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D’Silva SZ, Singh M, Pinto AS. NK cell defects: implication in acute myeloid leukemia. Front Immunol 2023; 14:1112059. [PMID: 37228595 PMCID: PMC10203541 DOI: 10.3389/fimmu.2023.1112059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Acute Myeloid Leukemia (AML) is a complex disease with rapid progression and poor/unsatisfactory outcomes. In the past few years, the focus has been on developing newer therapies for AML; however, relapse remains a significant problem. Natural Killer cells have strong anti-tumor potential against AML. This NK-mediated cytotoxicity is often restricted by cellular defects caused by disease-associated mechanisms, which can lead to disease progression. A stark feature of AML is the low/no expression of the cognate HLA ligands for the activating KIR receptors, due to which these tumor cells evade NK-mediated lysis. Recently, different Natural Killer cell therapies have been implicated in treating AML, such as the adoptive NK cell transfer, Chimeric antigen receptor-modified NK (CAR-NK) cell therapy, antibodies, cytokine, and drug treatment. However, the data available is scarce, and the outcomes vary between different transplant settings and different types of leukemia. Moreover, remission achieved by some of these therapies is only for a short time. In this mini-review, we will discuss the role of NK cell defects in AML progression, particularly the expression of different cell surface markers, the available NK cell therapies, and the results from various preclinical and clinical trials.
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Affiliation(s)
- Selma Z. D’Silva
- Transplant Immunology and Immunogenetics Lab, Advanced Centre for Treatment, Education and Research in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Meenakshi Singh
- Transplant Immunology and Immunogenetics Lab, Advanced Centre for Treatment, Education and Research in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Andrea S. Pinto
- Transplant Immunology and Immunogenetics Lab, Advanced Centre for Treatment, Education and Research in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
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2
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Mill CP, Fiskus W, Das K, Davis JA, Birdwell CE, Kadia TM, DiNardo CD, Daver N, Takahashi K, Sasaki K, McGeehan GM, Ruan X, Su X, Loghavi S, Kantarjian H, Bhalla KN. Causal linkage of presence of mutant NPM1 to efficacy of novel therapeutic agents against AML cells with mutant NPM1. Leukemia 2023:10.1038/s41375-023-01882-4. [PMID: 36977823 DOI: 10.1038/s41375-023-01882-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023]
Abstract
In AML with NPM1 mutation causing cytoplasmic dislocation of NPM1, treatments with Menin inhibitor (MI) and standard AML chemotherapy yield complete remissions. However, the causal and mechanistic linkage of mtNPM1 to the efficacy of these agents has not been definitively established. Utilizing CRISPR-Cas9 editing to knockout (KO) or knock-in a copy of mtNPM1 in AML cells, present studies demonstrate that KO of mtNPM1 from AML cells abrogates sensitivity to MI, selinexor (exportin-1 inhibitor), and cytarabine. Conversely, the knock-in of a copy of mtNPM1 markedly sensitized AML cells to treatment with MI or cytarabine. Following AML therapy, most elderly patients with AML with mtNPM1 and co-mutations in FLT3 suffer AML relapse with poor outcomes, creating a need for novel effective therapies. Utilizing the RNA-Seq signature of CRISPR-edited AML cells with mtNPM1 KO, we interrogated the LINCS1000-CMap data set and found several pan-HDAC inhibitors and a WEE1 tyrosine kinase inhibitor among the top expression mimickers (EMs). Additionally, treatment with adavosertib (WEE1 inhibitor) or panobinostat (pan-HDAC inhibitor) exhibited synergistic in vitro lethal activity with MI against AML cells with mtNPM1. Treatment with adavosertib or panobinostat also reduced AML burden and improved survival in AML xenograft models sensitive or resistant to MI.
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Affiliation(s)
- Christopher P Mill
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Warren Fiskus
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kaberi Das
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - John A Davis
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Tapan M Kadia
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Courtney D DiNardo
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Naval Daver
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Koichi Takahashi
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Koji Sasaki
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Xinjia Ruan
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoping Su
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sanam Loghavi
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hagop Kantarjian
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kapil N Bhalla
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.
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3
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Urwanisch L, Unger MS, Sieberer H, Dang HH, Neuper T, Regl C, Vetter J, Schaller S, Winkler SM, Kerschbamer E, Weichenberger CX, Krenn PW, Luciano M, Pleyer L, Greil R, Huber CG, Aberger F, Horejs-Hoeck J. The Class IIA Histone Deacetylase (HDAC) Inhibitor TMP269 Downregulates Ribosomal Proteins and Has Anti-Proliferative and Pro-Apoptotic Effects on AML Cells. Cancers (Basel) 2023; 15:cancers15041039. [PMID: 36831382 PMCID: PMC9953883 DOI: 10.3390/cancers15041039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by altered myeloid progenitor cell proliferation and differentiation. As in many other cancers, epigenetic transcriptional repressors such as histone deacetylases (HDACs) are dysregulated in AML. Here, we investigated (1) HDAC gene expression in AML patients and in different AML cell lines and (2) the effect of treating AML cells with the specific class IIA HDAC inhibitor TMP269, by applying proteomic and comparative bioinformatic analyses. We also analyzed cell proliferation, apoptosis, and the cell-killing capacities of TMP269 in combination with venetoclax compared to azacitidine plus venetoclax, by flow cytometry. Our results demonstrate significantly overexpressed class I and class II HDAC genes in AML patients, a phenotype which is conserved in AML cell lines. In AML MOLM-13 cells, TMP269 treatment downregulated a set of ribosomal proteins which are overexpressed in AML patients at the transcriptional level. TMP269 showed anti-proliferative effects and induced additive apoptotic effects in combination with venetoclax. We conclude that TMP269 exerts anti-leukemic activity when combined with venetoclax and has potential as a therapeutic drug in AML.
