1
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Hongo H, Kosaka T, Takayama KI, Baba Y, Yasumizu Y, Ueda K, Suzuki Y, Inoue S, Beltran H, Oya M. G-protein signaling of oxytocin receptor as a potential target for cabazitaxel-resistant prostate cancer. PNAS NEXUS 2024; 3:pgae002. [PMID: 38250514 PMCID: PMC10799637 DOI: 10.1093/pnasnexus/pgae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Although the treatment armamentarium for patients with metastatic prostate cancer has improved recently, treatment options after progression on cabazitaxel (CBZ) are limited. To identify the mechanisms underlying CBZ resistance and therapeutic targets, we performed single-cell RNA sequencing of circulating tumor cells (CTCs) from patients with CBZ-resistant prostate cancer. Cells were clustered based on gene expression profiles. In silico screening was used to nominate candidate drugs for overcoming CBZ resistance in castration-resistant prostate cancer. CTCs were divided into three to four clusters, reflecting intrapatient tumor heterogeneity in refractory prostate cancer. Pathway analysis revealed that clusters in two cases showed up-regulation of the oxytocin (OXT) receptor-signaling pathway. Spatial gene expression analysis of CBZ-resistant prostate cancer tissues confirmed the heterogeneous expression of OXT-signaling molecules. Cloperastine (CLO) had significant antitumor activity against CBZ-resistant prostate cancer cells. Mass spectrometric phosphoproteome analysis revealed the suppression of OXT signaling specific to CBZ-resistant models. These results support the potential of CLO as a candidate drug for overcoming CBZ-resistant prostate cancer via the inhibition of OXT signaling.
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Affiliation(s)
- Hiroshi Hongo
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takeo Kosaka
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-001, Japan
| | - Yuto Baba
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yota Yasumizu
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-001, Japan
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1298, Japan
| | - Himisha Beltran
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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2
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Hongo H, Kosaka T, Suzuki Y, Oya M. Discovery of a new candidate drug to overcome cabazitaxel-resistant gene signature in castration-resistant prostate cancer by in silico screening. Prostate Cancer Prostatic Dis 2023; 26:59-66. [PMID: 34593983 PMCID: PMC10023558 DOI: 10.1038/s41391-021-00426-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/12/2021] [Accepted: 06/29/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The taxane cabazitaxel (CBZ) is a promising treatment for docetaxel-resistant castration-resistant prostate cancer (CRPC). However, the survival benefit with CBZ for patients with CRPC is limited. This study used screening tests for candidate drugs targeting CBZ-resistant-related gene expression and identified pimozide as a potential candidate for overcoming CBZ resistance in CRPC. METHODS We established CBZ-resistant cell lines, DU145CR and PC3CR by incubating DU145 cells and PC3 cells with gradually increasing concentrations of CBZ. We performed in silico drug screening for candidate drugs that could reprogram the gene expression signature of a CBZ-resistant prostate cancer cells using a Connectivity Map. The in vivo effect of the drug combination was tested in xenograft mice models. RESULTS We identified pimozide as a promising candidate drug for CBZ-resistant CRPC. Pimozide had a significant antitumor effect on DU145CR cells. Moreover, combination treatment with pimozide and CBZ had a synergic effect for DU145CR cells in vitro and in vivo. Microarray analysis identified AURKB and KIF20A as potential targets of pimozide in CBZ-resistant CRPC. DU145CR had significantly higher AURKB and KIF20A expression compared with a non-CBZ-resistant cell line. Inhibition of AURKB and KIF20A had an antitumor effect in DU145CR xenograft tumors. Higher expression of AURKB and KIF20A was a poor prognostic factor of TGCA prostate cancer cohort. CBZ-resistant prostate cancer tissues in our institution had higher AURKB and KIF20A expression. CONCLUSIONS Pimozide appears to be a promising drug to overcome CBZ resistance in CRPC by targeting AURKB and KIF20A.
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Grants
- the Ministry of Education, Culture, Sports, Science and Technology of Japan; Grant No. #17K11158 the Takeda Science Foundation Japan Research Foundation for Clinical Pharmacology (JRFCP)
- the Ministry of Education, Culture, Sports, Science and Technology of Japan; Grant No. #21K09436, #20K22822, #17K16813, #15K20109 Keio University School of Medicine; Grant No. 02-002-0014, 02-002-0020 Sakaguchi Mitsunada Memorial Fund
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Affiliation(s)
- Hiroshi Hongo
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takeo Kosaka
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Yoko Suzuki
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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3
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Hongo H, Kosaka T, Suzuki Y, Mikami S, Fukada J, Oya M. Topoisomerase II alpha inhibition can overcome taxane-resistant prostate cancer through DNA repair pathways. Sci Rep 2021; 11:22284. [PMID: 34782700 PMCID: PMC8593019 DOI: 10.1038/s41598-021-01697-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
Cabazitaxel (CBZ) is approved for the treatment of docetaxel-resistant castration-resistant prostate cancer (CRPC). However, its efficacy against CRPC is limited, and there are no effective treatments for CBZ-resistant CRPC. This study explored the optimal treatment for CRPC in the post-cabazitaxel setting. PC3 (CBZ-sensitive) and PC3CR cells (CBZ-resistant) were used in this study. We performed in silico drug screening for candidate drugs that could reprogram the gene expression signature of PC3CR cells. The in vivo effect of the drug combination was tested in xenograft mice models. We identified etoposide (VP16) as a promising treatment candidate for CBZ-resistant CRPC. The WST assay revealed that VP16 had a significant antitumor effect on PC3CR cells. PC3CR cells exhibited significantly higher topoisomerase II alpha (TOP2A) expression than PC3 cells. Higher TOP2A expression was a poor prognostic factor in The Cancer Genome Atlas prostate cancer cohort. In the Fred Hutchinson Cancer Research Center dataset, docetaxel-exposed tissues and metastatic tumors had higher TOP2A expression. In addition, VP16 significantly inhibited the growth of tumors generated from both cell lines. Based on these findings, VP16-based chemotherapy may be an optimal treatment for CPRC in the post-CBZ setting.
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Affiliation(s)
- Hiroshi Hongo
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takeo Kosaka
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Yoko Suzuki
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Shuji Mikami
- Department of Diagnostic Pathology, Keio University Hospital, Tokyo, Japan
| | - Junichi Fukada
- Department of Radiology, Keio University School of Medicine, Tokyo, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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4
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Mus LM, Lambertz I, Claeys S, Kumps C, Van Loocke W, Van Neste C, Umapathy G, Vaapil M, Bartenhagen C, Laureys G, De Wever O, Bexell D, Fischer M, Hallberg B, Schulte J, De Wilde B, Durinck K, Denecker G, De Preter K, Speleman F. The ETS transcription factor ETV5 is a target of activated ALK in neuroblastoma contributing to increased tumour aggressiveness. Sci Rep 2020; 10:218. [PMID: 31937834 PMCID: PMC6959226 DOI: 10.1038/s41598-019-57076-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/05/2019] [Indexed: 02/08/2023] Open
Abstract
Neuroblastoma is an aggressive childhood cancer arising from sympatho-adrenergic neuronal progenitors. The low survival rates for high-risk disease point to an urgent need for novel targeted therapeutic approaches. Detailed molecular characterization of the neuroblastoma genomic landscape indicates that ALK-activating mutations are present in 10% of primary tumours. Together with other mutations causing RAS/MAPK pathway activation, ALK mutations are also enriched in relapsed cases and ALK activation was shown to accelerate MYCN-driven tumour formation through hitherto unknown ALK-driven target genes. To gain further insight into how ALK contributes to neuroblastoma aggressiveness, we searched for known oncogenes in our previously reported ALK-driven gene signature. We identified ETV5, a bona fide oncogene in prostate cancer, as robustly upregulated in neuroblastoma cells harbouring ALK mutations, and show high ETV5 levels downstream of the RAS/MAPK axis. Increased ETV5 expression significantly impacted migration, invasion and colony formation in vitro, and ETV5 knockdown reduced proliferation in a murine xenograft model. We also established a gene signature associated with ETV5 knockdown that correlates with poor patient survival. Taken together, our data highlight ETV5 as an intrinsic component of oncogenic ALK-driven signalling through the MAPK axis and propose that ETV5 upregulation in neuroblastoma may contribute to tumour aggressiveness.
