ZNF384-positive patients was enriched in hematopoietic stem cell features and related to that of EP300-ZNF384-positive patients, but was significantly distinct from that of TCF3-PBX1-positive and ZNF384-fusion-negative patients. However, clinical features of TCF3-ZNF384-positive patients are markedly different from those of EP300-ZNF384-positive patients, exhibiting higher cell counts and a younger age at presentation. TCF3-ZNF384-positive patients revealed a significantly poorer steroid response and a higher frequency of relapse, and the additional activating mutations in RAS signaling pathway genes were detected by whole exome analysis in some of the cases. Our observations indicate that ZNF384-related fusion genes consist of a distinct subgroup of B-cell precursor acute lymphoblastic leukemia with a characteristic immunophenotype, while the clinical features depend on the functional properties of individual fusion partners.
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Affiliation(s)
- Shinsuke Hirabayashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.,Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hitoshi Ichikawa
- Division of Genetics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences (IMS), RIKEN, Yokohama-shi, Kanagawa, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Akinori Yaguchi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.,Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Kazuki Terada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Yuya Saito
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.,Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Fuchu-shi, Tokyo, Japan
| | - Ai Yoshimi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.,Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito-shi, Ibaraki, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.,Division of Stem Cell Transplant and Cellular Therapy, Children's Cancer Center, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Junya Fujimura
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Moeko Hino
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba-shi, Chiba, Japan
| | - Akitoshi Kinoshita
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki-shi, Kanagawa, Japan
| | - Harumi Kakuda
- Department of Haematology/Oncology, Chiba Children's Hospital, Chiba-shi, Chiba, Japan
| | - Hidemitsu Kurosawa
- Department of Pediatrics, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Keisuke Kato
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito-shi, Ibaraki, Japan
| | - Ryosuke Kajiwara
- Department of Pediatrics, Yokohama City University Hospital, Yokohama-shi, Kanagawa, Japan
| | - Koichi Moriwaki
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University, Kawagoe-shi, Saitama, Japan
| | - Tsuyoshi Morimoto
- Department of Pediatrics, Tokai University School of Medicine, Isehara-shi, Kanagawa, Japan
| | - Kozue Nakamura
- Department of Pediatrics, Teikyo University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Narita-shi, Chiba, Japan
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.,Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Kazuo Sakashita
- Department of Hematology/Oncology, Nagano Children's Hospital, Azumino-shi, Nagano, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuki Yuza
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Fuchu-shi, Tokyo, Japan
| | - Koich Matsuda
- Laboratory of Clinical Sequence, Department of Computational biology and medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences (IMS), RIKEN, Yokohama-shi, Kanagawa, Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Takashi Fukushima
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba-shi, Ibaraki, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama-shi, Saitama, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Chuo-ku, Tokyo, Japan
| | - Akira Ohara
- Department of Pediatrics, Toho University Omori Medical Center, Ohta-ku, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
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Establishment and genetic characterization of a novel mixed-phenotype acute leukemia cell line with EP300-ZNF384 fusion. J Hematol Oncol 2015; 8:100. [PMID: 26293203 PMCID: PMC4546145 DOI: 10.1186/s13045-015-0197-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 11/25/2022] Open
Abstract
Herein, we describe the establishment and characterization of the first mixed-phenotype acute leukemia cell line (JIH-5). The JIH-5 cell line was established from leukemia cells with B lymphoid/myeloid phenotype from a female mixed-phenotype acute leukemia patient. JIH-5 cells exhibit an immunophenotype comprised of myeloid and B lymphoid antigens. Whole-exome sequencing revealed somatic mutations in nine genes in JIH-5 cells. Transcriptional sequencing of JIH-5 cells identified EP300-ZNF384 fusion transcript, which is a recurrent alteration in B cell acute lymphoblastic leukemia. Our results suggest that the JIH-5 cell line may serve as a tool for the study of mixed-phenotype acute leukemia or EP300-ZNF384.
