1
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Kim J, Park SH, Lee H. PANCDR: precise medicine prediction using an adversarial network for cancer drug response. Brief Bioinform 2024; 25:bbae088. [PMID: 38487849 PMCID: PMC10940842 DOI: 10.1093/bib/bbae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/09/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024] Open
Abstract
Pharmacogenomics aims to provide personalized therapy to patients based on their genetic variability. However, accurate prediction of cancer drug response (CDR) is challenging due to genetic heterogeneity. Since clinical data are limited, most studies predicting drug response use preclinical data to train models. However, such models might not be generalizable to external clinical data due to differences between the preclinical and clinical datasets. In this study, a Precision Medicine Prediction using an Adversarial Network for Cancer Drug Response (PANCDR) model is proposed. PANCDR consists of two sub-models, an adversarial model and a CDR prediction model. The adversarial model reduces the gap between the preclinical and clinical datasets, while the CDR prediction model extracts features and predicts responses. PANCDR was trained using both preclinical data and unlabeled clinical data. Subsequently, it was tested on external clinical data, including The Cancer Genome Atlas and brain tumor patients. PANCDR outperformed other machine learning models in predicting external test data. Our results demonstrate the robustness of PANCDR and its potential in precision medicine by recommending patient-specific drug candidates. The PANCDR codes and data are available at https://github.com/DMCB-GIST/PANCDR.
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Affiliation(s)
- Juyeon Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, 61005, Gwangju, South Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 03080, Seoul, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 03080, Seoul, South Korea
| | - Hyunju Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, 61005, Gwangju, South Korea
- Artificial Intelligence Graduate School, Gwangju Institute of Science and Technology, 61005, Gwangju, South Korea
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2
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Zhang W, Oh JH, Zhang W, Rathi S, Larson JD, Wechsler-Reya RJ, Sirianni RW, Elmquist WF. Central Nervous System Distribution of Panobinostat in Preclinical Models to Guide Dosing for Pediatric Brain Tumors. J Pharmacol Exp Ther 2023; 387:315-327. [PMID: 37827699 PMCID: PMC10658912 DOI: 10.1124/jpet.123.001826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
Achieving adequate exposure of the free therapeutic agent at the target is a critical determinant of efficacious chemotherapy. With this in mind, a major challenge in developing therapies for central nervous system (CNS) tumors is to overcome barriers to delivery, including the blood-brain barrier (BBB). Panobinostat is a nonselective pan-histone deacetylase inhibitor that is being tested in preclinical and clinical studies, including for the treatment of pediatric medulloblastoma, which has a propensity for leptomeningeal spread and diffuse midline glioma, which can infiltrate into supratentorial brain regions. In this study, we examined the rate, extent, and spatial heterogeneity of panobinostat CNS distribution in mice. Transporter-deficient mouse studies show that panobinostat is a dual substrate of P-glycoprotein (P-gp) and breast cancer resistant protein (Bcrp), which are major efflux transporters expressed at the BBB. The CNS delivery of panobinostat was moderately limited by P-gp and Bcrp, and the unbound tissue-to-plasma partition coefficient of panobinostat was 0.32 and 0.21 in the brain and spinal cord in wild-type mice. In addition, following intravenous administration, panobinostat demonstrated heterogeneous distribution among brain regions, indicating that its efficacy would be influenced by tumor location or the presence and extent of leptomeningeal spread. Simulation using a compartmental BBB model suggests inadequate exposure of free panobinostat in the brain following a recommended oral dosing regimen in patients. Therefore, alternative approaches to CNS delivery may be necessary to have adequate exposure of free panobinostat for the treatment of a broad range of pediatric brain tumors. SIGNIFICANCE STATEMENT: This study shows that the central nervous system (CNS) penetration of panobinostat is limited by P-gp and Bcrp, and its efficacy may be limited by inadequate distribution to the tumor. Panobinostat has heterogeneous distribution into various brain regions, indicating that its efficacy might depend on the anatomical location of the tumors. These distributional parameters in the mouse CNS can inform both preclinical and clinical trial study design and may guide treatment for these devastating brain tumors in children.
