1
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Sehgal M, Nayak SP, Sahoo S, Somarelli JA, Jolly MK. Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma. Cancer Biol Ther 2024; 25:2301802. [PMID: 38230570 PMCID: PMC10795782 DOI: 10.1080/15384047.2024.2301802] [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: 09/08/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Neuroblastoma is the most frequent extracranial pediatric tumor and leads to 15% of all cancer-related deaths in children. Tumor relapse and therapy resistance in neuroblastoma are driven by phenotypic plasticity and heterogeneity between noradrenergic (NOR) and mesenchymal (MES) cell states. Despite the importance of this phenotypic plasticity, the dynamics and molecular patterns associated with these bidirectional cell-state transitions remain relatively poorly understood. Here, we analyze multiple RNA-seq datasets at both bulk and single-cell resolution, to understand the association between NOR- and MES-specific factors. We observed that NOR-specific and MES-specific expression patterns are largely mutually exclusive, exhibiting a "teams-like" behavior among the genes involved, reminiscent of our earlier observations in lung cancer and melanoma. This antagonism between NOR and MES phenotypes was also associated with metabolic reprogramming and with immunotherapy targets PD-L1 and GD2 as well as with experimental perturbations driving the NOR-MES and/or MES-NOR transition. Further, these "teams-like" patterns were seen only among the NOR- and MES-specific genes, but not in housekeeping genes, possibly highlighting a hallmark of network topology enabling cancer cell plasticity.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Sonali Priyadarshini Nayak
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
- Max Planck School Matter to Life, University of Göttingen, Göttingen, Germany
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
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2
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Ataei A, Tahsili M, Hayadokht G, Daneshvar M, Mohammadi Nour S, Soofi A, Masoudi A, Kabiri M, Natami M. Targeting long noncoding RNAs in neuroblastoma: Progress and prospects. Chem Biol Drug Des 2023; 102:640-652. [PMID: 37291742 DOI: 10.1111/cbdd.14263] [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: 02/04/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 06/10/2023]
Abstract
Neuroblastoma (NB) is the third most prevalent tumor that mostly influences infants and young children. Although different treatments have been developed for the treatment of NB, high-risk patients have been reported to have low survival rates. Currently, long noncoding RNAs (lncRNAs) have shown an attractive potential in cancer research and a party of investigations have been performed to understand mechanisms underlying tumor development through lncRNA dysregulation. Researchers have just newly initiated to exhibit the involvement of lncRNAs in NB pathogenesis. In this review article, we tried to clarify the point we stand with respect to the involvement of lncRNAs in NB. Moreover, implications for the pathologic roles of lncRNAs in the development of NB have been discussed. It seems that some of these lncRNAs have promising potential to be applied as biomarkers for NB prognosis and treatment.
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Affiliation(s)
- Ali Ataei
- School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Golsa Hayadokht
- School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | | | | | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Alireza Masoudi
- Department of Laboratory Sciences, Faculty of Alied Medical Sciences, Qom University of Medical Sciences, Qom, Iran
| | - Maryam Kabiri
- Faculty of Medicine, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Mohammad Natami
- Department of Urology, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Gupta M, Kannappan S, Jain M, Douglass D, Shah R, Bose P, Narendran A. Development and validation of a 21-gene prognostic signature in neuroblastoma. Sci Rep 2023; 13:12526. [PMID: 37532697 PMCID: PMC10397261 DOI: 10.1038/s41598-023-37714-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
Survival outcomes for patients with neuroblastoma vary markedly and reliable prognostic markers and risk stratification tools are lacking. We sought to identify and validate a transcriptomic signature capable of predicting risk of mortality in patients with neuroblastoma. The TARGET NBL dataset (n = 243) was used to develop the model and two independent cohorts, E-MTAB-179 (n = 478) and GSE85047 (n = 240) were used as validation sets. EFS was the primary outcome and OS was the secondary outcome of interest for all analysis. We identified a 21-gene signature capable of stratifying neuroblastoma patients into high and low risk groups in the E-MTAB-179 (HR 5.87 [3.83-9.01], p < 0.0001, 5 year AUC 0.827) and GSE85047 (HR 3.74 [2.36-5.92], p < 0.0001, 5 year AUC 0.815) validation cohorts. Moreover, the signature remained independent of known clinicopathological variables, and remained prognostic within clinically important subgroups. Further, the signature was effectively incorporated into a risk model with clinicopathological variables to improve prognostic performance across validation cohorts (Pooled Validation HR 6.93 [4.89-9.83], p < 0.0001, 5 year AUC 0.839). Similar prognostic utility was also demonstrated with OS. The identified signature is a robust independent predictor of EFS and OS outcomes in neuroblastoma patients and can be combined with clinically utilized clinicopathological variables to improve prognostic performance.
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Affiliation(s)
- Mehul Gupta
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Sunand Kannappan
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Mohit Jain
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - David Douglass
- Department of Pediatrics, Hematology/Oncology Section, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
| | - Ravi Shah
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Pinaki Bose
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Cumming School of Medicine, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Aru Narendran
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Cumming School of Medicine, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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4
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Sugino RP, Ohira M, Mansai SP, Kamijo T. Comparative epigenomics by machine learning approach for neuroblastoma. BMC Genomics 2022; 23:852. [PMID: 36572864 PMCID: PMC9793522 DOI: 10.1186/s12864-022-09061-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the second most common pediatric solid tumor. Because the number of genetic mutations found in tumors are small, even in some patients with unfavorable NB, epigenetic variation is expected to play an important role in NB progression. DNA methylation is a major epigenetic mechanism, and its relationship with NB prognosis has been a concern. One limitation with the analysis of variation in DNA methylation is the lack of a suitable analytical model. Therefore, in this study, we performed a random forest (RF) analysis of the DNA methylome data of NB from multiple databases. RESULTS RF is a popular machine learning model owing to its simplicity, intuitiveness, and computational cost. RF analysis identified novel intermediate-risk patient groups with characteristic DNA methylation patterns within the low-risk group. Feature selection analysis based on probe annotation revealed that enhancer-annotated regions had strong predictive power, particularly for MYCN-amplified NBs. We developed a gene-based analytical model to identify candidate genes related to disease progression, such as PRDM8 and FAM13A-AS1. RF analysis revealed sufficient predictive power compared to other machine learning models. CONCLUSIONS RF is a useful tool for DNA methylome analysis in cancer epigenetic studies, and has potential to identify a novel cancer-related genes.
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Affiliation(s)
- Ryuichi P. Sugino
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Miki Ohira
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Sayaka P. Mansai
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Takehiko Kamijo
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan ,grid.263023.60000 0001 0703 3735Laboratory of Tumor Molecular Biology, Department of Graduate School of Science and Engineering, Saitama University, Kita-Urawa, Saitama, Japan
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5
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Kańduła MM, Aldoshin AD, Singh S, Kolaczyk ED, Kreil D. ViLoN-a multi-layer network approach to data integration demonstrated for patient stratification. Nucleic Acids Res 2022; 51:e6. [PMID: 36395816 PMCID: PMC9841426 DOI: 10.1093/nar/gkac988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
With more and more data being collected, modern network representations exploit the complementary nature of different data sources as well as similarities across patients. We here introduce the Variation of information fused Layers of Networks algorithm (ViLoN), a novel network-based approach for the integration of multiple molecular profiles. As a key innovation, it directly incorporates prior functional knowledge (KEGG, GO). In the constructed network of patients, patients are represented by networks of pathways, comprising genes that are linked by common functions and joint regulation in the disease. Patient stratification remains a key challenge both in the clinic and for research on disease mechanisms and treatments. We thus validated ViLoN for patient stratification on multiple data type combinations (gene expression, methylation, copy number), showing substantial improvements and consistently competitive performance for all. Notably, the incorporation of prior functional knowledge was critical for good results in the smaller cohorts (rectum adenocarcinoma: 90, esophageal carcinoma: 180), where alternative methods failed.
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Affiliation(s)
- Maciej M Kańduła
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Swati Singh
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Eric D Kolaczyk
- Correspondence may also be addressed to Eric D. Kolaczyk. Tel: +1 514 398 3805;
| | - David P Kreil
- To whom correspondence should be addressed. Tel: +43 1 47654 79009;
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6
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Gallez B. The Role of Imaging Biomarkers to Guide Pharmacological Interventions Targeting Tumor Hypoxia. Front Pharmacol 2022; 13:853568. [PMID: 35910347 PMCID: PMC9335493 DOI: 10.3389/fphar.2022.853568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/23/2022] [Indexed: 12/12/2022] Open
Abstract
Hypoxia is a common feature of solid tumors that contributes to angiogenesis, invasiveness, metastasis, altered metabolism and genomic instability. As hypoxia is a major actor in tumor progression and resistance to radiotherapy, chemotherapy and immunotherapy, multiple approaches have emerged to target tumor hypoxia. It includes among others pharmacological interventions designed to alleviate tumor hypoxia at the time of radiation therapy, prodrugs that are selectively activated in hypoxic cells or inhibitors of molecular targets involved in hypoxic cell survival (i.e., hypoxia inducible factors HIFs, PI3K/AKT/mTOR pathway, unfolded protein response). While numerous strategies were successful in pre-clinical models, their translation in the clinical practice has been disappointing so far. This therapeutic failure often results from the absence of appropriate stratification of patients that could benefit from targeted interventions. Companion diagnostics may help at different levels of the research and development, and in matching a patient to a specific intervention targeting hypoxia. In this review, we discuss the relative merits of the existing hypoxia biomarkers, their current status and the challenges for their future validation as companion diagnostics adapted to the nature of the intervention.
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7
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Sha Y, Han L, Sun B, Zhao Q. Identification of a Glycosyltransferase Signature for Predicting Prognosis and Immune Microenvironment in Neuroblastoma. Front Cell Dev Biol 2022; 9:769580. [PMID: 35071226 PMCID: PMC8773256 DOI: 10.3389/fcell.2021.769580] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/30/2021] [Indexed: 01/17/2023] Open
Abstract
Neuroblastoma (NB) is one of the most common solid tumors in children. Glycosyltransferases (GTs) play a crucial role in tumor development and immune escape and have been used as prognostic biomarkers in various tumors. However, the biological functions and prognostic significance of GTs in NB remain poorly understood. The expression data from Gene Expression Omnibus (GEO) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) were collected as training and testing data. Based on a progression status, differentially expressed GTs were identified. We constructed a GTscore through support vector machine, least absolute shrinkage and selection operator, and Cox regression in NB, which included four prognostic GTs and was an independent prognostic risk factor for NB. Patients in the high GTscore group had an older age, MYCN amplification, advanced International Neuroblastoma Staging System stage, and high risk. Samples with high GTscores revealed high disialoganglioside (GD2) and neuron-specific enolase expression levels. In addition, a lack of immune cell infiltration was observed in the high GTscore group. This GTscore was also associated with the expression of chemokines (CCL2, CXCL9, and CXCL10) and immune checkpoint genes (cytotoxic T-lymphocyte–associated protein 4, granzyme H, and granzyme K). A low GTscore was also linked to an enhanced response to anti–PD-1 immunotherapy in melanoma patients, and one type of tumor was also derived from neuroectodermal cells such as NB. In conclusion, the constructed GTscore revealed the relationship between GT expression and the NB outcome, GD2 phenotype, and immune infiltration and provided novel clues for the prediction of prognosis and immunotherapy response in NB.
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Affiliation(s)
- Yongliang Sha
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Lei Han
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bei Sun
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Outpatient Office, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qiang Zhao
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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8
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Cowman SJ, Koh MY. Revisiting the HIF switch in the tumor and its immune microenvironment. Trends Cancer 2022; 8:28-42. [PMID: 34743924 PMCID: PMC8702465 DOI: 10.1016/j.trecan.2021.10.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 01/03/2023]
Abstract
Hypoxia is a hallmark of all solid tumors and their metastases. This leads to activation of the hypoxia-inducible factor (HIF) family of transcription factors, which modulate gene expression within both tumor cells and immune cells within the tumor microenvironment, influencing tumor progression and treatment response. The best characterized HIF isoforms, HIF-1α and HIF-2α, show nonoverlapping and often antagonistic roles. With the recent availability of inhibitors that target one or both HIFs, including the first-in-class selective HIF-2α inhibitor belzutifan, the prospect of HIF-α isoform-selective targeting is now a reality. Here, we summarize current knowledge on the unique contributions of the two HIF-α isoforms to tumor progression in the context of the complex tumor immune microenvironment, highlighting important considerations for therapy.
