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Tan IL, Perez AR, Lew RJ, Sun X, Baldwin A, Zhu YK, Shah MM, Berger MS, Doudna JA, Fellmann C. Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis. Cell Rep 2023; 42:113339. [PMID: 37917583 PMCID: PMC10725516 DOI: 10.1016/j.celrep.2023.113339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 07/25/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Glioblastoma (GBM) is the most common lethal primary brain cancer in adults. Despite treatment regimens including surgical resection, radiotherapy, and temozolomide (TMZ) chemotherapy, growth of residual tumor leads to therapy resistance and death. At recurrence, a quarter to a third of all gliomas have hypermutated genomes, with mutational burdens orders of magnitude greater than in normal tissue. Here, we quantified the mutational landscape progression in a patient's primary and recurrent GBM, and we uncovered Cas9-targetable repeat elements. We show that CRISPR-mediated targeting of highly repetitive loci enables rapid elimination of GBM cells, an approach we term "genome shredding." Importantly, in the patient's recurrent GBM, we identified unique repeat sequences with TMZ mutational signature and demonstrated that their CRISPR targeting enables cancer-specific cell ablation. "Cancer shredding" leverages the non-coding genome and therapy-induced mutational signatures for targeted GBM cell depletion and provides an innovative paradigm to develop treatments for hypermutated glioma.
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Affiliation(s)
- I-Li Tan
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexendar R Perez
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94131, USA; Silico Therapeutics, San Francisco, CA 94131, USA
| | - Rachel J Lew
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Xiaoyu Sun
- Silico Therapeutics, San Francisco, CA 94131, USA
| | - Alisha Baldwin
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yong K Zhu
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mihir M Shah
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94131, USA
| | - Jennifer A Doudna
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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2
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Que Z, Yang K, Wang N, Li S, Li T. Functional Role of RBP in Osteosarcoma: Regulatory Mechanism and Clinical Therapy. Anal Cell Pathol (Amst) 2023; 2023:9849719. [PMID: 37426488 PMCID: PMC10328736 DOI: 10.1155/2023/9849719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023] Open
Abstract
Malignant bone neoplasms can be represented by osteosarcoma (OS), which accounts for 36% of all sarcomas. To reduce tumor malignancy, extensive efforts have been devoted to find an ideal target from numerous candidates, among which RNA-binding proteins (RBPs) have shown their unparalleled competitiveness. With the special structure of RNA-binding domains, RBPs have the potential to establish relationships with RNAs or small molecules and are considered regulators of different sections of RNA processes, including splicing, transport, translation, and degradation of RNAs. RBPs have considerable significant roles in various cancers, and experiments revealed that there was a strong association of RBPs with tumorigenesis and tumor cell progression. Regarding OS, RBPs are a new orientation, but achievements in hand are noteworthy. Higher or lower expression of RBPs was first found in tumor cells compared to normal tissue. By binding to different molecules, RBPs are capable of influencing tumor cell phenotypes through different signaling pathways or other axes, and researches on medical treatment have been largely inspired. Exploring the prognostic and therapeutic values of RBPs in OS is a hotspot where diverse avenues on regulating RBPs have achieved dramatical effects. In this review, we briefly summarize the contribution of RBPs and their binding molecules to OS oncogenicity and generally introduce distinctive RBPs as samples. Moreover, we focus on the attempts to differentiate RBP's opposite functions in predicting prognosis and collect possible strategies for treatment. Our review provides forwards insight into improving the understanding of OS and suggests RBPs as potential biomarkers for therapies.
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Affiliation(s)
- Ziyuan Que
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Kang Yang
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Nan Wang
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Shuying Li
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Tao Li
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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3
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Aksoy Yasar FB, Shingu T, Zamler DB, Zaman MF, Chien DL, Zhang Q, Ren J, Hu J. Quaking but not parkin is the major tumor suppressor in 6q deleted region in glioblastoma. Front Cell Dev Biol 2022; 10:931387. [PMID: 36051438 PMCID: PMC9424994 DOI: 10.3389/fcell.2022.931387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is a high-grade, aggressive brain tumor with dismal median survival time of 15 months. Chromosome 6q (Ch6q) is a hotspot of genomic alterations, which is commonly deleted or hyper-methylated in GBM. Two neighboring genes in this region, QKI and PRKN have been appointed as tumor suppressors in GBM. While a genetically modified mouse model (GEMM) of GBM has been successfully generated with Qk deletion in the central nervous system (CNS), in vivo genetic evidence supporting the tumor suppressor function of Prkn has not been established. In the present study, we generated a mouse model with Prkn-null allele and conditional Trp53 and Pten deletions in the neural stem cells (NSCs) and compared the tumorigenicity of this model to our previous GBM model with Qk deletion within the same system. We find that Qk but not Prkn is the potent tumor suppressor in the frequently altered Ch6q region in GBM.
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Affiliation(s)
- Fatma Betul Aksoy Yasar
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Takashi Shingu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Daniel B. Zamler
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mohammad Fayyad Zaman
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Derek Lin Chien
- School of Arts and Sciences, University of Rochester, Rochester, NY, United States
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Jiangong Ren
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jian Hu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- *Correspondence: Jian Hu,
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4
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Bale TA, Rosenblum MK. The 2021 WHO Classification of Tumors of the Central Nervous System: An update on pediatric low-grade gliomas and glioneuronal tumors. Brain Pathol 2022; 32:e13060. [PMID: 35218102 PMCID: PMC9245930 DOI: 10.1111/bpa.13060] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
The 2021 5th edition of the WHO Classification of Tumors of the Central Nervous System reflects the discovery of genetic alterations underlying many central nervous system (CNS) neoplasms. Insights gained from technologic advances and novel applications in molecular diagnostics, including next‐generation sequencing and DNA methylation‐based profiling, coupled with the recognition of clinicopathologic correlates, have prompted substantial changes to CNS tumor classification; this is particularly true for pediatric low‐grade gliomas and glioneuronal tumors (pLGG/GNTs). The 2021 WHO now classifies gliomas, glioneuronal tumors and neuronal tumors into 6 families, three of which encompass pLGG/LGNTs: “Pediatric type diffuse low‐grade gliomas,” “circumscribed astrocytic gliomas,” and “glioneuronal and neuronal tumors.” Among these are six newly recognized tumor types: “diffuse astrocytoma, MYB or MYBL1‐altered”; “polymorphous low grade neuroepithelial tumor of the young (PLNTY)”; “diffuse low‐grade glioma‐MAPK altered”; “Diffuse glioneuronal tumor with oligodendroglioma‐like features and nuclear clusters (DGONC)”; “myxoid glioneuronal tumor (MGT)”; and “multinodular and vacuolating neuronal tumor (MVNT).” We review these newly recognized entities in the context of general changes to the WHO schema, discuss implications of the new classification for treatment of pLGG/LGNT, and consider strategies for molecular testing and interpretation.