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Affiliation(s)
- Wenqiu Zhang
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - Ju-Hee Oh
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - Wenjuan Zhang
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - Sneha Rathi
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - Jon D Larson
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - Robert J Wechsler-Reya
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - Rachael W Sirianni
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
| | - William F Elmquist
- Department of Pharmaceutics, Brain Barriers Research Center, University of Minnesota, Minneapolis, Minnesota (Wenq.Z, J.-H.O., Wenj.Z., S.R., W.F.E.); Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California (J.D.L.); Herbert Irving Comprehensive Cancer Center, Columbia University Medical, New York, New York (R.J.W.-R.); and Department of Neurologic Surgery, UMass Chan Medical School, Worcester, Massachusetts (R.W.S.)
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3
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Nawar N, Garcha HK, Sedighi A, de Araujo ED, Gunning PT. Evaluation of Small-Molecule HDAC Inhibitors Through In Vitro and In Cellulo Approaches. Methods Mol Biol 2023; 2589:157-177. [PMID: 36255624 DOI: 10.1007/978-1-0716-2788-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The aberrant activity of histone deacetylases (HDACs) across a broad range of cancers and other disease indications has led to the development of small-molecule inhibitors that target one or more members of the HDAC protein family. Emerging HDAC inhibitors that show promise in drug discovery programs must be assessed across a range of in vitro assays to establish an inhibitor profile for potency and cellular selectivity towards target HDAC(s) as well as preliminary absorption, distribution, metabolism, and excretion (ADME) features. Here we provide an overview of methods to determine a subset of pivotal in vitro drug-like parameters for HDAC inhibitors (HDACi). We initially describe protocols for parallel artificial membrane permeability assays (PAMPA) to evaluate the passive permeability of small molecules across lipid membranes. Subsequently, we elaborate on cytotoxicity assays using CellTiter-Blue to determine HDACi-induced cell death in healthy/diseased cellular models. We next focus on assessing the target engagement of inhibitors with the appropriate HDAC isoforms in a cellular environment via Western blotting of acetylated HDAC substrates. Finally, we provide detailed guidelines on how to assess the metabolic stability of HDACi through whole blood stability assays. Collectively, these assays provide an overview of the permeability, selectivity, and stability of the HDAC inhibitor under development.
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Affiliation(s)
- Nabanita Nawar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Harsimran Kaur Garcha
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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4
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Skouras P, Markouli M, Strepkos D, Piperi C. Advances on Epigenetic Drugs for Pediatric Brain Tumors. Curr Neuropharmacol 2023; 21:1519-1535. [PMID: 36154607 PMCID: PMC10472812 DOI: 10.2174/1570159x20666220922150456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Pediatric malignant brain tumors represent the most frequent cause of cancer-related deaths in childhood. The therapeutic scheme of surgery, radiotherapy and chemotherapy has improved patient management, but with minimal progress in patients' prognosis. Emerging molecular targets and mechanisms have revealed novel approaches for pediatric brain tumor therapy, enabling personalized medical treatment. Advances in the field of epigenetic research and their interplay with genetic changes have enriched our knowledge of the molecular heterogeneity of these neoplasms and have revealed important genes that affect crucial signaling pathways involved in tumor progression. The great potential of epigenetic therapy lies mainly in the widespread location and the reversibility of epigenetic alterations, proposing a wide range of targeting options, including the possible combination of chemoand immunotherapy, significantly increasing their efficacy. Epigenetic drugs, including inhibitors of DNA methyltransferases, histone deacetylases and demethylases, are currently being tested in clinical trials on pediatric brain tumors. Additional novel epigenetic drugs include protein and enzyme inhibitors that modulate epigenetic modification pathways, such as Bromodomain and Extraterminal (BET) proteins, Cyclin-Dependent Kinase 9 (CDK9), AXL, Facilitates Chromatin Transcription (FACT), BMI1, and CREB Binding Protein (CBP) inhibitors, which can be used either as standalone or in combination with current treatment approaches. In this review, we discuss recent progress on epigenetic drugs that could possibly be used against the most common malignant tumors of childhood, such as medulloblastomas, high-grade gliomas and ependymomas.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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5
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Kling MJ, Kesherwani V, Mishra NK, Alexander G, McIntyre EM, Ray S, Challagundla KB, Joshi SS, Coulter DW, Chaturvedi NK. A novel dual epigenetic approach targeting BET proteins and HDACs in Group 3 (MYC-driven) Medulloblastoma. J Exp Clin Cancer Res 2022; 41:321. [DOI: 10.1186/s13046-022-02530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Medulloblastoma (MB) patients with MYC oncogene amplification or overexpression exhibit extremely poor clinical outcomes and respond poorly to current therapies. Epigenetic deregulation is very common in MYC-driven MB. The bromodomain extra-terminal (BET) proteins and histone deacetylases (HDACs) are epigenetic regulators of MYC transcription and its associated tumorigenic programs. This study aimed to investigate the therapeutic potential of inhibiting the BET proteins and HDACs together in MB.