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Affiliation(s)
- Laura Urwanisch
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Michael Stefan Unger
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Helene Sieberer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Hieu-Hoa Dang
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Theresa Neuper
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Christof Regl
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg im Muehlkreis, Austria
| | - Stephan M. Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg im Muehlkreis, Austria
| | - Emanuela Kerschbamer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via A. Volta 21, 39100 Bolzano, Italy
| | - Christian X. Weichenberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via A. Volta 21, 39100 Bolzano, Italy
| | - Peter W. Krenn
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Michela Luciano
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Lisa Pleyer
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- IIIrd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, 5020 Salzburg, Austria
| | - Richard Greil
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- IIIrd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Fritz Aberger
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
| | - Jutta Horejs-Hoeck
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Correspondence: ; Tel.: +43-(0)662-8044-5709
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Maetzig T, Lieske A, Dörpmund N, Rothe M, Kleppa MJ, Dziadek V, Hassan JJ, Dahlke J, Borchert D, Schambach A. Real-Time Characterization of Clonal Fate Decisions in Complex Leukemia Samples by Fluorescent Genetic Barcoding. Cells 2022; 11:cells11244045. [PMID: 36552809 PMCID: PMC9776743 DOI: 10.3390/cells11244045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Clonal heterogeneity in acute myeloid leukemia (AML) forms the basis for treatment failure and relapse. Attempts to decipher clonal evolution and clonal competition primarily depend on deep sequencing approaches. However, this prevents the experimental confirmation of the identified disease-relevant traits on the same cell material. Here, we describe the development and application of a complex fluorescent genetic barcoding (cFGB) lentiviral vector system for the labeling and subsequent multiplex tracking of up to 48 viable AML clones by flow cytometry. This approach allowed the visualization of longitudinal changes in the in vitro growth behavior of multiplexed color-coded AML clones for up to 137 days. Functional studies of flow cytometry-enriched clones documented their stably inherited increase in competitiveness, despite the absence of growth-promoting mutations in exome sequencing data. Transplantation of aliquots of a color-coded AML cell mix into mice revealed the initial engraftment of similar clones and their subsequent differential distribution in the animals over time. Targeted RNA-sequencing of paired pre-malignant and de novo expanded clones linked gene sets associated with Myc-targets, embryonic stem cells, and RAS signaling to the foundation of clonal expansion. These results demonstrate the potency of cFGB-mediated clonal tracking for the deconvolution of verifiable driver-mechanisms underlying clonal selection in leukemia.
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Affiliation(s)
- Tobias Maetzig
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
- Correspondence: ; Tel.: +49-511-532-7808
| | - Anna Lieske
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Nicole Dörpmund
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Marc-Jens Kleppa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Violetta Dziadek
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Jacob Jalil Hassan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Julia Dahlke
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Dorit Borchert
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Tang Y, Xiao S, Wang Z, Liang Y, Xing Y, Wu J, Lu M. A Prognostic Model for Acute Myeloid Leukemia Based on IL-2/STAT5 Pathway-Related Genes. Front Oncol 2022; 12:785899. [PMID: 35186733 PMCID: PMC8847395 DOI: 10.3389/fonc.2022.785899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Accurate prognostic stratification of patients can provide guidance for personalized therapy. Many prognostic models for acute myeloid leukemia (AML) have been reported, but most have considerable inaccuracies due to contained variables with insufficient capacity of predicting survival and lack of adequate verification. Here, 235 genes strongly related to survival in AML were systematically identified through univariate Cox regression analysis of eight independent AML datasets. Pathway enrichment analysis of these 235 genes revealed that the IL-2/STAT5 signaling pathway was the most highly enriched. Through Cox proportional-hazards regression model and stepwise algorithm, we constructed a six-gene STAT5-associated signature based on the most robustly survival-related genes related to the IL-2/STAT5 signaling pathway. Good prognostic performance was observed in the training cohort (GSE37642-GPL96), and the signature was validated in seven other validation cohorts. As an independent prognostic factor, the STAT5-associated signature was positively correlated with patient age and ELN2017 risk levels. An integrated score based on these three prognostic factors had higher prognostic accuracy than the ELN2017 risk category. Characterization of immune cell infiltration indicated that impaired B-cell adaptive immunity, immunosuppressive effects, serious infection, and weakened anti-inflammatory function tended to accompany high-risk patients. Analysis of in-house clinical samples revealed that the STAT5-assocaited signature risk scores of AML patients were significantly higher than those of healthy people. Five chemotherapeutic drugs that were effective in these high-risk patients were screened in silico. Among the five drugs, MS.275, a known HDAC inhibitor, selectively suppressed the proliferation of cancer cells with high STAT5 phosphorylation levels in vitro. Taken together, the data indicate that the STAT5-associated signature is a reliable prognostic model that can be used to optimize prognostic stratification and guide personalized AML treatments.
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Affiliation(s)
- Yigang Tang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shujun Xiao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengyuan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Liang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yangfei Xing
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiale Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Aung MMK, Mills ML, Bittencourt‐Silvestre J, Keeshan K. Insights into the molecular profiles of adult and paediatric acute myeloid leukaemia. Mol Oncol 2021; 15:2253-2272. [PMID: 33421304 PMCID: PMC8410545 DOI: 10.1002/1878-0261.12899] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a clinically and molecularly heterogeneous disease characterised by uncontrolled proliferation, block in differentiation and acquired self-renewal of hematopoietic stem and myeloid progenitor cells. This results in the clonal expansion of myeloid blasts within the bone marrow and peripheral blood. The incidence of AML increases with age, and in childhood, AML accounts for 20% of all leukaemias. Whilst there are many clinical and biological similarities between paediatric and adult AML with continuum across the age range, many characteristics of AML are associated with age of disease onset. These include chromosomal aberrations, gene mutations and differentiation lineage. Following chemotherapy, AML cells that survive and result in disease relapse exist in an altered chemoresistant state. Molecular profiling currently represents a powerful avenue of experimentation to study AML cells from adults and children pre- and postchemotherapy as a means of identifying prognostic biomarkers and targetable molecular vulnerabilities that may be age-specific. This review highlights recent advances in our knowledge of the molecular profiles with a focus on transcriptomes and metabolomes, leukaemia stem cells and chemoresistant cells in adult and paediatric AML and focus on areas that hold promise for future therapies.
