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Youn M, Smith SM, Lee AG, Chae HD, Spiteri E, Erdmann J, Galperin I, Jones LM, Donato M, Abidi P, Bittencourt H, Lacayo N, Dahl G, Aftandilian C, Davis KL, Matthews JA, Kornblau SM, Huang M, Sumarsono N, Redell MS, Fu CH, Chen IM, Alonzo TA, Eklund E, Gotlib J, Khatri P, Sweet-Cordero EA, Hijiya N, Sakamoto KM. Comparison of the Transcriptomic Signatures in Pediatric and Adult CML. Cancers (Basel) 2021; 13:cancers13246263. [PMID: 34944883 PMCID: PMC8699058 DOI: 10.3390/cancers13246263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary To investigate whether pediatric and adult chronic myeloid leukemia (CML) have unique molecular characteristics, we studied the transcriptomic signature of pediatric and adult CML cells using high-throughput RNA sequencing. We identified differentially expressed genes and pathways unique to pediatric CML cells compared to adult CML cells. The Rho pathway was significantly dysregulated in pediatric CML cells compared to adult CML cells, suggesting the potential importance in the pathogenesis of pediatric CML. Our study is the first to compare transcriptome profiles of CML across different age groups. A better understanding of the biology of CML across different ages may inform future treatment approaches. Abstract Children with chronic myeloid leukemia (CML) tend to present with higher white blood counts and larger spleens than adults with CML, suggesting that the biology of pediatric and adult CML may differ. To investigate whether pediatric and adult CML have unique molecular characteristics, we studied the transcriptomic signature of pediatric and adult CML CD34+ cells and healthy pediatric and adult CD34+ control cells. Using high-throughput RNA sequencing, we found 567 genes (207 up- and 360 downregulated) differentially expressed in pediatric CML CD34+ cells compared to pediatric healthy CD34+ cells. Directly comparing pediatric and adult CML CD34+ cells, 398 genes (258 up- and 140 downregulated), including many in the Rho pathway, were differentially expressed in pediatric CML CD34+ cells. Using RT-qPCR to verify differentially expressed genes, VAV2 and ARHGAP27 were significantly upregulated in adult CML CD34+ cells compared to pediatric CML CD34+ cells. NCF1, CYBB, and S100A8 were upregulated in adult CML CD34+ cells but not in pediatric CML CD34+ cells, compared to healthy controls. In contrast, DLC1 was significantly upregulated in pediatric CML CD34+ cells but not in adult CML CD34+ cells, compared to healthy controls. These results demonstrate unique molecular characteristics of pediatric CML, such as dysregulation of the Rho pathway, which may contribute to clinical differences between pediatric and adult patients.
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Affiliation(s)
- Minyoung Youn
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Stephanie M. Smith
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Alex Gia Lee
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA; (A.G.L.); (E.A.S.-C.)
| | - Hee-Don Chae
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Elizabeth Spiteri
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Cytogenetics Laboratory, Stanford Health Care, Stanford, CA 94304, USA; (J.E.); (I.G.)
| | - Jason Erdmann
- Cytogenetics Laboratory, Stanford Health Care, Stanford, CA 94304, USA; (J.E.); (I.G.)
| | - Ilana Galperin
- Cytogenetics Laboratory, Stanford Health Care, Stanford, CA 94304, USA; (J.E.); (I.G.)
| | - Lara Murphy Jones
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; (M.D.); (P.K.)
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; (M.D.); (P.K.)
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | - Parveen Abidi
- Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.A.); (J.G.)
| | - Henrique Bittencourt
- Hematology-Oncology Division, Charles Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC H3T 1C5, Canada;
| | - Norman Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Gary Dahl
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Catherine Aftandilian
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Kara L. Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Jairo A. Matthews
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; (J.A.M.); (S.M.K.)
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; (J.A.M.); (S.M.K.)
| | - Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Nathan Sumarsono
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Michele S. Redell
- Division of Pediatric Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Cecilia H. Fu
- Division of Hematology/Oncology, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - I-Ming Chen
- Department of Pathology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87102, USA;
| | - Todd A. Alonzo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA;
| | - Elizabeth Eklund
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Jason Gotlib
- Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.A.); (J.G.)