Methods
Using clinically relevant BET inhibitors (JQ1 or OTX015) and a pan-HDAC inhibitor (panobinostat), we evaluated the effects of combined inhibition on cell growth/survival in MYC-amplified MB cell lines and xenografts and examined underlying molecular mechanism(s).
Results
Co-treatment of JQ1 or OTX015 with panobinostat synergistically suppressed growth/survival of MYC-amplified MB cells by inducing G2 cell cycle arrest and apoptosis. Mechanistic investigation using RNA-seq revealed that co-treatment of JQ1 with panobinostat synergistically modulated global gene expression including MYC/HDAC targets. SYK and MSI1 oncogenes were among the top 50 genes synergistically downregulated by JQ1 and panobinostat. RT-PCR and western blot analyses confirmed that JQ1 and panobinostat synergistically inhibited the mRNA and protein expression of MSI1/SYK along with MYC expression. Reduced SYK/MSI expression after BET (specifically, BRD4) gene-knockdown further confirmed the epigenetic regulation of SYK and MSI1 genes. In addition, the combination of OTX015 and panobinostat significantly inhibited tumor growth in MYC-amplified MB xenografted mice by downregulating expression of MYC, compared to single-agent therapy.
Conclusions
Together, our findings demonstrated that dual-inhibition of BET and HDAC proteins of the epigenetic pathway can be a novel therapeutic approach against MYC-driven MB.
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6
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Garcha HK, Nawar N, Sorger H, Erdogan F, Aung MMK, Sedighi A, Manaswiyoungkul P, Seo HS, Schönefeldt S, Pölöske D, Dhe-Paganon S, Neubauer HA, Mustjoki SM, Herling M, de Araujo ED, Moriggl R, Gunning PT. High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor NN-429 in Natural Killer (NK)/T-Cell Lymphoma. Pharmaceuticals (Basel) 2022; 15:1321. [PMID: 36355493 PMCID: PMC9692247 DOI: 10.3390/ph15111321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 09/29/2023] Open
Abstract
NK/T-cell lymphoma (NKTCL) and γδ T-cell non-Hodgkin lymphomas (γδ T-NHL) are highly aggressive lymphomas that lack rationally designed therapies and rely on repurposed chemotherapeutics from other hematological cancers. Histone deacetylases (HDACs) have been targeted in a range of malignancies, including T-cell lymphomas. This study represents exploratory findings of HDAC6 inhibition in NKTCL and γδ T-NHL through a second-generation inhibitor NN-429. With nanomolar in vitro HDAC6 potency and high in vitro and in cellulo selectivity for HDAC6, NN-429 also exhibited long residence time and improved pharmacokinetic properties in contrast to older generation inhibitors. Following unique selective cytotoxicity towards γδ T-NHL and NKTCL, NN-429 demonstrated a synergistic relationship with the clinical agent etoposide and potential synergies with doxorubicin, cytarabine, and SNS-032 in these disease models, opening an avenue for combination treatment strategies.
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Affiliation(s)
- Harsimran Kaur Garcha
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Nabanita Nawar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Helena Sorger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Fettah Erdogan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Myint Myat Khine Aung
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Pimyupa Manaswiyoungkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Susann Schönefeldt
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Daniel Pölöske
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Heidi A. Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Satu M. Mustjoki
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Marco Herling
- Department of Hematology, Cellular Therapy, and Hemostaseology, University of Leipzig, 04109 Leipzig, Germany
| | - Elvin D. de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Patrick T. Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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7
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Epigenetic mechanisms in paediatric brain tumours: regulators lose control. Biochem Soc Trans 2022; 50:167-185. [PMID: 35076654 DOI: 10.1042/bst20201227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms are essential to regulate gene expression during normal development. However, they are often disrupted in pathological conditions including tumours, where they contribute to their formation and maintenance through altered gene expression. In recent years, next generation genomic techniques has allowed a remarkable advancement of our knowledge of the genetic and molecular landscape of paediatric brain tumours and have highlighted epigenetic deregulation as a common hallmark in their pathogenesis. This review describes the main epigenetic dysregulations found in paediatric brain tumours, including at DNA methylation and histone modifications level, in the activity of chromatin-modifying enzymes and in the expression of non-coding RNAs. How these altered processes influence tumour biology and how they can be leveraged to dissect the molecular heterogeneity of these tumours and contribute to their classification is also addressed. Finally, the availability and value of preclinical models as well as the current clinical trials exploring targeting key epigenetic mediators in paediatric brain tumours are discussed.