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Affiliation(s)
- Myint Myat Khine Aung
- Paul O’Gorman Leukaemia Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
| | - Megan L. Mills
- Paul O’Gorman Leukaemia Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
| | | | - Karen Keeshan
- Paul O’Gorman Leukaemia Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
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Al-Natour B, Rankin R, McKenna R, McMillan H, Zhang SD, About I, Khan AA, Galicia JC, Lundy FT, El-Karim IA. Identification and validation of novel biomarkers and therapeutics for pulpitis using connectivity mapping. Int Endod J 2021; 54:1571-1580. [PMID: 33964033 DOI: 10.1111/iej.13547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/04/2021] [Indexed: 12/21/2022]
Abstract
AIM To create an irreversible pulpitis gene signature from microarray data of healthy and inflamed dental pulps, followed by a bioinformatics approach using connectivity mapping to identify therapeutic compounds that could potentially treat pulpitis. METHODOLOGY The Gene Expression Omnibus (GEO) database, an international public repository of genomics data sets, was searched for human microarray datasets assessing pulpitis. An irreversible pulpitis gene expression signature was generated by differential expression analysis. The statistically significant connectivity map (ssCMap) method was used to identify compounds with a highly correlating gene expression pattern. qPCR was used to validate novel pulpitis genes. An ex vivo pulpitis model was used to test the effects of the compounds identified, and the level of inflammatory cytokines was measured with qPCR, ELISA and multiplex array. Means were compared using the t-test or ANOVA with the level of significance set at p ≤ .05. RESULTS Pulpitis gene signatures were created using differential gene expression analysis at cutoff points p = .0001 and .000018. Top upregulated genes were selected as potential pulpitis biomarkers. Among these, IL8, IL6 and MMP9 were previously identified as pulpitis biomarkers. Novel upregulated genes, chemokine (C-C motif) ligand 21 (CCL21), metallothionein 1H (MT1H) and aquaporin 9 (AQP9) were validated in the pulp tissue of teeth clinically diagnosed with irreversible pulpitis using qPCR. ssCMap analysis identified fluvastatin (Statin) and dequalinium chloride (Quaternary ammonium) as compounds with the strongest correlation to the gene signatures (p = .0001). Fluvastatin reduced IL8, IL6, CCL21, AQP9 (p < .001) and MMP9 (p < .05) in the ex vivo pulpitis model, while dequalinium chloride reduced AQP9 (p < .001) but had no significant effect on the other biomarkers. CONCLUSIONS AQP9, MT1H and CCL21 were identified and validated as novel biomarkers for pulpitis. Fluvastatin and dequalinium chloride identified by the ssCMap as potential therapeutics for pulpitis reduced selected pulpitis biomarkers in an ex vivo pulpitis model. In vivo testing of these licenced drugs is warranted.
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Affiliation(s)
- Banan Al-Natour
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.,Department of Oral Medicine and Oral Surgery, Jordan University of Science and Technology, Irbid, Jordan
| | - Robby Rankin
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Robyn McKenna
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Hayley McMillan
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, University of Ulster, Londonderry, UK
| | - Imad About
- Aix-Marseille Univ, CNRS, ISM, Inst Movement Sci, Marseille, France
| | - Asma A Khan
- Department of Endodontics, Dental School, UT Health San Antonio, San Antonio, TX, USA
| | - Johnah C Galicia
- Department of Restorative Dentistry (Endodontics), University College London Eastman Dental Institute, London, UK
| | - Fionnuala T Lundy
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Ikhlas A El-Karim
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
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9
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Li H, Xu X, Zhang Y, Tang X, Li W. Tetrandrine enhances antitumor effects of the histone deacetylase inhibitor MS-275 in human cancer in a Bax- and p53-dependent manner. Eur J Pharmacol 2020; 888:173575. [PMID: 32950498 DOI: 10.1016/j.ejphar.2020.173575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
MS-275 (Entinostat), is an oral histone deacetylase (HDAC) inhibitor with a high specificity for class 1 HDACs. As single agent, MS-275 exerts only modest antitumor activity against most solid malignancies. The use of MS-275 in combination with other anticancer agents is currently being evaluated to determine whether this approach can achieve superior therapeutic efficacy. Tetrandrine, a bisbenzylisoquinoline alkaloid isolated from the root of a Chinese medicinal herb, is safe and exhibits low toxicity, showing great potential to enhance chemotherapeutic efficacy. In the present study, we investigated the synergistic antitumor effects of MS-275 in combination with tetrandrine. Based on the results of in vitro experiments, the application of MS-275 in combination with tetrandrine induced selective apoptotic death in various cancer cells but spared normal cells. Mechanistically, the combination treatment induced a dramatic accumulation of reactive oxygen species (ROS), and a pretreatment with the ROS scavenger N-acetyl-L-cysteine (NAC) significantly prevented the cellular apoptosis induced by MS-275/tetrandrine. Moreover, molecular assays indicated that Bax and p53 were the key regulators of MS-275/tetrandrine induced apoptosis. The results of the in vivo studies were consistent with the results of the in vitro studies. Based on our findings, tetrandrine enhanced the antitumor effects of MS-275 in a Bax- and p53-dependent manner. The combination of MS-275 and tetrandrine may represent a novel and promising therapeutic strategy for cancer.
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Affiliation(s)
- Han Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Xiaoqing Xu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Yudi Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Xianying Tang
- College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, PR China
| | - Wenhua Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, PR China.
