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Gomez RL, Woods LM, Ramachandran R, Abou Tayoun AN, Philpott A, Ali FR. Super-enhancer associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells. Front Cell Dev Biol 2022; 10:943924. [PMID: 36147741 PMCID: PMC9485839 DOI: 10.3389/fcell.2022.943924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Neuroblastoma is a pediatric tumour that accounts for more than 15% of cancer-related deaths in children. High-risk tumours are often difficult to treat, and patients' survival chances are less than 50%. Retinoic acid treatment is part of the maintenance therapy given to neuroblastoma patients; however, not all tumours differentiate in response to retinoic acid. Within neuroblastoma tumors, two phenotypically distinct cell types have been identified based on their super-enhancer landscape and transcriptional core regulatory circuitries: adrenergic (ADRN) and mesenchymal (MES). We hypothesized that the distinct super-enhancers in these different tumour cells mediate differential response to retinoic acid. To this end, three different neuroblastoma cell lines, ADRN (MYCN amplified and non-amplified) and MES cells, were treated with retinoic acid, and changes in the super-enhancer landscape upon treatment and after subsequent removal of retinoic acid was studied. Using ChIP-seq for the active histone mark H3K27ac, paired with RNA-seq, we compared the super-enhancer landscape in cells that undergo neuronal differentiation in response to retinoic acid versus those that fail to differentiate and identified unique super-enhancers associated with neuronal differentiation. Among the ADRN cells that respond to treatment, MYCN-amplified cells remain differentiated upon removal of retinoic acid, whereas MYCN non-amplified cells revert to an undifferentiated state, allowing for the identification of super-enhancers responsible for maintaining differentiation. This study identifies key super-enhancers that are crucial for retinoic acid-mediated differentiation.
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Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Laura M. Woods
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ahmad N. Abou Tayoun
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
| | - Anna Philpott
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad R. Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Li J, Wang Y, Li L, Or PMY, Wai Wong C, Liu T, Ho WLH, Chan AM. Tumour-derived substrate-adherent cells promote neuroblastoma survival through secreted trophic factors. Mol Oncol 2021; 15:2011-2025. [PMID: 33932101 PMCID: PMC8334291 DOI: 10.1002/1878-0261.12969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/10/2021] [Accepted: 04/14/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumour in children. NB is highly heterogeneous and is comprised of a mixture of neuroblastic cancer cells and stromal cells. We previously reported that N‐type cells (neuroblastic cells) and S‐type cells (substrate‐adherent cells) in the SK‐N‐SH cell line shared almost identical genetic backgrounds. Sublines of N‐ and S‐type cells were isolated from an early passage (P35) of SK‐N‐SH. Sequencing analysis revealed that all sublines harboured the anaplastic lymphoma kinase (ALK) F1174L mutation, indicating that they were tumour derived. Surprisingly, over 74% resembled S‐type cells. In coculture experiments, S‐type cells protected N‐type cells from apoptosis induced by the oncogenic ALK inhibitor TAE684. Western blotting analyses showed that ALK, protein kinase A (AKT) and STAT3 signalling were stimulated in the cocultures. Furthermore, the conditioned medium from S‐type cells activated these downstream signalling molecules in the N‐type cells. The activation of STAT3 in the N‐type cells was ALK‐independent, while AKT was regulated by the ALK activation status. To identify the responsible soluble factors, we used a combination of transcriptomic and proteomic analysis and found that plasminogen activator inhibitor 1, secreted protein acidic and cysteine rich, periostin and galectin‐1 were potential mediators of STAT3 signalling. The addition of recombinant proteins to the tumour cells treated with the ALK inhibitor partially enhanced cell viability. Overall, the tumour‐derived S‐type cells prevented apoptosis in the N‐type cells via ALK‐independent STAT3 activation triggered by secreted factors. The inhibition of these factors in combination with ALK inhibition could provide a new direction for targeted therapies to treat high‐risk NB.