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8
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Nawar N, Bukhari S, Adile AA, Suk Y, Manaswiyoungkul P, Toutah K, Olaoye OO, Raouf YS, Sedighi A, Garcha HK, Hassan MM, Gwynne W, Israelian J, Radu TB, Geletu M, Abdeldayem A, Gawel JM, Cabral AD, Venugopal C, de Araujo ED, Singh SK, Gunning PT. Discovery of HDAC6-Selective Inhibitor NN-390 with in Vitro Efficacy in Group 3 Medulloblastoma. J Med Chem 2022; 65:3193-3217. [PMID: 35119267 DOI: 10.1021/acs.jmedchem.1c01585] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Histone deacetylase 6 (HDAC6) has been targeted in clinical studies for anticancer effects due to its role in oncogenic transformation and metastasis. Through a second-generation structure-activity relationship (SAR) study, the design, and biological evaluation of the selective HDAC6 inhibitor NN-390 is reported. With nanomolar HDAC6 potency, >200-550-fold selectivity for HDAC6 in analogous HDAC isoform functional assays, potent intracellular target engagement, and robust cellular efficacy in cancer cell lines, NN-390 is the first HDAC6-selective inhibitor to show therapeutic potential in metastatic Group 3 medulloblastoma (MB), an aggressive pediatric brain tumor often associated with leptomeningeal metastases and therapy resistance. MB stem cells contribute to these patients' poor clinical outcomes. NN-390 selectively targets this cell population with a 44.3-fold therapeutic margin between patient-derived Group 3 MB cells in comparison to healthy neural stem cells. NN-390 demonstrated a 45-fold increased potency over HDAC6-selective clinical candidate citarinostat. In summary, HDAC6-selective molecules demonstrated in vitro therapeutic potential against Group 3 MB.
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Affiliation(s)
- Nabanita Nawar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Shazreh Bukhari
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Ashley A Adile
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Yujin Suk
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Pimyupa Manaswiyoungkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Krimo Toutah
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Yasir S Raouf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Harsimran Kaur Garcha
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - William Gwynne
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Johan Israelian
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Tudor B Radu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mulu Geletu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Ayah Abdeldayem
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Justyna M Gawel
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Aaron D Cabral
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Chitra Venugopal
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Department of Surgery, Faculty of Health Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Sheila K Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Department of Surgery, Faculty of Health Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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9
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The Current Landscape of Targeted Clinical Trials in Non-WNT/Non-SHH Medulloblastoma. Cancers (Basel) 2022; 14:cancers14030679. [PMID: 35158947 PMCID: PMC8833659 DOI: 10.3390/cancers14030679] [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: 12/15/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Medulloblastoma is a form of malignant brain tumor that arises predominantly in infants and young children and can be divided into different groups based on molecular markers. The group of non-WNT/non-SHH medulloblastoma includes a spectrum of heterogeneous subgroups that differ in their biological characteristics, genetic underpinnings, and clinical course of disease. Non-WNT/non-SHH medulloblastoma is currently treated with surgery, chemotherapy, and radiotherapy; however, new drugs are needed to treat patients who are not yet curable and to reduce treatment-related toxicity and side effects. We here review which new treatment options for non-WNT/non-SHH medulloblastoma are currently clinically tested. Furthermore, we illustrate the challenges that have to be overcome to reach a new therapeutic standard for non-WNT/non-SHH medulloblastoma, for instance the current lack of good preclinical models, and the necessity to conduct trials in a comparably small patient collective. Abstract Medulloblastoma is an embryonal pediatric brain tumor and can be divided into at least four molecularly defined groups. The category non-WNT/non-SHH medulloblastoma summarizes medulloblastoma groups 3 and 4 and is characterized by considerable genetic and clinical heterogeneity. New therapeutic strategies are needed to increase survival rates and to reduce treatment-related toxicity. We performed a noncomprehensive targeted review of the current clinical trial landscape and literature to summarize innovative treatment options for non-WNT/non-SHH medulloblastoma. A multitude of new drugs is currently evaluated in trials for which non-WNT/non-SHH patients are eligible, for instance immunotherapy, kinase inhibitors, and drugs targeting the epigenome. However, the majority of these trials is not restricted to medulloblastoma and lacks molecular classification. Whereas many new molecular targets have been identified in the last decade, which are currently tested in clinical trials, several challenges remain on the way to reach a new therapeutic strategy for non-WNT/non-SHH medulloblastoma. These include the severe lack of faithful preclinical models and predictive biomarkers, the question on how to stratify patients for clinical trials, and the relative lack of studies that recruit large, homogeneous patient collectives. Innovative trial designs and international collaboration will be a key to eventually overcome these obstacles.