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10
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Rankin R, Lundy FT, Schock BC, Zhang S, Al‐Natour B, About I, Irwin C, Linden GJ, El‐Karim IA. A connectivity mapping approach predicted acetylsalicylic acid (aspirin) to induce osteo/odontogenic differentiation of dental pulp cells. Int Endod J 2020; 53:834-845. [DOI: 10.1111/iej.13281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 12/27/2022]
Affiliation(s)
- R. Rankin
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
| | - F. T. Lundy
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
| | - B. C. Schock
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
| | - S.‐D. Zhang
- School of Biomedical Sciences University of Ulster Derry~Londonderry UK
| | - B. Al‐Natour
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
| | - I. About
- Aix Marseille Univ CNRS ISM Inst Movement Sci Marseille France
| | - C. Irwin
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
| | - G. J. Linden
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
| | - I. A. El‐Karim
- School of Medicine Dentistry and Biomedical Sciences Queen’s University Belfast Belfast UK
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11
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Xu QY, Yu L. Epigenetic therapies in acute myeloid leukemia: the role of hypomethylating agents, histone deacetylase inhibitors and the combination of hypomethylating agents with histone deacetylase inhibitors. Chin Med J (Engl) 2020; 133:699-715. [PMID: 32044818 PMCID: PMC7190219 DOI: 10.1097/cm9.0000000000000685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulation includes changes of DNA methylation and modifications of histone proteins and is essential for normal physiologic functions, especially for controlling gene expression. Epigenetic dysregulation plays a key role in disease pathogenesis and progression of some malignancies, including acute myeloid leukemia (AML). Epigenetic therapies, including hypomethylating agents (HMAs) and histone deacetylase (HDAC) inhibitors, were developed to reprogram the epigenetic abnormalities in AML. However, the molecular mechanisms and therapeutic effects of the two agents alone or their combination remain unknown. An overview of these epigenetic therapies is given here. A literature search was conducted through PubMed database, looking for important biological or clinical studies related to the epigenetic regimens in the treatment of AML until October 15th, 2019. Various types of articles, including original research and reviews, were assessed, identified, and eventually summarized as a collection of data pertaining the mechanisms and clinical effects of HMAs and HDAC inhibitors in AML patients. We provided here an overview of the current understanding of the mechanisms and clinical therapeutic effects involved in the treatment with HMAs and HDAC inhibitors alone, the combination of epigenetic therapies with intensive chemotherapy, and the combination of both types of epigenetic therapies. Relevant clinical trials were also discussed. Generally speaking, the large number of studies and their varied outcomes demonstrate that effects of epigenetic therapies are heterogeneous, and that HMAs combination regimens probably contribute to significant response rates. However, more research is needed to explore therapeutic effects of HDAC inhibitors and various combinations of HMAs and HDAC inhibitors.
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Affiliation(s)
- Qing-Yu Xu
- Department of Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, Guangdong 518000, China
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim 68169, Germany
| | - Li Yu
- Department of Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, Guangdong 518000, China
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12
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San José-Enériz E, Gimenez-Camino N, Agirre X, Prosper F. HDAC Inhibitors in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:cancers11111794. [PMID: 31739588 PMCID: PMC6896008 DOI: 10.3390/cancers11111794] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by uncontrolled proliferation, differentiation arrest, and accumulation of immature myeloid progenitors. Although clinical advances in AML have been made, especially in young patients, long-term disease-free survival remains poor, making this disease an unmet therapeutic challenge. Epigenetic alterations and mutations in epigenetic regulators contribute to the pathogenesis of AML, supporting the rationale for the use of epigenetic drugs in patients with AML. While hypomethylating agents have already been approved in AML, the use of other epigenetic inhibitors, such as histone deacetylases (HDAC) inhibitors (HDACi), is under clinical development. HDACi such as Panobinostat, Vorinostat, and Tricostatin A have been shown to promote cell death, autophagy, apoptosis, or growth arrest in preclinical AML models, yet these inhibitors do not seem to be effective as monotherapies, but rather in combination with other drugs. In this review, we discuss the rationale for the use of different HDACi in patients with AML, the results of preclinical studies, and the results obtained in clinical trials. Although so far the results with HDACi in clinical trials in AML have been modest, there are some encouraging data from treatment with the HDACi Pracinostat in combination with DNA demethylating agents.
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Affiliation(s)
- Edurne San José-Enériz
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Naroa Gimenez-Camino
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: (X.A.); (F.P.); Tel.: +34-948-194700 (ext. 1002) (X.A.); +34-948-255400 (ext. 5807) (F.P.)
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IDISNA), Universidad de Navarra, 31008 Pamplona, Spain; (E.S.J.-E.); (N.G.-C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, 31008 Pamplona, Spain
- Correspondence: (X.A.); (F.P.); Tel.: +34-948-194700 (ext. 1002) (X.A.); +34-948-255400 (ext. 5807) (F.P.)
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13
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Zhou Z, Fang Q, Li P, Ma D, Zhe N, Ren M, Chen B, He Z, Wang J, Zhong Q, Wang J. Entinostat combined with Fludarabine synergistically enhances the induction of apoptosis in TP53 mutated CLL cells via the HDAC1/HO-1 pathway. Life Sci 2019; 232:116583. [PMID: 31226417 DOI: 10.1016/j.lfs.2019.116583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 02/02/2023]
Abstract
TP53 mutation is an indicator of poor prognostic in chronic lymphocytic leukemia (CLL). Worse still, CLL patients with TP53 mutation are associated with poor efficacy to current chemotherapeutic, such as Fludarabine. Here, we confirmed that high expression of HDAC1 in CLL patients with TP53 mutation, which is closely related to poor prognosis and drug-resistance. Subsequently, we demonstrated Entinostat (HDAC1 inhibitor) combination with Fludarabine significantly induced apoptosis in TP53 mutations CLL cells. Its mechanism was associated with up-regulation of the pro-apoptotic protein Bax and the down-regulation of HDAC1, HO-1 and BCL-2 proteins. More importantly, we also confirmed that upregulation of HDAC1 could resistant Entinostat-induced apoptosis in TP53 mutations CLL cells by activating the HDAC1/P38/HO-1 pathway. In vivo, we found that Entinostat combination with Fludarabine significantly induced tumor cells apoptosis and prolong survival time in xenograft mouse model. Finally, combining vitro and vivo experiments, we presented the first demonstration that Entinostat combination with Fludarabine had a synergistic effect on the induction of apoptosis in TP53 mutations CLL cells. In conclusion, we provide valuable pre-clinical experimental evidence for the treatment of CLL patients with poor prognosis, especially for TP53 mutations.