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Affiliation(s)
- Jing Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yubing Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lisha Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Penelope M-Y Or
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chi Wai Wong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tian Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wayne L H Ho
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Andrew M Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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ALK positively regulates MYCN activity through repression of HBP1 expression. Oncogene 2018; 38:2690-2705. [PMID: 30538293 DOI: 10.1038/s41388-018-0595-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 05/03/2018] [Accepted: 10/23/2018] [Indexed: 02/08/2023]
Abstract
ALK mutations occur in 10% of primary neuroblastomas and represent a major target for precision treatment. In combination with MYCN amplification, ALK mutations infer an ultra-high-risk phenotype resulting in very poor patient prognosis. To open up opportunities for future precision drugging, a deeper understanding of the molecular consequences of constitutive ALK signaling and its relationship to MYCN activity in this aggressive pediatric tumor entity will be essential. We show that mutant ALK downregulates the 'HMG-box transcription factor 1' (HBP1) through the PI3K-AKT-FOXO3a signaling axis. HBP1 inhibits both the transcriptional activating and repressing activity of MYCN, the latter being mediated through PRC2 activity. HBP1 itself is under negative control of MYCN through miR-17~92. Combined targeting of HBP1 by PI3K antagonists and MYCN signaling by BET- or HDAC-inhibitors blocks MYCN activity and significantly reduces tumor growth, suggesting a novel targeted therapy option for high-risk neuroblastoma.
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Claeys S, Denecker G, Cannoodt R, Kumps C, Durinck K, Speleman F, De Preter K. Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome. Oncotarget 2017; 8:106820-106832. [PMID: 29290991 PMCID: PMC5739776 DOI: 10.18632/oncotarget.22423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/17/2017] [Indexed: 11/25/2022] Open
Abstract
Background Neuroblastoma is an aggressive childhood malignancy of the sympathetic nervous system. Despite multi-modal therapy, survival of high-risk patients remains disappointingly low, underscoring the need for novel treatment strategies. The discovery of ALK activating mutations opened the way to precision treatment in a subset of these patients. Previously, we investigated the transcriptional effects of pharmacological ALK inhibition on neuroblastoma cell lines, six hours after TAE684 administration, resulting in the 77-gene ALK signature, which was shown to gradually decrease from 120 minutes after TAE684 treatment, to gain deeper insight into the molecular effects of oncogenic ALK signaling. Aim Here, we further dissected the transcriptional dynamic profiles of neuroblastoma cells upon TAE684 treatment in a detailed timeframe of ten minutes up to six hours after inhibition, in order to identify additional early targets for combination treatment. Results We observed an unexpected initial upregulation of positively regulated MYCN target genes following subsequent downregulation of overall MYCN activity. In addition, we identified adrenomedullin (ADM), previously shown to be implicated in sunitinib resistance, as the earliest response gene upon ALK inhibition. Conclusions We describe the early and late effects of ALK inhibitor TAE684 treatment on the neuroblastoma transcriptome. The observed unexpected upregulation of ADM warrants further investigation in relation to putative ALK resistance in neuroblastoma patients currently undergoing ALK inhibitor treatment.
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Affiliation(s)
- Shana Claeys
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Geertrui Denecker
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent, Belgium.,Data Mining and Modelling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium.,Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | - Candy Kumps
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Department of Uro-Gynaecology, Ghent University Hospital, Ghent, Belgium
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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Westhoff MA, Karpel-Massler G, Brühl O, Enzenmüller S, La Ferla-Brühl K, Siegelin MD, Nonnenmacher L, Debatin KM. A critical evaluation of PI3K inhibition in Glioblastoma and Neuroblastoma therapy. MOLECULAR AND CELLULAR THERAPIES 2014; 2:32. [PMID: 26056598 PMCID: PMC4452069 DOI: 10.1186/2052-8426-2-32] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/16/2014] [Indexed: 12/11/2022]
Abstract
Members of the PI3K/Akt/mTor signaling cascade are among the most frequently altered proteins in cancer, yet the therapeutic application of pharmacological inhibitors of this signaling network, either as monotherapy or in combination therapy (CT) has so far not been particularly successful. In this review we will focus on the role of PI3K/Akt/mTOR in two distinct tumors, Glioblastoma multiforme (GBM), an adult brain tumor which frequently exhibits PTEN inactivation, and Neuroblastoma (NB), a childhood malignancy that affects the central nervous system and does not harbor any classic alterations in PI3K/Akt signaling. We will argue that inhibitors of PI3K/Akt signaling can be components for potentially promising new CTs in both tumor entities, but further understanding of the signal cascade's complexity is essential for successful implementation of these CTs. Importantly, failure to do this might lead to severe adverse effects, such as treatment failure and enhanced therapy resistance.