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Affiliation(s)
| | - Mei Yee Koh
- University of Utah, Salt Lake City, UT 84112, USA.
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9
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Uva P, Bosco MC, Eva A, Conte M, Garaventa A, Amoroso L, Cangelosi D. Connectivity Map Analysis Indicates PI3K/Akt/mTOR Inhibitors as Potential Anti-Hypoxia Drugs in Neuroblastoma. Cancers (Basel) 2021; 13:cancers13112809. [PMID: 34199959 PMCID: PMC8200206 DOI: 10.3390/cancers13112809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Neuroblastoma (NB) is one of the deadliest pediatric cancers, accounting for 15% of deaths in childhood. Hypoxia is a condition of low oxygen tension occurring in solid tumors and has an unfavorable prognostic factor for NB. In the present study, we aimed to identify novel promising drugs for NB treatment. Connectivity Map (CMap), an online resource for drug repurposing, was used to identify connections between hypoxia-modulated genes in NB tumors and compounds. Two sets of 34 and 21 genes up- and down-regulated between hypoxic and normoxic primary NB tumors, respectively, were analyzed with CMap. The analysis reported a significant negative connectivity score across nine cell lines for 19 compounds mainly belonging to the class of PI3K/Akt/mTOR inhibitors. The gene expression profiles of NB cells cultured under hypoxic conditions and treated with the mTORC complex inhibitor PP242, referred to as the Mohlin dataset, was used to validate the CMap findings. A heat map representation of hypoxia-modulated genes in the Mohlin dataset and the gene set enrichment analysis (GSEA) showed an opposite regulation of these genes in the set of NB cells treated with the mTORC inhibitor PP242. In conclusion, our analysis identified inhibitors of the PI3K/Akt/mTOR signaling pathway as novel candidate compounds to treat NB patients with hypoxic tumors and a poor prognosis.
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Affiliation(s)
- Paolo Uva
- Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
- Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (M.C.B.); (A.E.)
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (M.C.B.); (A.E.)
| | - Massimo Conte
- UOC Oncologia, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (M.C.); (A.G.); (L.A.)
| | - Alberto Garaventa
- UOC Oncologia, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (M.C.); (A.G.); (L.A.)
| | - Loredana Amoroso
- UOC Oncologia, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (M.C.); (A.G.); (L.A.)
| | - Davide Cangelosi
- Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
- Correspondence:
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10
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Chen C, Zhou H, Liu Z, Ma X. Dysregulation of Zinc Finger Protein 395 Contributes to the Pathogenesis of Chondrosarcoma. Onco Targets Ther 2021; 14:3545-3553. [PMID: 34113121 PMCID: PMC8183675 DOI: 10.2147/ott.s310164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction The transcription factor zinc finger protein 395 (ZNF395) is involved in several cellular responses and tumorigenesis. However, the potential role and clinical significance of ZNF395 in chondrosarcoma are not well investigated. This study determines the expression profile, prognostic value and biological function of ZNF395 in human chondrosarcoma. Methods The mRNA and protein expressions of ZNF395 in fresh chondrosarcomas and the matched adjacent non-tumor tissues were assessed using real-time PCR and immunoblotting, respectively. The protein expression of ZNF395 in chondrosarcoma specimens was evaluated by immunohistochemistry, and the relationships among its protein level, clinicopathological parameters and prognosis were further detected. Cell viability, colony formation, migration, invasion and apoptosis assay were evaluated in chondrosarcoma cells with depletion of ZNF395. Results The mRNA and protein expressions of ZNF395 in chondrosarcoma tissues were significantly higher than those in the matched adjacent non-tumor tissues and benign cartilage tumors. Clinical analysis displayed that ZNF395 was expressed at higher levels in chondrosarcoma patients with higher histological grade and advanced MSTS stage. Furthermore, we demonstrated that high expression of ZNF395 correlated with a worse overall survival of chondrosarcoma patients. Multivariate Cox regression analysis indicated that ZNF395 was an independent prognostic marker in chondrosarcoma patients. Functional studies revealed that depletion of ZNF395 markedly inhibited cell viability, colony formation, migration and invasion, and promoted apoptosis in chondrosarcoma. Conclusion These findings suggest that dysregulation of ZNF395 contributes to chondrosarcoma development, and ZNF395 may act as a potent oncogene and serve as a independently prognostic factor, highlight the potential of ZNF395 as a novel biomarker and therapeutic target for chondrosarcoma.
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Affiliation(s)
- Changbao Chen
- Department of Spinal Surgery, Tianjin Hospital, Tianjin, 300211, People's Republic of China
| | - Hua Zhou
- Department of Orthopaedic Surgery, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Zhongjun Liu
- Department of Orthopaedic Surgery, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Xinlong Ma
- Department of Spinal Surgery, Tianjin Hospital, Tianjin, 300211, People's Republic of China
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11
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Molecular Genetics in Neuroblastoma Prognosis. CHILDREN-BASEL 2021; 8:children8060456. [PMID: 34072462 PMCID: PMC8226597 DOI: 10.3390/children8060456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
In recent years, much research has been carried out to identify the biological and genetic characteristics of the neuroblastoma (NB) tumor in order to precisely define the prognostic subgroups for improving treatment stratification. This review will describe the major genetic features and the recent scientific advances, focusing on their impact on diagnosis, prognosis, and therapeutic solutions in NB clinical management.
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12
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Duan B, Fu D, Zhang C, Ding P, Dong X, Xia B. Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains. J Am Chem Soc 2021; 143:7688-7697. [PMID: 33983734 DOI: 10.1021/jacs.1c00599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Methylation of DNA at CpG sites is a major mark for epigenetic regulation, but how transcription factors are influenced by CpG methylation is not well understood. Here, we report the molecular mechanisms of how the TCF (T-cell factor) and GEF (glucose transporter 4 enhancer factor) families of proteins selectively target unmethylated DNA sequences with a C-clamp type zinc finger domain. The structure of the C-clamp domain from human GEF family protein HDBP1 (C-clampHDBP1) in complex with DNA was determined using NMR spectroscopy, which adopts a unique zinc finger fold and selectively binds RCCGG (R = A/G) DNA sequences with an "Arg···Trp-Lys-Lys" DNA recognition motif inserted in the major groove. The CpG base pairs are central to the binding due to multiple hydrogen bonds formed with the backbone carbonyl groups of Trp378 and Lys379, as well as the side chain ε-amino groups of Lys379 and Lys380 from C-clampHDBP1. Consequently, methylation of the CpG dinucleotide almost abolishes the binding. Homology modeling reveals that the C-clamp domain from human TCF1E (C-clampTCF1E) binds DNA through essentially the same mechanism, with a similar "Arg···Arg-Lys-Lys" DNA recognition motif. The substitution of tryptophan by arginine makes C-clampHDBP1 prefer RCCGC DNA sequences. The two signature DNA recognition motifs are invariant in the GEF and TCF families of proteins, respectively, from fly to human. The recognition of the CpG dinucleotide through two consecutive backbone carbonyl groups is the same as that of the CXXC type unmethylated CpG DNA binding domains, suggesting a common mechanism shared by unmethylated CpG binding proteins.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dihong Fu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoqun Zhang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianzhi Dong
- Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
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13
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Thiruthaneeswaran N, Bibby BAS, Yang L, Hoskin PJ, Bristow RG, Choudhury A, West C. Lost in application: Measuring hypoxia for radiotherapy optimisation. Eur J Cancer 2021; 148:260-276. [PMID: 33756422 DOI: 10.1016/j.ejca.2021.01.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 12/15/2022]
Abstract
The history of radiotherapy is intertwined with research on hypoxia. There is level 1a evidence that giving hypoxia-targeting treatments with radiotherapy improves locoregional control and survival without compromising late side-effects. Despite coming in and out of vogue over decades, there is now an established role for hypoxia in driving molecular alterations promoting tumour progression and metastases. While tumour genomic complexity and immune profiling offer promise, there is a stronger evidence base for personalising radiotherapy based on hypoxia status. Despite this, there is only one phase III trial targeting hypoxia modification with full transcriptomic data available. There are no biomarkers in routine use for patients undergoing radiotherapy to aid management decisions, and a roadmap is needed to ensure consistency and provide a benchmark for progression to application. Gene expression signatures address past limitations of hypoxia biomarkers and could progress biologically optimised radiotherapy. Here, we review recent developments in generating hypoxia gene expression signatures and highlight progress addressing the challenges that must be overcome to pave the way for their clinical application.
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Affiliation(s)
- Niluja Thiruthaneeswaran
- Division of Cancer Sciences, The University of Manchester, Manchester, UK; Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
| | - Becky A S Bibby
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Lingjang Yang
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Peter J Hoskin
- Division of Cancer Sciences, The University of Manchester, Manchester, UK; Mount Vernon Cancer Centre, Northwood, UK
| | - Robert G Bristow
- Division of Cancer Sciences, The University of Manchester, Manchester, UK; CRUK Manchester Institute and Manchester Cancer Research Centre, Manchester, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, The University of Manchester, Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Catharine West
- Division of Cancer Sciences, The University of Manchester, Christie Hospital NHS Foundation Trust, Manchester, UK
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14
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Ornell KJ, Mistretta KS, Ralston CQ, Coburn JM. Development of a stacked, porous silk scaffold neuroblastoma model for investigating spatial differences in cell and drug responsiveness. Biomater Sci 2021; 9:1272-1290. [PMID: 33336667 DOI: 10.1039/d0bm01153c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Development of in vitro, preclinical cancer models that contain cell-driven microenvironments remains a challenge. Engineering of millimeter-scale, in vitro tumor models with spatially distinct regions that can be independently assessed to study tumor microenvironments has been limited. Here, we report the use of porous silk scaffolds to generate a high cell density neuroblastoma (NB) model that can spatially recapitulate changes resulting from cell and diffusion driven changes. Using COMSOL modeling, a scaffold holder design that facilitates stacking of thin, 200 μm silk scaffolds into a thick, bulk millimeter-scale tumor model (2, 4, 6, and 8 stacked scaffolds) and supports cell-driven oxygen gradients was developed. Cell-driven oxygen gradients were confirmed through pimonidazole staining. Post-culture, the stacked scaffolds were separated for analysis on a layer-by-layer basis. The analysis of each scaffold layer demonstrated decreasing DNA and increasing expression of hypoxia related genes (VEGF, CAIX, and GLUT1) from the exterior scaffolds to the interior scaffolds. Furthermore, the expression of hypoxia related genes at the interior of the stacks was comparable to that of a single scaffold cultured under 1% O2 and at the exterior of the stacks was comparable to that of a single scaffold cultured under 21% O2. The four-stack scaffold model underwent further evaluation to determine if a hypoxia activated drug, tirapazamine, induced reduced cell viability within the internal stacks (region of reduced oxygen) as compared with the external stacks. Decreased DNA content was observed in the internal stacks as compared to the external stacks when treated with tirapazamine, which suggests the internal scaffold stacks had higher levels of hypoxia than the external scaffolds. This stacked silk scaffold system presents a method for creating a single culture model capable of generating controllable cell-driven microenvironments through different stacks that can be individually assessed and used for drug screening.