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Affiliation(s)
- Zhen Zhou
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Department of Pharmacy, Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China
| | - Qin Fang
- Department of Pharmacy, Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang 550004, China; Department of Pharmacy, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Peifan Li
- Clinical Research Centre, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Dan Ma
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China; Department of Hematology, Guizhou Provincial Laboratory of Hematopoietic Stem Cell Transplantation Center, Guiyang 550004, China
| | - Nana Zhe
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China; Department of Hematology, Guizhou Provincial Laboratory of Hematopoietic Stem Cell Transplantation Center, Guiyang 550004, China
| | - Mei Ren
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China; Department of Hematology, Guizhou Provincial Laboratory of Hematopoietic Stem Cell Transplantation Center, Guiyang 550004, China
| | - Bingqing Chen
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China; Department of Hematology, Guizhou Provincial Laboratory of Hematopoietic Stem Cell Transplantation Center, Guiyang 550004, China
| | - Zhengchang He
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China
| | - Jun Wang
- Clinical Research Centre, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Qin Zhong
- Clinical Research Centre, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Jishi Wang
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China; Key Laboratory of Hematological Disease Diagnostic and Treat Centre of Guizhou Province, Guiyang 550004, China; Department of Hematology, Guizhou Provincial Laboratory of Hematopoietic Stem Cell Transplantation Center, Guiyang 550004, China.
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14
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Napolitano F, Carrella D, Mandriani B, Pisonero-Vaquero S, Sirci F, Medina DL, Brunetti-Pierri N, di Bernardo D. gene2drug: a computational tool for pathway-based rational drug repositioning. Bioinformatics 2019; 34:1498-1505. [PMID: 29236977 DOI: 10.1093/bioinformatics/btx800] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/10/2017] [Indexed: 02/06/2023] Open
Abstract
Motivation Drug repositioning has been proposed as an effective shortcut to drug discovery. The availability of large collections of transcriptional responses to drugs enables computational approaches to drug repositioning directly based on measured molecular effects. Results We introduce a novel computational methodology for rational drug repositioning, which exploits the transcriptional responses following treatment with small molecule. Specifically, given a therapeutic target gene, a prioritization of potential effective drugs is obtained by assessing their impact on the transcription of genes in the pathway(s) including the target. We performed in silico validation and comparison with a state-of-art technique based on similar principles. We next performed experimental validation in two different real-case drug repositioning scenarios: (i) upregulation of the glutamate-pyruvate transaminase (GPT), which has been shown to induce reduction of oxalate levels in a mouse model of primary hyperoxaluria, and (ii) activation of the transcription factor TFEB, a master regulator of lysosomal biogenesis and autophagy, whose modulation may be beneficial in neurodegenerative disorders. Availability and implementation A web tool for Gene2drug is freely available at http://gene2drug.tigem.it. An R package is under development and can be obtained from https://github.com/franapoli/gep2pep. Contact dibernardo@tigem.it. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Francesco Napolitano
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
| | - Diego Carrella
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
| | - Barbara Mandriani
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
| | - Sandra Pisonero-Vaquero
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
| | - Francesco Sirci
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Diego L Medina
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
| | - Nicola Brunetti-Pierri
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
- Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Diego di Bernardo
- Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy
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15
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ASXL1 and SETBP1 mutations promote leukaemogenesis by repressing TGFβ pathway genes through histone deacetylation. Sci Rep 2018; 8:15873. [PMID: 30367089 PMCID: PMC6203835 DOI: 10.1038/s41598-018-33881-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/06/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in ASXL1 and SETBP1 genes have been frequently detected and often coexist in myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). We previously showed that coexpression of mutant ASXL1 and SETBP1 in hematopoietic progenitor cells induced downregulation of TGFβ pathway genes and promoted the development of MDS/AML in a mouse model of bone marrow transplantation. However, whether the repression of TGFβ pathway in fact contributes to leukaemogenesis remains unclear. Moreover, mechanisms for the repression of TGFβ pathway genes in ASXL1/SETBP1-mutated MDS/AML cells have not been fully understood. In this study, we showed that expression of a constitutively active TGFβ type I receptor (ALK5-TD) inhibited leukaemic proliferation of MDS/AML cells expressing mutant ASXL1/SETBP1. We also found aberrantly reduced acetylation of several lysine residues on histone H3 and H4 around the promoter regions of multiple TGFβ pathway genes. The histone deacetylase (HDAC) inhibitor vorinostat reversed histone acetylation at these promoter regions, and induced transcriptional derepression of the TGFβ pathway genes. Furthermore, vorinostat showed robust growth-inhibitory effect in cells expressing mutant ASXL1, whereas it showed only a marginal effect in normal bone marrow cells. These data indicate that HDAC inhibitors will be promising therapeutic drugs for MDS and AML with ASXL1 and SETBP1 mutations.