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Affiliation(s)
- Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc K Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Xu Y, Li Z, Huai T, Huo X, Wang H, Bian E, Zhao B. DNMT1 Mediated CAHM Repression Promotes Glioma Invasion via SPAK/JNK Pathway. Cell Mol Neurobiol 2021; 42:2643-2653. [PMID: 34227028 DOI: 10.1007/s10571-021-01125-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Gliomas are the most common and fatal brain tumors worldwide. Abnormal DNA promoter methylation is an important mechanism for gene loss of tumor suppressors. A long non-coding RNA colorectal adenocarcinoma hypermethylated (CAHM) has been reported to be nearly deleted in glioblastomas (GBMs). Nevertheless, the roles of CAHM in gliomas remain unknown up to now. In the present study, 969 glioma samples downloaded from the CGGA and Gravendeel databases were included. We found that CAHM expression was correlated with glioma grades, molecular subtype, IDH mutation status, and 1q/19p codel status. In glioma cells, CAHM is hypermethylated by DNA methyltransferase1 (DNMT1) and the loss of CAHM expression could be reversed by 5-Aza-2'-deoxycytidine (5-Aza), a specific inhibitor of DNA methyltransferases. Besides, the expression of CAHM was negatively associated with overall survival in both primary and recurrent gliomas. Moreover, the result of Gene Ontology (GO) analysis suggested that CAHM participated in negatively regulating cell development, nervous system development, neurogenesis, and integrin-mediated signaling pathway. Overexpression of CAHM inhibited glioma cell proliferation, clone formation, and invasion. Further exploring results showed that CAHM overexpression suppressed glioma migration and invasion through SPAK/MAPK pathway. Collectively, this study disclosed that CAHM might be a suppressor in gliomas.
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Affiliation(s)
- Yadi Xu
- Ultrasonography Department, Hubei Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Zelin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Tian Huai
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Xiuhao Huo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Hongliang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China. .,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
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6
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Functional Expression, Purification and Identification of Interaction Partners of PACRG. Molecules 2021; 26:molecules26082308. [PMID: 33923444 PMCID: PMC8074078 DOI: 10.3390/molecules26082308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
PACRG (Parkin co-regulated gene) shares a bi-directional promoter with the Parkinson’s disease-associated gene Parkin, but the physiological roles of PACRG have not yet been fully elucidated. Recombinant expression methods are indispensable for protein structural and functional studies. In this study, the coding region of PACRG was cloned to a conventional vector pQE80L, as well as two cold-shock vectors pCold II and pCold-GST, respectively. The constructs were transformed into Escherichia coli (DE3), and the target proteins were overexpressed. The results showed that the cold-shock vectors are more suitable for PACRG expression. The soluble recombinant proteins were purified with Ni2+ chelating column, glutathione S-transferase (GST) affinity chromatography and gel filtration. His6 pull down assay and LC-MS/MS were carried out for identification of PACRG-binding proteins in HEK293T cell lysates, and a total number of 74 proteins were identified as potential interaction partners of PACRG. GO (Gene ontology) enrichment analysis (FunRich) of the 74 proteins revealed multiple molecular functions and biological processes. The highest proportion of the 74 proteins functioned as transcription regulator and transcription factor activity, suggesting that PACRG may play important roles in regulation of gene transcription.
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7
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MYB oncoproteins: emerging players and potential therapeutic targets in human cancer. Oncogenesis 2021; 10:19. [PMID: 33637673 PMCID: PMC7910556 DOI: 10.1038/s41389-021-00309-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
MYB transcription factors are highly conserved from plants to vertebrates, indicating that their functions embrace fundamental mechanisms in the biology of cells and organisms. In humans, the MYB gene family is composed of three members: MYB, MYBL1 and MYBL2, encoding the transcription factors MYB, MYBL1, and MYBL2 (also known as c-MYB, A-MYB, and B-MYB), respectively. A truncated version of MYB, the prototype member of the MYB family, was originally identified as the product of the retroviral oncogene v-myb, which causes leukaemia in birds. This led to the hypothesis that aberrant activation of vertebrate MYB could also cause cancer. Despite more than three decades have elapsed since the isolation of v-myb, only recently investigators were able to detect MYB genes rearrangements and mutations, smoking gun evidence of the involvement of MYB family members in human cancer. In this review, we will highlight studies linking the activity of MYB family members to human malignancies and experimental therapeutic interventions tailored for MYB-expressing cancers.