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Affiliation(s)
- Kimberly J Ornell
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
| | - Katelyn S Mistretta
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
| | - Coulter Q Ralston
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
| | - Jeannine M Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
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15
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Cangelosi D, Morini M, Zanardi N, Sementa AR, Muselli M, Conte M, Garaventa A, Pfeffer U, Bosco MC, Varesio L, Eva A. Hypoxia Predicts Poor Prognosis in Neuroblastoma Patients and Associates with Biological Mechanisms Involved in Telomerase Activation and Tumor Microenvironment Reprogramming. Cancers (Basel) 2020; 12:E2343. [PMID: 32825087 PMCID: PMC7563184 DOI: 10.3390/cancers12092343] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 12/23/2022] Open
Abstract
The biological and clinical heterogeneity of neuroblastoma (NB) demands novel biomarkers and therapeutic targets in order to drive the most appropriate treatment for each patient. Hypoxia is a condition of low-oxygen tension occurring in poorly vascularized tumor tissues. In this study, we aimed to assess the role of hypoxia in the pathogenesis of NB and at developing a new clinically relevant hypoxia-based predictor of outcome. We analyzed the gene expression profiles of 1882 untreated NB primary tumors collected at diagnosis and belonging to four existing data sets. Analyses took advantage of machine learning methods. We identified NB-hop, a seven-gene hypoxia biomarker, as a predictor of NB patient prognosis, which is able to discriminate between two populations of patients with unfavorable or favorable outcome on a molecular basis. NB-hop retained its prognostic value in a multivariate model adjusted for established risk factors and was able to additionally stratify clinically relevant groups of patients. Tumors with an unfavorable NB-hop expression showed a significant association with telomerase activation and a hypoxic, immunosuppressive, poorly differentiated, and apoptosis-resistant tumor microenvironment. NB-hop defines a new population of NB patients with hypoxic tumors and unfavorable prognosis and it represents a critical factor for the stratification and treatment of NB patients.
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Affiliation(s)
- Davide Cangelosi
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Nicolò Zanardi
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Angela Rita Sementa
- Laboratory of Pathology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Marco Muselli
- Institute of Electronics, Computer and Telecommunication Engineering, Italian National Research Council, 16149 Genova, Italy;
| | - Massimo Conte
- Pediatric Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.C.); (A.G.)
| | - Alberto Garaventa
- Pediatric Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.C.); (A.G.)
| | - Ulrich Pfeffer
- Integrated Oncology Therapies Department, Molecular Pathology, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy;
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Luigi Varesio
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
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16
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Prognostic significance of MYCN related genes in pediatric neuroblastoma: a study based on TARGET and GEO datasets. BMC Pediatr 2020; 20:314. [PMID: 32593299 PMCID: PMC7320557 DOI: 10.1186/s12887-020-02219-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/22/2020] [Indexed: 02/08/2023] Open
Abstract
Background Neuroblastoma patients with MYCN amplification are associated with poor prognosis. However, the prognostic relevance of MYCN associated genes in neuroblastoma is unclear. Methods The expression profiles of MYCN associated genes were identified from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) datasets. Enriched transcription factors and signaling pathways were determined using gene set enrichment analysis (GSEA). Kaplan-Meier plotter was used to identify the prognostic relevance of MYCN associated genes. Multivariate cox regression and Spearman’s correlation were used to determine the correlation coefficients of MYCN associated genes. Results In TARGET and GSE85047 datasets, neuroblastoma patients with MYCN amplification were associated with worse prognosis. Transcription factor MYC was positively associated with MYCN amplification in GSEA assay. We identified 13 MYC target genes which were increased in neuroblastoma patients with MYCN amplification in TARGET, GSE19274 and GSE85047 datasets. Moreover, six out of the 13 MYC target genes ARMC6, DCTPP1, EIF4G1, ELOVL6, FBL and PRMT1 were associated with adverse prognosis in TARGET and GSE85047 datasets. Transcription factor E2F1 was up-regulated by MYCN amplification and associated with the poor prognosis of neuroblastoma. Furthermore, RPS19 in ribosome signaling pathway was also associated with MYCN amplification and correlated with the poor prognosis of neuroblastoma. At last, we showed that most of MYCN target genes were correlated with each other. However, EIF4G1 was an independent prognostic marker. And the prognostic effects of the combination of MYCN amplification and EIF4G1 expression were more significant than MYCN or EIF4G1 alone. Conclusions MYCN target genes ARMC6, DCTPP1, EIF4G1, ELOVL6, FBL, PRMT1, E2F1 and RPS19 had significant prognostic effects in pediatric neuroblastoma. And neuroblastoma patients without MYCN amplification and low EIF4G1 expression had best prognosis.
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17
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Soltanalizadeh B, Gonzalez Rodriguez E, Maroufy V, Zheng WJ, Wu H. Modelling of hypoxia gene expression for three different cancer cell lines. ACTA ACUST UNITED AC 2020; 13:124-143. [PMID: 32153660 DOI: 10.1504/ijcbdd.2020.10026794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gene dynamic analysis is essential in identifying target genes involved pathogenesis of various diseases, including cancer. Cancer prognosis is often influenced by hypoxia. We apply a multi-step pipeline to study dynamic gene expressions in response to hypoxia in three cancer cell lines: prostate (DU145), colon (HT29), and breast (MCF7) cancers. We identified 26 distinct temporal expression patterns for prostate cell line, and 29 patterns for colon and breast cell lines. The module-based dynamic networks have been developed for all three cell lines. Our analyses improve the existing results in multiple ways. It exploits the time-dependence nature of gene expression values in identifying the dynamically significant genes; hence, more key significant genes and transcription factors have been identified. Our gene network returns significant information regarding biologically important modules of genes. Furthermore, the network has potential in learning the regulatory path between transcription factors and the downstream genes. In addition, our findings suggest that changes in genes BMP6 and ARSJ expression might have a key role in the time-dependent response to hypoxia in breast cancer.
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Affiliation(s)
- Babak Soltanalizadeh
- Department of Biostatistics & Data Science, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Erika Gonzalez Rodriguez
- Center for translational Injury Research, Department of Surgery, McGovern Medical School, UT Houston, Houston, TX, USA
| | - Vahed Maroufy
- Department of Biostatistics & Data Science, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hulin Wu
- Department of Biostatistics & Data Science, University of Texas Health Science Center at Houston, Houston, TX, USA
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18
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Persson CU, von Stedingk K, Fredlund E, Bexell D, Påhlman S, Wigerup C, Mohlin S. ARNT-dependent HIF-2 transcriptional activity is not sufficient to regulate downstream target genes in neuroblastoma. Exp Cell Res 2020; 388:111845. [PMID: 31945318 DOI: 10.1016/j.yexcr.2020.111845] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Hypoxia-inducible factor (HIF)-2α associates with poor outcome in neuroblastoma and glioblastoma, and gain-of-function mutations in the EPAS1 gene (encoding HIF-2α) have been reported in paragangliomas and pheochromocytomas. Specific targeting of a druggable hydrophobic pocket in the HIF-2α PAS-B domain with PT2385 have demonstrated promising clinical results for clear cell renal cell carcinoma (ccRCC). Here, we investigated the effect of PT2385-mediated inhibition of ARNT dependent HIF-2 activity. METHODS Neuroblastoma patient-derived xenograft (PDX) cells were treated with PT2385 and analyzed for HIF-2-dependent gene expression, HIF activity, HIF-2α protein localization, response to chemotherapy and orthotopic tumor growth in vivo. Two-sided student t-test was used. RESULTS We detected high levels of HIF-2α protein in perivascular niches in neuroblastoma PDXs in vivo and at oxygenated conditions in PDX-derived cell cultures in vitro, particularly in the cytoplasmic fraction. Nuclear HIF-2α expression was reduced following PT2385 treatment, but surprisingly, virtually no effects on tumor growth in vivo or expression of canonical HIF downstream target genes in vitro were observed. In coherence, RNA sequencing of PT2385-treated PDX cells revealed a virtually unaffected transcriptome. Treatment with PT2385 did not affect cellular response to chemotherapy. In contrast, HIF-2α protein knockdown resulted in profound downregulation of target genes. CONCLUSIONS The lack of effect from PT2385 treatment in combination with high cytoplasmic HIF-2α expression at normoxia suggest that HIF-2α have additional roles than acting as an ARNT dependent transcription factor. It is important to further unravel the conditions at which HIF-2α has transcriptional and non-transcriptional roles in neuroblastoma.
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Affiliation(s)
- Camilla U Persson
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Kristoffer von Stedingk
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Oncogenomic, University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elina Fredlund
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden; Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Daniel Bexell
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Sven Påhlman
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Caroline Wigerup
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Sofie Mohlin
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden; Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden.
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19
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Raggi F, Cangelosi D, Becherini P, Blengio F, Morini M, Acquaviva M, Belli ML, Panizzon G, Cervo G, Varesio L, Eva A, Bosco MC. Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass. J Transl Med 2020; 18:21. [PMID: 31924244 PMCID: PMC6954611 DOI: 10.1186/s12967-020-02210-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 01/03/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tetralogy of Fallot (ToF) and Atrial Septal Defects (ASD) are the most common types of congenital heart diseases and a major cause of childhood morbidity and mortality. Cardiopulmonary bypass (CPB) is used during corrective cardiac surgery to support circulation and heart stabilization. However, this procedure triggers systemic inflammatory and stress response and consequent increased risk of postoperative complications. The aim of this study was to define the molecular bases of ToF and ASD pathogenesis and response to CPB and identify new potential biomarkers. METHODS Comparative transcriptome analysis of right atrium specimens collected from 10 ToF and 10 ASD patients was conducted before (Pre-CPB) and after (Post-CPB) corrective surgery. Total RNA isolated from each sample was individually hybridized on Affymetrix HG-U133 Plus Array Strips containing 38,500 unique human genes. Differences in the gene expression profiles and functional enrichment/network analyses were assessed using bioinformatic tools. qRT-PCR analysis was used to validate gene modulation. RESULTS Pre-CPB samples showed significant differential expression of a total of 72 genes, 28 of which were overexpressed in ToF and 44 in ASD. According to Gene Ontology annotation, the mostly enriched biological processes were represented by matrix organization and cell adhesion in ToF and by muscle development and contractility in ASD specimens. GSEA highlighted the specific enrichment of hypoxia gene sets in ToF samples, pointing to a role for hypoxia in disease pathogenesis. The post-CPB myocardium exhibited significant alterations in the expression profile of genes related to transcription regulation, growth/apoptosis, inflammation, adhesion/matrix organization, and oxidative stress. Among them, only 70 were common to the two disease groups, whereas 110 and 24 were unique in ToF and ASD, respectively. Multiple functional interactions among differentially expressed gene products were predicted by network analysis. Interestingly, gene expression changes in ASD samples followed a consensus hypoxia profile. CONCLUSION Our results provide a comprehensive view of gene reprogramming in right atrium tissues of ToF and ASD patients before and after CPB, defining specific molecular pathways underlying disease pathophysiology and myocardium response to CPB. These findings have potential translational value because they identify new candidate prognostic markers and targets for tailored cardioprotective post-surgical therapies.
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Affiliation(s)
- Federica Raggi
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy
| | - Davide Cangelosi
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy
| | - Pamela Becherini
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy.,Department of Internal Medicine, University of Genova, Genova, Italy
| | - Fabiola Blengio
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy.,INSERM U955 Equipe 16, Creteil, France
| | - Martina Morini
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy
| | - Massimo Acquaviva
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy.,Immunobiology of Neurological Disorders Unit, Institute of Experimental Neurology INSPE, Ospedale San Raffaele, Milano, Italy
| | - Maria Luisa Belli
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy.,Cytomorphology Laboratory, Heamo-Onco-TMO Department, IRCSS Istituto Giannina Gaslini, Genova, Italy
| | - Giuseppe Panizzon
- Department of Cardiology, IRCSS Istituto Giannina Gaslini, Genova, Italy
| | - Giuseppe Cervo
- Department of Cardiology, IRCSS Istituto Giannina Gaslini, Genova, Italy
| | - Luigi Varesio
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, IRCSS Istituto Giannina Gaslini, Padiglione 2, L.go G.Gaslini 5, 16147, Genova, Italy.