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Affiliation(s)
- Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Irina Lambertz
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Shana Claeys
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Candy Kumps
- Department of Uro-gynaecology, Ghent University Hospital, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Christophe Van Neste
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marica Vaapil
- Translational Cancer Research, Lund University, Lund, Sweden
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany.,Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Genevieve Laureys
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Paediatric Haematology and Oncology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Laboratory of Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Daniel Bexell
- Translational Cancer Research, Lund University, Lund, Sweden
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany.,Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Schulte
- Department of Paediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany.,Department of Paediatric Oncology and Haematology, Charité University Medical Centre Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Paediatric Haematology and Oncology, Ghent University Hospital, Ghent, Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Geertrui Denecker
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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5
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Zhang L, Zhou H, Li J, Wang X, Zhang X, Shi T, Feng G. Comprehensive Characterization of Circular RNAs in Neuroblastoma Cell Lines. Technol Cancer Res Treat 2020; 19:1533033820957622. [PMID: 33000697 PMCID: PMC7533920 DOI: 10.1177/1533033820957622] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/15/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Neuroblastoma (NB) is a rare type of cancer but frequently occurred in children. However, it is still unclear whether circular RNAs (circRNAs) play key roles in NB tumorigenesis or progression. In this study, we identified 39,022 circRNAs across the 39 neuroblastoma and 2 normal cell lines. With the gene and circRNA expression data, we classified the NB cell lines, identified and characterized the functional circRNAs in the 3 NB classes. Specifically, 29 circRNAs were found to be dysregulated in the NB classes. Notably, 7 circRNAs located within MYCN-amplified regions were upregulated in cell lines with the high activities of MYC targets and MYCN amplification, and were highly correlated with expression of their parental gene, NBAS. Subsequently, we constructed ceRNA networks for the functional circRNAs. Specifically, hsa_circ_0005379 was identified as a critical regulator in the ceRNA networks because of targeting 13 genes, which formed a complex competing endogenous RNA (ceRNA) network. Moreover, hsa_circ_0002343, which was connected with few genes, might regulate the PI3K/Akt/mTOR signaling via RAC1. Furthermore, 3 genes, including NOTCH2, SERPINH1, and LAMC1, involved in epithelial mesenchymal transition (EMT) were observed to connect with hsa_circ_0001361, suggesting that this circRNA was closely associated with EMT. Consequently, 7 genes, such as DAD1, PPIA, NOTCH2, PGK1, BUB1, EIF2S1, and TCF7L2, were found to be closely associated with both event-free survival (EFS) and overall survival (OS). In conclusion, the present study identified functional circRNAs and predicted their functionality in neuroblastoma cell lines, which not only improved the understanding of circRNAs in neuroblastoma, but also provided the evidences for the related researchers.
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Affiliation(s)
- Li Zhang
- Big Data and Engineering Research Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, China
- The authors contributed equally to this paper
| | - Hangyu Zhou
- Department of Clinical Laboratory, Dongzhimen Hospital Beijing University of Chinese Medicine, Beijing, China
- The authors contributed equally to this paper
| | - Jing Li
- Department of Neurosurgery, Huai’an Second People’s Hospital, the Affiliated Huai’an Hospital of Xuzhou Medical University, Huai’an, China
- The authors contributed equally to this paper
| | - Xinyu Wang
- Big Data and Engineering Research Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China
| | - Xin Zhang
- Big Data and Engineering Research Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Guoshuang Feng
- Big Data and Engineering Research Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, China
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6
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Russo R, Cimmino F, Pezone L, Manna F, Avitabile M, Langella C, Koster J, Casale F, Raia M, Viola G, Fischer M, Iolascon A, Capasso M. Kinome expression profiling of human neuroblastoma tumors identifies potential drug targets for ultra high-risk patients. Carcinogenesis 2017; 38:1011-1020. [DOI: 10.1093/carcin/bgx077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/22/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
| | - Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
| | - Lucia Pezone
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
- Department of Medicine, University of Verona,
| | - Francesco Manna
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
| | - Marianna Avitabile
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
| | - Concetta Langella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Meibergdreef, Amsterdam, The Netherlands,
| | - Fiorina Casale
- Servizio di Oncologia Pediatrica, Dipartimento della Donna, del Bambino e di Chirurgia Generale e Specialistica—Seconda Università degli Studi di Napoli, Italy,
| | | | - Giampietro Viola
- Dipartimento di Salute della Donna e del Bambino, Università degli Studi di Padova, Italy,
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, University of Cologne Children’s Hospital, Cologne, Germany,
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany and
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy,
- CEINGE Biotecnologie Avanzate, Napoli, Italy,
- IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, Napoli, Italy
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7
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Salazar BM, Balczewski EA, Ung CY, Zhu S. Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. Int J Mol Sci 2016; 18:E37. [PMID: 28035989 PMCID: PMC5297672 DOI: 10.3390/ijms18010037] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 12/13/2022] Open
Abstract
Pediatric cancers rarely exhibit recurrent mutational events when compared to most adult cancers. This poses a challenge in understanding how cancers initiate, progress, and metastasize in early childhood. Also, due to limited detected driver mutations, it is difficult to benchmark key genes for drug development. In this review, we use neuroblastoma, a pediatric solid tumor of neural crest origin, as a paradigm for exploring "big data" applications in pediatric oncology. Computational strategies derived from big data science-network- and machine learning-based modeling and drug repositioning-hold the promise of shedding new light on the molecular mechanisms driving neuroblastoma pathogenesis and identifying potential therapeutics to combat this devastating disease. These strategies integrate robust data input, from genomic and transcriptomic studies, clinical data, and in vivo and in vitro experimental models specific to neuroblastoma and other types of cancers that closely mimic its biological characteristics. We discuss contexts in which "big data" and computational approaches, especially network-based modeling, may advance neuroblastoma research, describe currently available data and resources, and propose future models of strategic data collection and analyses for neuroblastoma and other related diseases.
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Affiliation(s)
- Brittany M Salazar
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Emily A Balczewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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8
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Liu X, Yang X, Chen X, Zhang Y, Pan X, Wang G, Ye Y. Expression Profiling Identifies Bezafibrate as Potential Therapeutic Drug for Lung Adenocarcinoma. J Cancer 2015; 6:1214-21. [PMID: 26535062 PMCID: PMC4622851 DOI: 10.7150/jca.12191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/27/2015] [Indexed: 12/13/2022] Open
Abstract
Drug-induced gene expression patterns that invert disease profiles have recently been illustrated to be a new strategy for drug-repositioning. In the present study, we validated this approach and focused on prediction of novel drugs for lung adenocarcinoma (AC), for which there is a pressing need to find novel therapeutic compounds. Firstly, connectivity map (CMap) analysis computationally predicted bezafibrate as a putative compound against lung AC. Then this hypothesis was verified by in vitro assays of anti-proliferation and cell cycle arrest. In silico docking evidence indicated that bezafibrate could target cyclin dependent kinase 2(CDK2), which regulates progression through the cell cycle. Furthermore, we found that bezafibrate can significantly down-regulate the expression of CDK2 mRNA and p-CDK2. Using a nude mice xenograft model, we also found that bezafibrate could inhibit tumor growth of lung AC in vivo. In conclusion, this study proposed bezafibrate as a potential therapeutic option for lung AC patients, illustrating the potential of in silico drug screening.
