1
|
Buckley DN, Tew BY, Gooden C, Salhia B. A comprehensive analysis of minimally differentially methylated regions common to pediatric and adult solid tumors. NPJ Precis Oncol 2024; 8:125. [PMID: 38824198 PMCID: PMC11144230 DOI: 10.1038/s41698-024-00590-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2024] [Indexed: 06/03/2024] Open
Abstract
Cancer is the second most common cause of death in children aged 1-14 years in the United States, with 11,000 new cases and 1200 deaths annually. Pediatric cancers typically have lower mutational burden compared to adult-onset cancers, however, the epigenomes in pediatric cancer are highly altered, with widespread DNA methylation changes. The rarity of pediatric cancers poses a significant challenge to developing cancer-type specific biomarkers for diagnosis, prognosis, or treatment monitoring. In the current study, we explored the potential of a DNA methylation profile common across various pediatric cancers. To do this, we conducted whole genome bisulfite sequencing (WGBS) on 31 recurrent pediatric tumor tissues, 13 normal tissues, and 20 plasma cell-free (cf)DNA samples, representing 11 different pediatric cancer types. We defined minimal focal regions that were differentially methylated across samples in the multiple cancer types which we termed minimally differentially methylated regions (mDMRs). These methylation changes were also observed in 506 pediatric and 5691 adult cancer samples accessed from publicly available databases, and in 44 pediatric cancer samples we analyzed using a targeted hybridization probe capture assay. Finally, we found that these methylation changes were detectable in cfDNA and could serve as potential cfDNA methylation biomarkers for early detection or minimal residual disease.
Collapse
Affiliation(s)
- David N Buckley
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ben Yi Tew
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chris Gooden
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
2
|
Glunčić M, Vlahović I, Rosandić M, Paar V. Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly. Sci Rep 2023; 13:14420. [PMID: 37660151 PMCID: PMC10475015 DOI: 10.1038/s41598-023-41517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
Collapse
Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia.
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (Ret.), 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
| |
Collapse
|
3
|
Agarwal P, Glowacka A, Mahmoud L, Bazzar W, Larsson LG, Alzrigat M. MYCN Amplification Is Associated with Reduced Expression of Genes Encoding γ-Secretase Complex and NOTCH Signaling Components in Neuroblastoma. Int J Mol Sci 2023; 24:8141. [PMID: 37175848 PMCID: PMC10179553 DOI: 10.3390/ijms24098141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Amplification of the MYCN oncogene is found in ~20% of neuroblastoma (NB) cases and correlates with high-risk disease and poor prognosis. Despite the plethora of studies describing the role of MYCN in NB, the exact molecular mechanisms underlying MYCN's contribution to high-risk disease are not completely understood. Herein, we implemented an integrative approach combining publicly available RNA-Seq and MYCN ChIP-Seq datasets derived from human NB cell lines to define biological processes directly regulated by MYCN in NB. Our approach revealed that MYCN-amplified NB cell lines, when compared to non-MYCN-amplified cell lines, are characterized by reduced expression of genes involved in NOTCH receptor processing, axoneme assembly, and membrane protein proteolysis. More specifically, we found genes encoding members of the γ-secretase complex, which is known for its ability to liberate several intracellular signaling molecules from membrane-bound proteins such as NOTCH receptors, to be down-regulated in MYCN-amplified NB cell lines. Analysis of MYCN ChIP-Seq data revealed an enrichment of MYCN binding at the transcription start sites of genes encoding γ-secretase complex subunits. Notably, using publicly available gene expression data from NB primary tumors, we revealed that the expression of γ-secretase subunits encoding genes and other components of the NOTCH signaling pathway was also reduced in MYCN-amplified tumors and correlated with worse overall survival in NB patients. Genetic or pharmacological depletion of MYCN in NB cell lines induced the expression of γ-secretase genes and NOTCH-target genes. Chemical inhibition of γ-secretase activity dampened the expression of NOTCH-target genes upon MYCN depletion in NB cells. In conclusion, this study defines a set of MYCN-regulated pathways that are specific to MYCN-amplified NB tumors, and it suggests a novel role for MYCN in the suppression of genes of the γ-secretase complex, with an impact on the NOTCH-target gene expression in MYCN-amplified NB.
Collapse
Affiliation(s)
- Prasoon Agarwal
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, 22362 Lund, Sweden
| | - Aleksandra Glowacka
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Loay Mahmoud
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Wesam Bazzar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
- Department of Pharmaceutical Biosciences, Biomedical Center, Uppsala University, 75124 Uppsala, Sweden
| | - Lars-Gunnar Larsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
- Department of Pharmaceutical Biosciences, Biomedical Center, Uppsala University, 75124 Uppsala, Sweden
| | - Mohammad Alzrigat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
- Department of Pharmaceutical Biosciences, Biomedical Center, Uppsala University, 75124 Uppsala, Sweden
| |
Collapse
|
4
|
MYCN in Neuroblastoma: "Old Wine into New Wineskins". Diseases 2021; 9:diseases9040078. [PMID: 34842635 PMCID: PMC8628738 DOI: 10.3390/diseases9040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
MYCN Proto-Oncogene, BHLH Transcription Factor (MYCN) has been one of the most studied genes in neuroblastoma. It is known for its oncogenetic mechanisms, as well as its role in the prognosis of the disease and it is considered one of the prominent targets for neuroblastoma therapy. In the present work, we attempted to review the literature, on the relation between MYCN and neuroblastoma from all possible mechanistic sites. We have searched the literature for the role of MYCN in neuroblastoma based on the following topics: the references of MYCN in the literature, the gene's anatomy, along with its transcripts, the protein's anatomy, the epigenetic mechanisms regulating MYCN expression and function, as well as MYCN amplification. MYCN plays a significant role in neuroblastoma biology. Its functions and properties range from the forming of G-quadraplexes, to the interaction with miRNAs, as well as the regulation of gene methylation and histone acetylation and deacetylation. Although MYCN is one of the most primary genes studied in neuroblastoma, there is still a lot to be learned. Our knowledge on the exact mechanisms of MYCN amplification, etiology and potential interventions is still limited. The knowledge on the molecular mechanisms of MYCN in neuroblastoma, could have potential prognostic and therapeutic advantages.