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26
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A novel recurrent EP300-ZNF384 gene fusion in B-cell precursor acute lymphoblastic leukemia. Leukemia 2015; 29:2445-8. [PMID: 25943178 DOI: 10.1038/leu.2015.111] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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27
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Lou Y, Suo S, Tong H, Ye X, Wang Y, Chen Z, Qian W, Meng H, Mai W, Huang J, Tong Y, Jin J. Characteristics and prognosis analysis of additional chromosome abnormalities in newly diagnosed acute promyelocytic leukemia treated with arsenic trioxide as the front-line therapy. Leuk Res 2013; 37:1451-6. [DOI: 10.1016/j.leukres.2013.07.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 07/19/2013] [Indexed: 01/08/2023]
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28
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Huang RY, Chen GB, Matsumura N, Lai HC, Mori S, Li J, Wong MK, Konishi I, Thiery JP, Goh L. Histotype-specific copy-number alterations in ovarian cancer. BMC Med Genomics 2012; 5:47. [PMID: 23078675 PMCID: PMC3567940 DOI: 10.1186/1755-8794-5-47] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 10/11/2012] [Indexed: 12/12/2022] Open
Abstract
Background Epithelial ovarian cancer is characterized by multiple genomic alterations; most are passenger alterations which do not confer tumor growth. Like many cancers, it is a heterogeneous disease and can be broadly categorized into 4 main histotypes of clear cell, endometrioid, mucinous, and serous. To date, histotype-specific copy number alterations have been difficult to elucidate. The difficulty lies in having sufficient sample size in each histotype for statistical analyses. Methods To dissect the heterogeneity of ovarian cancer and identify histotype-specific alterations, we used an in silico hypothesis-driven approach on multiple datasets of epithelial ovarian cancer. Results In concordance with previous studies on global copy number alterations landscape, the study showed similar alterations. However, when the landscape was de-convoluted into histotypes, distinct alterations were observed. We report here significant histotype-specific copy number alterations in ovarian cancer and showed that there is genomic diversity amongst the histotypes. 76 cancer genes were found to be significantly altered with several as potential copy number drivers, including ERBB2 in mucinous, and TPM3 in endometrioid histotypes. ERBB2 was found to have preferential alterations, where it was amplified in mucinous (28.6%) but deleted in serous tumors (15.1%). Validation of ERBB2 expression showed significant correlation with microarray data (p=0.007). There also appeared to be reciprocal relationship between KRAS mutation and copy number alterations. In mucinous tumors where KRAS mutation is common, the gene was not significantly altered. However, KRAS was significantly amplified in serous tumors where mutations are rare in high grade tumors. Conclusions The study demonstrates that the copy number landscape is specific to the histotypes and identification of these alterations can pave the way for targeted drug therapy specific to the histotypes.
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Affiliation(s)
- Ruby Yunju Huang
- Department of Obstetrics & Gynaecology, National University Hospital, 5 Lower Kent Ridge Road, Singapore 119074, Singapore
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29
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Ortiz de Mendíbil I, Vizmanos JL, Novo FJ. Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer. PLoS One 2009; 4:e4805. [PMID: 19279687 PMCID: PMC2653638 DOI: 10.1371/journal.pone.0004805] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 01/30/2009] [Indexed: 11/27/2022] Open
Abstract
Background The recurrence and non-random distribution of translocation breakpoints in human tumors are usually attributed to local sequence features present in the vicinity of the breakpoints. However, it has also been suggested that functional constraints might contribute to delimit the position of translocation breakpoints within the genes involved, but a quantitative analysis of such contribution has been lacking. Methodology We have analyzed two well-known signatures of functional selection, such as reading-frame compatibility and non-random combinations of protein domains, on an extensive dataset of fusion proteins resulting from chromosomal translocations in cancer. Conclusions Our data provide strong experimental support for the concept that the position of translocation breakpoints in the genome of cancer cells is determined, to a large extent, by the need to combine certain protein domains and to keep an intact reading frame in fusion transcripts. Additionally, the information that we have assembled affords a global view of the oncogenic mechanisms and domain architectures that are used by fusion proteins. This can be used to assess the functional impact of novel chromosomal translocations and to predict the position of breakpoints in the genes involved.
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Affiliation(s)
| | | | - Francisco J. Novo
- Department of Genetics, University of Navarra, Pamplona, Spain
- * E-mail:
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