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Affiliation(s)
- Xinyan Liu
- 1. Magazine office, Guangzhou Medical University, Guangzhou 510182, P.R. China
| | - Xiaoqin Yang
- 3. Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Xinmei Chen
- 4. Department of Biochemistry, School of Basic Science, Guangzhou Medical University, Guangzhou 510182, P.R. China
| | - Yantao Zhang
- 2. Department of Pharmacy, College of Health sciences, Guangzhou Medical University, Guangzhou 510180, P.R. China
| | - Xuebin Pan
- 2. Department of Pharmacy, College of Health sciences, Guangzhou Medical University, Guangzhou 510180, P.R. China
| | - Guiping Wang
- 2. Department of Pharmacy, College of Health sciences, Guangzhou Medical University, Guangzhou 510180, P.R. China
| | - Yun Ye
- 5. College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou 545006, P.R. China
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9
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Faria CC, Agnihotri S, Mack SC, Golbourn BJ, Diaz RJ, Olsen S, Bryant M, Bebenek M, Wang X, Bertrand KC, Kushida M, Head R, Clark I, Dirks P, Smith CA, Taylor MD, Rutka JT. Identification of alsterpaullone as a novel small molecule inhibitor to target group 3 medulloblastoma. Oncotarget 2015; 6:21718-29. [PMID: 26061748 PMCID: PMC4673298 DOI: 10.18632/oncotarget.4304] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/13/2015] [Indexed: 12/22/2022] Open
Abstract
Advances in the molecular biology of medulloblastoma revealed four genetically and clinically distinct subgroups. Group 3 medulloblastomas are characterized by frequent amplifications of the oncogene MYC, a high incidence of metastasis, and poor prognosis despite aggressive therapy. We investigated several potential small molecule inhibitors to target Group 3 medulloblastomas based on gene expression data using an in silico drug screen. The Connectivity Map (C-MAP) analysis identified piperlongumine as the top candidate drug for non-WNT medulloblastomas and the cyclin-dependent kinase (CDK) inhibitor alsterpaullone as the compound predicted to have specific antitumor activity against Group 3 medulloblastomas. To validate our findings we used these inhibitors against established Group 3 medulloblastoma cell lines. The C-MAP predicted drugs reduced cell proliferation in vitro and increased survival in Group 3 medulloblastoma xenografts. Alsterpaullone had the highest efficacy in Group 3 medulloblastoma cells. Genomic profiling of Group 3 medulloblastoma cells treated with alsterpaullone confirmed inhibition of cell cycle-related genes, and down-regulation of MYC. Our results demonstrate the preclinical efficacy of using a targeted therapy approach for Group 3 medulloblastomas. Specifically, we provide rationale for advancing alsterpaullone as a targeted therapy in Group 3 medulloblastoma.
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Affiliation(s)
- Claudia C. Faria
- Division of Neurosurgery, Department of Surgery, The Hospital for Sick Children, Toronto, Canada
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, EPE, Lisbon, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sameer Agnihotri
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Stephen C. Mack
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Brian J. Golbourn
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Roberto J. Diaz
- Division of Neurosurgery, Department of Surgery, The Hospital for Sick Children, Toronto, Canada
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Samantha Olsen
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Melissa Bryant
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Matthew Bebenek
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Xin Wang
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Kelsey C. Bertrand
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Michelle Kushida
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Renee Head
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Ian Clark
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Peter Dirks
- Division of Neurosurgery, Department of Surgery, The Hospital for Sick Children, Toronto, Canada
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Christian A. Smith
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, Department of Surgery, The Hospital for Sick Children, Toronto, Canada
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - James T. Rutka
- Division of Neurosurgery, Department of Surgery, The Hospital for Sick Children, Toronto, Canada
- Program in Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
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10
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Lambertz I, Kumps C, Claeys S, Lindner S, Beckers A, Janssens E, Carter DR, Cazes A, Cheung BB, De Mariano M, De Bondt A, De Brouwer S, Delattre O, Gibbons J, Janoueix-Lerosey I, Laureys G, Liang C, Marchall GM, Porcu M, Takita J, Trujillo DC, Van Den Wyngaert I, Van Roy N, Van Goethem A, Van Maerken T, Zabrocki P, Cools J, Schulte JH, Vialard J, Speleman F, De Preter K. Upregulation of MAPK Negative Feedback Regulators and RET in Mutant ALK Neuroblastoma: Implications for Targeted Treatment. Clin Cancer Res 2015; 21:3327-39. [PMID: 25805801 DOI: 10.1158/1078-0432.ccr-14-2024] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 03/13/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Activating ALK mutations are present in almost 10% of primary neuroblastomas and mark patients for treatment with small-molecule ALK inhibitors in clinical trials. However, recent studies have shown that multiple mechanisms drive resistance to these molecular therapies. We anticipated that detailed mapping of the oncogenic ALK-driven signaling in neuroblastoma can aid to identify potential fragile nodes as additional targets for combination therapies. EXPERIMENTAL DESIGN To achieve this goal, transcriptome profiling was performed in neuroblastoma cell lines with the ALK(F1174L) or ALK(R1275Q) hotspot mutations, ALK amplification, or wild-type ALK following pharmacologic inhibition of ALK using four different compounds. Next, we performed cross-species genomic analyses to identify commonly transcriptionally perturbed genes in MYCN/ALK(F1174L) double transgenic versus MYCN transgenic mouse tumors as compared with the mutant ALK-driven transcriptome in human neuroblastomas. RESULTS A 77-gene ALK signature was established and successfully validated in primary neuroblastoma samples, in a neuroblastoma cell line with ALK(F1174L) and ALK(R1275Q) regulable overexpression constructs and in other ALKomas. In addition to the previously established PI3K/AKT/mTOR, MAPK/ERK, and MYC/MYCN signaling branches, we identified that mutant ALK drives a strong upregulation of MAPK negative feedback regulators and upregulates RET and RET-driven sympathetic neuronal markers of the cholinergic lineage. CONCLUSIONS We provide important novel insights into the transcriptional consequences and the complexity of mutant ALK signaling in this aggressive pediatric tumor. The negative feedback loop of MAPK pathway inhibitors may affect novel ALK inhibition therapies, whereas mutant ALK induced RET signaling can offer novel opportunities for testing ALK-RET oriented molecular combination therapies.
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Affiliation(s)
- Irina Lambertz
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Shana Claeys
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sven Lindner
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Germany
| | - Anneleen Beckers
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Els Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Daniel R Carter
- Kids Cancer Center, Sydneys Children's Hospital, Children's Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, Australia
| | - Alex Cazes
- Unité Inserm U830, Centre de Recherche, Institut Curie, Paris, France
| | - Belamy B Cheung
- Kids Cancer Center, Sydneys Children's Hospital, Children's Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, Australia
| | - Marilena De Mariano
- Biotherapy Unit, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - An De Bondt
- Oncology Discovery Research and Early Development, Johnson & Johnson, Beerse, Belgium
| | - Sara De Brouwer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Olivier Delattre
- Unité Inserm U830, Centre de Recherche, Institut Curie, Paris, France
| | - Jay Gibbons
- VP Oncology, Xcovery LLC, West Palm Beach, Florida
| | | | - Geneviève Laureys
- Department of Pediatric Oncology and Haematology, Ghent University Hospital, Ghent, Belgium
| | - Chris Liang
- VP Oncology, Xcovery LLC, West Palm Beach, Florida
| | - Glenn M Marchall
- Kids Cancer Center, Sydneys Children's Hospital, Children's Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, Australia
| | - Michael Porcu
- Center for Human Genetics, K.U. Leuven-VIB, Leuven, Belgium
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | | | - Ilse Van Den Wyngaert
- Oncology Discovery Research and Early Development, Johnson & Johnson, Beerse, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alan Van Goethem
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Piotr Zabrocki
- Center for Human Genetics, K.U. Leuven-VIB, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, K.U. Leuven-VIB, Leuven, Belgium
| | - Johannes H Schulte
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Germany. German Cancer Consortium (DKTK), Germany. Translational Neuro-Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany. Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Jorge Vialard
- Oncology Discovery Biology, Janssen Research & Development, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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11
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Prioritizing therapeutics for lung cancer: an integrative meta-analysis of cancer gene signatures and chemogenomic data. PLoS Comput Biol 2015; 11:e1004068. [PMID: 25786242 PMCID: PMC4364883 DOI: 10.1371/journal.pcbi.1004068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 12/02/2014] [Indexed: 01/22/2023] Open
Abstract
Repurposing FDA-approved drugs with the aid of gene signatures of disease can accelerate the development of new therapeutics. A major challenge to developing reliable drug predictions is heterogeneity. Different gene signatures of the same disease or drug treatment often show poor overlap across studies, as a consequence of both biological and technical variability, and this can affect the quality and reproducibility of computational drug predictions. Existing algorithms for signature-based drug repurposing use only individual signatures as input. But for many diseases, there are dozens of signatures in the public domain. Methods that exploit all available transcriptional knowledge on a disease should produce improved drug predictions. Here, we adapt an established meta-analysis framework to address the problem of drug repurposing using an ensemble of disease signatures. Our computational pipeline takes as input a collection of disease signatures, and outputs a list of drugs predicted to consistently reverse pathological gene changes. We apply our method to conduct the largest and most systematic repurposing study on lung cancer transcriptomes, using 21 signatures. We show that scaling up transcriptional knowledge significantly increases the reproducibility of top drug hits, from 44% to 78%. We extensively characterize drug hits in silico, demonstrating that they slow growth significantly in nine lung cancer cell lines from the NCI-60 collection, and identify CALM1 and PLA2G4A as promising drug targets for lung cancer. Our meta-analysis pipeline is general, and applicable to any disease context; it can be applied to improve the results of signature-based drug repurposing by leveraging the large number of disease signatures in the public domain. Computer algorithms that find new uses for known drugs can accelerate the development of new therapies for many diseases, including cancer. One promising strategy is to identify drugs that, at the transcriptional level, reverse the gene expression signature of a disease. A major difficulty with this strategy is variability: different gene expression signatures of the same disease or drug treatment can show poor overlap across studies. Since existing algorithms analyze one signature at a time, this means that the drug candidates they identify may reverse some signatures of a disease but not others. For many diseases, dozens of signatures from different labs are now available in online databases. Combining knowledge across all signatures should lead to better drug predictions. Here, we design a meta-analysis pipeline that takes in a large set of disease signatures and then identifies drugs that consistently reverse deleterious gene changes. We apply our method to find new drug candidates for lung cancer, using 21 signatures. We show that our meta-analysis pipeline increases the reproducibility of top drug hits, and then extensively characterize new lung cancer drug candidates in silico.