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10
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Epigenetic-Based Therapy-A Prospective Chance for Medulloblastoma Patients' Recovery. Int J Mol Sci 2021; 22:ijms22094925. [PMID: 34066495 PMCID: PMC8124462 DOI: 10.3390/ijms22094925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/25/2022] Open
Abstract
Medulloblastoma (MB) is one of the most frequent and malignant brain tumors in children. The prognosis depends on the advancement of the disease and the patient's age. Current therapies, which include surgery, chemotherapy, and irradiation, despite being quite effective, cause significant side effects that influence the central nervous system's function and cause neurocognitive deficits. Therefore, they substantially lower the quality of life, which is especially severe in a developing organism. Thus, there is a need for new therapies that are less toxic and even more effective. Recently, knowledge about the epigenetic mechanisms that are responsible for medulloblastoma development has increased. Epigenetics is a phenomenon that influences gene expression but can be easily modified by external factors. The best known epigenetic mechanisms are histone modifications, DNA methylation, or noncoding RNAs actions. Epigenetic mechanisms comprehensively explain the complex phenomena of carcinogenesis. At the same time, they seem to be a potential key to treating medulloblastoma with fewer complications than past therapies. This review presents the currently known epigenetic mechanisms that are involved in medulloblastoma pathogenesis and the potential therapies that use epigenetic traits to cure medulloblastoma while maintaining a good quality of life and ensuring a higher median overall survival rate.
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11
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Medulloblastoma drugs in development: Current leads, trials and drawbacks. Eur J Med Chem 2021; 215:113268. [PMID: 33636537 DOI: 10.1016/j.ejmech.2021.113268] [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: 01/11/2021] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022]
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children. Current treatment for MB includes surgical resection, radiotherapy and chemotherapy. Despite significant progress in its management, a portion of children relapse and tumor recurrence carries a poor prognosis. Based on their molecular and clinical characteristics, MB patients are clinically classified into four groups: Wnt, Hh, Group 3, and Group 4. With our increased understanding of relevant molecular pathways disrupted in MB, the development of targeted therapies for MB has also increased. Targeted drugs have shown unique privileges over traditional cytotoxic therapies in balancing efficacy and toxicity, with many of them approved and widely used clinically. The aim of this review is to present the recent progress on targeted chemotherapies for the treatment of all classes of MB.
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12
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Rausch M, Weiss A, Zoetemelk M, Piersma SR, Jimenez CR, van Beijnum JR, Nowak-Sliwinska P. Optimized Combination of HDACI and TKI Efficiently Inhibits Metabolic Activity in Renal Cell Carcinoma and Overcomes Sunitinib Resistance. Cancers (Basel) 2020; 12:cancers12113172. [PMID: 33126775 PMCID: PMC7693411 DOI: 10.3390/cancers12113172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary To ameliorate the situation for kidney cancer patients and to broaden the application of available drugs, we initiated this research to enhance the anti-cancer activity through combination treatment. There is an unmet need for innovative treatment strategies and optimized drug combinations haven proven to be an adequate solution. We identified a four-drug combination of two histone deacetylate and two tyrosine kinase inhibitors that is effective in sunitinib-naïve and -resistant human renal cell carcinoma cells. Through our research, we demonstrated the superior anti-cancer activity of an optimized drug combination in comparison to single drugs, while maintaining a good safety/selectivity profile. We anticipate that the development and use of well-established drug combinations will be enforced offering personalized and more diverse treatment options in clinical conditions. Abstract Clear cell renal cell carcinoma (ccRCC) is characterized by high histone deacetylase (HDAC) activity triggering both cell motility and the development of metastasis. Therefore, there is an unmet need to establish innovative strategies to advance the use of HDAC inhibitors (HDACIs). We selected a set of tyrosine kinase inhibitors (TKIs) and HDACIs to test them in combination, using the validated therapeutically guided multidrug optimization (TGMO) technique based on experimental testing and in silico data modeling. We determined a synergistic low-dose three-drug combination decreasing the cell metabolic activity in metastatic ccRCC cells, Caki-1, by over 80%. This drug combination induced apoptosis and showed anti-angiogenic activity, both in original Caki-1 and in sunitinib-resistant Caki-1 cells. Through phosphoproteomic analysis, we revealed additional targets to improve the translation of this combination in 3-D (co-)culture systems. Cell–cell and cell–environment interactions increased, reverting the invasive and metastatic phenotype of Caki-1 cells. Our data suggest that our optimized low-dose drug combination is highly effective in complex in vitro settings and promotes the activity of HDACIs.