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8
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Yang H, Li Y, Peng Z, Wang Y. Overexpression of miR-20a promotes the progression of osteosarcoma by directly targeting QKI2. Oncol Lett 2019; 18:87-94. [PMID: 31289476 PMCID: PMC6540454 DOI: 10.3892/ol.2019.10313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 01/22/2019] [Indexed: 11/15/2022] Open
Abstract
Osteosarcoma (OS) is the most common type of malignant primary bone neoplasm. Although the application of neoadjuvant chemotherapy has improved the 5-year survival rate of patients suffering from OS, prognosis remains poor. Therefore, it is important to elucidate the molecular mechanisms underlying the occurrence, progression and metastasis of OS. The RNA-binding protein Quaking (QKI) is a member of the STAR family of proteins, and can function as a tumor suppressor gene to suppress the occurrence and progression of a variety of tumors; however, the role of QKI in OS remains to be fully elucidated. In the present study, it was identified that the expression of QKI2 was downregulated in OS using western blot analysis. In addition, subsequent functional investigations, including MTT, Transwell invasion and migration assays, revealed that QKI2 inhibited the proliferation, invasion and migration of an OS cell line in vitro. By implementing a series of experimental techniques in molecular biology, including reverse transcription-quantitative polymerase chain reaction and a double fluorescence reporter assay, it was demonstrated that the expression of miR-20a was high and inhibited the expression of QKI2 in OS. In conclusion, it was revealed that aberrantly upregulated miR-20a inhibited the expression of QKI2 in OS by targeting QKI2 mRNA, subsequently promoting the proliferation, migration and invasion of OS cells.
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Affiliation(s)
- Hongbo Yang
- Department of Orthopedic Surgery, Affiliated Hospital of Chifeng University, Chifeng, Inner Mongolia 024000, P.R. China
| | - Yongli Li
- Department of Tumor Radiotherapy, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150000, P.R. China
| | - Zhibin Peng
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yansong Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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9
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Mo HY, Jo YS, Yoo NJ, Kim MS, Song SY, Lee SH. Frameshift mutation of candidate tumor suppressor genes QK1 and TMEFF2 in gastric and colorectal cancers. Cancer Biomark 2019; 24:1-6. [PMID: 30614793 DOI: 10.3233/cbm-160559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Both QKI and TMEFF2 genes are considered putative tumor suppressor genes (TSGs). In gastric (GC) and colorectal (CRC) cancers, downregulation of their expressions is known to be frequent. However, QKI and TMEFF2 mutations that could potentially inactivate their functions are not reported in cancers. METHODS In a genome database, we observed that both QKI and TMEFF2 harbor mononucleotide repeats, which could be mutated in cancers with high microsatellite instability (MSI-H). For this, we studied 79 GCs and 124 CRCs for the mutations and their intratumoral heterogeneity (ITH). RESULTS Six of 34 GCs (17.6%) and 10 of 79 CRCs (12.7%) with MSI-H exhibited QKI frameshift mutations while five of 79 CRCs (6.3%) with high MSI (MSI-H) exhibited TMEFF2 frameshift mutations. However, we found no such mutation in microsatellite stable/low MSI (MSS/MSI-L) cancers within the mononucleotide repeats. We also studied ITH for the detected frameshift mutations in 16 cases of CRCs and detected that QKI and TMEFF2 frameshift mutations showed regional ITH in 2 (12.5%) and 1 (6.3%) cases, respectively. CONCLUSIONS Our data show that candidate TSG genes QKI and TMEFF2 harbor mutational ITH as well as the frameshift mutations in GC and CRC with MSI-H. From this observation, frameshift mutations of QKI and TMEFF2 may play a role in tumorigenesis through their TSG inactivation in GC and CRC.
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Affiliation(s)
- Ha Yoon Mo
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yun Sol Jo
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Nam Jin Yoo
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Min Sung Kim
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang Yong Song
- Department of Pathology and Translational Genomics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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10
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Lee SH, Kim JS, Zheng S, Huse JT, Bae JS, Lee JW, Yoo KH, Koo HH, Kyung S, Park WY, Sung KW. ARID1B alterations identify aggressive tumors in neuroblastoma. Oncotarget 2018; 8:45943-45950. [PMID: 28521285 PMCID: PMC5542239 DOI: 10.18632/oncotarget.17500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 04/11/2017] [Indexed: 12/01/2022] Open
Abstract
Targeted panel sequencing was performed to determine molecular targets and biomarkers in 72 children with neuroblastoma. Frequent genetic alterations were detected in ALK (16.7%), BRCA1 (13.9%), ATM (12.5%), and PTCH1 (11.1%) in an 83-gene panel. Molecular targets for targeted therapy were identified in 16 of 72 patients (22.2%). Two-thirds of ALK mutations were known to increase sensitivity to ALK inhibitors. Sequence alterations in ARID1B were identified in 5 of 72 patients (6.9%). Four of five ARID1B alterations were detected in tumors of high-risk patients. Two of five patients with ARID1B alterations died of disease progression. Relapse-free survival was lower in patients with ARID1B alterations than in those without (p = 0.01). In analysis confined to high-risk patients, 3-year overall survival was lower in patients with an ARID1B alteration (33.3 ± 27.2%) or MYCN amplification (30.0 ± 23.9%) than in those with neither ARID1B alteration nor MYCN amplification (90.5 ± 6.4%, p = 0.05). These results provide possibilities for targeted therapy and a new biomarker identifying a subgroup of neuroblastoma patients with poor prognosis.
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Affiliation(s)
- Soo Hyun Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.,Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jung-Sun Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Siyuan Zheng
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason T Huse
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joon Seol Bae
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sungkyu Kyung
- Department of Bioinformatics, Sungsil University, Seoul, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ki W Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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11
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Yang H, Peng Z, Liang M, Zhang Y, Wang Y, Huang T, Jiang Y, Jiang B, Wang Y. The miR-17-92 cluster/QKI2/β-catenin axis promotes osteosarcoma progression. Oncotarget 2018; 9:25285-25293. [PMID: 29861871 PMCID: PMC5982768 DOI: 10.18632/oncotarget.23935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
Quaking(QKI) is an RNA binding protein, and it has been shown to serve as a tumor suppressor. However, the expression and functions of QKI in osteosarcoma progression remain poorly understood. In this study, we aimed to explore the expression of QKI2 in osteosarcoma tissues and to determine the mechanisms underlying aberrant QKI2 expression and the effect of QKI2 on osteosarcoma progression. We found that QKI2 was significantly down-regulated in osteosarcoma tissues compared with adjacent normal bone tissues. Using a series of molecular biological techniques, we demonstrated that all members of the miR-17-92 cluster were up-regulated and contributed to the down-regulation of QKI2 expression in osteosarcoma. Functional examination showed that QKI2 inhibited the proliferation, migration and invasion of osteosarcoma cells via decreasing the expression of β-catenin. Conclusively, we revealed that the regulatory axis consisting of the miR-17-92 cluster/QKI2/β-catenin plays a crucial role in the development and progression of osteosarcoma.