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12
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BMCC1, which is an interacting partner of BCL2, attenuates AKT activity, accompanied by apoptosis. Cell Death Dis 2015; 6:e1607. [PMID: 25611382 PMCID: PMC4669766 DOI: 10.1038/cddis.2014.568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/19/2014] [Accepted: 10/30/2014] [Indexed: 11/08/2022]
Abstract
BNIP2 and Cdc42GAP homology (BCH) motif-containing molecule at the carboxyl-terminal region 1 (BMCC1) gene is highly expressed in patients with favorable neuroblastoma (NB). It encodes a 340-kDa protein with a conserved BCH scaffold domain that may regulate signaling networks and multiple cellular functions, including apoptosis. In this study, we determined the mechanism by which BMCC1 promotes apoptosis in human NB and non-NB cells, as BMCC1 is normally expressed in various organs, particularly in neuronal and epithelial tissues. We demonstrated in this report that BMCC1 was induced by DNA damage, one of the triggers of intrinsic apoptosis. Accordingly, we investigated whether BMCC1 expression impacts intracellular signals in the regulation of apoptosis via its C-terminal region containing BCH scaffold domain. BMCC1 decreased phosphorylation of survival signals on AKT and its upstream kinase PDK1. BMCC1 upregulation was correlated with the activation of forkhead box-O3a (FOXO3a) (a downstream inducer of apoptosis, which is suppressed by AKT) and induction of BCL2 inhibitor BIM, suggesting that BMCC1 negatively regulates phosphorylation pathway of AKT, resulted in apoptosis. In addition, we found that BNIP2 homology region of BMCC1 interacts with BCL2. Intrinsic apoptosis induced by DNA damage was enhanced by BMCC1 overexpression, and was diminished by knockdown of BMCC1. Taken together, we conclude that BMCC1 promotes apoptosis at multiple steps in AKT-mediated survival signal pathway. These steps include physical interaction with BCL2 and attenuation of AKT-dependent inhibition of FOXO3a functions, such as transcriptional induction of BIM and phosphorylation of ataxia telangiectasia-mutated (ATM) after DNA damage. We propose that downregulation of BMCC1 expression, which is frequently observed in unfavorable NB and epithelial-derived cancers, may facilitate tumor development by abrogating DNA damage repair and apoptosis.
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13
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Sidarovich V, Adami V, Gatto P, Greco V, Tebaldi T, Tonini GP, Quattrone A. Translational downregulation of HSP90 expression by iron chelators in neuroblastoma cells. Mol Pharmacol 2015; 87:513-24. [PMID: 25564462 DOI: 10.1124/mol.114.095729] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Iron is an essential cellular nutrient, being a critical cofactor of several proteins involved in cell growth and replication. Compared with normal cells, neoplastic cells have been shown to require a greater amount of iron, thus laying the basis for the promising anticancer activity of iron chelators. In this work, we evaluated the effects of molecules with iron chelation activity on neuroblastoma (NB) cell lines. Of the 17 iron chelators tested, six reduced cell viability of two NB cell lines with an inhibition of growth of 50% below 10 µM; four of the six molecules-ciclopirox olamine (CPX), piroctone, 8-hydroxyquinoline, and deferasirox-were also shown to efficiently chelate intracellular iron within minutes after addition. Effects on cell viability of one of the compounds, CPX, were indeed dependent on chelation of intracellular iron and mediated by both G0/G1 cell cycle block and induction of apoptosis. By combined transcriptome and translatome profiling we identified early translational downregulation of several members of the heat shock protein group as a specific effect of CPX treatment. We functionally confirmed iron-dependent depletion of HSP90 and its client proteins at pharmacologically achievable concentrations of CPX, and we extended this effect to piroctone, 8-hydroxyquinoline, and deferasirox. Given the documented sensitivity of NB cells to HSP90 inhibition, we propose CPX and other iron chelators as investigational antitumor agents in NB therapy.
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Affiliation(s)
- Viktoryia Sidarovich
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
| | - Valentina Adami
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
| | - Pamela Gatto
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
| | - Valentina Greco
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
| | - Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
| | - Gian Paolo Tonini
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy (V.S., P.G., V.G., T.T., A.Q.); High-Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento, Trento, Italy (V.A.); and Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy (G.P.T.)
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14
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Isozaki Y, Hoshino I, Akutsu Y, Hanari N, Mori M, Nishimori T, Murakami K, Akanuma N, Toyozumi T, Takahashi M, Suito H, Takeshita N, Maruyama T, Suzuki A, Nakayama T, Matsubara H. Screening of alternative drugs to the tumor suppressor miR-375 in esophageal squamous cell carcinoma using the connectivity map. Oncology 2014; 87:351-63. [PMID: 25195536 DOI: 10.1159/000365592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 06/25/2014] [Indexed: 11/19/2022]
Abstract
OBJECTIVE The aim of this study was to identify alternative compounds to the tumor suppressor miR-375 using the connectivity map (CMAP) and to validate the antitumor effects of the identified drugs in esophageal squamous cell carcinoma (ESCC). METHODS Gene profiling of miR-375-treated TE2 and T.Tn cells was applied in order to search the CMAP database. Among the compounds identified using the CMAP, we focused on 8 drugs [(-)-epigallocatechin-3-gallate, metformin, rosiglitazone among others], excluding 2 drugs among the top 10 compounds. We evaluated whether these compounds possess tumor-suppressive functions in ESCC. RESULTS A cytotoxicity assay showed that the sensitivity of TE2 and T.Tn cells treated with the 8 compounds was evaluated based on IC50 values of 42.9 µM to 3.8 mM. A cell cycle analysis revealed that the percentage of TE2 and T.Tn cells incubated with 6 compounds in the G0/G1 phase or the G2/M phase increased by approximately 40-80%. A TUNEL assay showed that the percentages of apoptotic cells treated with almost all compounds were significantly increased (p < 0.05) compared with the control cells. CONCLUSION The CMAP database is a useful tool for identifying compounds affecting the same molecular pathways, particularly products that are difficult to apply via practical approaches, such as microRNAs.
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Affiliation(s)
- Yuka Isozaki
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
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15
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Li J, Pak SC, O’Reilly LP, Benson JA, Wang Y, Hidvegi T, Hale P, Dippold C, Ewing M, Silverman GA, Perlmutter DH. Fluphenazine reduces proteotoxicity in C. elegans and mammalian models of alpha-1-antitrypsin deficiency. PLoS One 2014; 9:e87260. [PMID: 24498058 PMCID: PMC3909079 DOI: 10.1371/journal.pone.0087260] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/27/2013] [Indexed: 12/15/2022] Open
Abstract
The classical form of α1-antitrypsin deficiency (ATD) is associated with hepatic fibrosis and hepatocellular carcinoma. It is caused by the proteotoxic effect of a mutant secretory protein that aberrantly accumulates in the endoplasmic reticulum of liver cells. Recently we developed a model of this deficiency in C. Elegans and adapted it for high-content drug screening using an automated, image-based array scanning. Screening of the Library of Pharmacologically Active Compounds identified fluphenazine (Flu) among several other compounds as a drug which reduced intracellular accumulation of mutant α1-antitrypsin Z (ATZ). Because it is representative of the phenothiazine drug class that appears to have autophagy enhancer properties in addition to mood stabilizing activity, and can be relatively easily re-purposed, we further investigated its effects on mutant ATZ. The results indicate that Flu reverses the phenotypic effects of ATZ accumulation in the C. elegans model of ATD at doses which increase the number of autophagosomes in vivo. Furthermore, in nanomolar concentrations, Flu enhances the rate of intracellular degradation of ATZ and reduces the cellular ATZ load in mammalian cell line models. In the PiZ mouse model Flu reduces the accumulation of ATZ in the liver and mediates a decrease in hepatic fibrosis. These results show that Flu can reduce the proteotoxicity of ATZ accumulation in vivo and, because it has been used safely in humans, this drug can be moved rapidly into trials for liver disease due to ATD. The results also provide further validation for drug discovery using C. elegans models that can be adapted to high-content drug screening platforms and used together with mammalian cell line and animal models.