Collapse
|
5
|
Parodi S, Pistorio A, Erminio G, Ognibene M, Morini M, Garaventa A, Gigliotti AR, Haupt R, Frassoni F, Pezzolo A. Loss of whole chromosome X predicts prognosis of neuroblastoma patients with numerical genomic profile. Pediatr Blood Cancer 2019; 66:e27635. [PMID: 30688024 DOI: 10.1002/pbc.27635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/17/2018] [Accepted: 01/05/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND Neuroblastoma (NB), a pediatric tumor of the sympathetic nervous system, is characterized by very frequent chromosomal aberrations at the onset of the disease. Identification of further risk factors for relapse, which could lead to increased survival and potentially reduced late effects among survivors, is still urgently needed. Segmental chromosome aberrations (SCA) are associated with poor prognosis, whereas numerical whole-chromosome aberrations (NCA) are found in patients with a good prognosis; however, a small percentage of the latter patients (10%-15%) subsequently relapse and/or die of disease. PROCEDURE DNA copy-number data from 174 NB patients with an NCA genomic profile were analyzed. Association between NCA and event-free survival (EFS) was investigated by the Kaplan-Meier estimator and prognostic decision tree (DT). RESULTS DT identified 65 patients with normal chromosome X and an excellent five-year EFS (100%) independently from the stage at diagnosis. The association between poor EFS and whole chromosome X alterations was confirmed after stratification into two groups of different expected prognosis and by internal validation via bootstrap analysis. Furthermore, the association was also observed in an independent cohort of NB patients extracted from the data set of the National Cancer Institute TARGET Project for Neuroblastoma, but sample size was small (n = 75) and statistical significance was not achieved. CONCLUSIONS Loss of whole chromosome X may represent a new prognostic marker for NB patients with an NCA genomic profile. If confirmed by further studies, this finding could indicate that such patients should be reclassified as intermediate risk and treated accordingly.
Collapse
Affiliation(s)
- Stefano Parodi
- Epidemiologia e Biostatistica, IRCCS Istituto Giannina, Genova, Italy
| | - Angela Pistorio
- Epidemiologia e Biostatistica, IRCCS Istituto Giannina, Genova, Italy
| | - Giovanni Erminio
- Epidemiologia e Biostatistica, IRCCS Istituto Giannina, Genova, Italy
| | - Marzia Ognibene
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina, Genova, Italy
| | - Martina Morini
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina, Genova, Italy
| | - Alberto Garaventa
- Dipartimento di Emato-oncologia, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | - Riccardo Haupt
- Epidemiologia e Biostatistica, IRCCS Istituto Giannina, Genova, Italy
| | - Francesco Frassoni
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina, Genova, Italy
| | - Annalisa Pezzolo
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina, Genova, Italy
| |
Collapse
|
6
|
Sakka L, Delétage N, Chalus M, Aissouni Y, Sylvain-Vidal V, Gobron S, Coll G. Assessment of citalopram and escitalopram on neuroblastoma cell lines. Cell toxicity and gene modulation. Oncotarget 2018; 8:42789-42807. [PMID: 28467792 PMCID: PMC5522106 DOI: 10.18632/oncotarget.17050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/15/2017] [Indexed: 12/13/2022] Open
Abstract
Selective serotonin reuptake inhibitors (SSRI) are common antidepressants which cytotoxicity has been assessed in cancers notably colorectal carcinomas and glioma cell lines. We assessed and compared the cytotoxicity of 2 SSRI, citalopram and escitalopram, on neuroblastoma cell lines. The study was performed on 2 non-MYCN amplified cell lines (rat B104 and human SH-SY5Y) and 2 human MYCN amplified cell lines (IMR32 and Kelly). Citalopram and escitalopram showed concentration-dependent cytotoxicity on all cell lines. Citalopram was more cytotoxic than escitalopram. IMR32 was the most sensitive cell line. The absence of toxicity on human primary Schwann cells demonstrated the safety of both molecules for myelin. The mechanisms of cytotoxicity were explored using gene-expression profiles and quantitative real-time PCR (qPCR). Citalopram modulated 1 502 genes and escitalopram 1 164 genes with a fold change ≥ 2. 1 021 genes were modulated by both citalopram and escitalopram; 481 genes were regulated only by citalopram while 143 genes were regulated only by escitalopram. Citalopram modulated 69 pathways (KEGG) and escitalopram 42. Ten pathways were differently modulated by citalopram and escitalopram. Citalopram drastically decreased the expression of MYBL2, BIRC5 and BARD1 poor prognosis factors of neuroblastoma with fold-changes of -107 (p<2.26 10−7), -24.1 (p<5.6 10−9) and -17.7 (p<1.2 10−7). CCNE1, AURKA, IGF2, MYCN and ERBB2 were more moderately down-regulated by both molecules. Glioma markers E2F1, DAPK1 and CCND1 were down-regulated. Citalopram displayed more powerful action with broader and distinct spectrum of action than escitalopram.
Collapse
Affiliation(s)
- Laurent Sakka
- Laboratoire d'Anatomie et d'Organogenèse, Laboratoire de Biophysique Sensorielle, NeuroDol, Faculté de Médecine, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.,Service de Neurochirurgie, Pole RMND, CHU de Clermont-Ferrand, Hôpital Gabriel-Montpied, 63003 Clermont-Ferrand Cedex, France
| | - Nathalie Delétage
- Neuronax SAS, Biopôle Clermont-Limagne, F-63360 Saint-Beauzire, France
| | - Maryse Chalus
- Laboratoire d'Anatomie et d'Organogenèse, Laboratoire de Biophysique Sensorielle, NeuroDol, Faculté de Médecine, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Youssef Aissouni
- Laboratoire de Pharmacologie Fondamentale et Clinique de la Douleur, NeuroDol, Faculté de Médecine, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | | | - Stéphane Gobron
- Neuronax SAS, Biopôle Clermont-Limagne, F-63360 Saint-Beauzire, France
| | - Guillaume Coll
- Service de Neurochirurgie, Pole RMND, CHU de Clermont-Ferrand, Hôpital Gabriel-Montpied, 63003 Clermont-Ferrand Cedex, France
| |
Collapse
|
7
|
Swift CC, Eklund MJ, Kraveka JM, Alazraki AL. Updates in Diagnosis, Management, and Treatment of Neuroblastoma. Radiographics 2018. [DOI: 10.1148/rg.2018170132] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Caroline C. Swift
- From the Department of Radiology and Radiological Science (C.C.S., M.J.E.) and Department of Pediatrics (J.M.K.), Medical University of South Carolina, 96 Jonathan Lucas St, MSC 323, Suite 210, Charleston, SC 29425; and Department of Radiology and Imaging Sciences, Emory University, Atlanta, Ga (A.L.A.)