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Affiliation(s)
- Hongbo Yang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhibin Peng
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Min Liang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yubo Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yangyang Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianwen Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yudong Jiang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bo Jiang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yansong Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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12
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Gimenez U, Perles-Barbacaru AT, Millet A, Appaix F, El-Atifi M, Pernet-Gallay K, van der Sanden B, Berger F, Lahrech H. Microscopic DTI accurately identifies early glioma cell migration: correlation with multimodal imaging in a new glioma stem cell model. NMR IN BIOMEDICINE 2016; 29:1553-1562. [PMID: 27717043 DOI: 10.1002/nbm.3608] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Monitoring glioma cell infiltration in the brain is critical for diagnosis and therapy. Using a new glioma Glio6 mouse model derived from human stem cells we show how diffusion tensor imaging (DTI) may predict glioma cell migration/invasion. In vivo multiparametric MRI was performed at one, two and three months of Glio6 glioma growth (Glio6 (n = 6), sham (n = 3)). This longitudinal study reveals the existence of a time window to study glioma cell/migration/invasion selectively. Indeed, at two months only Glio6 cell invasion was detected, while tumor mass formation, edema, blood-brain barrier leakage and tumor angiogenesis were detected later, at three months. To robustly confirm the potential of DTI for detecting glioma cell migration/invasion, a microscopic 3D-DTI (80 μm isotropic spatial resolution) technique was developed and applied to fixed mouse brains (Glio6 (n = 6), sham (n = 3)). DTI changes were predominant in the corpus callosum (CC), a known path of cell migration. Fractional anisotropy (FA) and perpendicular diffusivity (D⊥ ) changes derived from ex vivo microscopic 3D-DTI were significant at two months of tumor growth. In the caudate putamen an FA increase of +38% (p < 0.001) was observed, while in the CC a - 28% decrease in FA (p < 0.005) and a + 95% increase in D⊥ (p < 0.005) were observed. In the CC, DTI changes and fluorescent Glio6 cell density obtained by two-photon microscopy in the same brains were correlated (p < 0.001, r = 0.69), validating FA and D⊥ as early quantitative biomarkers to detect glioma cell migration/invasion. The origin of DTI changes was assessed by electron microscopy of the same tract, showing axon bundle disorganization. During the first two months, Glio6 cells display a migratory phenotype without being associated with the constitution of a brain tumor mass. This offers a unique opportunity to apply microscopic 3D-DTI and to validate DTI parameters FA and D⊥ as biomarkers for glioma cell invasion.
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Affiliation(s)
| | | | | | - Florence Appaix
- Grenoble Institut des Neurosciences Inserm U836, Grenoble, France
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Darbelli L, Richard S. Emerging functions of the Quaking RNA-binding proteins and link to human diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:399-412. [PMID: 26991871 DOI: 10.1002/wrna.1344] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/23/2016] [Accepted: 02/01/2016] [Indexed: 01/16/2023]
Abstract
RNA-binding proteins (RBPs) are essential players in RNA metabolism including key cellular processes from pre-mRNA splicing to mRNA translation. The K homology-type QUAKING RBP is emerging as a vital factor for oligodendrocytes, monocytes/macrophages, endothelial cell, and myocyte function. Interestingly, the qkI gene has now been identified as the culprit gene for a patient with intellectual disabilities and is translocated in a pediatric ganglioglioma as a fusion protein with MYB. In this review, we will focus on the emerging discoveries of the QKI proteins as well as highlight the recent advances in understanding the role of QKI in human disease pathology including myelin disorders, schizophrenia and cancer. WIREs RNA 2016, 7:399-412. doi: 10.1002/wrna.1344 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Lama Darbelli
- Terry Fox Molecular Oncology Group, Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, Canada, H3T 1E2
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group, Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, Canada, H3T 1E2
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14
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Radomska KJ, Sager J, Farnsworth B, Tellgren-Roth Å, Tuveri G, Peuckert C, Kettunen P, Jazin E, Emilsson LS. Characterization and Expression of the Zebrafish qki Paralogs. PLoS One 2016; 11:e0146155. [PMID: 26727370 PMCID: PMC4699748 DOI: 10.1371/journal.pone.0146155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 12/13/2015] [Indexed: 11/21/2022] Open
Abstract
Quaking (QKI) is an RNA-binding protein involved in post-transcriptional mRNA processing. This gene is found to be associated with several human neurological disorders. Early expression of QKI proteins in the developing mouse neuroepithelium, together with neural tube defects in Qk mouse mutants, suggest the functional requirement of Qk for the establishment of the nervous system. As a knockout of Qk is embryonic lethal in mice, other model systems like the zebrafish could serve as a tool to study the developmental functions of qki. In the present study we sought to characterize the evolutionary relationship and spatiotemporal expression of qkia, qki2, and qkib; zebrafish homologs of human QKI. We found that qkia is an ancestral paralog of the single tetrapod Qk gene that was likely lost during the fin-to-limb transition. Conversely, qkib and qki2 are orthologs, emerging at the root of the vertebrate and teleost lineage, respectively. Both qki2 and qkib, but not qkia, were expressed in the progenitor domains of the central nervous system, similar to expression of the single gene in mice. Despite having partially overlapping expression domains, each gene has a unique expression pattern, suggesting that these genes have undergone subfunctionalization following duplication. Therefore, we suggest the zebrafish could be used to study the separate functions of qki genes during embryonic development.