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Affiliation(s)
- Jie Li
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Stephen C. Pak
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Linda P. O’Reilly
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Joshua A. Benson
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Yan Wang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Tunda Hidvegi
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Pamela Hale
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Christine Dippold
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Michael Ewing
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Gary A. Silverman
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - David H. Perlmutter
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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16
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Carotenuto M, Pedone E, Diana D, de Antonellis P, Džeroski S, Marino N, Navas L, Di Dato V, Scoppettuolo MN, Cimmino F, Correale S, Pirone L, Monti SM, Bruder E, Zenko B, Slavkov I, Pastorino F, Ponzoni M, Schulte JH, Schramm A, Eggert A, Westermann F, Arrigoni G, Accordi B, Basso G, Saviano M, Fattorusso R, Zollo M. Neuroblastoma tumorigenesis is regulated through the Nm23-H1/h-Prune C-terminal interaction. Sci Rep 2013; 3:1351. [PMID: 23448979 PMCID: PMC3584926 DOI: 10.1038/srep01351] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/12/2013] [Indexed: 12/21/2022] Open
Abstract
Nm23-H1 is one of the most interesting candidate genes for a relevant role in Neuroblastoma pathogenesis. H-Prune is the most characterized Nm23-H1 binding partner, and its overexpression has been shown in different human cancers. Our study focuses on the role of the Nm23-H1/h-Prune protein complex in Neuroblastoma. Using NMR spectroscopy, we performed a conformational analysis of the h-Prune C-terminal to identify the amino acids involved in the interaction with Nm23-H1. We developed a competitive permeable peptide (CPP) to impair the formation of the Nm23-H1/h-Prune complex and demonstrated that CPP causes impairment of cell motility, substantial impairment of tumor growth and metastases formation. Meta-analysis performed on three Neuroblastoma cohorts showed Nm23-H1 as the gene highly associated to Neuroblastoma aggressiveness. We also identified two other proteins (PTPRA and TRIM22) with expression levels significantly affected by CPP. These data suggest a new avenue for potential clinical application of CPP in Neuroblastoma treatment.
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17
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Wilzén A, Krona C, Sveinbjörnsson B, Kristiansson E, Dalevi D, Øra I, De Preter K, Stallings RL, Maris J, Versteeg R, Nilsson S, Kogner P, Abel F. ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours. Mol Cancer 2013; 12:70. [PMID: 23835063 PMCID: PMC3766266 DOI: 10.1186/1476-4598-12-70] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/25/2013] [Indexed: 12/21/2022] Open
Abstract
Background Neuroblastoma (NB) tumours are commonly divided into three cytogenetic subgroups. However, by unsupervised principal components analysis of gene expression profiles we recently identified four distinct subgroups, r1-r4. In the current study we characterized these different subgroups in more detail, with a specific focus on the fourth divergent tumour subgroup (r4). Methods Expression microarray data from four international studies corresponding to 148 neuroblastic tumour cases were subject to division into four expression subgroups using a previously described 6-gene signature. Differentially expressed genes between groups were identified using Significance Analysis of Microarray (SAM). Next, gene expression network modelling was performed to map signalling pathways and cellular processes representing each subgroup. Findings were validated at the protein level by immunohistochemistry and immunoblot analyses. Results We identified several significantly up-regulated genes in the r4 subgroup of which the tyrosine kinase receptor ERBB3 was most prominent (fold change: 132–240). By gene set enrichment analysis (GSEA) the constructed gene network of ERBB3 (n = 38 network partners) was significantly enriched in the r4 subgroup in all four independent data sets. ERBB3 was also positively correlated to the ErbB family members EGFR and ERBB2 in all data sets, and a concurrent overexpression was seen in the r4 subgroup. Further studies of histopathology categories using a fifth data set of 110 neuroblastic tumours, showed a striking similarity between the expression profile of r4 to ganglioneuroblastoma (GNB) and ganglioneuroma (GN) tumours. In contrast, the NB histopathological subtype was dominated by mitotic regulating genes, characterizing unfavourable NB subgroups in particular. The high ErbB3 expression in GN tumour types was verified at the protein level, and showed mainly expression in the mature ganglion cells. Conclusions Conclusively, this study demonstrates the importance of performing unsupervised clustering and subtype discovery of data sets prior to analyses to avoid a mixture of tumour subtypes, which may otherwise give distorted results and lead to incorrect conclusions. The current study identifies ERBB3 as a clear-cut marker of a GNB/GN-like expression profile, and we suggest a 7-gene expression signature (including ERBB3) as a complement to histopathology analysis of neuroblastic tumours. Further studies of ErbB3 and other ErbB family members and their role in neuroblastic differentiation and pathogenesis are warranted.
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Affiliation(s)
- Annica Wilzén
- Department of Clinical Genetics, Institution of Biomedicine, Box 413, S- 405 30, Gothenburg University, Gothenburg, Sweden.
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Karube K, Tsuzuki S, Yoshida N, Arita K, Kato H, Katayama M, Ko YH, Ohshima K, Nakamura S, Kinoshita T, Seto M. Comprehensive gene expression profiles of NK cell neoplasms identify vorinostat as an effective drug candidate. Cancer Lett 2013; 333:47-55. [PMID: 23348693 DOI: 10.1016/j.canlet.2012.12.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/06/2012] [Accepted: 12/25/2012] [Indexed: 12/27/2022]
Abstract
NK cell neoplasms are lymphoid malignancies with an aggressive clinical course. In the present study, we analyzed gene expression profiling of NK cell neoplasms and attempted to identify important molecular pathways and new effective drugs. Pathway analysis of gene expression profiles suggested the important roles of the JAK-STAT pathway, NF-κB pathway or Wnt pathways in NK cell neoplasms. Notably, western blot analysis revealed that STAT3 was expressed and phosphorylated at a higher level in NK cell lines than in normal NK cells or other cell lines. These findings indicate the occurrence of JAK-STAT activation in NK cell neoplasms. Connectivity Map (CMAP) analysis of gene expression profiles identified candidate drugs against NK cell neoplasms. Among the drugs suggested by CMAP analysis, we focused on puromycin, phenoxybenzamine, LY294002, wortmannin, vorinostat and trichostatin A because they exhibited high enrichment scores. We added these drugs to NK cell lines and other cell lines. Among the drugs, vorinostat suppressed NK cell line proliferation at a significantly lower concentration compared to other cell lines. Suppression of the JAK-STAT pathway appeared to contribute to this effect. Vorinostat may be a good candidate for use in the therapy against NK cell neoplasms.
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Affiliation(s)
- Kennosuke Karube
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
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Comparative gene expression profiling of benign and malignant lesions reveals candidate therapeutic compounds for leiomyosarcoma. Sarcoma 2012; 2012:805614. [PMID: 22919280 PMCID: PMC3420093 DOI: 10.1155/2012/805614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 06/05/2012] [Indexed: 01/15/2023] Open
Abstract
Leiomyosarcoma (LMS) is a malignant, soft-tissue tumor for which few effective therapies exist. Previously, we showed that there are three molecular subtypes of LMS. Here, we analyzed genes differentially expressed in each of the three LMS subtypes as compared to benign leiomyomas and then used the Connectivity Map (cmap) to calculate enrichment scores for the 1309 cmap drugs in order to identify candidate molecules with the potential to induce a benign, leiomyoma-like phenotype in LMS cells. 11 drugs were selected and tested for their ability to inhibit the growth of three human LMS cell lines. We identified two drugs with in vitro efficacy against LMS, one of which had a strongly negative enrichment score (Cantharidin) and the other of which had a strongly positive enrichment score (MG-132). Given MG-132's strong inhibitory effect on LMS cell viability, we hypothesized that LMS cells may be sensitive to treatment with other proteasome inhibitors and demonstrated that bortezomib, a clinically-approved proteasome inhibitor not included in the original cmap screen, potently inhibited the viability of the LMS cell lines. These findings suggest that systematically linking LMS subtype-specific expression signatures with drug-associated expression profiles represents a promising approach for the identification of new drugs for LMS.