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20
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Abou Khouzam R, Goutham HV, Zaarour RF, Chamseddine AN, Francis A, Buart S, Terry S, Chouaib S. Integrating tumor hypoxic stress in novel and more adaptable strategies for cancer immunotherapy. Semin Cancer Biol 2020; 65:140-154. [PMID: 31927131 DOI: 10.1016/j.semcancer.2020.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/10/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
Immunotherapy is poised to become an increasingly utilized therapy in the treatment of cancer. However, several abnormalities in the tumor microenvironment (TME) that can thwart the efficacy of immunotherapies have been established. Microenvironmental hypoxia is a determining factor in shaping aggressiveness, metastatic potential and treatment resistance of solid tumors. The characterization of this phenomenon could prove beneficial for determining a patient's treatment path and for the introduction of novel targetable factors that can enhance therapeutic outcome. Indeed, the ablation of hypoxia has the potential to sensitize tumors to immunotherapy by metabolically remodeling their microenvironment. In this review, we discuss the intrinsic contributions of hypoxia to cellular plasticity, heterogeneity, stemness and genetic instability in the context of immune escape. In addition, we will shed light on how managing hypoxia can ameliorate response to immunotherapy and how integrating hypoxia gene signatures could play a role in this pursuit.
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Affiliation(s)
- Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, 4184, United Arab Emirates.
| | - Hassan Venkatesh Goutham
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, 4184, United Arab Emirates.
| | - Rania Faouzi Zaarour
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, 4184, United Arab Emirates.
| | - Ali N Chamseddine
- Département d'Oncologie Médicale, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France.
| | - Amirtharaj Francis
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, 4184, United Arab Emirates.
| | - Stéphanie Buart
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Faculty. De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif F-94805, France
| | - Stéphane Terry
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Faculty. De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif F-94805, France.
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, 4184, United Arab Emirates; INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Faculty. De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif F-94805, France.
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21
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Ornell KJ, Mistretta KS, Newman E, Ralston CQ, Coburn JM. Three-Dimensional, Scaffolded Tumor Model to Study Cell-Driven Microenvironment Effects and Therapeutic Responses. ACS Biomater Sci Eng 2019; 5:6742-6754. [DOI: 10.1021/acsbiomaterials.9b01267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kimberly J. Ornell
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Rd., Worcester 01609-2280, Massachusetts, United States
| | - Katelyn S. Mistretta
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Rd., Worcester 01609-2280, Massachusetts, United States
| | - Emily Newman
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Rd., Worcester 01609-2280, Massachusetts, United States
| | - Coulter Q. Ralston
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Rd., Worcester 01609-2280, Massachusetts, United States
| | - Jeannine M. Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Rd., Worcester 01609-2280, Massachusetts, United States
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22
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Exosomal microRNAs from Longitudinal Liquid Biopsies for the Prediction of Response to Induction Chemotherapy in High-Risk Neuroblastoma Patients: A Proof of Concept SIOPEN Study. Cancers (Basel) 2019; 11:cancers11101476. [PMID: 31575060 PMCID: PMC6826693 DOI: 10.3390/cancers11101476] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/10/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
Despite intensive treatment, 50% of children with high-risk neuroblastoma (HR-NB) succumb to their disease. Progression through current trials evaluating the efficacy of new treatments for children with HR disease usually depends on an inadequate response to induction chemotherapy, assessed using imaging modalities. In this study, we sought to identify circulating biomarkers that might be detected in a simple blood sample to predict patient response to induction chemotherapy. Since exosomes released by tumor cells can drive tumor growth and chemoresistance, we tested the hypothesis that exosomal microRNA (exo-miRNAs) in blood might predict response to induction chemotherapy. The exo-miRNAs expression profile in plasma samples collected from children treated in HR-NBL-1/SIOPEN before and after induction chemotherapy was compared to identify a three exo-miRs signature that could discriminate between poor and good responders. Exo-miRNAs expression also provided a chemoresistance index predicting the good or poor prognosis of HR-NB patients.
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23
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Cowman S, Fan YN, Pizer B, Sée V. Decrease of Nibrin expression in chronic hypoxia is associated with hypoxia-induced chemoresistance in some brain tumour cells. BMC Cancer 2019; 19:300. [PMID: 30943920 PMCID: PMC6446413 DOI: 10.1186/s12885-019-5476-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 03/14/2019] [Indexed: 12/03/2022] Open
Abstract
Background Solid tumours are less oxygenated than normal tissues. This is called tumour hypoxia and leads to resistance to radiotherapy and chemotherapy. The molecular mechanisms underlying such resistance have been investigated in a range of tumour types, including the adult brain tumours glioblastoma, yet little is known for paediatric brain tumours. Medulloblastoma (MB) is the most common malignant brain tumour in children. We aimed to elucidate the impact of hypoxia on the sensitivity of MB cells to chemo- and radiotherapy. Methods We used two MB cell line (D283-MED and MEB-Med8A) and a widely used glioblastoma cell line (U87MG) for comparison. We applied a range of molecular and cellular techniques to measure cell survival, cell cycle progression, protein expression and DNA damage combined with a transcriptomic micro-array approach in D283-MED cells, for global gene expression analysis in acute and chronic hypoxic conditions. Results In D283-MED and U87MG, chronic hypoxia (5 days), but not acute hypoxia (24 h) induced resistance to chemotherapy and X-ray irradiation. This acquired resistance upon chronic hypoxia was present but less pronounced in MEB-Med8A cells. Using transcriptomic analysis in D283-MED cells, we found a large transcriptional remodelling upon long term hypoxia, in particular the expression of a number of genes involved in detection and repair of double strand breaks (DSB) was altered. The levels of Nibrin (NBN) and MRE11, members of the MRN complex (MRE11/Rad50/NBN) responsible for DSB recognition, were significantly down-regulated. This was associated with a reduction of Ataxia Telangiectasia Mutated (ATM) activation by etoposide, indicating a profound dampening of the DNA damage signalling in hypoxic conditions. As a consequence, p53 activation by etoposide was reduced, and cell survival enhanced. Whilst U87MG shared the same dampened p53 activity, upon chemotherapeutic drug treatment in chronic hypoxic conditions, these cells used a different mechanism, independent of the DNA damage pathway. Conclusion Together our results demonstrate a new mechanism explaining hypoxia-induced resistance involving the alteration of the response to DSB in D283-MED cells, but also highlight the cell type to cell type diversity and the necessity to take into account the differing tumour genetic make-up when considering re-sensitisation therapeutic protocols. Electronic supplementary material The online version of this article (10.1186/s12885-019-5476-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Cowman
- University of Liverpool, Institute of Integrated Biology, Department of Biochemistry, Centre for Cell Imaging, L69 7ZB, Liverpool, UK
| | - Yuen Ngan Fan
- University of Liverpool, Institute of Integrated Biology, Department of Biochemistry, Centre for Cell Imaging, L69 7ZB, Liverpool, UK.,University of Manchester, Faculty of Biology, Medicine and Health, M13 9PT, Manchester, UK
| | - Barry Pizer
- University of Liverpool and Alder Hey Children's NHS Foundation Trust, member of Liverpool Health Partners., Liverpool, UK
| | - Violaine Sée
- University of Liverpool, Institute of Integrated Biology, Department of Biochemistry, Centre for Cell Imaging, L69 7ZB, Liverpool, UK.
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24
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Morgenstern DA, Bagatell R, Cohn SL, Hogarty MD, Maris JM, Moreno L, Park JR, Pearson AD, Schleiermacher G, Valteau-Couanet D, London WB, Irwin MS. The challenge of defining "ultra-high-risk" neuroblastoma. Pediatr Blood Cancer 2019; 66:e27556. [PMID: 30479064 DOI: 10.1002/pbc.27556] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/08/2018] [Accepted: 10/27/2018] [Indexed: 12/17/2022]
Abstract
Given the biological and clinical heterogeneity of neuroblastoma, risk stratification is vital to determining appropriate treatment. Historically, most patients with high-risk neuroblastoma (HR-NBL) have been treated uniformly without further stratification. Attempts have been made to identify factors that can be used to risk stratify these patients and to characterize an "ultra-high-risk" (UHR) subpopulation with particularly poor outcome. However, among published data, there is a lack of consensus in the definition of the UHR population and heterogeneity in the endpoints and statistical methods used. This review summarizes our current understanding of stratification of HR-NBL and discusses the complex issues in defining UHR neuroblastoma.
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Affiliation(s)
| | - Rochelle Bagatell
- Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | | | - Michael D Hogarty
- Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - John M Maris
- Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Lucas Moreno
- Hospital Universitario Niño Jesus, Madrid, Spain
| | - Julie R Park
- Seattle Children's Hospital and University of Washington School of Medicine, Seattle, Washington
| | - Andrew D Pearson
- Institute of Cancer Research and Royal Marsden National Health Service (NHS) Foundation Trust, Sutton, Surrey, UK
| | | | | | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Meredith S Irwin
- Hospital for Sick Children and University of Toronto, Toronto, Canada
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25
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Paterson BM, Cullinane C, Crouch PJ, White AR, Barnham KJ, Roselt PD, Noonan W, Binns D, Hicks RJ, Donnelly PS. Modification of Biodistribution and Brain Uptake of Copper Bis(thiosemicarbazonato) Complexes by the Incorporation of Amine and Polyamine Functional Groups. Inorg Chem 2019; 58:4540-4552. [PMID: 30869878 DOI: 10.1021/acs.inorgchem.9b00117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of new bis(thiosemicarbazonato)copper(II) complexes featuring polyamine substituents via selective transamination reactions is presented. Polyamines of different lengths, with different ionizable substituent groups, were used to modify and adjust the hydrophilic/lipophilic balance of the copper complexes. The new analogues were radiolabeled with copper-64 and their lipophilicities estimated using distribution coefficients. The cell uptake of the new polyamine complexes was investigated with preliminary in vitro biological studies using a neuroblastoma cancer cell line. The in vivo biodistribution of three of the new analogues was investigated in vivo in mice using positron-emission tomography imaging, and one of the new complexes was compared to [64Cu]Cu(atsm) in an A431 squamous cell carcinoma xenograft model. Modification of the copper complexes with various amine-containing functional groups alters the biodistribution of the complexes in mice. One complex, with a pendent ( N, N-dimethylamino)ethane functional group, displayed tumor uptake similar to that of [64Cu]Cu(atsm) but higher brain uptake, suggesting that this compound has the potential to be of use in the diagnostic brain imaging of tumors and neurodegenerative diseases.
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Affiliation(s)
| | - Carleen Cullinane
- The Centre for Molecular Imaging and Translational Research Laboratory , The Peter MacCallum Cancer Centre , Melbourne , Victoria 3000 , Australia
| | | | | | | | - Peter D Roselt
- The Centre for Molecular Imaging and Translational Research Laboratory , The Peter MacCallum Cancer Centre , Melbourne , Victoria 3000 , Australia
| | - Wayne Noonan
- The Centre for Molecular Imaging and Translational Research Laboratory , The Peter MacCallum Cancer Centre , Melbourne , Victoria 3000 , Australia
| | - David Binns
- The Centre for Molecular Imaging and Translational Research Laboratory , The Peter MacCallum Cancer Centre , Melbourne , Victoria 3000 , Australia
| | - Rodney J Hicks
- The Centre for Molecular Imaging and Translational Research Laboratory , The Peter MacCallum Cancer Centre , Melbourne , Victoria 3000 , Australia
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26
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Wang F, Zhou S, Qi D, Xiang SH, Wong ET, Wang X, Fonkem E, Hsieh TC, Yang J, Kirmani B, Shabb JB, Wu JM, Wu M, Huang JH, Yu WH, Wu E. Nucleolin Is a Functional Binding Protein for Salinomycin in Neuroblastoma Stem Cells. J Am Chem Soc 2019; 141:3613-3622. [PMID: 30689374 DOI: 10.1021/jacs.8b12872] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aim of this study is to illuminate a novel therapeutic approach by identifying a functional binding target of salinomycin, an emerging anticancer stem cell (CSC) agent, and to help dissect the underlying action mechanisms. By utilizing integrated strategies, we identify that nucleolin (NCL) is likely a salinomycin-binding target and a critical regulator involved in human neuroblastoma (NB) CSC activity. Salinomycin markedly suppresses NB CD34 expression and reduces CD34+ cell population in an NCL-dependent manner via disruption of the interaction of NCL with CD34 promoter. The elevated levels of NCL expression in NB tumors are associated with poor patient survival. Altogether, these results indicate that NCL is likely a novel functional salinomycin-binding target that exhibits the potential to be a prognostic marker for NB therapy.