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Affiliation(s)
- Katarzyna J. Radomska
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jonathan Sager
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Bryn Farnsworth
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Åsa Tellgren-Roth
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Giulia Tuveri
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Christiane Peuckert
- Department of Neuroscience, Uppsala Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Petronella Kettunen
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Elena Jazin
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Lina S. Emilsson
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
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15
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Wang H, Pan JQ, Luo L, Ning XJ, Ye ZP, Yu Z, Li WS. NF-κB induces miR-148a to sustain TGF-β/Smad signaling activation in glioblastoma. Mol Cancer 2015; 14:2. [PMID: 25971746 PMCID: PMC4429406 DOI: 10.1186/1476-4598-14-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023] Open
Abstract
Background Inflammatory cytokines and transforming growth factor-β (TGF-β) are mutually inhibitory. However, hyperactivation of nuclear factor-κB (NF-κB) and TGF-β signaling both emerge in glioblastoma. Here, we report microRNA-148a (miR-148a) overexpression in glioblastoma and that miR-148a directly suppressed Quaking (QKI), a negative regulator of TGF-β signaling. Methods We determined NF-κB and TGF-β/Smad signaling activity using pNF-κB-luc, pSMAD-luc, and control plasmids. The association between an RNA-induced silencing complex and QKI, mitogen-inducible gene 6 (MIG6), S-phase kinase–associated protein 1 (SKP1), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA was tested with microribonucleoprotein immunoprecipitation and real-time PCR. Xenograft tumors were established in the brains of nude mice. Results QKI suppression induced an aggressive phenotype of glioblastoma cells both in vitro and in vivo. Interestingly, we found that NF-κB induced miR-148a expression, leading to enhanced-strength and prolonged-duration TGF-β/Smad signaling. Notably, these findings were consistent with the significant correlation between miR-148a levels with NF-κB hyperactivation and activated TGF-β/Smad signaling in a cohort of human glioblastoma specimens. Conclusions These findings uncover a plausible mechanism for NF-κB–sustained TGF-β/Smad activation via miR-148a in glioblastoma, and may suggest a new target for clinical intervention in human cancer. Electronic supplementary material The online version of this article (doi:10.1186/1476-4598-14-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Wang
- Department of Neurosurgery, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tian He Road, Tian He District, Guangzhou, Guangdong, 510630, China.
| | - Jian-Qing Pan
- Department of Neurosurgery, The Affiliated Shenzhen Nanshan Hospital, Guangdong Medical College, Shenzhen, 518052, China. .,Guangzhou Biocare Cancer Institute, Guangzhou, 510663, China.
| | - Lun Luo
- Department of Neurosurgery, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tian He Road, Tian He District, Guangzhou, Guangdong, 510630, China.
| | - Xin-Jie Ning
- Department of Neurosurgery, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tian He Road, Tian He District, Guangzhou, Guangdong, 510630, China.
| | - Zhuo-Peng Ye
- Department of Neurosurgery, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tian He Road, Tian He District, Guangzhou, Guangdong, 510630, China.
| | - Zhe Yu
- Guangzhou Biocare Cancer Institute, Guangzhou, 510663, China.
| | - Wen-Sheng Li
- Department of Neurosurgery, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tian He Road, Tian He District, Guangzhou, Guangdong, 510630, China.
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16
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Zhang X, Jia H, Lu Y, Dong C, Hou J, Wang Z, Wang F, Zhong H, Wang L, Wang K. Exome sequencing on malignant meningiomas identified mutations in neurofibromatosis type 2 (NF2) and meningioma 1 (MN1) genes. DISCOVERY MEDICINE 2014; 18:301-311. [PMID: 25549701 PMCID: PMC4720499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Meningiomas are tumors originating from the membranous layers surrounding the central nervous system, and are generally regarded as "benign" tumors of the brain. Malignant meningiomas are rare and are typically associated with a higher risk of local tumor recurrence and a poorer prognosis (median survival time <2 years). Previous genome-wide association studies and exome sequencing studies have identified genes that play a role in susceptibility to meningiomas, but these studies did not focus specifically on malignant tumors. METHODS We performed exome sequencing on five malignant meningiomas on the Illumina HiSeq2000 platform using Agilent SureSelect Human All Exon kits. We used wANNOVAR web server to annotate and prioritize variants, identified candidate genes with recurrent mutations, and validated selected mutations by Sanger sequencing. We next designed custom NimbleGen targeted region arrays on five candidate genes, and sequenced four additional malignant meningiomas. RESULTS From exome sequencing data, we identified several frequently mutated genes including NF2, MN1, ARID1B, SEMA4D, and MUC2, with private mutations in tumors. We sequenced these genes in four additional samples and identified potential driver mutations in NF2 (neurofibromatosis type 2) and MN1 (meningioma 1). CONCLUSIONS We confirmed that mutations in NF2 may play a role in progression of meningiomas, and nominated MN1 as a candidate gene for malignant transformation of meningiomas. Our sample size is limited by the extreme rarity of malignant meningiomas, but our study represents one of the first sequencing studies focusing on the malignant subtype.