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Navarro S, Piqueras M, Villamón E, Yáñez Y, Balaguer J, Cañete A, Noguera R. New prognostic markers in neuroblastoma. ACTA ACUST UNITED AC 2012; 6:555-67. [PMID: 23480837 DOI: 10.1517/17530059.2012.704018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The hallmark of neuroblastoma is its clinical and biological heterogeneity, with the likelihood of cure varying widely according to age at diagnosis, extent of disease and tumor biology. We hope this review will be useful for understanding part of the unfamiliar neuroblastoma codex. AREAS COVERED In the first part of this review, the authors summarize the currently used prognostic factors for risk-adapted therapy, with the focus on clinical management of neuroblastoma patients. In the second part, the authors discuss the evolving prognostic factors for future treatment schemes. A search of online medical research databases was undertaken focusing especially on literature published in the last six years. EXPERT OPINION Harnessing the synergy of the various forms of data, including clinical variables and biomarker profiles, would allow mathematical predictive models to be built for the individual patient, which could eventually become molecular targets of specific therapies.
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Affiliation(s)
- Samuel Navarro
- Department of Pathology, Medical School, University of Valencia , Avda. Blasco Ibañez 15 Valencia 46010 , Spain +34 96 3864146 ; +34 96 3864173 ;
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21
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Johnstone AL, Reierson GW, Smith RP, Goldberg JL, Lemmon VP, Bixby JL. A chemical genetic approach identifies piperazine antipsychotics as promoters of CNS neurite growth on inhibitory substrates. Mol Cell Neurosci 2012; 50:125-35. [PMID: 22561309 DOI: 10.1016/j.mcn.2012.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 03/23/2012] [Accepted: 04/20/2012] [Indexed: 01/22/2023] Open
Abstract
Injury to the central nervous system (CNS) can result in lifelong loss of function due in part to the regenerative failure of CNS neurons. Inhibitory proteins derived from myelin and the astroglial scar are major barriers for the successful regeneration of injured CNS neurons. Previously, we described the identification of a novel compound, F05, which promotes neurite growth from neurons challenged with inhibitory substrates in vitro, and promotes axonal regeneration in vivo (Usher et al., 2010). To identify additional regeneration-promoting compounds, we used F05-induced gene expression profiles to query the Broad Institute Connectivity Map, a gene expression database of cells treated with >1300 compounds. Despite no shared chemical similarity, F05-induced changes in gene expression were remarkably similar to those seen with a group of piperazine phenothiazine antipsychotics (PhAPs). In contrast to antipsychotics of other structural classes, PhAPs promoted neurite growth of CNS neurons challenged with two different glial derived inhibitory substrates. Our pharmacological studies suggest a mechanism whereby PhAPs promote growth through antagonism of calmodulin signaling, independent of dopamine receptor antagonism. These findings shed light on mechanisms underlying neurite-inhibitory signaling, and suggest that clinically approved antipsychotic compounds may be repurposed for use in CNS injured patients.
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Affiliation(s)
- Andrea L Johnstone
- The Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1400 NW 12th Ave, Miami, FL 33136, USA
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22
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Azad MA, Wright GD. Determining the mode of action of bioactive compounds. Bioorg Med Chem 2012; 20:1929-39. [DOI: 10.1016/j.bmc.2011.10.088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/14/2011] [Accepted: 10/30/2011] [Indexed: 10/14/2022]
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Identifying inhibitors of epithelial-mesenchymal transition by connectivity map-based systems approach. J Thorac Oncol 2012; 6:1784-92. [PMID: 21964532 DOI: 10.1097/jto.0b013e31822adfb0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Acquisition of mesenchymal phenotype by epithelial cells by means of epithelial-mesenchymal transition (EMT) is considered as an early event in the multistep process of tumor metastasis. Therefore, inhibition of EMT might be a rational strategy to prevent metastasis. METHODS Using the global gene expression profile from a cell culture model of transforming growth factor-β (TGF-β)-induced EMT, we identified potential EMT inhibitors. We used a publicly available database (www.broad.mit.edu/cmap) comprising gene expression profiles obtained from multiple different cell lines in response to various drugs to derive negative correlations to EMT gene expression profile using Connectivity Map, a pattern matching tool. RESULTS Experimental validation of the identified compounds showed rapamycin as a novel inhibitor of TGF-β signaling along with 17-AAG, a known modulator of TGF-β pathway. Both of these compounds completely blocked EMT and the associated migratory and invasive phenotype. The other identified compound, LY294002, demonstrated a selective inhibition of mesenchymal markers, cell migration and invasion, without affecting the loss of E-cadherin expression or Smad phosphorylation. CONCLUSIONS Our data reveal that rapamycin is a novel modulator of TGF-β signaling, and along with 17-AAG and LY294002, could be used as therapeutic agent for inhibiting EMT. This study demonstrates the potential of a systems approach in identifying novel modulators of a complex biological process.
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Neuroblastoma genetics and phenotype: a tale of heterogeneity. Semin Cancer Biol 2011; 21:238-44. [PMID: 21839839 DOI: 10.1016/j.semcancer.2011.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/13/2011] [Indexed: 12/31/2022]
Abstract
Cancer is a complex disease driven by multiple genetic and epigenetic alterations. Understanding the (epi-)genetic changes and consequent deregulation of regulatory networks controlling the various normal critical cellular phenotypes that are perturbed in cancer cells can provide clues to new therapeutic opportunities. Moreover, such insights into the molecular pathology of a given cancer type can offer clinical relevant genetic markers or molecular signatures for assessment of prognosis and response to therapy, and prediction of risk for relapse. Therefore, as for many other tumour entities, neuroblastoma (NB) has been the subject of intensive ongoing genomic research. Here we will summarize the current state-of-the-art of these studies with focus on genome wide DNA copy number and gene expression analyses in relation to the relevance for present and future clinical management of NB patients.
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Abel F, Dalevi D, Nethander M, Jörnsten R, De Preter K, Vermeulen J, Stallings R, Kogner P, Maris J, Nilsson S. A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int 2011; 11:9. [PMID: 21492432 PMCID: PMC3095533 DOI: 10.1186/1475-2867-11-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 04/14/2011] [Indexed: 12/03/2022] Open
Abstract
Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p < 0.05, one-way ANOVA test). PCA clusters p1, p2, and p3 were found to correspond well to the postulated subtypes 1, 2A, and 2B, respectively. Remarkably, a fourth novel cluster was detected in all three independent data sets. This cluster comprised mainly 11q-deleted MNA-negative tumours with low expression of ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and/or dead of disease, p < 0.05, Fisher's exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics.
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Affiliation(s)
- Frida Abel
- Department of Clinical Genetics, Gothenburg University, Gothenburg, Sweden.
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26
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Wen Z, Wang Z, Wang S, Ravula R, Yang L, Xu J, Wang C, Zuo Z, Chow MSS, Shi L, Huang Y. Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map. PLoS One 2011; 6:e18278. [PMID: 21464939 PMCID: PMC3065471 DOI: 10.1371/journal.pone.0018278] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 02/25/2011] [Indexed: 12/14/2022] Open
Abstract
To pursue a systematic approach to discovery of mechanisms of action of traditional Chinese medicine (TCM), we used microarrays, bioinformatics and the “Connectivity Map” (CMAP) to examine TCM-induced changes in gene expression. We demonstrated that this approach can be used to elucidate new molecular targets using a model TCM herbal formula Si-Wu-Tang (SWT) which is widely used for women's health. The human breast cancer MCF-7 cells treated with 0.1 µM estradiol or 2.56 mg/ml of SWT showed dramatic gene expression changes, while no significant change was detected for ferulic acid, a known bioactive compound of SWT. Pathway analysis using differentially expressed genes related to the treatment effect identified that expression of genes in the nuclear factor erythroid 2-related factor 2 (Nrf2) cytoprotective pathway was most significantly affected by SWT, but not by estradiol or ferulic acid. The Nrf2-regulated genes HMOX1, GCLC, GCLM, SLC7A11 and NQO1 were upreguated by SWT in a dose-dependent manner, which was validated by real-time RT-PCR. Consistently, treatment with SWT and its four herbal ingredients resulted in an increased antioxidant response element (ARE)-luciferase reporter activity in MCF-7 and HEK293 cells. Furthermore, the gene expression profile of differentially expressed genes related to SWT treatment was used to compare with those of 1,309 compounds in the CMAP database. The CMAP profiles of estradiol-treated MCF-7 cells showed an excellent match with SWT treatment, consistent with SWT's widely claimed use for women's diseases and indicating a phytoestrogenic effect. The CMAP profiles of chemopreventive agents withaferin A and resveratrol also showed high similarity to the profiles of SWT. This study identified SWT as an Nrf2 activator and phytoestrogen, suggesting its use as a nontoxic chemopreventive agent, and demonstrated the feasibility of combining microarray gene expression profiling with CMAP mining to discover mechanisms of actions and to identify new health benefits of TCMs.