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16
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform 2018; 19:506-523. [PMID: 28069634 PMCID: PMC5952941 DOI: 10.1093/bib/bbw112] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Laleh Soltan Ghoraie
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
| | - Galina Glazko
- University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York, USA
| | - Olli Yli-Harja
- Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, Hall in Tyrol, Austria
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Frank Emmert-Streib
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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17
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De Wolf H, Cougnaud L, Van Hoorde K, De Bondt A, Wegner JK, Ceulemans H, Göhlmann H. High-Throughput Gene Expression Profiles to Define Drug Similarity and Predict Compound Activity. Assay Drug Dev Technol 2018; 16:162-176. [DOI: 10.1089/adt.2018.845] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Hans De Wolf
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Computational Sciences, Discovery Sciences, Beerse, Belgium
| | | | | | - An De Bondt
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Computational Sciences, Discovery Sciences, Beerse, Belgium
| | - Joerg K. Wegner
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Computational Sciences, Discovery Sciences, Beerse, Belgium
| | - Hugo Ceulemans
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Computational Sciences, Discovery Sciences, Beerse, Belgium
| | - Hinrich Göhlmann
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Computational Sciences, Discovery Sciences, Beerse, Belgium
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18
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Roulston GDR, Burt CL, Kettyle LMJ, Matchett KB, Keenan HL, Mulgrew NM, Ramsey JM, Dougan C, McKiernan J, Grishagin IV, Mills KI, Thompson A. Low-dose salinomycin induces anti-leukemic responses in AML and MLL. Oncotarget 2018; 7:73448-73461. [PMID: 27612428 PMCID: PMC5341990 DOI: 10.18632/oncotarget.11866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
Development of anti-cancer drugs towards clinical application is costly and inefficient. Large screens of drugs, efficacious for non-cancer disease, are currently being used to identify candidates for repurposing based on their anti-cancer properties. Here, we show that low-dose salinomycin, a coccidiostat ionophore previously identified in a breast cancer screen, has anti-leukemic efficacy. AML and MLLr cell lines, primary cells and patient samples were sensitive to submicromolar salinomycin. Most strikingly, colony formation of normal hematopoietic cells was unaffected by salinomycin, demonstrating a lack of hemotoxicity at the effective concentrations. Furthermore, salinomycin treatment of primary cells resulted in loss of leukemia repopulation ability following transplantation, as demonstrated by extended recipient survival compared to controls. Bioinformatic analysis of a 17-gene signature identified and validated in primary MLLr cells, uncovered immunomodulatory pathways, hubs and protein interactions as potential transducers of low dose salinomycin treatment. Additionally, increased protein expression of p62/Sqstm1, encoded for by one of the 17 signature genes, demonstrates a role for salinomycin in aggresome/vesicle formation indicative of an autophagic response. Together, the data support the efficacy of salinomycin as an anti-leukemic at non-hemotoxic concentrations. Further investigation alone or in combination with other therapies is warranted for future clinical trial.
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Affiliation(s)
- Gary D R Roulston
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Charlotte L Burt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Laura M J Kettyle
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Kyle B Matchett
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Heather L Keenan
- Cambridge University School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, CB2 0SP, United Kingdom
| | - Nuala M Mulgrew
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Joanne M Ramsey
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Caoifa Dougan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - John McKiernan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Ivan V Grishagin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Ken I Mills
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom
| | - Alexander Thompson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, United Kingdom.,Division of Cancer and Stem Cells, School of Medicine, Wolfson Centre for Stem Cells, Tissue Engineering & Modelling (STEM), University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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19
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Thillaiyampalam G, Liberante F, Murray L, Cardwell C, Mills K, Zhang SD. An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping. BMC Bioinformatics 2017; 18:581. [PMID: 29268695 PMCID: PMC5740937 DOI: 10.1186/s12859-017-1989-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 12/06/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Gene expression connectivity mapping has gained much popularity in recent years with a number of successful applications in biomedical research testifying its utility and promise. A major application of connectivity mapping is the identification of small molecule compounds capable of inhibiting a disease state. In this study, we are additionally interested in small molecule compounds that may enhance a disease state or increase the risk of developing that disease. Using breast cancer as a case study, we aim to develop and test a methodology for identifying commonly prescribed drugs that may have a suppressing or inducing effect on the target disease (breast cancer). RESULTS We obtained from public data repositories a collection of breast cancer gene expression datasets with over 7000 patients. An integrated meta-analysis approach to gene expression connectivity mapping was developed, which involved unified processing and normalization of raw gene expression data, systematic removal of batch effects, and multiple runs of balanced sampling for differential expression analysis. Differentially expressed genes stringently selected were used to construct multiple non-joint gene signatures representing the same biological state. Remarkably these non-joint gene signatures retrieved from connectivity mapping separate lists of candidate drugs with significant overlaps, providing high confidence in their predicted effects on breast cancers. Of particular note, among the top 26 compounds identified as inversely connected to the breast cancer gene signatures, 14 of them are known anti-cancer drugs. CONCLUSIONS A few candidate drugs with potential to enhance breast cancer or increase the risk of the disease were also identified; further investigation on a large population is required to firmly establish their effects on breast cancer risks. This work thus provides a novel approach and an applicable example for identifying medications with potential to alter cancer risks through gene expression connectivity mapping.
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Affiliation(s)
| | - Fabio Liberante
- Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, UK
| | - Liam Murray
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
| | - Chris Cardwell
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
| | - Ken Mills
- Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, UK
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, UK
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, L/Derry, Northern Ireland, BT47 6SB UK
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20
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Maetzig T, Ruschmann J, Sanchez Milde L, Lai CK, von Krosigk N, Humphries RK. Lentiviral Fluorescent Genetic Barcoding for Multiplex Fate Tracking of Leukemic Cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 6:54-65. [PMID: 28664166 PMCID: PMC5480982 DOI: 10.1016/j.omtm.2017.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 02/06/2023]
Abstract
Tracking the behavior of leukemic samples both in vitro and in vivo plays an increasingly large role in efforts to better understand the leukemogenic processes and the effects of potential new therapies. Such work can be accelerated and made more efficient by methodologies enabling the characterization of leukemia samples in multiplex assays. We recently developed three sets of lentiviral fluorescent genetic barcoding (FGB) vectors that create 26, 14, and 6 unique immunophenotyping-compatible color codes from GFP-, yellow fluorescent protein (YFP)-, and monomeric kusabira orange 2 (mKO2)-derived fluorescent proteins. These vectors allow for labeling and tracking of individual color-coded cell populations in mixed samples by real-time flow cytometry. Using the prototypical Hoxa9/Meis1 murine model of acute myeloid leukemia, we describe the application of the 6xFGB vector system for assessing leukemic cell characteristics in multiplex assays. By transplanting color-coded cell mixes, we investigated the competitive growth behavior of individual color-coded populations, determined leukemia-initiating cell frequencies, and assessed the dose-dependent potential of cells exposed to the histone deacetylase inhibitor Entinostat for bone marrow homing. Thus, FGB provides a useful tool for the multiplex characterization of leukemia samples in a wide variety of applications with a concomitant reduction in workload, processing times, and mouse utilization.