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Affiliation(s)
- Xu Zhang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510641, China and BGI Diagnosis, Tianjin, Tianjin 300308, China
| | - Haiying Jia
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA and The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yao Lu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510641, China and BGI Tech Solutions, Shenzhen, Guangdong 518083, China
| | - Chengliang Dong
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jinghui Hou
- Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong 510632, China
| | - Zheng Wang
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Feng Wang
- BGI Tech Solutions, Shenzhen, Guangdong 518083, China
| | - Hongbin Zhong
- BGI Tech Solutions, Shenzhen, Guangdong 518083, China
| | - Lin Wang
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Kai Wang
- Zilkha Neurogenetic Institute and Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA
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17
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Vyazunova I, Maklakova VI, Berman S, De I, Steffen MD, Hong W, Lincoln H, Morrissy AS, Taylor MD, Akagi K, Brennan CW, Rodriguez FJ, Collier LS. Sleeping Beauty mouse models identify candidate genes involved in gliomagenesis. PLoS One 2014; 9:e113489. [PMID: 25423036 PMCID: PMC4244117 DOI: 10.1371/journal.pone.0113489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 10/27/2014] [Indexed: 01/01/2023] Open
Abstract
Genomic studies of human high-grade gliomas have discovered known and candidate tumor drivers. Studies in both cell culture and mouse models have complemented these approaches and have identified additional genes and processes important for gliomagenesis. Previously, we found that mobilization of Sleeping Beauty transposons in mice ubiquitously throughout the body from the Rosa26 locus led to gliomagenesis with low penetrance. Here we report the characterization of mice in which transposons are mobilized in the Glial Fibrillary Acidic Protein (GFAP) compartment. Glioma formation in these mice did not occur on an otherwise wild-type genetic background, but rare gliomas were observed when mobilization occurred in a p19Arf heterozygous background. Through cloning insertions from additional gliomas generated by transposon mobilization in the Rosa26 compartment, several candidate glioma genes were identified. Comparisons to genetic, epigenetic and mRNA expression data from human gliomas implicates several of these genes as tumor suppressor genes and oncogenes in human glioblastoma.
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Affiliation(s)
- Irina Vyazunova
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Vilena I. Maklakova
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Samuel Berman
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ishani De
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Megan D. Steffen
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Won Hong
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Hayley Lincoln
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - A. Sorana Morrissy
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Keiko Akagi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States of America
| | - Cameron W. Brennan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Fausto J. Rodriguez
- Department of Pathology, Division of Neuropathology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Lara S. Collier
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
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Pedersen SK, Mitchell SM, Graham LD, McEvoy A, Thomas ML, Baker RT, Ross JP, Xu ZZ, Ho T, LaPointe LC, Young GP, Molloy PL. CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia. Epigenetics 2014; 9:1071-82. [PMID: 24799664 PMCID: PMC4164492 DOI: 10.4161/epi.29046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The CAHM gene (Colorectal Adenocarcinoma HyperMethylated), previously LOC100526820, is located on chromosome 6, hg19 chr6:163 834 097–163 834 982. It lacks introns, encodes a long non-coding RNA (lncRNA) and is located adjacent to the gene QKI, which encodes an RNA binding protein. Deep bisulphite sequencing of ten colorectal cancer (CRC) and matched normal tissues demonstrated frequent hypermethylation within the CAHM gene in cancer. A quantitative methylation-specific PCR (qMSP) was used to characterize additional tissue samples. With a threshold of 5% methylation, the CAHM assay was positive in 2/26 normal colorectal tissues (8%), 17/21 adenomas (81%), and 56/79 CRC samples (71%). A reverse transcriptase-qPCR assay showed that CAHM RNA levels correlated negatively with CAHM % methylation, and therefore CAHM gene expression is typically decreased in CRC. The CAHM qMSP assay was applied to DNA isolated from plasma specimens from 220 colonoscopy-examined patients. Using a threshold of 3 pg methylated genomic DNA per mL plasma, methylated CAHM sequences were detected in the plasma DNA of 40/73 (55%) of CRC patients compared with 3/73 (4%) from subjects with adenomas and 5/74 (7%) from subjects without neoplasia. Both the frequency of detection and the amount of methylated CAHM DNA released into plasma increased with increasing cancer stage. Methylated CAHM DNA shows promise as a plasma biomarker for use in screening for CRC.
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Affiliation(s)
| | - Susan M Mitchell
- CSIRO Preventative Health Flagship; Animal, Food & Health Sciences Division; North Ryde, NSW Australia
| | - Lloyd D Graham
- CSIRO Preventative Health Flagship; Animal, Food & Health Sciences Division; North Ryde, NSW Australia
| | - Aidan McEvoy
- Clinical Genomics Pty Ltd; North Ryde, NSW Australia
| | | | - Rohan T Baker
- Clinical Genomics Pty Ltd; North Ryde, NSW Australia
| | - Jason P Ross
- CSIRO Preventative Health Flagship; Animal, Food & Health Sciences Division; North Ryde, NSW Australia
| | - Zheng-Zhou Xu
- CSIRO Preventative Health Flagship; Animal, Food & Health Sciences Division; North Ryde, NSW Australia
| | - Thu Ho
- CSIRO Preventative Health Flagship; Animal, Food & Health Sciences Division; North Ryde, NSW Australia
| | | | - Graeme P Young
- Flinders Centre for Innovation in Cancer; Flinders University (FMC); Adelaide, SA Australia
| | - Peter L Molloy
- CSIRO Preventative Health Flagship; Animal, Food & Health Sciences Division; North Ryde, NSW Australia
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19
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Riehmer V, Gietzelt J, Beyer U, Hentschel B, Westphal M, Schackert G, Sabel MC, Radlwimmer B, Pietsch T, Reifenberger G, Weller M, Weber RG, Loeffler M. Genomic profiling reveals distinctive molecular relapse patterns in IDH1/2 wild-type glioblastoma. Genes Chromosomes Cancer 2014; 53:589-605. [PMID: 24706357 DOI: 10.1002/gcc.22169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/12/2014] [Indexed: 12/28/2022] Open