| | - Meryle J. Eklund
- From the Department of Radiology and Radiological Science (C.C.S., M.J.E.) and Department of Pediatrics (J.M.K.), Medical University of South Carolina, 96 Jonathan Lucas St, MSC 323, Suite 210, Charleston, SC 29425; and Department of Radiology and Imaging Sciences, Emory University, Atlanta, Ga (A.L.A.)
| | - Jacqueline M. Kraveka
- From the Department of Radiology and Radiological Science (C.C.S., M.J.E.) and Department of Pediatrics (J.M.K.), Medical University of South Carolina, 96 Jonathan Lucas St, MSC 323, Suite 210, Charleston, SC 29425; and Department of Radiology and Imaging Sciences, Emory University, Atlanta, Ga (A.L.A.)
| | - Adina L. Alazraki
- From the Department of Radiology and Radiological Science (C.C.S., M.J.E.) and Department of Pediatrics (J.M.K.), Medical University of South Carolina, 96 Jonathan Lucas St, MSC 323, Suite 210, Charleston, SC 29425; and Department of Radiology and Imaging Sciences, Emory University, Atlanta, Ga (A.L.A.)
| |
Collapse
|
8
|
Liu PY, Sokolowski N, Guo ST, Siddiqi F, Atmadibrata B, Telfer TJ, Sun Y, Zhang L, Yu D, Mccarroll J, Liu B, Yang RH, Guo XY, Tee AE, Itoh K, Wang J, Kavallaris M, Haber M, Norris MD, Cheung BB, Byrne JA, Ziegler DS, Marshall GM, Dinger ME, Codd R, Zhang XD, Liu T. The BET bromodomain inhibitor exerts the most potent synergistic anticancer effects with quinone-containing compounds and anti-microtubule drugs. Oncotarget 2018; 7:79217-79232. [PMID: 27764794 PMCID: PMC5346709 DOI: 10.18632/oncotarget.12640] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/28/2016] [Indexed: 11/25/2022] Open
Abstract
BET bromodomain inhibitors are very promising novel anticancer agents, however, single therapy does not cause tumor regression in mice, suggesting the need for combination therapy. After screening a library of 2697 small molecule compounds, we found that two classes of compounds, the quinone-containing compounds such as nanaomycin and anti-microtubule drugs such as vincristine, exerted the best synergistic anticancer effects with the BET bromodomain inhibitor JQ1 in neuroblastoma cells. Mechanistically, the quinone-containing compound nanaomycin induced neuroblastoma cell death but also activated the Nrf2-antioxidant signaling pathway, and the BET bromodomain proteins BRD3 and BRD4 formed a protein complex with Nrf2. Treatment with JQ1 blocked the recruitment of Nrf2 to the antioxidant responsive elements at Nrf2 target gene promoters, and JQ1 exerted synergistic anticancer effects with nanaomycin by blocking the Nrf2-antioxidant signaling pathway. JQ1 and vincristine synergistically induced neuroblastoma cell cycle arrest at the G2/M phase, aberrant mitotic spindle assembly formation and apoptosis, but showed no effect on cell survival in normal non-malignant cells. Importantly, co-treatment with JQ1 and vincristine synergistically suppressed tumor progression in neuroblastoma-bearing mice. These results strongly suggest that patients treated with BET bromodomain inhibitors in clinical trials should be co-treated with vincristine.
Collapse
Affiliation(s)
- Pei Y Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Nicholas Sokolowski
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Su T Guo
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Faraz Siddiqi
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Bernard Atmadibrata
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Thomas J Telfer
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, Australia
| | - Yuting Sun
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Lihong Zhang
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Denise Yu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Joshua Mccarroll
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Bing Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Rui H Yang
- Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Affiliated Hospital of Shanxi Medical University, Shanxi, China
| | - Xiang Y Guo
- Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Affiliated Hospital of Shanxi Medical University, Shanxi, China
| | - Andrew E Tee
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Jenny Wang
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Centre for Childhood Cancer Research, University of New South Wales Medicine, University of New South Wales Australia, Sydney, Australia
| | - Maria Kavallaris
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Michelle Haber
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Murray D Norris
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Centre for Childhood Cancer Research, University of New South Wales Medicine, University of New South Wales Australia, Sydney, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Jennifer A Byrne
- Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, Australia
| | - David S Ziegler
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, Australia
| | - Glenn M Marshall
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales Medicine, University of New South Wales Australia, Darlinghurst, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, Australia
| | - Xu D Zhang
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.,Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Affiliated Hospital of Shanxi Medical University, Shanxi, China
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Centre for Childhood Cancer Research, University of New South Wales Medicine, University of New South Wales Australia, Sydney, Australia
| |
Collapse
|
9
|
Galli S, Naranjo A, Van Ryn C, Tilan JU, Trinh E, Yang C, Tsuei J, Hong SH, Wang H, Izycka-Swieszewska E, Lee YC, Rodriguez OC, Albanese C, Kitlinska J. Neuropeptide Y as a Biomarker and Therapeutic Target for Neuroblastoma. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:3040-3053. [PMID: 27743558 DOI: 10.1016/j.ajpath.2016.07.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 12/17/2022]
Abstract
Neuroblastoma (NB) is a pediatric malignant neoplasm of sympathoadrenal origin. Challenges in its management include stratification of this heterogeneous disease and a lack of both adequate treatments for high-risk patients and noninvasive biomarkers of disease progression. Our previous studies have identified neuropeptide Y (NPY), a sympathetic neurotransmitter expressed in NB, as a potential therapeutic target for these tumors by virtue of its Y5 receptor (Y5R)-mediated chemoresistance and Y2 receptor (Y2R)-mediated proliferative and angiogenic activities. The goal of this study was to determine the clinical relevance and utility of these findings. Expression of NPY and its receptors was evaluated in corresponding samples of tumor RNA, tissues, and sera from 87 patients with neuroblastic tumors and in tumor tissues from the TH-MYCN NB mouse model. Elevated serum NPY levels correlated with an adverse clinical presentation, poor survival, metastasis, and relapse, whereas strong Y5R immunoreactivity was a marker of angioinvasive tumor cells. In NB tissues from TH-MYCN mice, high immunoreactivity of both NPY and Y5R marked angioinvasive NB cells. Y2R was uniformly expressed in undifferentiated tumor cells, which supports its previously reported role in NB cell proliferation. Our findings validate NPY as a therapeutic target for advanced NB and implicate the NPY/Y5R axis in disease dissemination. The correlation between elevated systemic NPY and NB progression identifies serum NPY as a novel NB biomarker.