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Affiliation(s)
- Fengfei Wang
- Department of Neurosurgery , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Neuroscience Institute , Baylor Scott & White Health , Temple , Texas 76502 , United States
- Department of Neurology , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Department of Surgery , Texas A & M University College of Medicine , Temple , Texas 76504 , United States
| | - Shuang Zhou
- Department of Neurosurgery , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Neuroscience Institute , Baylor Scott & White Health , Temple , Texas 76502 , United States
- Cancer Research Institute, Department of Medicine, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , Massachusetts 02215 , United States
| | - Dan Qi
- Department of Neurosurgery , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Neuroscience Institute , Baylor Scott & White Health , Temple , Texas 76502 , United States
| | - Shi-Hua Xiang
- Nebraska Center for Virology, School of Veterinary Medicine and Biomedical Sciences , University of Nebraska-Lincoln , Lincoln , Nebraska 68583 , United States
| | - Eric T Wong
- Cancer Research Institute, Department of Medicine, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , Massachusetts 02215 , United States
| | - Xuejing Wang
- Department of Neurology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan 450052 , China
| | - Ekokobe Fonkem
- Department of Neurosurgery , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Neuroscience Institute , Baylor Scott & White Health , Temple , Texas 76502 , United States
- Department of Neurology , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Department of Surgery , Texas A & M University College of Medicine , Temple , Texas 76504 , United States
- LIVESTRONG Cancer Institutes, Dell Medical School , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Tze-Chen Hsieh
- Department of Biochemistry and Molecular Biology , New York Medical College , Valhalla , New York 10595 , United States
| | - Jianhua Yang
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Batool Kirmani
- Department of Neurology , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Department of Surgery , Texas A & M University College of Medicine , Temple , Texas 76504 , United States
| | - John B Shabb
- Department of Biomedical Sciences, School of Medicine and Health Sciences , University of North Dakota , Grand Forks , North Dakota 58202 , United States
| | - Joseph M Wu
- Department of Biochemistry and Molecular Biology , New York Medical College , Valhalla , New York 10595 , United States
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences , University of North Dakota , Grand Forks , North Dakota 58202 , United States
| | - Jason H Huang
- Department of Neurosurgery , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Neuroscience Institute , Baylor Scott & White Health , Temple , Texas 76502 , United States
- Department of Surgery , Texas A & M University College of Medicine , Temple , Texas 76504 , United States
| | - Wei-Hsuan Yu
- Institute of Biochemistry and Molecular Biology, College of Medicine , National Taiwan University , Taipei 10051 , Taiwan
| | - Erxi Wu
- Department of Neurosurgery , Baylor Scott & White Health , Temple , Texas 78508 , United States
- Neuroscience Institute , Baylor Scott & White Health , Temple , Texas 76502 , United States
- Department of Surgery , Texas A & M University College of Medicine , Temple , Texas 76504 , United States
- LIVESTRONG Cancer Institutes, Dell Medical School , The University of Texas at Austin , Austin , Texas 78712 , United States
- Department of Pharmaceutical Sciences , Texas A & M University College of Pharmacy , College Station , Texas 77843 , United States
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27
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Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma. Int J Mol Sci 2018; 19:ijms19102903. [PMID: 30257451 PMCID: PMC6212863 DOI: 10.3390/ijms19102903] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/15/2018] [Accepted: 09/20/2018] [Indexed: 01/09/2023] Open
Abstract
Glioma growth is often accompanied by a hypoxic microenvironment favorable for the induction and maintenance of the glioma stem cell (GSC) phenotype. Due to the paucity of cell models of Isocitrate Dehydrogenase 1 mutant (IDH1mut) GSCs, biology under hypoxic conditions has not been sufficiently studied as compared to IDH1 wildtype (IDH1wt) GSCs. We therefore grew well-characterized IDH1mut (n = 4) and IDH1wt (n = 4) GSC lines under normoxic (20%) and hypoxic (1.5%) culture conditions and harvested mRNA after 72 h. Transcriptome analyses were performed and hypoxia regulated genes were further analyzed using the expression and clinical data of the lower grade glioma cohort of The Cancer Genome Atlas (LGG TCGA) in a confirmatory approach and to test for possible survival associations. Results show that global expression changes were more pronounced in IDH1wt than in IDH1mut GSCs. However, when focusing on known hypoxia-regulated gene sets, enrichment analyses showed a comparable regulation in both IDH1mut and IDH1wt GSCs. Of 272 significantly up-regulated genes under hypoxic conditions in IDH1mut GSCs a hypoxia-related survival score (HRS-score) of five genes (LYVE1, FAM162A, WNT6, OTP, PLOD1) was identified by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm which was able to predict survival independent of age, 1p19q co-deletion status and WHO grade (II vs. III) in the LGG TCGA cohort and in the Rembrandt dataset. Altogether, we were able to identify and validate a novel hypoxia-related survival score in IDH1mut GSCs consisting of five hypoxia-regulated genes which was significantly associated with patient survival independent of known prognostic confounders.
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28
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Effects of hypoxic preconditioning on neuroblastoma tumour oxygenation and metabolic signature in a chick embryo model. Biosci Rep 2018; 38:BSR20180185. [PMID: 30026261 PMCID: PMC6131206 DOI: 10.1042/bsr20180185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/02/2018] [Accepted: 07/09/2018] [Indexed: 01/01/2023] Open
Abstract
Hypoxia episodes and areas in tumours have been associated with metastatic dissemination and poor prognosis. Given the link between tumour tissue oxygen levels and cellular metabolic activity, we hypothesised that the metabolic profile between metastatic and non-metastatic tumours would reveal potential new biomarkers and signalling cues. We have used a previously established chick embryo model for neuroblastoma growth and metastasis, where the metastatic phenotype can be controlled by neuroblastoma cell hypoxic preconditioning (3 days at 1% O2). We measured, with fibre-optic oxygen sensors, the effects of the hypoxic preconditioning on the tumour oxygenation, within tumours formed by SK-N-AS cells on the chorioallantoic membrane (CAM) of chick embryos. We found that the difference between the metastatic and non-metastatic intratumoural oxygen levels was small (0.35% O2), with a mean below 1.5% O2 for most tumours. The metabolomic profiling, using NMR spectroscopy, of neuroblastoma cells cultured in normoxia or hypoxia for 3 days, and of the tumours formed by these cells showed that the effects of hypoxia in vitro did not compare with in vivo tumours. One notable difference was the high levels of the glycolytic end-products triggered by hypoxia in vitro, but not by hypoxia preconditioning in tumours, likely due to the very high basal levels of these metabolites in tumours compared with cells. In conclusion, we have identified high levels of ketones (3-hydroxybutyrate), lactate and phosphocholine in hypoxic preconditioned tumours, all known to fuel tumour growth, and we herein point to the poor relevance of in vitro metabolomic experiments for cancer research.
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29
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Giordano TJ. 65 YEARS OF THE DOUBLE HELIX: Classification of endocrine tumors in the age of integrated genomics. Endocr Relat Cancer 2018; 25:T171-T187. [PMID: 29980645 DOI: 10.1530/erc-18-0116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/31/2018] [Indexed: 12/26/2022]
Abstract
The classification of human cancers represents one of the cornerstones of modern pathology. Over the last century, surgical pathologists established the current taxonomy of neoplasia using traditional histopathological parameters, which include tumor architecture, cytological features and cellular proliferation. This morphological classification is efficient and robust with high reproducibility and has served patients and health care providers well. The most recent decade has witnessed an explosion of genome-wide molecular genetic and epigenetic data for most cancers, including tumors of endocrine organs. The availability of this expansive multi-dimensional genomic data, collectively termed the cancer genome, has catalyzed a re-examination of the classification of endocrine tumors. Here, recent cancer genome studies of various endocrine tumors, including those of the thyroid, pituitary and adrenal glands, pancreas, small bowel, lung and skin, are presented with special emphasis on how genomic insights are impacting endocrine tumor classification.
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Affiliation(s)
- Thomas J Giordano
- Divisions of Anatomic Pathology and Molecular & Genomic PathologyDepartments of Pathology and Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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30
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Sahu D, Ho SY, Juan HF, Huang HC. High-risk, Expression-Based Prognostic Long Noncoding RNA Signature in Neuroblastoma. JNCI Cancer Spectr 2018; 2:pky015. [PMID: 31360848 PMCID: PMC6649748 DOI: 10.1093/jncics/pky015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/13/2018] [Accepted: 03/29/2018] [Indexed: 12/19/2022] Open
Abstract
Background Current clinical risk factors stratify patients with neuroblastoma (NB) for appropriate treatments, yet patients with similar clinical behaviors evoke variable responses. MYCN amplification is one of the established drivers of NB and, when combined with high-risk displays, worsens outcomes. Growing high-throughput transcriptomics studies suggest long noncoding RNA (lncRNA) dysregulation in cancers, including NB. However, expression-based lncRNA signatures are altered by MYCN amplification, which is associated with high-risk, and patient prognosis remains limited. Methods We investigated RNA-seq-based expression profiles of lncRNAs in MYCN status and risk status in a discovery cohort (n = 493) and validated them in three independent cohorts. In the discovery cohort, a prognostic association of lncRNAs was determined by univariate Cox regression and integrated into a signature using the risk score method. A novel risk score threshold selection criterion was developed to stratify patients into risk groups. Outcomes by risk group and clinical subgroup were assessed using Kaplan-Meier survival curves and multivariable Cox regression. The performance of lncRNA signatures was evaluated by receiver operating characteristic curve. All statistical tests were two-sided. Results In the discovery cohort, 16 lncRNAs that were differentially expressed (fold change ≥ 2 and adjusted P ≤ 0.01) integrated into a prognostic signature. A high risk score group of lncRNA signature had poor event-free survival (EFS; P < 1E-16). Notably, lncRNA signature was independent of other clinical risk factors when predicting EFS (hazard ratio = 3.21, P = 5.95E-07). The findings were confirmed in independent cohorts (P = 2.86E-02, P = 6.18E-03, P = 9.39E-03, respectively). Finally, the lncRNA signature had higher accuracy for EFS prediction (area under the curve = 0.788, 95% confidence interval = 0.746 to 0.831). Conclusions Here, we report the first (to our knowledge) RNA-seq 16-lncRNA prognostic signature for NB that may contribute to precise clinical stratification and EFS prediction.
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Affiliation(s)
- Divya Sahu
- Institute of Bioinformatics and Systems Biology.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Fen Juan
- Department of Life Science, Institute of Molecular and Cellular Biology, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Cheng Huang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
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31
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CHL1 gene acts as a tumor suppressor in human neuroblastoma. Oncotarget 2018; 9:25903-25921. [PMID: 29899830 PMCID: PMC5995240 DOI: 10.18632/oncotarget.25403] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/28/2018] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma is an aggressive, relapse-prone childhood tumor of the sympathetic nervous system that accounts for 15% of pediatric cancer deaths. A distal portion of human chromosome 3p is often deleted in neuroblastoma, this region may contain one or more putative tumor suppressor genes. A 2.54 Mb region at 3p26.3 encompassing the smallest region of deletion pinpointed CHL1 gene, the locus for neuronal cell adhesion molecule close homolog of L1. We found that low CHL1 expression predicted poor outcome in neuroblastoma patients. Here we have used two inducible cell models to analyze the impact of CHL1 on neuroblastoma biology. Over-expression of CHL1 induced neurite-like outgrowth and markers of neuronal differentiation in neuroblastoma cells, halted tumor progression, inhibited anchorage-independent colony formation, and suppressed the growth of human tumor xenografts. Conversely, knock-down of CHL1 induced neurite retraction and activation of Rho GTPases, enhanced cell proliferation and migration, triggered colony formation and anchorage-independent growth, accelerated growth in orthotopic xenografts mouse model. Our findings demonstrate unambiguously that CHL1 acts as a regulator of proliferation and differentiation of neuroblastoma cells through inhibition of the MAPKs and Akt pathways. CHL1 is a novel candidate tumor suppressor in neuroblastoma, and its associated pathways may represent a promising target for future therapeutic interventions.