Abstract
Molecular changes associated with the progression of glioblastoma after standard radiochemotherapy remain poorly understood. We compared genomic profiles of 27 paired primary and recurrent IDH1/2 wild-type glioblastomas by genome-wide array-based comparative genomic hybridization. By bioinformatic analysis, primary and recurrent tumor profiles were normalized and segmented, chromosomal gains and losses identified taking the tumor cell content into account, and difference profiles deduced. Seven of 27 (26%) pairs lacked DNA copy number differences between primary and recurrent tumors (equal pairs). The recurrent tumors in 9/27 (33%) pairs contained all chromosomal imbalances of the primary tumors plus additional ones, suggesting a sequential acquisition of and/or selection for aberrations during progression (sequential pairs). In 11/27 (41%) pairs, the profiles of primary and recurrent tumors were divergent, i.e., the recurrent tumors contained additional aberrations but had lost others, suggesting a polyclonal composition of the primary tumors and considerable clonal evolution (discrepant pairs). Losses on 9p21.3 harboring the CDKN2A/B locus were significantly more common in primary tumors from sequential and discrepant (nonequal) pairs. Nonequal pairs showed ten regions of recurrent genomic differences between primary and recurrent tumors harboring 46 candidate genes associated with tumor recurrence. In particular, copy numbers of genes encoding apoptosis regulators were frequently changed at progression. In summary, approximately 25% of IDH1/2 wild-type glioblastoma pairs have stable genomic imbalances. In contrast, approximately 75% of IDH1/2 wild-type glioblastomas undergo further genomic aberrations and alter their clonal composition upon recurrence impacting their genomic profile, a process possibly facilitated by 9p21.3 loss in the primary tumor. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Vera Riehmer
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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Zhao Y, Zhang G, Wei M, Lu X, Fu H, Feng F, Wang S, Lu W, Wu N, Lu Z, Yuan J. The tumor suppressing effects of QKI-5 in prostate cancer: a novel diagnostic and prognostic protein. Cancer Biol Ther 2013; 15:108-18. [PMID: 24153116 DOI: 10.4161/cbt.26722] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In recent years, the RNA-binding protein quaking 5 (QKI-5) has been recognized as a novel tumor suppressor in many cancers. To date, no studies have examined the role of QKI-5 in prostate cancer. The present study was designed to elucidate the correlation of QKI-5 expression with the clinical pathological features and prognosis of prostate cancer. In an overwhelming majority of the 184 cases of prostate cancer samples analyzed, the QKI-5 expression was significantly decreased, which was largely due to the high promoter methylation levels. Using lentiviral vectors, we established two stable prostate cancer cell lines with altered QKI-5 expression, including a QKI-5 overexpressing PC3 cell line and a DU145 cell line with knocked-down QKI-5 expression. The effects of the lentiviral-mediated QKI-5 knockdown on the PC3 cells and DU145 cells were assessed by cell growth curves, flow cytometry (FCM), and an invasion assay. The PC3 cells were transplanted into nude mice, and then, the tumor growth curves and TUNEL staining were determined. These results demonstrated that QKI-5 was highly expressed in benign prostatic hyperplasia (BPH) tissues but not in carcinomatous tissues and that QKI-5 effectively inhibited prostate cancer cell proliferation in vitro and in vivo. In addition, the decrease in QKI-5 expression was closely correlated with the prostate cancer Gleason score, poor differentiation, degree of invasion, lymph node metastasis, distant metastasis, TNM grading, and poor survival. These results indicate that the QKI-5 expression may be a novel, independent factor in the prognosis of prostate cancer patients.
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Affiliation(s)
- Yi Zhao
- Department of Urology; Xijing Hospital; Fourth Military Medical University; Xi'an, PR China; Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Gen Zhang
- Department of Urology; Xijing Hospital; Fourth Military Medical University; Xi'an, PR China
| | - Mengying Wei
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Xiaozhao Lu
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Hanyan Fu
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Feixue Feng
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Shan Wang
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Wei Lu
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Ning Wu
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Zifan Lu
- Department of Biochemistry and Molecular Biology; State Key Laboratory of Cancer Biology; Fourth Military Medical University; Xi'an, PR China
| | - Jianlin Yuan
- Department of Urology; Xijing Hospital; Fourth Military Medical University; Xi'an, PR China
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Diaz G, Melis M, Tice A, Kleiner DE, Mishra L, Zamboni F, Farci P. Identification of microRNAs specifically expressed in hepatitis C virus-associated hepatocellular carcinoma. Int J Cancer 2013; 133:816-24. [PMID: 23390000 PMCID: PMC3830961 DOI: 10.1002/ijc.28075] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/14/2013] [Indexed: 12/12/2022]
Abstract
Although several studies have investigated the association of miRNAs with hepatocellular carcinoma (HCC), the data published so far are not concordant. A reason for these discrepancies may be the fact that most studies used the nontumorous tissue surrounding the HCC lesion as a control, which is almost invariably affected by cirrhosis or chronic hepatitis, as well as other pathological conditions such as hepatitis B virus (HBV) or hepatitis C virus (HCV) infection. Moreover, HCC is often analyzed as a single group regardless of the different viral etiologies. The miRNAs differentially expressed in HCV-related HCC were investigated by comparing the tumorous tissues to a wide range of liver specimens, including healthy livers obtained from liver donors and patients who underwent liver resection for angioma, in addition to tissues from various acute and chronic liver diseases, including HCV-related cirrhosis not associated with HCC, HCV-related cirrhosis associated with HCC and HBV-associated acute liver failure. The whole set of 2,226 human miRNAs were examined, including 1,121 pre-miRNAs and 1,105 mature miRNAs, available in a microarray platform. Stringent statistical methods were applied to reduce the risk of false discoveries to less than 1%. These data identified 18 miRNAs exclusively expressed in HCV-associated HCC, characterized by high specificity and selectivity versus all other liver diseases and healthy conditions and connected into a regulatory network pivoting on p53, phosphatase and tensin homolog and all-trans retinoic acid signaling.