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; (M.D.); (P.K.)
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | | | - Nobuko Hijiya
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Kathleen M. Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
- Correspondence: ; Tel.: +1-650-725-7126; Fax: +1-650-723-6700
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Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia. Oncogene 2021; 40:6166-6179. [PMID: 34535769 PMCID: PMC8556320 DOI: 10.1038/s41388-021-02012-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 08/25/2021] [Accepted: 09/07/2021] [Indexed: 12/22/2022]
Abstract
The transcription factors PAX5, IKZF1, and EBF1 are frequently mutated in B cell acute lymphoblastic leukemia (B-ALL). We demonstrate that compound heterozygous loss of multiple genes critical for B and T cell development drives transformation, including Pax5+/-xEbf1+/-, Pax5+/-xIkzf1+/-, and Ebf1+/-xIkzf1+/- mice for B-ALL, or Tcf7+/-xIkzf1+/- mice for T-ALL. To identify genetic defects that cooperate with Pax5 and Ebf1 compound heterozygosity to initiate leukemia, we performed a Sleeping Beauty (SB) transposon screen that identified cooperating partners including gain-of-function mutations in Stat5b (~65%) and Jak1 (~68%), or loss-of-function mutations in Cblb (61%) and Myb (32%). These findings underscore the role of JAK/STAT5B signaling in B cell transformation and demonstrate roles for loss-of-function mutations in Cblb and Myb in transformation. RNA-Seq studies demonstrated upregulation of a PDK1>SGK3>MYC pathway; treatment of Pax5+/-xEbf1+/- leukemia cells with PDK1 inhibitors blocked proliferation in vitro. In addition, we identified a conserved transcriptional gene signature between human and murine leukemias characterized by upregulation of myeloid genes, most notably involving the GM-CSF pathway, that resemble a B cell/myeloid mixed-lineage leukemia. Thus, our findings identify multiple mechanisms that cooperate with defects in B cell transcription factors to generate either progenitor B cell or mixed B/myeloid-like leukemias.
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Potential functions of hsa-miR-155-5p and core genes in chronic myeloid leukemia and emerging role in human cancer: A joint bioinformatics analysis. Genomics 2021; 113:1647-1658. [PMID: 33862181 DOI: 10.1016/j.ygeno.2021.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/07/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Considering the critical roles of hsa-miR-155-5p participated in hematopoietic system, this study aims to clarify the possible pathogenesis of chronic myeloid leukemia (CML) induced by hsa-miR-155-5p.Three different strategies were employed, namely a network-based pipeline, a survival analysis and genetic screening method, and a simulation modeling approach, to assess the oncogenic role of hsa-miR-155-5p in CML. We identified new potential roles of hsa-miR-155-5p in CML, involving the BCR/ABL-mediated leukemogenesis through MAPK signaling. Several promising targets including E2F2, KRAS and FLI1 were screened as candidate diagnostic marker genes. The survival analysis revealed that mRNA expression of E2F2, KRAS and FLI1 was negatively correlated with hsa-miR-155-5p and these targets were significantly associated with poor overall survival. Furthermore, an overlap between CML-related genes and hsa-miR-155-5p target genes was revealed using competing endogenous RNA (ceRNA) networks analysis. Taken together, our results reveal the dynamic regulatory aspect of hsa-miR-155-5p as potential player in CML pathogenesis.
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Cutler JA, Udainiya S, Madugundu AK, Renuse S, Xu Y, Jung J, Kim KP, Wu X, Pandey A. Integrative phosphoproteome and interactome analysis of the role of Ubash3b in BCR-ABL signaling. Leukemia 2019; 34:301-305. [PMID: 31399640 PMCID: PMC6934410 DOI: 10.1038/s41375-019-0535-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/16/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02210, USA
| | - Savita Udainiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, Karnataka, 560 029, India
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560 066, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yaoyu Xu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, 100005, Beijing, China
| | - Jaehun Jung
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Departments of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Kwang Pyo Kim
- Departments of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, Republic of Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, 02453, Republic of Korea
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA. .,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, Karnataka, 560 029, India.