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Affiliation(s)
- Magdalena Rausch
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
| | - Andrea Weiss
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Marloes Zoetemelk
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan, 1117 Amsterdam, The Netherlands; (S.R.P.); (C.R.J.)
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1117 Amsterdam, The Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan, 1117 Amsterdam, The Netherlands; (S.R.P.); (C.R.J.)
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1117 Amsterdam, The Netherlands
| | - Judy R. van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC-Location VUmc, VU University Amsterdam, 1117 Amsterdam, The Netherlands;
| | - Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
- Correspondence: ; Tel.: +41-22-3793352
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13
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Perla A, Fratini L, Cardoso PS, Nör C, Brunetto AT, Brunetto AL, de Farias CB, Jaeger M, Roesler R. Histone Deacetylase Inhibitors in Pediatric Brain Cancers: Biological Activities and Therapeutic Potential. Front Cell Dev Biol 2020; 8:546. [PMID: 32754588 PMCID: PMC7365945 DOI: 10.3389/fcell.2020.00546] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
Brain cancers are the leading cause of cancer-related deaths in children. Biological changes in these tumors likely include epigenetic deregulation during embryonal development of the nervous system. Histone acetylation is one of the most widely investigated epigenetic processes, and histone deacetylase inhibitors (HDACis) are increasingly important candidate treatments in many cancer types. Here, we review advances in our understanding of how HDACis display antitumor effects in experimental models of specific pediatric brain tumor types, i.e., medulloblastoma (MB), ependymoma (EPN), pediatric high-grade gliomas (HGGs), and rhabdoid and atypical teratoid/rhabdoid tumors (ATRTs). We also discuss clinical perspectives for the use of HDACis in the treatment of pediatric brain tumors.
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Affiliation(s)
- Alexandre Perla
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Lívia Fratini
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Paula S Cardoso
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Carolina Nör
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - André T Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Algemir L Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Mariane Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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14
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Anti-leukemic effects of histone deacetylase (HDAC) inhibition in acute lymphoblastic leukemia (ALL) cells: Shedding light on mitigating effects of NF-κB and autophagy on panobinostat cytotoxicity. Eur J Pharmacol 2020; 875:173050. [PMID: 32142770 DOI: 10.1016/j.ejphar.2020.173050] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/22/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022]
Abstract
Identification of the roles of epigenetic alterations in cancers has suggested that different molecules involved in this process are potentially therapeutic targets. Given the role of histone deacetylases (HDACs) enzymes in leukemogenesis, we designed a study to investigate the anti-leukemic property of panobinostat, a HDAC inhibitor, in acute lymphoblastic leukemia (ALL) cells. Our results showed that panobinostat decreased cell viability of pre-B ALL-derived cells. The favorable anti-leukemic effects of the inhibitor was further confirmed by cell cycle analysis, where we found that panobinostat prolonged the transition of the cells from G1 phase probably through c-Myc-mediated up-regulation of cyclin-dependent kinase inhibitors. Unlike the apoptotic effect of panobinostat on Nalm-6 cells, the expression of anti-apoptotic nuclear factor-kappa B (NF-κB) target genes remained unchanged. Accordingly, we found that the inhibition of NF-κB pathway using bortezomib boosted the effect of panobinostat, indicating that panobinostat-induced apoptosis could be attenuated through the activation of the NF-κB pathway. The results of the present study reflected another aspect of autophagy in leukemic cells, as we showed that although Nalm-6 cells could exploit autophagy to override the anti-survival effect of HDAC inhibition, the presence of an autophagy inhibitor could alter the compensatory circumstance to induce cell death. Beyond panobinostat cytotoxicity as a single agent, synergistic experiments outlined that pharmaceutical targeting of HDACs could amplify the cytotoxicity of vincristine in ALL cells, delineating that panobinostat, either as a single agent or in a combined modality, possesses novel promising potentials for the treatment of ALL.