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Affiliation(s)
- Tobias Maetzig
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jens Ruschmann
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Lea Sanchez Milde
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Courteney K Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Niklas von Krosigk
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
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21
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Connectivity mapping (ssCMap) to predict A20-inducing drugs and their antiinflammatory action in cystic fibrosis. Proc Natl Acad Sci U S A 2016; 113:E3725-34. [PMID: 27286825 DOI: 10.1073/pnas.1520289113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cystic fibrosis (CF) lung disease is characterized by chronic and exaggerated inflammation in the airways. Despite recent developments to therapeutically overcome the underlying functional defect in the cystic fibrosis transmembrane conductance regulator, there is still an unmet need to also normalize the inflammatory response. The prolonged and heightened inflammatory response in CF is, in part, mediated by a lack of intrinsic down-regulation of the proinflammatory NF-κB pathway. We have previously identified reduced expression of the NF-κB down-regulator A20 in CF as a key target to normalize the inflammatory response. Here, we have used publicly available gene array expression data together with a statistically significant connections' map (sscMap) to successfully predict drugs already licensed for the use in humans to induce A20 mRNA and protein expression and thereby reduce inflammation. The effect of the predicted drugs on A20 and NF-κB(p65) expression (mRNA) as well as proinflammatory cytokine release (IL-8) in the presence and absence of bacterial LPS was shown in bronchial epithelial cells lines (16HBE14o-, CFBE41o-) and in primary nasal epithelial cells from patients with CF (Phe508del homozygous) and non-CF controls. Additionally, the specificity of the drug action on A20 was confirmed using cell lines with tnfαip3 (A20) knockdown (siRNA). We also show that the A20-inducing effect of ikarugamycin and quercetin is lower in CF-derived airway epithelial cells than in non-CF cells.
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22
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A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping. BMC Bioinformatics 2016; 17:211. [PMID: 27170106 PMCID: PMC4864913 DOI: 10.1186/s12859-016-1066-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/29/2016] [Indexed: 01/14/2023] Open
Abstract
Background Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research in connectivity mapping mainly focused on two of the key components in the framework, namely, the reference gene expression profiles and the connectivity mapping algorithms. The other key component in this framework, the query gene signature, has been left to users to construct without much consensus on how this should be done, albeit it has been an issue most relevant to end users. As a key input to the connectivity mapping process, gene signature is crucially important in returning biologically meaningful and relevant results. This paper intends to formulate a standardized procedure for constructing high quality gene signatures from a user’s perspective. Results We describe a two-stage process for making quality gene signatures using gene expression data as initial inputs. First, a differential gene expression analysis comparing two distinct biological states; only the genes that have passed stringent statistical criteria are considered in the second stage of the process, which involves ranking genes based on statistical as well as biological significance. We introduce a “gene signature progression” method as a standard procedure in connectivity mapping. Starting from the highest ranked gene, we progressively determine the minimum length of the gene signature that allows connections to the reference profiles (drugs) being established with a preset target false discovery rate. We use a lung cancer dataset and a breast cancer dataset as two case studies to demonstrate how this standardized procedure works, and we show that highly relevant and interesting biological connections are returned. Of particular note is gefitinib, identified as among the candidate therapeutics in our lung cancer case study. Our gene signature was based on gene expression data from Taiwan female non-smoker lung cancer patients, while there is evidence from independent studies that gefitinib is highly effective in treating women, non-smoker or former light smoker, advanced non-small cell lung cancer patients of Asian origin. Conclusions In summary, we introduced a gene signature progression method into connectivity mapping, which enables a standardized procedure for constructing high quality gene signatures. This progression method is particularly useful when the number of differentially expressed genes identified is large, and when there is a need to prioritize them to be included in the query signature. The results from two case studies demonstrate that the approach we have developed is capable of obtaining pertinent candidate drugs with high precision. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1066-x) contains supplementary material, which is available to authorized users.
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23
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O'Reilly PG, Wen Q, Bankhead P, Dunne PD, McArt DG, McPherson S, Hamilton PW, Mills KI, Zhang SD. QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics. BMC Bioinformatics 2016; 17:198. [PMID: 27143038 PMCID: PMC4855472 DOI: 10.1186/s12859-016-1062-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022] Open
Abstract
Background Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying potential small molecule compounds, which may be further investigated as candidates for repurposing to treat diseases. The public release of voluminous data from the Library of Integrated Cellular Signatures (LINCS) programme further enhanced the utilities and potentials of gene expression connectivity mapping in biomedicine. Results We describe QUADrATiC (http://go.qub.ac.uk/QUADrATiC), a user-friendly tool for the exploration of gene expression connectivity on the subset of the LINCS data set corresponding to FDA-approved small molecule compounds. It enables the identification of compounds for repurposing therapeutic potentials. The software is designed to cope with the increased volume of data over existing tools, by taking advantage of multicore computing architectures to provide a scalable solution, which may be installed and operated on a range of computers, from laptops to servers. This scalability is provided by the use of the modern concurrent programming paradigm provided by the Akka framework. The QUADrATiC Graphical User Interface (GUI) has been developed using advanced Javascript frameworks, providing novel visualization capabilities for further analysis of connections. There is also a web services interface, allowing integration with other programs or scripts. Conclusions QUADrATiC has been shown to provide an improvement over existing connectivity map software, in terms of scope (based on the LINCS data set), applicability (using FDA-approved compounds), usability and speed. It offers potential to biological researchers to analyze transcriptional data and generate potential therapeutics for focussed study in the lab. QUADrATiC represents a step change in the process of investigating gene expression connectivity and provides more biologically-relevant results than previous alternative solutions. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1062-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul G O'Reilly
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Qing Wen
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Peter Bankhead
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Darragh G McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Suzanne McPherson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Peter W Hamilton
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Ken I Mills
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK.
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK. .,Northern Ireland Centre for Stratified Medicine, University of Ulster, C-TRIC Building, Altnagelvin Hospital campus, Glenshane Road, Derry/Londonderry, BT47 6SB, UK.