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Affiliation(s)
- Mike-Andrew Westhoff
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Georg Karpel-Massler
- Department of Neurosurgery, University Medical Center Ulm, Ulm, Germany ; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY USA
| | - Oliver Brühl
- Laboratorio Analisi Sicilia Catania, Lentini, SR Italy
| | - Stefanie Enzenmüller
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | | | - Markus D Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY USA
| | - Lisa Nonnenmacher
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
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Westhoff MA, Karpel-Massler G, Brühl O, Enzenmüller S, La Ferla-Brühl K, Siegelin MD, Nonnenmacher L, Debatin KM. A critical evaluation of PI3K inhibition in Glioblastoma and Neuroblastoma therapy. MOLECULAR AND CELLULAR THERAPIES 2014; 2:32. [PMID: 26056598 PMCID: PMC4452069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/16/2014] [Indexed: 11/21/2023]
Abstract
Members of the PI3K/Akt/mTor signaling cascade are among the most frequently altered proteins in cancer, yet the therapeutic application of pharmacological inhibitors of this signaling network, either as monotherapy or in combination therapy (CT) has so far not been particularly successful. In this review we will focus on the role of PI3K/Akt/mTOR in two distinct tumors, Glioblastoma multiforme (GBM), an adult brain tumor which frequently exhibits PTEN inactivation, and Neuroblastoma (NB), a childhood malignancy that affects the central nervous system and does not harbor any classic alterations in PI3K/Akt signaling. We will argue that inhibitors of PI3K/Akt signaling can be components for potentially promising new CTs in both tumor entities, but further understanding of the signal cascade's complexity is essential for successful implementation of these CTs. Importantly, failure to do this might lead to severe adverse effects, such as treatment failure and enhanced therapy resistance.
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Affiliation(s)
- Mike-Andrew Westhoff
- />Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Georg Karpel-Massler
- />Department of Neurosurgery, University Medical Center Ulm, Ulm, Germany
- />Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY USA
| | - Oliver Brühl
- />Laboratorio Analisi Sicilia Catania, Lentini, SR Italy
| | - Stefanie Enzenmüller
- />Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | | | - Markus D Siegelin
- />Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY USA
| | - Lisa Nonnenmacher
- />Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Klaus-Michael Debatin
- />Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
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Abstract
The burgeoning field of anaplastic lymphoma kinase (ALK) in cancer encompasses many cancer types, from very rare cancers to the more prevalent non-small-cell lung cancer (NSCLC). The common activation of ALK has led to the use of the ALK tyrosine kinase inhibitor (TKI) crizotinib in a range of patient populations and to the rapid development of second-generation drugs targeting ALK. In this Review, we discuss our current understanding of ALK function in human cancer and the implications for tumour treatment.
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MESH Headings
- Anaplastic Lymphoma Kinase
- Animals
- Antineoplastic Agents/therapeutic use
- Caenorhabditis elegans Proteins/physiology
- Cell Transformation, Neoplastic/genetics
- Clinical Trials as Topic
- Crizotinib
- Drosophila Proteins/physiology
- Drug Resistance, Neoplasm
- Enzyme Induction
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphoma, Large-Cell, Anaplastic/enzymology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Mice
- Models, Biological
- Models, Molecular
- Mutation
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Neoplasms/drug therapy
- Neoplasms/enzymology
- Neoplasms/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/physiology
- Protein Conformation
- Protein-Tyrosine Kinases/physiology
- Pyrazoles/therapeutic use
- Pyridines/therapeutic use
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/physiology
- Signal Transduction
- Translocation, Genetic
- Zebrafish Proteins/physiology
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Affiliation(s)
- Bengt Hallberg
- Department of Molecular Biology, Building 6L, Umeå University, Umeå S-90187, Sweden
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8
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Wu D, Yu H, Li J. [Mechanisms of resistance to EML4-ALK inhibitors in non-small cell lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2013; 16:48-53. [PMID: 23327874 PMCID: PMC6000462 DOI: 10.3779/j.issn.1009-3419.2013.01.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Di Wu
- Department of Medical Oncology, Jilin Province Tumor Hospital, Changchun 130012, China;Tumor Center, First Hospital of Jilin University, Changchun 130021, China
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