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15
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da Cunha Jaeger M, Ghisleni EC, Cardoso PS, Siniglaglia M, Falcon T, Brunetto AT, Brunetto AL, de Farias CB, Taylor MD, Nör C, Ramaswamy V, Roesler R. HDAC and MAPK/ERK Inhibitors Cooperate To Reduce Viability and Stemness in Medulloblastoma. J Mol Neurosci 2020; 70:981-992. [PMID: 32056089 DOI: 10.1007/s12031-020-01505-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023]
Abstract
Medulloblastoma (MB), which originates from embryonic neural stem cells (NSCs) or neural precursors in the developing cerebellum, is the most common malignant brain tumor of childhood. Recurrent and metastatic disease is the principal cause of death and may be related to resistance within cancer stem cells (CSCs). Chromatin state is involved in maintaining signaling pathways related to stemness, and inhibition of histone deacetylase enzymes (HDAC) has emerged as an experimental therapeutic strategy to target this cell population. Here, we observed antitumor actions and changes in stemness induced by HDAC inhibition in MB. Analyses of tumor samples from patients with MB showed that the stemness markers BMI1 and CD133 are expressed in all molecular subgroups of MB. The HDAC inhibitor (HDACi) NaB reduced cell viability and expression of BMI1 and CD133 and increased acetylation in human MB cells. Enrichment analysis of genes associated with CD133 or BMI1 expression showed mitogen-activated protein kinase (MAPK)/ERK signaling as the most enriched processes in MB tumors. MAPK/ERK inhibition reduced expression of the stemness markers, hindered MB neurosphere formation, and its antiproliferative effect was enhanced by combination with NaB. These results suggest that combining HDAC and MAPK/ERK inhibitors may be a novel and more effective approach in reducing MB proliferation when compared to single-drug treatments, through modulation of the stemness phenotype of MB cells.
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Affiliation(s)
- Mariane da Cunha Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Eduarda Chiesa Ghisleni
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Paula Schoproni Cardoso
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marialva Siniglaglia
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Tiago Falcon
- Bioinformatics Core, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - André T Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Algemir L Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Children's Cancer Institute, Porto Alegre, RS, Brazil
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
| | - Carolina Nör
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Rua Sarmento Leite, 500 (ICBS, Campus Centro/UFRGS), Porto Alegre, RS, 90050-170, Brazil.
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16
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Ballabio C, Anderle M, Gianesello M, Lago C, Miele E, Cardano M, Aiello G, Piazza S, Caron D, Gianno F, Ciolfi A, Pedace L, Mastronuzzi A, Tartaglia M, Locatelli F, Ferretti E, Giangaspero F, Tiberi L. Modeling medulloblastoma in vivo and with human cerebellar organoids. Nat Commun 2020; 11:583. [PMID: 31996670 PMCID: PMC6989674 DOI: 10.1038/s41467-019-13989-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/06/2019] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children and among the subtypes, Group 3 MB has the worst outcome. Here, we perform an in vivo, patient-specific screen leading to the identification of Otx2 and c-MYC as strong Group 3 MB inducers. We validated our findings in human cerebellar organoids where Otx2/c-MYC give rise to MB-like organoids harboring a DNA methylation signature that clusters with human Group 3 tumors. Furthermore, we show that SMARCA4 is able to reduce Otx2/c-MYC tumorigenic activity in vivo and in human cerebellar organoids while SMARCA4 T910M, a mutant form found in human MB patients, inhibits the wild-type protein function. Finally, treatment with Tazemetostat, a EZH2-specific inhibitor, reduces Otx2/c-MYC tumorigenesis in ex vivo culture and human cerebellar organoids. In conclusion, human cerebellar organoids can be efficiently used to understand the role of genes found altered in cancer patients and represent a reliable tool for developing personalized therapies.
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Affiliation(s)
- Claudio Ballabio
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Marica Anderle
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Matteo Gianesello
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Chiara Lago
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Evelina Miele
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marina Cardano
- University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Silvano Piazza
- University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Davide Caron
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Francesca Gianno
- Department of Radiologic, Oncologic and Anatomo Pathological Sciences, University Sapienza of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Pediatrics, Sapienza, University of Rome, Rome, Italy
| | | | - Felice Giangaspero
- Department of Radiologic, Oncologic and Anatomo Pathological Sciences, University Sapienza of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy.