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Affiliation(s)
- Zhining Wen
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Zhijun Wang
- Department of Pharmaceutical Sciences and Center for Advancement of Drug Research and Evaluation, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
| | - Steven Wang
- Department of Pharmaceutical Sciences and Center for Advancement of Drug Research and Evaluation, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
| | - Ranadheer Ravula
- Department of Pharmaceutical Sciences and Center for Advancement of Drug Research and Evaluation, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
| | - Lun Yang
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
- Department of Clinical Pharmacy and Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, China
| | - Jun Xu
- Clinical Transcriptional Genomics Core, Medical Genetics Institute, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Charles Wang
- Functional Genomics Core, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Zhong Zuo
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Moses S. S. Chow
- Department of Pharmaceutical Sciences and Center for Advancement of Drug Research and Evaluation, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
| | - Leming Shi
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
- Department of Clinical Pharmacy and Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, China
- * E-mail: (LS); (YH)
| | - Ying Huang
- Department of Pharmaceutical Sciences and Center for Advancement of Drug Research and Evaluation, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
- * E-mail: (LS); (YH)
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27
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Roet KCD, Bossers K, Franssen EHP, Ruitenberg MJ, Verhaagen J. A meta-analysis of microarray-based gene expression studies of olfactory bulb-derived olfactory ensheathing cells. Exp Neurol 2011; 229:10-45. [PMID: 21396936 DOI: 10.1016/j.expneurol.2011.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/28/2010] [Accepted: 03/02/2011] [Indexed: 12/23/2022]
Abstract
Genome wide transcriptional profiling and large scale proteomics have emerged as two powerful methods to dissect the molecular properties of specific neural tissues or cell types on a global scale. Several genome-wide transcriptional profiling and proteomics studies have been published on cultured olfactory ensheathing cells (OEC). In this article we present a meta-analysis of all five published and publicly available micro-array gene expression datasets of cultured early-passage-OB-OEC with other cell types (Schwann cells, late-passage-OB-OEC, mucosa-OEC, an OEC cell line, and acutely dissected OEC). The aim of this meta-analysis is to identify genes and molecular pathways that are found in multiple instead of one isolated study. 454 Genes were detected in at least three out of five microarray datasets. In this "Top-list", genes involved in the biological processes "growth of neurites", "blood vessel development", "migration of cells" and "immune response" were strongly overrepresented. By applying network analysis tools, molecular networks were constructed and Hub-genes were identified that may function as key genes in the above mentioned interrelated processes. We also identified 7 genes (ENTPD2, MATN2, CTSC, PTHLH, GLRX1, COL27A1 and ID2) with uniformly higher or lower expression in early-passage-OB-OEC in all five microarray comparisons. These genes have diverse but intriguing roles in neuroprotection, neurite extension and/or tissue repair. Our meta-analysis provides novel insights into the molecular basis of OB-OEC-mediated neural repair and can serve as a repository for investigators interested in the molecular biology of OEC. This article is part of a Special Issue entitled: Understanding olfactory ensheathing glia and their prospect for nervous system repair.
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Affiliation(s)
- Kasper C D Roet
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Meibergdreef 47, Amsterdam, The Netherlands.
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28
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McArt DG, Zhang SD. Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping. PLoS One 2011; 6:e16382. [PMID: 21305029 PMCID: PMC3031567 DOI: 10.1371/journal.pone.0016382] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 12/14/2010] [Indexed: 01/16/2023] Open
Abstract
Connectivity mapping is a recently developed technique for discovering the underlying connections between different biological states based on gene-expression similarities. The sscMap method has been shown to provide enhanced sensitivity in mapping meaningful connections leading to testable biological hypotheses and in identifying drug candidates with particular pharmacological and/or toxicological properties. Challenges remain, however, as to how to prioritise the large number of discovered connections in an unbiased manner such that the success rate of any following-up investigation can be maximised. We introduce a new concept, gene-signature perturbation, which aims to test whether an identified connection is stable enough against systematic minor changes (perturbation) to the gene-signature. We applied the perturbation method to three independent datasets obtained from the GEO database: acute myeloid leukemia (AML), cervical cancer, and breast cancer treated with letrozole. We demonstrate that the perturbation approach helps to identify meaningful biological connections which suggest the most relevant candidate drugs. In the case of AML, we found that the prevalent compounds were retinoic acids and PPAR activators. For cervical cancer, our results suggested that potential drugs are likely to involve the EGFR pathway; and with the breast cancer dataset, we identified candidates that are involved in prostaglandin inhibition. Thus the gene-signature perturbation approach added real values to the whole connectivity mapping process, allowing for increased specificity in the identification of possible therapeutic candidates.
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Affiliation(s)
- Darragh G. McArt
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
- * E-mail:
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29
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Palchaudhuri R, Hergenrother PJ. Transcript profiling and RNA interference as tools to identify small molecule mechanisms and therapeutic potential. ACS Chem Biol 2011; 6:21-33. [PMID: 21105689 DOI: 10.1021/cb100310h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The identification of the mechanism of action and therapeutic potential of bioactive small molecules remains a considerable challenge in the field of drug discovery and chemical biology. Apart from traditional target identification techniques, new tools have emerged that can significantly aid mechanism elucidation efforts. The development of pattern matching algorithms that compare transcription profile data to analogous data on compounds with known cellular targets allows for mechanistic insights without the need to synthesize chemically modified probes. In addition, such methods can be used to connect small molecules to particular disease states, thus aiding the rational identification of candidate therapeutics. Another method with considerable potential is whole-genome RNAi screening, a technique that can identify critical upstream proteins involved in a small molecule's mechanism of action. Several proof-of-concept studies using compounds with known cellular targets suggest this tool will enable mechanistic characterization of bioactive small molecules with unknown mechanisms. This Review highlights recent successes in using these pattern matching and chemical genetic tools, with the goal of uncovering small molecule mechanisms and identifying therapeutic candidates for disease treatment.
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Affiliation(s)
- Rahul Palchaudhuri
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul J. Hergenrother
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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30
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Wang G, Ye Y, Yang X, Liao H, Zhao C, Liang S. Expression-based in silico screening of candidate therapeutic compounds for lung adenocarcinoma. PLoS One 2011; 6:e14573. [PMID: 21283735 PMCID: PMC3024967 DOI: 10.1371/journal.pone.0014573] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 12/21/2010] [Indexed: 01/26/2023] Open
Abstract
Background Lung adenocarcinom (AC) is the most common form of lung cancer. Currently, the number of medical options to deal with lung cancer is very limited. In this study, we aimed to investigate potential therapeutic compounds for lung adenocarcinoma based on integrative analysis. Methodology/Principal Findings The candidate therapeutic compounds were identified in a two-step process. First, a meta-analysis of two published microarray data was conducted to obtain a list of 343 differentially expressed genes specific to lung AC. In the next step, expression profiles of these genes were used to query the Connectivity-Map (C-MAP) database to identify a list of compounds whose treatment reverse expression direction in various cancer cells. Several compounds in the categories of HSP90 inhibitor, HDAC inhibitor, PPAR agonist, PI3K inhibitor, passed our screening to be the leading candidates. On top of the list, three HSP90 inhibitors, i.e. 17-AAG (also known as tanespimycin), monorden, and alvespimycin, showed significant negative enrichment scores. Cytotoxicity as well as effects on cell cycle regulation and apoptosis were evaluated experimentally in lung adenocarcinoma cell line (A549 or GLC-82) with or without treatment with 17-AAG. In vitro study demonstrated that 17-AAG alone or in combination with cisplatin (DDP) can significantly inhibit lung adenocarcinoma cell growth by inducing cell cycle arrest and apoptosis. Conclusions/Significance We have used an in silico screening to identify compounds for treating lung cancer. One such compound 17-AAG demonstrated its anti-lung AC activity by inhibiting cell growth and promoting apoptosis and cell cycle arrest.