Collapse
Affiliation(s)
- Susana Galli
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Arlene Naranjo
- Department of Biostatistics, Children's Oncology Group Statistics & Data Center, University of Florida, Gainesville, Florida
| | - Collin Van Ryn
- Department of Biostatistics, Children's Oncology Group Statistics & Data Center, University of Florida, Gainesville, Florida
| | - Jason U Tilan
- Department of Nursing, School of Nursing and Health Studies, Georgetown University, Washington, District of Columbia; Department of Human Science, School of Nursing and Health Studies, Georgetown University, Washington, District of Columbia
| | - Emily Trinh
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Chao Yang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Jessica Tsuei
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Sung-Hyeok Hong
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Hongkun Wang
- Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, District of Columbia
| | - Ewa Izycka-Swieszewska
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Yi-Chien Lee
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Olga C Rodriguez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Chris Albanese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia; Department of Pathology, Georgetown University Medical Center, Washington, District of Columbia
| | - Joanna Kitlinska
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia.
| |
Collapse
|
10
|
Zhu S, Thomas Look A. Neuroblastoma and Its Zebrafish Model. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:451-78. [PMID: 27165366 DOI: 10.1007/978-3-319-30654-4_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neuroblastoma, an important developmental tumor arising in the peripheral sympathetic nervous system (PSNS), accounts for approximately 10 % of all cancer-related deaths in children. Recent genomic analyses have identified a spectrum of genetic alterations in this tumor. Amplification of the MYCN oncogene is found in 20 % of cases and is often accompanied by mutational activation of the ALK (anaplastic lymphoma kinase) gene, suggesting their cooperation in tumor initiation and spread. Understanding how complex genetic changes function together in oncogenesis has been a continuing and daunting task in cancer research. This challenge was addressed in neuroblastoma by generating a transgenic zebrafish model that overexpresses human MYCN and activated ALK in the PSNS, leading to tumors that closely resemble human neuroblastoma and new opportunities to probe the mechanisms that underlie the pathogenesis of this tumor. For example, coexpression of activated ALK with MYCN in this model triples the penetrance of neuroblastoma and markedly accelerates tumor onset, demonstrating the interaction of these modified genes in tumor development. Further, MYCN overexpression induces adrenal sympathetic neuroblast hyperplasia, blocks chromaffin cell differentiation, and ultimately triggers a developmentally-timed apoptotic response in the hyperplastic sympathoadrenal cells. In the context of MYCN overexpression, activated ALK provides prosurvival signals that block this apoptotic response, allowing continued expansion and oncogenic transformation of hyperplastic neuroblasts, thus promoting progression to neuroblastoma. This application of the zebrafish model illustrates its value in rational assessment of the multigenic changes that define neuroblastoma pathogenesis and points the way to future studies to identify novel targets for therapeutic intervention.
Collapse
Affiliation(s)
- Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Cancer Center and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55902, USA.
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
11
|
Selective inhibition of HDAC8 decreases neuroblastoma growth in vitro and in vivo and enhances retinoic acid-mediated differentiation. Cell Death Dis 2015; 6:e1657. [PMID: 25695609 PMCID: PMC4669789 DOI: 10.1038/cddis.2015.24] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/29/2014] [Accepted: 01/12/2015] [Indexed: 01/07/2023]
Abstract
For differentiation-defective malignancies, compounds that modulate transcription, such as retinoic acid and histone deacetylase (HDAC) inhibitors, are of particular interest. HDAC inhibitors are currently under investigation for the treatment of a broad spectrum of cancer diseases. However, one clinical drawback is class-specific toxicity of unselective inhibitors, limiting their full anticancer potential. Selective targeting of individual HDAC isozymes in defined tumor entities may therefore be an attractive alternative treatment approach. We have previously identified HDAC family member 8 (HDAC8) as a novel target in childhood neuroblastoma. Using small-molecule inhibitors, we now demonstrate that selective inhibition of HDAC8 exhibits antineuroblastoma activity without toxicity in two xenograft mouse models of MYCN oncogene-amplified neuroblastoma. In contrast, the unselective HDAC inhibitor vorinostat was more toxic in the same models. HDAC8-selective inhibition induced cell cycle arrest and differentiation in vitro and in vivo. Upon combination with retinoic acid, differentiation was significantly enhanced, as demonstrated by elongated neurofilament-positive neurites and upregulation of NTRK1. Additionally, MYCN oncogene expression was downregulated in vitro and tumor cell growth was markedly reduced in vivo. Mechanistic studies suggest that cAMP-response element-binding protein (CREB) links HDAC8- and retinoic acid-mediated gene transcription. In conclusion, HDAC-selective targeting can be effective in tumors exhibiting HDAC isozyme-dependent tumor growth in vivo and can be combined with differentiation-inducing agents.