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32
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Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, Chlenski A, Dobratic M, Mariani CJ, Godley LA, Prabhakar N, White K, Stranger BE, Cohn SL. Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients. Oncotarget 2018; 7:76816-76826. [PMID: 27765905 PMCID: PMC5340231 DOI: 10.18632/oncotarget.12713] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is notable for its broad spectrum of clinical behavior ranging from spontaneous regression to rapidly progressive disease. Hypoxia is well known to confer a more aggressive phenotype in neuroblastoma. We analyzed transcriptome data from diagnostic neuroblastoma tumors and hypoxic neuroblastoma cell lines to identify genes whose expression levels correlate with poor patient outcome and are involved in the hypoxia response. By integrating a diverse set of transcriptome datasets, including those from neuroblastoma patients and neuroblastoma derived cell lines, we identified nine genes (SLCO4A1, ENO1, HK2, PGK1, MTFP1, HILPDA, VKORC1, TPI1, and HIST1H1C) that are up-regulated in hypoxia and whose expression levels are correlated with poor patient outcome in three independent neuroblastoma cohorts. Analysis of 5-hydroxymethylcytosine and ENCODE data indicate that at least five of these nine genes have an increase in 5-hydroxymethylcytosine and a more open chromatin structure in hypoxia versus normoxia and are putative targets of hypoxia inducible factor (HIF) as they contain HIF binding sites in their regulatory regions. Four of these genes are key components of the glycolytic pathway and another three are directly involved in cellular metabolism. We experimentally validated our computational findings demonstrating that seven of the nine genes are significantly up-regulated in response to hypoxia in the four neuroblastoma cell lines tested. This compact and robustly validated group of genes, is associated with the hypoxia response in aggressive neuroblastoma and may represent a novel target for biomarker and therapeutic development.
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Affiliation(s)
- Mark A Applebaum
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America.,Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Aashish R Jha
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, 60637, United States of America.,Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Clara Kao
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Kyle M Hernandez
- Center for Research Informatics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Gillian DeWane
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Helen R Salwen
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Alexandre Chlenski
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Marija Dobratic
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Christopher J Mariani
- Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Lucy A Godley
- Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Nanduri Prabhakar
- Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Kevin White
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Barbara E Stranger
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, 60637, United States of America.,Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America.,Center for Data Intensive Science, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Susan L Cohn
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America.,Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, 60637, United States of America
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33
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Langer EM, Kendsersky ND, Daniel CJ, Kuziel GM, Pelz C, Murphy KM, Capecchi MR, Sears RC. ZEB1-repressed microRNAs inhibit autocrine signaling that promotes vascular mimicry of breast cancer cells. Oncogene 2018; 37:1005-1019. [PMID: 29084210 PMCID: PMC5823716 DOI: 10.1038/onc.2017.356] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
Abstract
During normal tumor growth and in response to some therapies, tumor cells experience acute or chronic deprivation of nutrients and oxygen and induce tumor vascularization. While this occurs predominately through sprouting angiogenesis, tumor cells have also been shown to directly contribute to vessel formation through vascular mimicry (VM) and/or endothelial transdifferentiation. The extrinsic and intrinsic mechanisms underlying tumor cell adoption of endothelial phenotypes, however, are not well understood. Here we show that serum withdrawal induces mesenchymal breast cancer cells to undergo VM and that knockdown of the epithelial-to-mesenchymal transition (EMT) regulator, Zinc finger E-box binding homeobox 1 (ZEB1), or overexpression of the ZEB1-repressed microRNAs (miRNAs), miR-200c, miR-183, miR-96 and miR-182 inhibits this process. We find that secreted proteins Fibronectin 1 (FN1) and serine protease inhibitor (serpin) family E member 2 (SERPINE2) are essential for VM in this system. These secreted factors are upregulated in mesenchymal cells in response to serum withdrawal, and overexpression of VM-inhibiting miRNAs abrogates this upregulation. Intriguingly, the receptors for these secreted proteins, low-density lipoprotein receptor-related protein 1 (LRP1) and Integrin beta 1 (ITGB1), are also targets of the VM-inhibiting miRNAs, suggesting that autocrine signaling stimulating VM is regulated by ZEB1-repressed miRNA clusters. Together, these data provide mechanistic insight into the regulation of VM and suggest that miRNAs repressed during EMT, in addition to suppressing migratory and stem-like properties of tumor cells, also inhibit endothelial phenotypes of breast cancer cells adopted in response to a nutrient-deficient microenvironment.
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Affiliation(s)
- E M Langer
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - N D Kendsersky
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - C J Daniel
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - G M Kuziel
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - C Pelz
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA
| | - K M Murphy
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Pathology & Immunology, Washington University, St. Louis, MO, USA
| | - M R Capecchi
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - R C Sears
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
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34
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Bhalla K, Jaber S, Nahid M N, Underwood K, Beheshti A, Landon A, Bhandary B, Bastian P, Evens AM, Haley J, Polster B, Gartenhaus RB. Role of hypoxia in Diffuse Large B-cell Lymphoma: Metabolic repression and selective translation of HK2 facilitates development of DLBCL. Sci Rep 2018; 8:744. [PMID: 29335581 PMCID: PMC5768748 DOI: 10.1038/s41598-018-19182-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/22/2017] [Indexed: 02/08/2023] Open
Abstract
Published molecular profiling studies in patients with lymphoma suggested the influence of hypoxia inducible factor-1 alpha (HIF1α) targets in prognosis of DLBCL. Yet, the role of hypoxia in hematological malignancies remains unclear. We observed that activation of HIF1α resulted in global translation repression during hypoxic stress in DLBCL. Protein translation efficiency as measured using 35S-labeled methionine incorporation revealed a ≥50% reduction in translation upon activation of HIF1α. Importantly, translation was not completely inhibited and expression of clinically correlated hypoxia targets such as GLUT1, HK2, and CYT-C was found to be refractory to translational repression under hypoxia in DLBCL cells. Notably, hypoxic induction of these genes was not observed in normal primary B-cells. Translational repression was coupled with a decrease in mitochondrial function. Screening of primary DLBCL patient samples revealed that expression of HK2, which encodes for the enzyme hexokinase 2, was significantly correlated with DLBCL phenotype. Genetic knockdown studies demonstrated that HK2 is required for promoting growth of DLBCL under hypoxic stress. Altogether, our findings provide strong support for the direct contribution of HK2 in B-cell lymphoma development and suggest that HK2 is a key metabolic driver of the DLBCL phenotype.
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Affiliation(s)
- Kavita Bhalla
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Department of Medicine, Baltimore, MD, 21201, USA.
| | - Sausan Jaber
- University of Maryland, Department of Biochemistry and Molecular Biology, Baltimore, MD, 21201, USA
| | - Nanaji Nahid M
- Veterans Administration Medical Center, Baltimore, MD, 21201, USA
| | - Karen Underwood
- University of Maryland, Flow Cytometry Core, Greenebaum Comprehensive Cancer Center, Baltimore, MD, 21201, USA
| | | | - Ari Landon
- Yale School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Binny Bhandary
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Department of Medicine, Baltimore, MD, 21201, USA
| | - Paul Bastian
- National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | | | - John Haley
- Department of Pathology, Stony Brook Medicine, Stony Brook, NY, 11794-8691, USA
| | - Brian Polster
- University of Maryland, Department of Biochemistry and Molecular Biology, Baltimore, MD, 21201, USA
| | - Ronald B Gartenhaus
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Department of Medicine, Baltimore, MD, 21201, USA.
- Veterans Administration Medical Center, Baltimore, MD, 21201, USA.
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35
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Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat Commun 2018; 9:20. [PMID: 29295995 PMCID: PMC5750219 DOI: 10.1038/s41467-017-02391-6] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/24/2017] [Indexed: 12/18/2022] Open
Abstract
Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug research. A common approach is to infer signaling activity of pathways from gene expression. However, mapping gene expression to pathway components disregards the effect of post-translational modifications, and downstream signatures represent very specific experimental conditions. Here we present PROGENy, a method that overcomes both limitations by leveraging a large compendium of publicly available perturbation experiments to yield a common core of Pathway RespOnsive GENes. Unlike pathway mapping methods, PROGENy can (i) recover the effect of known driver mutations, (ii) provide or improve strong markers for drug indications, and (iii) distinguish between oncogenic and tumor suppressor pathways for patient survival. Collectively, these results show that PROGENy accurately infers pathway activity from gene expression in a wide range of conditions.
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Affiliation(s)
- Michael Schubert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Bertram Klinger
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- IRI Life Sciences and Institute for Theoretical Biology, Humboldt University Berlin, Philippstr. 13/Haus 18, 10115, Berlin, Germany
| | - Martina Klünemann
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- IRI Life Sciences and Institute for Theoretical Biology, Humboldt University Berlin, Philippstr. 13/Haus 18, 10115, Berlin, Germany
| | - Anja Sieber
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- IRI Life Sciences and Institute for Theoretical Biology, Humboldt University Berlin, Philippstr. 13/Haus 18, 10115, Berlin, Germany
| | - Florian Uhlitz
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- IRI Life Sciences and Institute for Theoretical Biology, Humboldt University Berlin, Philippstr. 13/Haus 18, 10115, Berlin, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine (MDC), Berlin Institute for Medical Systems Biology/Berlin Institute of Health, Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Nils Blüthgen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- IRI Life Sciences and Institute for Theoretical Biology, Humboldt University Berlin, Philippstr. 13/Haus 18, 10115, Berlin, Germany
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, Aachen, 52057, Germany.
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36
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Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A. c-MYC inhibition impairs hypoxia response in glioblastoma multiforme. Oncotarget 2017; 7:33257-71. [PMID: 27119353 PMCID: PMC5078092 DOI: 10.18632/oncotarget.8921] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/31/2016] [Indexed: 01/09/2023] Open
Abstract
The c-MYC oncoprotein is a DNA binding transcription factor that enhances the expression of many active genes. c-MYC transcriptional signatures vary according to the transcriptional program defined in each cell type during differentiation. Little is known on the involvement of c-MYC in regulation of gene expression programs that are induced by extracellular cues such as a changing microenvironment. Here we demonstrate that inhibition of c-MYC in glioblastoma multiforme cells blunts hypoxia-dependent glycolytic reprogramming and mitochondria fragmentation in hypoxia. This happens because c-MYC inhibition alters the cell transcriptional response to hypoxia and finely tunes the expression of a subset of Hypoxia Inducible Factor 1-regulated genes. We also show that genes whose expression in hypoxia is affected by c-MYC inhibition are able to distinguish the Proneural subtype of glioblastoma multiforme, thus potentially providing a molecular signature for this class of tumors that are the least tractable among glioblastomas.