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Affiliation(s)
- Guiping Wang
- Bioinformatics Group, Institute of Genetic Engineering, Southern Medical University, Guangzhou, People's Republic of China
- Guangzhou Medical College, Guangzhou, People's Republic of China
| | - Yun Ye
- Bioinformatics Group, Institute of Genetic Engineering, Southern Medical University, Guangzhou, People's Republic of China
- Department of Biological and Chemical Engineering, Guangxi University of Technology, Liuzhou, People's Republic of China
| | - Xiaoqin Yang
- Bioinformatics Group, Institute of Genetic Engineering, Southern Medical University, Guangzhou, People's Republic of China
| | - Hongying Liao
- Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Canguo Zhao
- Guangzhou Medical College, Guangzhou, People's Republic of China
| | - Shuang Liang
- Bioinformatics Group, Institute of Genetic Engineering, Southern Medical University, Guangzhou, People's Republic of China
- * E-mail:
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31
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Smith KM, Datti A, Fujitani M, Grinshtein N, Zhang L, Morozova O, Blakely KM, Rotenberg SA, Hansford LM, Miller FD, Yeger H, Irwin MS, Moffat J, Marra MA, Baruchel S, Wrana JL, Kaplan DR. Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens. EMBO Mol Med 2011; 2:371-84. [PMID: 20721990 PMCID: PMC3377336 DOI: 10.1002/emmm.201000093] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Neuroblastoma (NB) is the most deadly extra-cranial solid tumour in children necessitating an urgent need for effective and less toxic treatments. One reason for the lack of efficacious treatments may be the inability of existing drugs to target the tumour-initiating or cancer stem cell population responsible for sustaining tumour growth, metastases and relapse. Here, we describe a strategy to identify compounds that selectively target patient-derived cancer stem cell-like tumour-initiating cells (TICs) while sparing normal paediatric stem cells (skin-derived precursors, SKPs) and characterize two therapeutic candidates. DECA-14 and rapamycin were identified as NB TIC-selective agents. Both compounds induced TIC death at nanomolar concentrations in vitro, significantly reduced NB xenograft tumour weight in vivo, and dramatically decreased self-renewal or tumour-initiation capacity in treated tumours. These results demonstrate that differential drug sensitivities between TICs and normal paediatric stem cells can be exploited to identify novel, patient-specific and potentially less toxic therapies.
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Affiliation(s)
- Kristen M Smith
- Cell Biology Program and James Burrell Laboratories, The Hospital for Sick Children, Toronto, Canada
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Lan MY, Chen CL, Lin KT, Lee SA, Yang WLR, Hsu CN, Wu JC, Ho CY, Lin JC, Huang CYF. From NPC therapeutic target identification to potential treatment strategy. Mol Cancer Ther 2010; 9:2511-23. [PMID: 20716640 DOI: 10.1158/1535-7163.mct-09-0966] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is relatively rare in Western countries but is a common cancer in southern Asia. Many differentially expressed genes have been linked to NPC; however, how to prioritize therapeutic targets and potential drugs from unsorted gene lists remains largely unknown. We first collected 558 upregulated and 993 downregulated NPC genes from published microarray data and the primary literatures. We then postulated that conversion of gene signatures into the protein-protein interaction network and analyzing the network topologically could provide insight into key regulators involved in tumorigenesis of NPC. Of particular interest was the presence of cliques, called fully connected subgraphs, in the inferred NPC networks. These clique-based hubs, connecting with more than three queries and ranked higher than other nodes in the NPC protein-protein interaction network, were further narrowed down by pathway analysis to retrieve 24 upregulated and 6 downregulated bottleneck genes for predicting NPC carcinogenesis. Moreover, additional oncogenes, tumor suppressor genes, genes involved in protein complexes, and genes obtained after functional profiling were merged with the bottleneck genes to form the final gene signature of 38 upregulated and 10 downregulated genes. We used the initial and final NPC gene signatures to query the Connectivity Map, respectively, and found that target reduction through our pipeline could efficiently uncover potential drugs with cytotoxicity to NPC cancer cells. An integrative Web site (http://140.109.23.188:8080/NPC) was established to facilitate future NPC research. This in silico approach, from target prioritization to potential drugs identification, might be an effective method for various cancer researches.
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Affiliation(s)
- Ming-Ying Lan
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
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Gheeya J, Johansson P, Chen QR, Dexheimer T, Metaferia B, Song YK, Wei JS, He J, Pommier Y, Khan J. Expression profiling identifies epoxy anthraquinone derivative as a DNA topoisomerase inhibitor. Cancer Lett 2010; 293:124-31. [PMID: 20133050 DOI: 10.1016/j.canlet.2010.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/04/2010] [Accepted: 01/11/2010] [Indexed: 11/19/2022]
Abstract
To discover novel drugs for neuroblastoma treatment, we have previously screened a panel of drugs and identified 30 active agents against neuroblastoma cells. Here we performed microarray gene expression analysis to monitor the impact of these agents on a neuroblastoma cell line and used the connectivity map (cMAP) to explore putative mechanism of action of unknown drugs. We first compared the expression profiles of 10 compounds shared in both our dataset and cMAP database and observed the high connectivity scores for 7 of 10 matched drugs regardless of the differences of cell lines utilized. The screen of cMAP for uncharacterized drugs indicated the signature of Epoxy anthraquinone derivative (EAD) matched the profiles of multiple known DNA targeted agents (topoisomerase I/II inhibitors, DNA intercalators, and DNA alkylation agents) as predicted by its structure. Similar result was obtained by querying against our internal NB-cMAP (http://pob.abcc.ncifcrf.gov/cgi-bin/cMAP), a database containing the profiles of 30 active drugs. These results suggest that Epoxy anthraquinone derivative may inhibit neuroblastoma cells by targeting DNA replication inhibition. Experimental data also demonstrate that Epoxy anthraquinone derivative indeed induces DNA double-strand breaks through DNA alkylation and inhibition of topoisomerase activity. Our study indicates that Epoxy anthraquinone derivative may be a novel DNA topoisomerase inhibitor that can be potentially used for treatment of neuroblastoma or other cancer patients.
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Affiliation(s)
- Jinesh Gheeya
- Oncogenomics Section, Pediatric Oncology Branch, Advanced Technology Center, National Cancer Institute, Gaithersburg, MD, USA
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Van Roy N, De Preter K, Hoebeeck J, Van Maerken T, Pattyn F, Mestdagh P, Vermeulen J, Vandesompele J, Speleman F. The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy. Genome Med 2009; 1:74. [PMID: 19638189 PMCID: PMC2717400 DOI: 10.1186/gm74] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Neuroblastoma is one of the most common solid tumors of childhood, arising from immature sympathetic nervous system cells. The clinical course of patients with neuroblastoma is highly variable, ranging from spontaneous regression to widespread metastatic disease. Although the outcome for children with cancer has improved considerably during the past decades, the prognosis of children with aggressive neuroblastoma remains dismal. The clinical heterogeneity of neuroblastoma mirrors the biological and genetic heterogeneity of these tumors. Ploidy and MYCN amplification have been used as genetic markers for risk stratification and therapeutic decision making, and, more recently, gene expression profiling and genome-wide DNA copy number analysis have come into the picture as sensitive and specific tools for assessing prognosis. The applica tion of new genetic tools also led to the discovery of an important familial neuroblastoma cancer gene, ALK, which is mutated in approximately 8% of sporadic tumors, and genome-wide association studies have unveiled loci with risk alleles for neuroblastoma development. For some of the genomic regions that are deleted in some neuroblastomas, on 1p, 3p and 11q, candidate tumor suppressor genes have been identified. In addition, evidence has emerged for the contribution of epigenetic disturbances in neuroblastoma oncogenesis. As in other cancer entities, altered microRNA expression is also being recognized as an important player in neuroblastoma. The recent successes in unraveling the genetic basis of neuroblastoma are now opening opportunities for development of targeted therapies.
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Affiliation(s)
- Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
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