Collapse
|
12
|
ALK: Anaplastic lymphoma kinase. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
13
|
Duijkers FAM, Meijerink JPP, Pieters R, van Noesel MM. Downregulation of Axl in non-MYCN amplified neuroblastoma cell lines reduces migration. Gene 2013; 521:62-8. [PMID: 23523856 DOI: 10.1016/j.gene.2013.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/07/2013] [Indexed: 12/14/2022]
Abstract
Neuroblastomas (NBL) are common pediatric solid tumors with a variable clinical course. At diagnosis half of all neuroblastoma patients presents with metastatic disease. The mechanisms of metastasis are largely unknown. Gene expression profiles (HU133plus2.0 arrays, Affymetrix) of 17 NBL and 5 peripheral neuro-ectodermal cell lines were used to identify a subgroup of non-MYCN amplified (non-NMA) NBL cell lines with a distinct gene expression profile and characterized by high expression of AXL. Axl is a tyrosine kinase receptor which plays a role in the metastatic process of several types of cancer. We hypothesized that Axl contributes to the metastasizing potential of non-NMA NBL and tested if AXL silencing diminishes malignant properties of high Axl expressing cell lines. AXL was silenced in two non-NMA NBL cell lines by using a lentiviral shRNA construct that was able to transduce these cell lines with more than 90% infection efficiency. Axl mRNA and protein level were efficiently knocked-down resulting in a decrease of migration of Axl positive cell lines GI-M-EN and SH-EP-2, and decreased invasion of GI-M-EN. Morphologically, Axl knockdown induced more rounded cells with a loss of contact. Intracellularly, we observed induction of stress fibers (immunofluorescence F-actin). These changes in cytoskeleton were associated with decreased migration, but were not accompanied by changes in genes involved in epithelial to mesenchymal transition such as CDH2, VIM or MMP9. No effects were observed for cell proliferation, apoptosis or downstream pathways. In conclusion, AXL is identified as a possible mediator of NBL metastasis.
Collapse
Affiliation(s)
- Floor A M Duijkers
- Department of Pediatric Oncology-Hematology, Erasmus MC-Sophia Children's Hospital, Dr. Molewaterplein 60, 3015 GJ Rotterdam, The Netherlands
| | | | | | | |
Collapse
|
14
|
Abstract
PURPOSE We evaluated in vitro the role of CO(2)-induced oxidative stress on the expression of proteins involved in cell-cycle regulation of neuroblastoma cells. METHODS SH-SY5Y cells were exposed to CO(2) at 15 mmHg pressure (100 %) for 4 h and then moved to normal condition for 24 h. Control cells were maintained in 5 % CO(2) for the same time. ROS production was determined by fluorescent staining with H2DCF-DA. DNA damage was measured by COMET assay. p53 protein expression was analyzed by western blot and confocal laser scanning microscopy was used to evaluate its sub-cellular localization. Cyclin expression was quantified by real-time PCR and western blot. Cell-cycle analysis was performed by FACS. RESULTS CO(2) incubation was associated with an increase in ROS production (p < 0.01), cell DNA damage mainly after 24 h (12 % increase of tail DNA content and 4-fold increase of tail length) and a significant up-regulation in p53 expression at 24 h with an intense nuclear staining. In CO(2)-treated cells, we observed an S-phase arrest in correlation with a reduction of cyclin B1 expression. CONCLUSIONS In vitro-simulated pneumoperitoneum environment with CO(2) induces oxidative stress and cell DNA damage, leading to p53 up-regulation involved in cell-cycle arrest of neuroblastoma cells.
Collapse
|
15
|
Jeison M, Yaniv I, Ash S. Genetic stratification of neuroblastoma for treatment tailoring. Future Oncol 2012; 7:1087-99. [PMID: 21919696 DOI: 10.2217/fon.11.87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Neuroblastoma is the most common extracranial tumor of childhood. The clinical behavior is variable, ranging from spontaneous regression to fatal progression despite aggressive therapy. The most highly statistically significant and clinically relevant factors that are currently used for classification include stage, age, histopathologic category, MYCN oncogene status, chromosome 11q status and DNA ploidy. These genetic markers were analyzed separately by classical methods until recently: mainly fluorescence in situ hybridization or loss of heterozygosity. The development of genome-wide techniques such as comparative genomic hybridization, array comparative genomic hybridization and single nucleotide polymorphism allows the analysis of copy number variations through the whole genome in one step. This enabled the investigators to refine different genetic subtypes for the better comprehension of neuroblastoma tumor behavior and reach the conclusion that these data together with a genomic profile based on gene expression should be included in future treatment stratification.
Collapse
Affiliation(s)
- Marta Jeison
- Department of Pediatric Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | | | | |
Collapse
|
16
|
Kwon MJ, Choi YL, Sung KW, Kang SY, Park SM, Choi SY, Kim JS, Suh YL. Oncogenic anaplastic lymphoma kinase (ALK) mutation in neuroblastomas and other pediatric tumors. Pathol Res Pract 2011; 207:634-9. [PMID: 21940108 DOI: 10.1016/j.prp.2011.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/14/2011] [Accepted: 07/30/2011] [Indexed: 11/28/2022]
Abstract
Neuroblastoma (NB) is one of the most common malignant pediatric tumors that show aggressive behavior. Most advanced-stage NBs have proven refractory to many treatment modalities, and a fundamental alternative therapy, such as inhibition of biological pathways, is now being explored. Anaplastic lymphoma kinase (ALK) has recently been identified as an activation mutation in familial or high-risk sporadic NBs. We examined the prevalence of the ALK mutation in 54 NB cases (23 pre-treatment cases and 31 cases for which specimens were available before and after treatment) and the presence of the ALK mutation in various pediatric tumors. We detected the ALK mutation (F1174C and R1275Q) in 2 (3.7%) of the 54 NB specimens. Both cases showed poorly differentiated and advanced-stage NBs. No ALK mutations were detected in other pediatric tumors. The frequency of the ALK mutation was somewhat lower than that expected in Korean patients with NBs. The mutation detected in the present study was one of the hotspot mutations, including positions of F1174 and R1275 reported previously. The results of the present study suggest the possibility of potential roles of ALK inhibitors in the therapeutics of a small population of neuroblastoma carrying mutated ALK kinases.
Collapse
Affiliation(s)
- Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F. Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. Int J Cancer 2011; 130:2599-606. [PMID: 21796619 DOI: 10.1002/ijc.26317] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/12/2011] [Indexed: 01/04/2023]
Abstract
Neuroblastoma is an aggressive embryonal tumor that accounts for ∼15% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p = 5.61 × 10(-5) ). Using ultra-high resolution (∼115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5-kb region, of which eight were found in a 7-kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4-Mb proximal. The commonly deleted region contains one miRNA (hsa-mir-1537), four transcribed ultra conserved region elements (uc.43-uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.