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Affiliation(s)
| | - Mauro Savino
- Nucleic Acids Laboratory, Institute of Molecular Biology and Pathology, National Research Council (IBPM-CNR) and Department of Biology and Biotechnologies, Sapienza University, 00185 Rome, Italy
| | | | - Barbara Illi
- Nucleic Acids Laboratory, Institute of Molecular Biology and Pathology, National Research Council (IBPM-CNR) and Department of Biology and Biotechnologies, Sapienza University, 00185 Rome, Italy
| | - Francesca Bozzo
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy.,Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy
| | - Cristiana Valle
- Institute of Cell Biology and Neurobiology, CNR, c/o CERC, 00143 Rome, Italy.,Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Fabrizio Ferrè
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, 40126 Bologna, Italy
| | - Sergio Nasi
- Nucleic Acids Laboratory, Institute of Molecular Biology and Pathology, National Research Council (IBPM-CNR) and Department of Biology and Biotechnologies, Sapienza University, 00185 Rome, Italy
| | - Andrea Levi
- Institute of Cell Biology and Neurobiology, CNR, c/o CERC, 00143 Rome, Italy
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37
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Yang L, Li Y, Wei Z, Chang X. Coexpression network analysis identifies transcriptional modules associated with genomic alterations in neuroblastoma. Biochim Biophys Acta Mol Basis Dis 2017; 1864:2341-2348. [PMID: 29247836 DOI: 10.1016/j.bbadis.2017.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/02/2017] [Accepted: 12/11/2017] [Indexed: 01/28/2023]
Abstract
Neuroblastoma is a highly complex and heterogeneous cancer in children. Acquired genomic alterations including MYCN amplification, 1p deletion and 11q deletion are important risk factors and biomarkers in neuroblastoma. Here, we performed a co-expression-based gene network analysis to study the intrinsic association between specific genomic changes and transcriptome organization. We identified multiple gene coexpression modules which are recurrent in two independent datasets and associated with functional pathways including nervous system development, cell cycle, immune system process and extracellular matrix/space. Our results also indicated that modules involved in nervous system development and cell cycle are highly associated with MYCN amplification and 1p deletion, while modules responding to immune system process are associated with MYCN amplification only. In summary, this integrated analysis provides novel insights into molecular heterogeneity and pathogenesis of neuroblastoma. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.
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Affiliation(s)
- Liulin Yang
- College of Electrical Engineering, Guangxi University, Nanning, Guangxi 530004, China; Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Yun Li
- Department of Biostatistics and Epidemiology, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
| | - Xiao Chang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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38
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Criscuoli M, Filippi I, Osti D, Aldinucci C, Guerrini G, Pelicci G, Carraro F, Naldini A. The Shc protein RAI promotes an adaptive cell survival program in hypoxic neuroblastoma cells. J Cell Physiol 2017; 233:4282-4293. [DOI: 10.1002/jcp.26247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/13/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Mattia Criscuoli
- Cellular and Molecular Physiology UnitDepartment of Molecular and Developmental MedicineUniversity of SienaSienaItaly
| | - Irene Filippi
- Cellular and Molecular Physiology UnitDepartment of Molecular and Developmental MedicineUniversity of SienaSienaItaly
- Istituto Toscano TumoriFirenzeItaly
| | - Daniela Osti
- Department of Experimental OncologyEuropean Institute of OncologyMilanItaly
| | - Carlo Aldinucci
- Cellular and Molecular Physiology UnitDepartment of Molecular and Developmental MedicineUniversity of SienaSienaItaly
| | - Giuditta Guerrini
- Cellular and Molecular Physiology UnitDepartment of Molecular and Developmental MedicineUniversity of SienaSienaItaly
| | - Giuliana Pelicci
- Department of Experimental OncologyEuropean Institute of OncologyMilanItaly
- Department of Translational MedicinePiemonte Orientale University “Amedeo Avogadro”NovaraItaly
| | - Fabio Carraro
- Cellular and Molecular Physiology UnitDepartment of Molecular and Developmental MedicineUniversity of SienaSienaItaly
- Istituto Toscano TumoriFirenzeItaly
| | - Antonella Naldini
- Cellular and Molecular Physiology UnitDepartment of Molecular and Developmental MedicineUniversity of SienaSienaItaly
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39
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Ognibene M, Cangelosi D, Morini M, Segalerba D, Bosco MC, Sementa AR, Eva A, Varesio L. Immunohistochemical analysis of PDK1, PHD3 and HIF-1α expression defines the hypoxic status of neuroblastoma tumors. PLoS One 2017; 12:e0187206. [PMID: 29117193 PMCID: PMC5678880 DOI: 10.1371/journal.pone.0187206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/16/2017] [Indexed: 01/31/2023] Open
Abstract
Neuroblastoma (NB) is the most common solid tumor during infancy and the first cause of death among the preschool age diseases. The availability of several NB genomic profiles improves the prognostic ability, but the outcome prediction for this pathology remains imperfect. We previously produced a novel prognostic gene signature based on the response of NB cells to hypoxia, a condition of tumor microenvironment strictly connected with cancer aggressiveness. Here we attempted to further define the expression of hypoxia-modulated specific genes, looking at their protein level in NB specimens, considering in particular the hypoxia inducible factor-1α (HIF-1α), the mitochondrial pyruvate dehydrogenase kinase 1 (PDK1), and the HIF-prolyl hydroxylase domain 3 (PHD3). The evaluation of expression was performed by Western blot and immunocytochemistry on NB cell lines and by immunohistochemistry on tumor specimens. Stimulation of both HIF-1α and PDK1 and inhibition of PHD3 expression were observed in NB cell lines cultured under prolonged hypoxic conditions as well as in most of the tumors with poor outcome. Our results indicate that the immunohistochemistry analysis of the protein expression of PDK1, PHD3, and HIF-1α defines the hypoxic status of NB tumors and can be used as a simple and relevant tool to stratify high-risk patients.
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Affiliation(s)
- Marzia Ognibene
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
- * E-mail: (AE); (MO)
| | - Davide Cangelosi
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | - Daniela Segalerba
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | | | - Alessandra Eva
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
- * E-mail: (AE); (MO)
| | - Luigi Varesio
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
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40
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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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41
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Yang L, Taylor J, Eustace A, Irlam JJ, Denley H, Hoskin PJ, Alsner J, Buffa FM, Harris AL, Choudhury A, West CML. A Gene Signature for Selecting Benefit from Hypoxia Modification of Radiotherapy for High-Risk Bladder Cancer Patients. Clin Cancer Res 2017; 23:4761-4768. [PMID: 28400426 DOI: 10.1158/1078-0432.ccr-17-0038] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/21/2017] [Accepted: 04/05/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Hypoxia modification improves overall survival in muscle-invasive bladder cancer patients who undergo radiotherapy. There is evidence that hypoxic tumors benefit most from hypoxia modification. The study aimed to identify or derive a hypoxia gene signature that predicts benefit from hypoxia-modifying treatment in bladder cancer.Experimental Design: Published hypoxia signatures were tested and a new one derived by analyzing bladder cancer transcriptomic data from public databases. Tumor samples were available from the BCON phase III randomized trial of radiotherapy alone or with carbogen and nicotinamide (CON). Gene expression data were generated for 151 tumors using Affymetrix Human 1.0 Exon ST arrays and used for independent validation.Results: A 24-gene signature was derived, which was prognostic in four of six independent surgical cohorts (n = 679; meta HR, 2.32; 95% CI, 1.73-3.12; P < 0.0001). The signature was also prognostic in BCON patients receiving radiotherapy alone (n = 75; HR for local relapse-free survival, 2.37; 95% CI, 1.26-4.47; P = 0.0076). The signature predicted benefit from CON (n = 76; HR, 0.47; 95% CI, 0.26-0.86; P = 0.015). Prognostic significance (P = 0.017) and predictive significance (P = 0.058) remained after adjusting for clinicopathologic variables. A test for interaction between hypoxia status and treatment arms was significant (P = 0.0094).Conclusions: A 24-gene hypoxia signature has strong and independent prognostic and predictive value for muscle-invasive bladder cancer patients. The signature can aid identification of patients likely to benefit from the addition of carbogen and nicotinamide to radiotherapy. Clin Cancer Res; 23(16); 4761-8. ©2017 AACR.
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Affiliation(s)
- Lingjian Yang
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Janet Taylor
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
- Applied Computational Biology and Bioinformatics Group, CRUK-MI, Manchester, United Kingdom
- HMDS, Leeds Cancer Centre, St James University Hospital, Leeds, United Kingdom
| | - Amanda Eustace
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Joely J Irlam
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Helen Denley
- Department of Cellular Pathology, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Peter J Hoskin
- Cancer Centre, Mount Vernon Hospital, Rickmansworth Road, Northwood, Middlesex, United Kingdom
| | - Jan Alsner
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Francesca M Buffa
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian L Harris
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom.
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Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression. Proc Natl Acad Sci U S A 2017; 114:E6137-E6146. [PMID: 28696319 DOI: 10.1073/pnas.1700655114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Neuroblastoma is a pediatric cancer characterized by variable outcomes ranging from spontaneous regression to life-threatening progression. High-risk neuroblastoma patients receive myeloablative chemotherapy with hematopoietic stem-cell transplant followed by adjuvant retinoid differentiation treatment. However, the overall survival remains low; hence, there is an urgent need for alternative therapeutic approaches. One feature of high-risk neuroblastoma is the high level of DNA methylation of putative tumor suppressors. Combining the reversibility of DNA methylation with the differentiation-promoting activity of retinoic acid (RA) could provide an alternative strategy to treat high-risk neuroblastoma. Here we show that treatment with the DNA-demethylating drug 5-Aza-deoxycytidine (AZA) restores high-risk neuroblastoma sensitivity to RA. Combined systemic distribution of AZA and RA impedes tumor growth and prolongs survival. Genome-wide analysis of treated tumors reveals that this combined treatment rapidly induces a HIF2α-associated hypoxia-like transcriptional response followed by an increase in neuronal gene expression and a decrease in cell-cycle gene expression. A small-molecule inhibitor of HIF2α activity diminishes the tumor response to AZA+RA treatment, indicating that the increase in HIF2α levels is a key component in tumor response to AZA+RA. The link between increased HIF2α levels and inhibited tumor growth is reflected in large neuroblastoma patient datasets. Therein, high levels of HIF2α, but not HIF1α, significantly correlate with expression of neuronal differentiation genes and better prognosis but negatively correlate with key features of high-risk tumors, such as MYCN amplification. Thus, contrary to previous studies, our findings indicate an unanticipated tumor-suppressive role for HIF2α in neuroblastoma.
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43
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ZNF395 Is an Activator of a Subset of IFN-Stimulated Genes. Mediators Inflamm 2017; 2017:1248201. [PMID: 28316371 PMCID: PMC5339479 DOI: 10.1155/2017/1248201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 11/17/2022] Open
Abstract
Activation of the interferon (IFN) pathway in response to infection with pathogens results in the induction of IFN-stimulated genes (ISGs) including proinflammatory cytokines, which mount the proper antiviral immune response. However, aberrant expression of these genes is pathogenic to the host. In addition to IFN-induced transcription factors non-IFN-regulated factors contribute to the transcriptional control of ISGs. Here, we show by genome wide expression analysis, siRNA-mediated suppression and Doxycycline-induced overexpression that the cellular transcription factor ZNF395 activates a subset of ISGs including the chemokines CXCL10 and CXCL11 in keratinocytes. We found that ZNF395 acts independently of IFN but enhances the IFN-induced expression of CXCL10 and CXCL11. Luciferase reporter assays revealed a requirement of intact NFκB-binding sites for ZNF395 to stimulate the CXCL10 promoter. The transcriptional activation of CXCL10 and CXCL11 by ZNF395 was abolished after inhibition of IKK by BMS-345541, which increased the stability of ZNF395. ZNF395 encodes at least two motifs that mediate the enhanced degradation of ZNF395 in response to IKK activation. Thus, IKK is required for ZNF395-mediated activation of transcription and enhances its turn-over to keep the activity of ZNF395 low. Our results support a previously unrecognized role of ZNF395 in the innate immune response and inflammation.