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FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer. PLoS Comput Biol 2018; 14:e1006266. [PMID: 30040819 PMCID: PMC6075785 DOI: 10.1371/journal.pcbi.1006266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/03/2018] [Accepted: 06/05/2018] [Indexed: 12/03/2022] Open
Abstract
Numerous gene fusions have been uncovered across multiple cancer types. Although the ability to target several of these fusions has led to the development of some successful anti-cancer drugs, most of them are not druggable. Understanding the molecular pathways of a fusion is important in determining its function in oncogenesis and in developing therapeutic strategies for patients harboring the fusion. However, the molecular pathways have been elucidated for only a few fusions, in part because of the labor-intensive nature of the required functional assays. Therefore, we developed a domain-based network approach to infer the pathways of a fusion. Molecular interactions of a fusion are first predicted by using its protein domain composition, and its associated pathways are then inferred from these molecular interactions. We demonstrated the capabilities of this approach by primarily applying it to the well-studied BCR-ABL1 fusion. The approach was also applied to two undruggable fusions in sarcoma, EWS-FL1 and FUS-DDIT3. We successfully identified known genes and pathways associated with these fusions and satisfactorily validated these predictions using several benchmark sets. The predictions of EWS-FL1 and FUS-DDIT3 also correlate with results of high-throughput drug screening. To our best knowledge, this is the first approach for inferring pathways of fusions. We present a computational framework, FusionPathway, to infer the oncogenesis pathways of a fusion and help develop therapeutic strategies in these pathways for patients harboring the fusion. In this work, we successfully validated the capabilities of this approach through its application to the well-studied BCR-ABL1 fusion and two undruggable fusions in sarcoma, EWS-FL1 and FUS-DDIT3. Especially, the predictions of EWS-FL1 and FUS-DDIT3 correlate well with results of high-throughput drug screening in sarcoma cells. Therefore, FusionPathway can be an effective method to infer pathways and potential therapeutic targets that are associated with those undruggable fusions. Our results of BCR-ABL1 also suggest that FusionPathway may be able to help elucidate pathway-dependent mechanisms of resistances to those kinase fusion-targeting therapies and develop strategies to overcome the resistances. In addition, the developed R package of FusionPathways (https://github.com/perwu/FusionPathway/) can help people easily apply our approach to study other important fusions in cancer.
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Fang ZH, Wang SL, Zhao JT, Lin ZJ, Chen LY, Su R, Xie ST, Carter BZ, Xu B. miR-150 exerts antileukemia activity in vitro and in vivo through regulating genes in multiple pathways. Cell Death Dis 2016; 7:e2371. [PMID: 27899822 PMCID: PMC5059860 DOI: 10.1038/cddis.2016.256] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 12/12/2022]
Abstract
MicroRNAs, a class of small noncoding RNAs, have been implicated to regulate gene expression in virtually all important biological processes. Although accumulating evidence demonstrates that miR-150, an important regulator in hematopoiesis, is deregulated in various types of hematopoietic malignancies, the precise mechanisms of miR-150 action are largely unknown. In this study, we found that miR-150 is downregulated in samples from patients with acute lymphoblastic leukemia, acute myeloid leukemia, and chronic myeloid leukemia, and normalized after patients achieved complete remission. Restoration of miR-150 markedly inhibited growth and induced apoptosis of leukemia cells, and reduced tumorigenicity in a xenograft leukemia murine model. Microarray analysis identified multiple novel targets of miR-150, which were validated by quantitative real-time PCR and luciferase reporter assay. Gene ontology and pathway analysis illustrated potential roles of these targets in small-molecule metabolism, transcriptional regulation, RNA metabolism, proteoglycan synthesis in cancer, mTOR signaling pathway, or Wnt signaling pathway. Interestingly, knockdown one of four miR-150 targets (EIF4B, FOXO4B, PRKCA, and TET3) showed an antileukemia activity similar to that of miR-150 restoration. Collectively, our study demonstrates that miR-150 functions as a tumor suppressor through multiple mechanisms in human leukemia and provides a rationale for utilizing miR-150 as a novel therapeutic agent for leukemia treatment.
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Affiliation(s)
- Zhi Hong Fang
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Si Li Wang
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Jin Tao Zhao
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Zhi Juan Lin
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Lin Yan Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Rui Su
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Si Ting Xie
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
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