Collapse
Affiliation(s)
- Annelies Fieuw
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Neuroblastoma genetics and phenotype: a tale of heterogeneity. Semin Cancer Biol 2011; 21:238-44. [PMID: 21839839 DOI: 10.1016/j.semcancer.2011.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/13/2011] [Indexed: 12/31/2022]
Abstract
Cancer is a complex disease driven by multiple genetic and epigenetic alterations. Understanding the (epi-)genetic changes and consequent deregulation of regulatory networks controlling the various normal critical cellular phenotypes that are perturbed in cancer cells can provide clues to new therapeutic opportunities. Moreover, such insights into the molecular pathology of a given cancer type can offer clinical relevant genetic markers or molecular signatures for assessment of prognosis and response to therapy, and prediction of risk for relapse. Therefore, as for many other tumour entities, neuroblastoma (NB) has been the subject of intensive ongoing genomic research. Here we will summarize the current state-of-the-art of these studies with focus on genome wide DNA copy number and gene expression analyses in relation to the relevance for present and future clinical management of NB patients.
Collapse
|
19
|
Murphy DM, Buckley PG, Das S, Watters KM, Bryan K, Stallings RL. Co-localization of the oncogenic transcription factor MYCN and the DNA methyl binding protein MeCP2 at genomic sites in neuroblastoma. PLoS One 2011; 6:e21436. [PMID: 21731748 PMCID: PMC3120883 DOI: 10.1371/journal.pone.0021436] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/01/2011] [Indexed: 12/20/2022] Open
Abstract
Background MYCN is a transcription factor that is expressed during the development of the neural crest and its dysregulation plays a major role in the pathogenesis of pediatric cancers such as neuroblastoma, medulloblastoma and rhabdomyosarcoma. MeCP2 is a CpG methyl binding protein which has been associated with a number of cancers and developmental disorders, particularly Rett syndrome. Methods and Findings Using an integrative global genomics approach involving chromatin immunoprecipitation applied to microarrays, we have determined that MYCN and MeCP2 co-localize to gene promoter regions, as well as inter/intragenic sites, within the neuroblastoma genome (MYCN amplified Kelly cells) at high frequency (70.2% of MYCN sites were also positive for MeCP2). Intriguingly, the frequency of co-localization was significantly less at promoter regions exhibiting substantial hypermethylation (8.7%), as determined by methylated DNA immunoprecipitation (MeDIP) applied to the same microarrays. Co-immunoprecipitation of MYCN using an anti-MeCP2 antibody indicated that a MYCN/MeCP2 interaction occurs at protein level. mRNA expression profiling revealed that the median expression of genes with promoters bound by MYCN was significantly higher than for genes bound by MeCP2, and that genes bound by both proteins had intermediate expression. Pathway analysis was carried out for genes bound by MYCN, MeCP2 or MYCN/MeCP2, revealing higher order functions. Conclusions Our results indicate that MYCN and MeCP2 protein interact and co-localize to similar genomic sites at very high frequency, and that the patterns of binding of these proteins can be associated with significant differences in transcriptional activity. Although it is not yet known if this interaction contributes to neuroblastoma disease pathogenesis, it is intriguing that the interaction occurs at the promoter regions of several genes important for the development of neuroblastoma, including ALK, AURKA and BDNF.
Collapse
Affiliation(s)
- Derek M. Murphy
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Patrick G. Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sudipto Das
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Karen M. Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Kenneth Bryan
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- * E-mail:
| |
Collapse
|
20
|
Piqueras M, Navarro S, Cañete A, Castel V, Noguera R. Prognostic value of partial genetic instability in neuroblastoma with ≤50% neuroblastic cell content. Histopathology 2011; 59:22-30. [PMID: 21668478 DOI: 10.1111/j.1365-2559.2011.03899.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Better understanding of neuroblastoma genetics will improve with genome-wide techniques. However, performing these analyses in samples with <60% neuroblast cells is not adequate. We evaluated the utility of fluorescence in situ hybridization (FISH) on tissue microarrays (TMA) in detecting partial genetic instability (PGI), focusing on samples with ≤50% neuroblast cells. METHODS AND RESULTS Alterations of 11q and 17q were detected by FISH on 369 neuroblastoma samples in TMA. Status of the MYCN gene and 1p36 region has been established previously by FISH diagnosis. Partial genetic instability (PGI) was defined as the ratio between segmental genetic alterations detected and number of genetic markers diagnosed in each tumour. Of primary tumours, 14.6% harboured 11q deletions, whereas 42.6% showed 17q gain. PGI was established in 260 primary tumours, 67 of which contained ≤50% neuroblasts. Outcomes were statistically worse for patients whose tumours presented high PGI (P < 0.0001). Multivariate analysis revealed moderate and high PGI as prognostic factors. CONCLUSIONS In the cohort examined in this study, univariate and multivariate analysis confirmed the effect of PGI in patient outcome. PGI established by FISH on TMA is a useful method to identify high-risk patients even if tumours have a cell content of ≤50% neuroblast cells.
Collapse
Affiliation(s)
- Marta Piqueras
- Department of Pathology, Medical School, University of Valencia, Spain
| | | | | | | | | |
Collapse
|
21
|
How to minimise the effect of tumour cell content in detection of aberrant genetic markers in neuroblastoma. Br J Cancer 2011; 105:89-92. [PMID: 21654680 PMCID: PMC3137406 DOI: 10.1038/bjc.2011.188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: Clinical heterogeneity reflects the complexity of genetic events associated with neuroblastoma (NB). To identify the status of all described genetic loci with possible prognostic interest, high-throughput approaches have been used, but only with tumour cell content >60%. In some tumours, necrotic, haemorrhagic and/or calcification areas influence the low amount of neuroblasts. We evaluated the effect of tumour cell content in the detection of relevant aberrant genetic markers (AGM) diagnosed by fluorescence in situ hybridisation (FISH) on tissue microarrays (TMA) in NB. Methods: Two hundred and thirty-three MYCN non-amplified primary NB included in 12 TMAs were analysed. Results: Presence of AGM reduced event-free survival (EFS) (P=0.004) as well as overall survival (OS) (P=0.004) of patients in the whole cohort. There were no differences in prognostic impact of presence of AGM according to tumour cell content. Conclusion: We propose the use of FISH to diagnose AGM of all NB samples having the above-mentioned areas to determine patient risk.