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44
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Cangelosi D, Pelassa S, Morini M, Conte M, Bosco MC, Eva A, Sementa AR, Varesio L. Artificial neural network classifier predicts neuroblastoma patients' outcome. BMC Bioinformatics 2016; 17:347. [PMID: 28185577 PMCID: PMC5123344 DOI: 10.1186/s12859-016-1194-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background More than fifty percent of neuroblastoma (NB) patients with adverse prognosis do not benefit from treatment making the identification of new potential targets mandatory. Hypoxia is a condition of low oxygen tension, occurring in poorly vascularized tissues, which activates specific genes and contributes to the acquisition of the tumor aggressive phenotype. We defined a gene expression signature (NB-hypo), which measures the hypoxic status of the neuroblastoma tumor. We aimed at developing a classifier predicting neuroblastoma patients’ outcome based on the assessment of the adverse effects of tumor hypoxia on the progression of the disease. Methods Multi-layer perceptron (MLP) was trained on the expression values of the 62 probe sets constituting NB-hypo signature to develop a predictive model for neuroblastoma patients’ outcome. We utilized the expression data of 100 tumors in a leave-one-out analysis to select and construct the classifier and the expression data of the remaining 82 tumors to test the classifier performance in an external dataset. We utilized the Gene set enrichment analysis (GSEA) to evaluate the enrichment of hypoxia related gene sets in patients predicted with “Poor” or “Good” outcome. Results We utilized the expression of the 62 probe sets of the NB-Hypo signature in 182 neuroblastoma tumors to develop a MLP classifier predicting patients’ outcome (NB-hypo classifier). We trained and validated the classifier in a leave-one-out cross-validation analysis on 100 tumor gene expression profiles. We externally tested the resulting NB-hypo classifier on an independent 82 tumors’ set. The NB-hypo classifier predicted the patients’ outcome with the remarkable accuracy of 87 %. NB-hypo classifier prediction resulted in 2 % classification error when applied to clinically defined low-intermediate risk neuroblastoma patients. The prediction was 100 % accurate in assessing the death of five low/intermediated risk patients. GSEA of tumor gene expression profile demonstrated the hypoxic status of the tumor in patients with poor prognosis. Conclusions We developed a robust classifier predicting neuroblastoma patients’ outcome with a very low error rate and we provided independent evidence that the poor outcome patients had hypoxic tumors, supporting the potential of using hypoxia as target for neuroblastoma treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1194-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Davide Cangelosi
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Simone Pelassa
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Massimo Conte
- Department of Hematology-Oncology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Angela Rita Sementa
- Department of Pathology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Luigi Varesio
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy.
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45
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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.
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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.
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Elkashef SM, Allison SJ, Sadiq M, Basheer HA, Ribeiro Morais G, Loadman PM, Pors K, Falconer RA. Polysialic acid sustains cancer cell survival and migratory capacity in a hypoxic environment. Sci Rep 2016; 6:33026. [PMID: 27611649 PMCID: PMC5017143 DOI: 10.1038/srep33026] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022] Open
Abstract
Polysialic acid (polySia) is a unique carbohydrate polymer expressed on the surface of NCAM (neuronal cell adhesion molecule) in a number of cancers where it modulates cell-cell and cell-matrix adhesion, migration, invasion and metastasis and is strongly associated with poor clinical prognosis. We have carried out the first investigation into the effect of polySia expression on the behaviour of cancer cells in hypoxia, a key source of chemoresistance in tumours. The role of polysialylation and associated tumour cell migration and cell adhesion were studied in hypoxia, along with effects on cell survival and the potential role of HIF-1. Our findings provide the first evidence that polySia expression sustains migratory capacity and is associated with tumour cell survival in hypoxia. Initial mechanistic studies indicate a potential role for HIF-1 in sustaining polySia-mediated migratory capacity, but not cell survival. These data add to the growing body of evidence pointing to a crucial role for the polysialyltransferases (polySTs) in neuroendocrine tumour progression and provide the first evidence to suggest that polySia is associated with an aggressive phenotype in tumour hypoxia. These results have significant potential implications for polyST inhibition as an anti-metastatic therapeutic strategy and for targeting hypoxic cancer cells.
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Affiliation(s)
- Sara M Elkashef
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
| | - Simon J Allison
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, U.K
| | - Maria Sadiq
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
| | - Haneen A Basheer
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
| | - Goreti Ribeiro Morais
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
| | - Paul M Loadman
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
| | - Klaus Pors
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
| | - Robert A Falconer
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, West Yorkshire BD7 1DP, U.K
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Lin X, Sun R, Zhao X, Zhu D, Zhao X, Gu Q, Dong X, Zhang D, Zhang Y, Li Y, Sun B. C-myc overexpression drives melanoma metastasis by promoting vasculogenic mimicry via c-myc/snail/Bax signaling. J Mol Med (Berl) 2016; 95:53-67. [PMID: 27543492 DOI: 10.1007/s00109-016-1452-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/14/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
c-Myc is a well-characterized proto-oncogene that induces cellular transformation and modulates programmed cell death. While recent studies have demonstrated high expression of c-Myc protein in advanced and metastatic melanoma, the clinical and biological implications remain to be fully elucidated. In this study, we investigated the effect of c-Myc overexpression in melanoma tumorigenesis. Clinicopathological analysis demonstrated that c-Myc expression positively correlated with the formation of vasculogenic mimicry (VM) and linearly patterned programmed cell necrosis (LPPCN). Clinically, high c-Myc expression was significantly associated with distant metastasis and poor prognosis, while biologically, c-Myc overexpression led to significant increases in cell motility, invasiveness and metastasis. Moreover, c-Myc induced the formation of VM and promoted the expression of epithelial-mesenchymal transition (EMT)-associated protein Snail both in vivo and in vitro. High expression of c-Myc increased Bax expression in hypoxic conditions and induced cell apoptosis. Taken together, we conclude that c-Myc overexpression promotes the formation of VM by EMT and LPPCN in melanoma. Our improved understanding of the clinical and biological effects of c-Myc overexpression in melanoma highlights the incomplete understanding of this oncogene, and indicates that c-Myc is a potential therapeutic target of this disease. KEY MESSAGE High c-Myc expression is associated with tumor metastasis and poor prognosis in human melanoma. c-Myc upregulates Snail expression to promote EMT via the TGF-β/Snail/Ecadherin signal pathway. c-Myc leads to cell death by upregulating Bax expression causing a lower Bcl2/Bax ratio under severe hypoxic conditions. c-Myc promotes vasculogenic mimicry and linearly patterned programmed cell necrosis.
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Affiliation(s)
- Xian Lin
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
| | - Ran Sun
- Department of Surgery, Tianjin Hospital of ITCWM Nankai Hospital, Tianjin, 300100, China
| | - Xiulan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
- Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, 300052, China
| | - Dongwang Zhu
- Department of Surgery, Stomatological Hospital of Tianjin Medical University, Tianjin, 300070, China
| | - Xueming Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
| | - Qiang Gu
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
- Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, 300052, China
| | - Xueyi Dong
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
| | - Danfang Zhang
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
| | - Yanhui Zhang
- Department of Pathology, Cancer Hospital of Tianjin Medical University, Tianjin, 300060, China
| | - Yanlei Li
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China
| | - Baocun Sun
- Department of Pathology, Tianjin Medical University, Tianjin, 300070, China.
- Department of Pathology, Cancer Hospital of Tianjin Medical University, Tianjin, 300060, China.
- Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, 300052, China.
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48
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Transcript signatures that predict outcome and identify targetable pathways in MYCN-amplified neuroblastoma. Mol Oncol 2016; 10:1461-1472. [PMID: 27599694 DOI: 10.1016/j.molonc.2016.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In the pediatric cancer neuroblastoma (NB), patients are stratified into low, intermediate or high-risk subsets based in part on MYCN amplification status. While MYCN amplification in general predicts unfavorable outcome, no clinical or genomic factors have been identified that predict outcome within these cohorts of high-risk patients. In particular, it is currently not possible at diagnosis to determine which high-risk neuroblastoma patients will ultimately fail upfront therapy. EXPERIMENTAL DESIGN We analyzed the prognostic potential of most published gene expression signatures for NB and developed a new prognostic signature to predict outcome for patients with MYCN amplification. Network and pathway analyses identified candidate therapeutic targets for this MYCN-amplified patient subset with poor outcome. RESULTS Most signatures have a high capacity to predict outcome of unselected NB patients. However, the majority of published signatures, as well as most randomly generated signatures, are highly confounded by MYCN amplification, and fail to predict outcome in subpopulations of high-risk patients with MYCN-amplified NB. We identify a MYCN module signature that predicts patient outcome for those with MYCN-amplified tumors, that also predicts potential tractable therapeutic signaling pathways and targets including the DNA repair enzyme Poly [ADP-ribose] polymerase 1 (PARP1). CONCLUSION Many prognostic signatures for NB are confounded by MYCN amplification and fail to predict outcome for the subset of high-risk patients with MYCN amplification. We report a MYCN module signature that is associated with distinct patient outcomes, and predicts candidate therapeutic targets in DNA repair pathways, including PARP1 in MYCN-amplified NB.
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49
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Squillario M, Barbieri M, Verri A, Barla A. Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. MICROARRAYS 2016; 5:microarrays5020015. [PMID: 27600081 PMCID: PMC5003491 DOI: 10.3390/microarrays5020015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Abstract
Biological interpretability is a key requirement for the output of microarray data analysis pipelines. The most used pipeline first identifies a gene signature from the acquired measurements and then uses gene enrichment analysis as a tool for functionally characterizing the obtained results. Recently Knowledge Driven Variable Selection (KDVS), an alternative approach which performs both steps at the same time, has been proposed. In this paper, we assess the effectiveness of KDVS against standard approaches on a Parkinson’s Disease (PD) dataset. The presented quantitative analysis is made possible by the construction of a reference list of genes and gene groups associated to PD. Our work shows that KDVS is much more effective than the standard approach in enhancing the interpretability of the obtained results.
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Affiliation(s)
| | - Matteo Barbieri
- DIBRIS, University of Genoa, Via Dodecaneso 35, I-16146 Genova, Italy.
| | - Alessandro Verri
- DIBRIS, University of Genoa, Via Dodecaneso 35, I-16146 Genova, Italy.
| | - Annalisa Barla
- DIBRIS, University of Genoa, Via Dodecaneso 35, I-16146 Genova, Italy.
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50
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Formicola D, Petrosino G, Lasorsa VA, Pignataro P, Cimmino F, Vetrella S, Longo L, Tonini GP, Oberthuer A, Iolascon A, Fischer M, Capasso M. An 18 gene expression-based score classifier predicts the clinical outcome in stage 4 neuroblastoma. J Transl Med 2016; 14:142. [PMID: 27188717 PMCID: PMC4870777 DOI: 10.1186/s12967-016-0896-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/05/2016] [Indexed: 12/21/2022] Open
Abstract
Background The prognosis of children with metastatic stage 4 neuroblastoma (NB) has remained poor in the past decade. Patients and methods Using microarray analyses of 342 primary tumors, we here developed and validated an easy to use gene expression-based risk score including 18 genes, which can robustly predict the outcome of stage 4 patients. Results This classifier was a significant predictor of overall survival in two independent validation cohorts [cohort 1 (n = 214): P = 6.3 × 10−5; cohort 2 (n = 27): P = 3.1 × 10−2]. The prognostic value of the risk score was validated by multivariate analysis including the established markers age and MYCN status (P = 0.027). In the pooled validation cohorts (n = 241), integration of the risk score with the age and/or MYCN status identified subgroups with significantly differing overall survival (ranging from 35 to 100 %). Conclusion Together, the 18-gene risk score classifier can identify patients with stage 4 NB with favorable outcome and may therefore improve risk assessment and treatment stratification of NB patients with disseminated disease. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0896-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Formicola
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy.,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy
| | - Giuseppe Petrosino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy.,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy
| | - Vito Alessandro Lasorsa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy.,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy
| | - Piero Pignataro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy.,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy
| | - Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy.,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy
| | - Simona Vetrella
- Department of Oncology, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Luca Longo
- U.O.C. Bioterapie, IRCCS AOU San Martino-IST, National Cancer Research Institute, Genoa, Italy
| | - Gian Paolo Tonini
- Laboratory of Neuroblastoma, Onco/Hematology Department SDB University of Padua, Pediatric Research Institute, Padua, Italy
| | - André Oberthuer
- Department of Pediatric Oncology and Hematology, and Center for Molecular Medicine Cologne (CMMC), University of Cologne Children's Hospital, Cologne, Germany
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy.,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, and Center for Molecular Medicine Cologne (CMMC), University of Cologne Children's Hospital, Cologne, Germany.,Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80145, Naples, Italy. .,CEINGE Biotecnolgie Avanzate Scarl, Naples, Italy.
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