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24
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Abstract
Abnormal activation of SETBP1 through overexpression or missense mutations is highly recurrent in various myeloid malignancies; however, it is unclear whether such activation alone is able to induce leukemia development. Here we show that Setbp1 overexpression in mouse bone marrow progenitors through retroviral transduction is capable of initiating leukemia development in irradiated recipient mice. Before leukemic transformation, Setbp1 overexpression significantly enhances the self-renewal of hematopoietic stem cells (HSCs) and expands granulocyte macrophage progenitors (GMPs). Interestingly, Setbp1 overexpression also causes transcriptional repression of critical hematopoiesis regulator gene Runx1 and this effect is crucial for Setbp1-induced transformation. Runx1 repression is induced by Setbp1-mediated recruitment of a nucleosome remodeling deacetylase (NuRD) complex to Runx1 promoters and can be reversed by treatment with histone deacetylase (HDAC) inhibitors Entinostat and Vorinostat. Moreover, treatment with these inhibitors caused efficient differentiation of Setbp1 activation-induced leukemia cells in vitro, and significantly extended the survival of mice transplanted with such leukemias, suggesting that HDAC inhibition could be an effective strategy for treating myeloid malignancies with SETBP1 activation.
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25
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Bannon A, Zhang SD, Schock BC, Ennis M. Cystic Fibrosis from Laboratory to Bedside: The Role of A20 in NF-κB-Mediated Inflammation. Med Princ Pract 2015; 24:301-10. [PMID: 25925366 PMCID: PMC5588248 DOI: 10.1159/000381423] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 03/05/2015] [Indexed: 01/28/2023] Open
Abstract
Cystic fibrosis (CF) is a lifelong, inflammatory multi-organ disease and the most common lethal, genetic condition in Caucasian populations, with a median survival rate of 41.5 years. Pulmonary disease, characterized by infective exacerbations, bronchiectasis and increasing airway insufficiency is the most serious manifestation of this disease process, currently responsible for over 80% of CF deaths. Chronic dysregulation of the innate immune and host inflammatory response has been proposed as a mechanism central to this genetic condition, primarily driven by the nuclear factor κB (NF-κB) pathway. Chronic activation of this transcription factor complex leads to the production of pro-inflammatory cytokines and mediators such as IL-6, IL-8 and TNF-α. A20 has been described as a central and inducible negative regulator of NF-κB. This intracellular molecule negatively regulates NF-κB-driven pro-inflammatory signalling upon toll-like receptor activation at the level of TRAF6 activation. Silencing of A20 increases cellular levels of p65 and induces a pro-inflammatory state. We have previously shown that A20 expression positively correlates with lung function (FEV1%) in CF. Despite improvement in survival rates in recent years, advancements in available therapies have been incremental. We demonstrate that the experimental use of naturally occurring plant diterpenes such as gibberellin on lipopolysaccharide-stimulated cell lines reduces IL-8 release in an A20-dependent manner. We discuss how the use of a novel bio-informatics gene expression connectivity-mapping technique to identify small molecule compounds that similarly mimic the action of A20 may lead to the development of new therapeutic approaches capable of reducing chronic airway inflammation in CF.
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Affiliation(s)
- Aidan Bannon
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Bettina C. Schock
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
| | - Madeleine Ennis
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
- *Prof. Madeleine Ennis, Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Health Sciences Building, Lisburn Road, Belfast BT9 7AE (UK), E-Mail
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Kettyle LMJ, Liberante FG, Thompson A. Rational drug repurposing using sscMap analysis in a HOX-TALE model of leukemia. Methods Mol Biol 2014; 1196:349-70. [PMID: 25151174 DOI: 10.1007/978-1-4939-1242-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Drug discovery and development are often hampered by lack of target identification and clinical tractability. Repurposing of approved drugs to life-threatening diseases such as leukemia is emerging as a promising alternative approach. Connectivity mapping systems link approved drugs with disease-related gene signatures. Relevant preclinical models provide essential tools for system validation and proof-of-concept studies. Herein we describe procedures aimed at generating disease-based gene signatures and applying them to established cross-referencing databases of potential candidate drugs. As a proof of principle, we present the identification of Entinostat as a candidate drug for the treatment of HOX-TALE-related leukemia.
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Affiliation(s)
- Laura M J Kettyle
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, BT9 7BL, UK
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27
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Mulgrew NM, Kettyle LMJ, Ramsey JM, Cull S, Smyth LJ, Mervyn DM, Bijl JJ, Thompson A. c-Met inhibition in a HOXA9/Meis1 model of CN-AML. Dev Dyn 2013; 243:172-81. [PMID: 24307265 DOI: 10.1002/dvdy.24070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 09/16/2013] [Accepted: 09/26/2013] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Hematopoiesis is a paradigm for developmental processes, hierarchically organized, with stem cells at its origin. Hematopoietic stem cells (HSCs) replenish progenitor and precursor cells of multiple lineages, which normally differentiate into short-lived mature circulating cells. Hematopoiesis has provided insight into the molecular basis of tissue homeostasis and malignancy. Malignant hematopoiesis, in particular acute myeloid leukemia (AML), results from impaired development or differentiation of HSCs and progenitors. Co-overexpression of HOX and TALE genes, particularly the HOXA cluster and MEIS1, is associated with AML. Clinically relevant models of AML are required to advance drug development for an aging patient cohort. RESULTS Molecular analysis identified altered gene, microRNA, and protein expression in HOXA9/Meis1 leukemic bone marrow compared to normal controls. A candidate drug screen identified the c-Met inhibitor SU11274 for further analysis. Altered cell cycle status, apoptosis, differentiation, and impaired colony formation were shown for SU11274 in AML cell lines and primary leukemic bone marrow. CONCLUSIONS The clonal HOXA9/Meis1 AML model is amenable to drug screening analysis. The data presented indicate that human AML cells respond in a similar manner to the HOXA9/Meis1 cells, indicating pre-clinical relevance of the mouse model.
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Affiliation(s)
- Nuala M Mulgrew
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, United Kingdom
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