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17
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Choi SA, Lee C, Kwak PA, Park CK, Wang KC, Phi JH, Lee JY, Chong S, Kim SK. Histone deacetylase inhibitor panobinostat potentiates the anti-cancer effects of mesenchymal stem cell-based sTRAIL gene therapy against malignant glioma. Cancer Lett 2018; 442:161-169. [PMID: 30367915 DOI: 10.1016/j.canlet.2018.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 09/25/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022]
Abstract
Human adipose tissue-derived mesenchymal stem cells expressing the secreted form of the tumor necrosis factor-related apoptosis-inducing ligand (hAT-MSC.sTRAIL) have demonstrated therapeutic activity against various tumors in preclinical studies. However, the limited expression of TRAIL death receptors remains a challenge. We evaluated the therapeutic efficacy of panobinostat in enhancing the sensitivity of hAT-MSC.sTRAIL-mediated apoptosis in malignant glioma. Panobinostat effectively inhibited all malignant glioma cells (IC50, 0.03-0.23 μM), enhancing the expression of DRs, but not in hAT-MSCs. Combined treatment with hAT-MSC.sTRAIL and panobinostat significantly suppressed cell viability and enhanced apoptosis. In a diffuse intrinsic pontine glioma (DIPG) mouse model, the combined treatment induced decreases in tumor volume and prolonged survival. Our study demonstrates that panobinostat enhances the expression of TRAIL DRs and potentiates the anti-cancer effects of hAT-MSC.sTRAIL.
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Affiliation(s)
- Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Adolescent Cancer Center, Seoul National University Cancer Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chanhee Lee
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Adolescent Cancer Center, Seoul National University Cancer Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pil Ae Kwak
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Adolescent Cancer Center, Seoul National University Cancer Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Chang Wang
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Adolescent Cancer Center, Seoul National University Cancer Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Yeoun Lee
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Anatomy, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sangjoon Chong
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Adolescent Cancer Center, Seoul National University Cancer Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Adolescent Cancer Center, Seoul National University Cancer Hospital, Seoul, Republic of Korea; Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
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18
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Histone deacetylases inhibition: a potential diagnostic and therapeutic target for cancers. Hum Pathol 2018; 71:166-167. [DOI: 10.1016/j.humpath.2017.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/19/2017] [Indexed: 11/19/2022]
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Zwergel C, Romanelli A, Stazi G, Besharat ZM, Catanzaro G, Tafani M, Valente S, Mai A. Application of Small Epigenetic Modulators in Pediatric Medulloblastoma. Front Pediatr 2018; 6:370. [PMID: 30560106 PMCID: PMC6286966 DOI: 10.3389/fped.2018.00370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/12/2018] [Indexed: 12/17/2022] Open
Abstract
Medulloblastoma is one of the most frequent among pediatric brain tumors, and it has been classified in various subgroups. Some of them already benefit from quite good therapeutic options, whereas others urgently need novel therapeutic approaches. Epigenetic modulators have long been studied in various types of cancer. Within this review, we summarize the main preclinical studies regarding epigenetic targets (such as HDAC, SIRT, BET, EZH2, G9a, LSD1, and DNMT) inhibitors in medulloblastoma. Furthermore, we shed light on the increasing number of applications of drug combinations as well as hybrid compounds involving epigenetic mechanisms. Nevertheless, in the studies published so far, mainly un-specific or old modulators have been used, and the PKs (brain permeability) have not been well-evaluated. Thus, these findings should be considered as a starting point for further improvement and not as a final result.
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Affiliation(s)
- Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Annalisa Romanelli
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Giulia Stazi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | | | | | - Marco Tafani
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
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Yi J, Wu J. Epigenetic regulation in medulloblastoma. Mol Cell Neurosci 2017; 87:65-76. [PMID: 29269116 DOI: 10.1016/j.mcn.2017.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma is the most common malignant childhood brain tumor. The heterogeneous tumors are classified into four subgroups based on transcription profiles. Recent developments in genome-wide sequencing techniques have rapidly advanced the understanding of these tumors. The high percentages of somatic alterations of genes encoding chromatin regulators in all subgroups suggest that epigenetic deregulation is a major driver of medulloblastoma. In this report, we review the current understanding of epigenetic regulation in medulloblastoma with a focus on the functional studies of chromatin regulators in the initiation and progression of specific subgroups of medulloblastoma. We also discuss the potential usage of epigenetic inhibitors for medulloblastoma treatment.
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Affiliation(s)
- Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
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