Collapse
|
22
|
|
23
|
Murphy DM, Buckley PG, Bryan K, Watters KM, Koster J, van Sluis P, Molenaar J, Versteeg R, Stallings RL. Dissection of the oncogenic MYCN transcriptional network reveals a large set of clinically relevant cell cycle genes as drivers of neuroblastoma tumorigenesis. Mol Carcinog 2010; 50:403-11. [PMID: 21557326 DOI: 10.1002/mc.20722] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 11/19/2010] [Indexed: 01/11/2023]
Abstract
Amplification of the oncogenic transcription factor MYCN plays a major role in the pathogenesis of several pediatric cancers, including neuroblastoma, medulloblastoma, and rhabodomyosarcoma. For neuroblastoma, MYCN amplification is the most powerful genetic predictor of poor patient survival, yet the mechanism by which MYCN drives tumorigenesis is only partially understood. To gain an insight into the distribution of MYCN binding and to identify clinically relevant MYCN target genes, we performed an integrated analysis of MYCN ChIP-chip and mRNA expression using the MYCN repressible SHEP-21N neuroblastoma cell line. We hypothesized that genes exclusively MYCN bound in SHEP-21N cells over-expressing MYCN would be enriched for direct targets which contribute to the process of disease progression. Integrated analysis revealed that MYCN drives tumorigenesis predominantly as a positive regulator of target gene transcription. A high proportion of genes (24%) that are MYCN bound and up-regulated in the SHEP-21N model are significantly associated with poor overall patient survival (OS) in a set of 88 tumors. In contrast, the proportion of genes down-regulated when bound by MYCN in the SHEP-21N model and which are significantly associated with poor overall patient survival when under-expressed in primary tumors was significantly lower (5%). Gene ontology analysis determined a highly statistically significant enrichment for cell cycle related genes within the over-expressed MYCN target group which were also associated with poor OS. We conclude that the over-expression of MYCN leads to aberrant binding and over-expression of genes associated with cell cycle regulation which are significantly correlated with poor OS and MYCN amplification.
Collapse
Affiliation(s)
- Derek M Murphy
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, Dublin, Ireland
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Ragusa M, Majorana A, Banelli B, Barbagallo D, Statello L, Casciano I, Guglielmino MR, Duro LR, Scalia M, Magro G, Di Pietro C, Romani M, Purrello M. MIR152, MIR200B, and MIR338, human positional and functional neuroblastoma candidates, are involved in neuroblast differentiation and apoptosis. J Mol Med (Berl) 2010; 88:1041-53. [PMID: 20574809 DOI: 10.1007/s00109-010-0643-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 05/10/2010] [Accepted: 06/03/2010] [Indexed: 11/26/2022]
Abstract
MicroRNAs (MIRs) perform critical regulatory functions within cell networks, both in physiology as well as in pathology. Through the positional gene candidate approach, we have identified three MIRs (MIR152, MIR200B, and MIR338) that are located in regions frequently altered in neuroblastoma (NB) and target mRNAs encoding proteins involved in cell proliferation, neuroblast differentiation, neuroblast migration, and apoptosis. Expression analysis in NB biopsies and NB cell lines showed that these MIRs are dysregulated. We have characterized a CpG island, close to the gene encoding MIR200B and hypermethylated in NB samples, that explains its negative regulation. Expression of MIR152, MIR200B, and MIR338 is specifically modulated in NB cell lines during differentiation and apoptosis. Functional genomic experiments through enforced expression of MIR200B and knockdown of MIR152 resulted in a significant decrease of the invasion activity of SH-SY5Y cells. Reconstruction of a NB network comprising MIR152, MIR200B, and MIR338 allowed us to confirm their role in the control of NB cell stemness and apoptosis: This suggests that altered regulation of these MIRs could have a role in NB pathogenesis by interfering with the molecular mechanisms, which physiologically control differentiation and death of neuroblasts. Accordingly, they could be considered as new NB biomarkers and potential targets of antagomirs or epigenetic therapies.
Collapse
Affiliation(s)
- Marco Ragusa
- Unità di BioMedicina Molecolare Genomica e dei Sistemi Complessi, Genetica, Biologia Computazionale G Sichel, Dipartimento di Scienze BioMediche, Sezione di Biologia Generale, Biologia Cellulare, Genetica Molecolare, Università degli Studi di Catania, 95123, Catania, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Kumps C, Van Roy N, Heyrman L, Goossens D, Del-Favero J, Noguera R, Vandesompele J, Speleman F, De Preter K. Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma. BMC Genomics 2010; 11:298. [PMID: 20459859 PMCID: PMC2879279 DOI: 10.1186/1471-2164-11-298] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 05/12/2010] [Indexed: 11/10/2022] Open
Abstract
Background Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors. Results We tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method on 52 neuroblastoma tumors showed that Multiplex Amplicon Quantification can reliably detect the important genomic aberrations. Conclusion Multiplex Amplicon Quantification is a low-cost and high-throughput PCR-based technique that can reliably detect copy number alterations in regions with prognostic relevance for neuroblastoma.
Collapse
Affiliation(s)
- Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Albihn A, Johnsen JI, Henriksson MA. MYC in oncogenesis and as a target for cancer therapies. Adv Cancer Res 2010; 107:163-224. [PMID: 20399964 DOI: 10.1016/s0065-230x(10)07006-5] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
MYC proteins (c-MYC, MYCN, and MYCL) regulate processes involved in many if not all aspects of cell fate. Therefore, it is not surprising that the MYC genes are deregulated in several human neoplasias as a result from genetic and epigenetic alterations. The near "omnipotency" together with the many levels of regulation makes MYC an attractive target for tumor intervention therapy. Here, we summarize some of the current understanding of MYC function and provide an overview of different cancer forms with MYC deregulation. We also describe available treatments and highlight novel approaches in the pursuit for MYC-targeting therapies. These efforts, at different stages of development, constitute a promising platform for novel, more specific treatments with fewer side effects. If successful a MYC-targeting therapy has the potential for tailored treatment of a large number of different tumors.
Collapse
Affiliation(s)
- Ami Albihn
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | | |
Collapse
|
27
|
Bettayeb K, Baunbæk D, Delehouze C, Loaëc N, Hole AJ, Baumli S, Endicott JA, Douc-Rasy S, Bénard J, Oumata N, Galons H, Meijer L. CDK Inhibitors Roscovitine and CR8 Trigger Mcl-1 Down-Regulation and Apoptotic Cell Death in Neuroblastoma Cells. Genes Cancer 2010; 1:369-80. [PMID: 21779453 PMCID: PMC3092200 DOI: 10.1177/1947601910369817] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma (NB), the most frequent extracranial solid tumor of children accounting for nearly 15% of all childhood cancer mortality, displays overexpression of antiapoptotic Bcl-2 and Mcl-1 in aggressive forms of the disease. The clinical phase 2 drug roscovitine (CYC202, seliciclib), a relatively selective inhibitor of cyclin-dependent kinases (CDKs), and CR8, a recently developed and more potent analog, induce concentration-dependent apoptotic cell death of NB cells (average IC(50) values: 24.2 µM and 0.4 µM for roscovitine and CR8, respectively). Both roscovitine and CR8 trigger rapid down-regulation of the short-lived survival factor Mcl-1 in the 9 investigated human NB cell lines. This effect was further analyzed in the human SH-SY5Y NB cell line. Down-regulation of Mcl-1 appears to depend on inhibition of CDKs rather than on interaction of roscovitine and CR8 with their secondary targets. CR8 is an adenosine triphosphate-competitive inhibitor of CDK9, and the structure of a CDK9/cyclin T/CR8 complex is described. Mcl-1 down-regulation occurs both at the mRNA and protein levels. This effect can be accounted for by a reduction in Mcl-1 protein synthesis, under stable Mcl-1 degradation conditions. Mcl-1 down-regulation is accompanied by a transient increase in free Noxa, a proapoptotic factor. Mcl-1 down-regulation occurs independently of the presence or up-regulation of p53 and of the MYCN status. Taken together, these results suggest that the clinical drug roscovitine and its novel analog CR8 induce apoptotic tumor cell death by down-regulating Mcl-1, a key survival factor expressed in all NB cell lines. CDK inhibition may thus constitute a new approach to treat refractory high-risk NB.
Collapse
Affiliation(s)
- Karima Bettayeb
- C.N.R.S. USR3151, ‘Protein Phosphorylation & Human Disease’ Group, Station Biologique, Bretagne, France
- Laboratory of Molecular & Cellular Neuroscience (Prof. Paul Greengard), The Rockefeller University, New York, NY, USA
| | - Dianne Baunbæk
- C.N.R.S. USR3151, ‘Protein Phosphorylation & Human Disease’ Group, Station Biologique, Bretagne, France
| | - Claire Delehouze
- C.N.R.S. USR3151, ‘Protein Phosphorylation & Human Disease’ Group, Station Biologique, Bretagne, France
- ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, 29680 Roscoff, France
| | - Nadège Loaëc
- C.N.R.S. USR3151, ‘Protein Phosphorylation & Human Disease’ Group, Station Biologique, Bretagne, France
| | - Alison J. Hole
- University of Oxford, Department of Biochemistry, Laboratory of Molecular Biophysics, Oxford, UK
| | - Sonja Baumli
- University of Oxford, Department of Biochemistry, Laboratory of Molecular Biophysics, Oxford, UK
| | - Jane A. Endicott
- University of Oxford, Department of Biochemistry, Laboratory of Molecular Biophysics, Oxford, UK
| | - Setha Douc-Rasy
- C.N.R.S. UMR8126, Département de Biologie et Pathologie Médicales, Institut Gustave Roussy, Villejuif, France
| | - Jean Bénard
- C.N.R.S. UMR8126, Département de Biologie et Pathologie Médicales, Institut Gustave Roussy, Villejuif, France
| | - Nassima Oumata
- Laboratoire de Chimie Organique 2, CNRS UMR8601, INSERM U 648, Université Paris-Descartes, Paris, France
- Laboratory of Molecular & Cellular Neuroscience (Prof. Paul Greengard), The Rockefeller University, New York, NY, USA
| | - Hervé Galons
- Laboratoire de Chimie Organique 2, CNRS UMR8601, INSERM U 648, Université Paris-Descartes, Paris, France
| | - Laurent Meijer
- C.N.R.S. USR3151, ‘Protein Phosphorylation & Human Disease’ Group, Station Biologique, Bretagne, France
| |
Collapse
|
28
|
Balamuth NJ, Wood A, Wang Q, Jagannathan J, Mayes P, Zhang Z, Chen Z, Rappaport E, Courtright J, Pawel B, Weber B, Wooster R, Sekyere EO, Marshall GM, Maris JM. Serial transcriptome analysis and cross-species integration identifies centromere-associated protein E as a novel neuroblastoma target. Cancer Res 2010; 70:2749-58. [PMID: 20233875 DOI: 10.1158/0008-5472.can-09-3844] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer genomic studies that rely on analysis of biopsies from primary tumors may not fully identify the molecular events associated with tumor progression. We hypothesized that characterizing the transcriptome during tumor progression in the TH-MYCN transgenic model would identify oncogenic drivers that would be targetable therapeutically. We quantified expression of 32,381 murine genes in nine hyperplastic ganglia harvested at three time points and four tumor cohorts of progressively larger size in mice homozygous for the TH-MYCN transgene. We found 93 genes that showed a linearly increasing or decreasing pattern of expression from the preneoplastic ganglia to end stage tumors. Cross-species integration identified 24 genes that were highly expressed in human MYCN-amplified neuroblastomas. The genes prioritized were not exclusively driven by increasing Myc transactivation or proliferative rate. We prioritized three targets [centromere-associated protein E (Cenpe), Gpr49, and inosine monophosphate dehydrogenase type II] with previously determined roles in cancer. Using siRNA knockdown in human neuroblastoma cell lines, we further prioritized CENPE due to inhibition of cellular proliferation. Targeting CENPE with the small molecular inhibitor GSK923295 showed inhibition of in vitro proliferation of 19 neuroblastoma cell lines (median IC(50), 41 nmol/L; range, 27-266 nmol/L) and delayed tumor growth in three xenograft models (P values ranged from P < 0.0001 to P = 0.018). We provide preclinical validation that serial transcriptome analysis of a transgenic mouse model followed by cross-species integration is a useful method to identify therapeutic targets and identify CENPE as a novel therapeutic candidate in neuroblastoma.
Collapse
Affiliation(s)
- Naomi J Balamuth
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|