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Affiliation(s)
- Giacomo Diaz
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Marta Melis
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashley Tice
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David E. Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lopa Mishra
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fausto Zamboni
- Liver Transplantation Center, Brotzu Hospital, 09134 Cagliari, Italy
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Ji S, Ye G, Zhang J, Wang L, Wang T, Wang Z, Zhang T, Wang G, Guo Z, Luo Y, Cai J, Yang JY. miR-574-5p negatively regulates Qki6/7 to impact β-catenin/Wnt signalling and the development of colorectal cancer. Gut 2013; 62:716-26. [PMID: 22490519 PMCID: PMC3618686 DOI: 10.1136/gutjnl-2011-301083] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Deficiency or reduced expression of signal transduction and activation of RNA family protein Quaking (Qki) is associated with developmental defects in neural and vascular tissues and the development of debilitating human diseases including colorectal cancer (CRC). However, the mechanisms underlying the aberrant downregulation or deficiency of Qki were uncertain. DESIGN Expression of miR-574-5p, Qki5/6/7/7b splicing variants, β-catenin and p27(Kip1) was determined in mouse and human CRC cells and tissues to investigate the post-transcriptional regulation of Qki isoforms by miR-574-5p and its impact on β-catenin/p27(Kip1) signalling, cell cycle progression, proliferation, migration, invasion and tumour growth. RESULTS In the CRC tissues of C57BL/6-Apc(min/+) mice, miR-574-5p was found to be significantly upregulated and negatively correlated with the expression of Qki but positively correlated with the expression of β-catenin. In mouse and human CRC cells, miR-574-5p was shown to regulate Qki isoforms (Qki6/7 in particular) post-transcriptionally and caused altered expression in β-catenin and p27(Kip1) , increased proliferation, migration and invasion and decreased differentiation and cell cycle exit. Furthermore, in clinical CRC tissues, miR-574-5p was shown to be greatly upregulated and inversely correlated with the expression of Qkis. Finally, inhibition of miR-574-5p was shown to suppress the growth of tumours in the nude mice. CONCLUSIONS Together, these novel findings suggest that miR-574-5p is a potent ribo-regulator for Qkis and that aberrant miR-574-5p upregulation can be oncogenic.
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Affiliation(s)
- Shunlong Ji
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Gengtai Ye
- Department of Surgical Oncology the First Affiliated Hospital of Xiamen University and Xiamen Cancer Center, Xiamen, People's Republic of China
| | - Jun Zhang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Linpei Wang
- Department of Surgical Oncology the First Affiliated Hospital of Xiamen University and Xiamen Cancer Center, Xiamen, People's Republic of China
| | - Tao Wang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Zhen Wang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Tiantian Zhang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Guanghui Wang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Zongsheng Guo
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Yu Luo
- School of Nursing, the Third Military Medical University, Chongqing, People's Republic of China
| | - Jianchun Cai
- Department of Surgical Oncology the First Affiliated Hospital of Xiamen University and Xiamen Cancer Center, Xiamen, People's Republic of China
| | - James Y Yang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, People's Republic of China,Fujian Provincial Transgenic Core, Xiamen University Laboratory Animal Center, Xiamen, People's Republic of China
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Baronchelli S, Bentivegna A, Redaelli S, Riva G, Butta V, Paoletta L, Isimbaldi G, Miozzo M, Tabano S, Daga A, Marubbi D, Cattaneo M, Biunno I, Dalprà L. Delineating the cytogenomic and epigenomic landscapes of glioma stem cell lines. PLoS One 2013; 8:e57462. [PMID: 23468990 PMCID: PMC3585345 DOI: 10.1371/journal.pone.0057462] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/24/2013] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma multiforme (GBM), the most common and malignant type of glioma, is characterized by a poor prognosis and the lack of an effective treatment, which are due to a small sub-population of cells with stem-like properties, termed glioma stem cells (GSCs). The term "multiforme" describes the histological features of this tumor, that is, the cellular and morphological heterogeneity. At the molecular level multiple layers of alterations may reflect this heterogeneity providing together the driving force for tumor initiation and development. In order to decipher the common "signature" of the ancestral GSC population, we examined six already characterized GSC lines evaluating their cytogenomic and epigenomic profiles through a multilevel approach (conventional cytogenetic, FISH, aCGH, MeDIP-Chip and functional bioinformatic analysis). We found several canonical cytogenetic alterations associated with GBM and a common minimal deleted region (MDR) at 1p36.31, including CAMTA1 gene, a putative tumor suppressor gene, specific for the GSC population. Therefore, on one hand our data confirm a role of driver mutations for copy number alterations (CNAs) included in the GBM genomic-signature (gain of chromosome 7- EGFR gene, loss of chromosome 13- RB1 gene, loss of chromosome 10-PTEN gene); on the other, it is not obvious that the new identified CNAs are passenger mutations, as they may be necessary for tumor progression specific for the individual patient. Through our approach, we were able to demonstrate that not only individual genes into a pathway can be perturbed through multiple mechanisms and at different levels, but also that different combinations of perturbed genes can incapacitate functional modules within a cellular networks. Therefore, beyond the differences that can create apparent heterogeneity of alterations among GSC lines, there's a sort of selective force acting on them in order to converge towards the impairment of cell development and differentiation processes. This new overview could have a huge importance in therapy.
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Affiliation(s)
- Simona Baronchelli
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
- Science and Technology Park, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Angela Bentivegna
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Gabriele Riva
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Valentina Butta
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Laura Paoletta
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | | | - Monica Miozzo
- Department of Pathophysiology and Organ Transplant, University of Milan, Milan, Italy
- Pathology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia Tabano
- Department of Pathophysiology and Organ Transplant, University of Milan, Milan, Italy
- Pathology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Daga
- Department of Hematology-Oncology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria San Martino- Istituto Scientifico Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Daniela Marubbi
- Department of Hematology-Oncology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria San Martino- Istituto Scientifico Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Monica Cattaneo
- Science and Technology Park, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Ida Biunno
- Institute of Genetics and Biomedical Research-National Research Council, Milan, Italy
| | - Leda Dalprà
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
- Department of Surgical Pathology, S. Gerardo Hospital, Monza, Italy
- * E-mail:
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The QKI-5 and QKI-6 RNA binding proteins regulate the expression of microRNA 7 in glial cells. Mol Cell Biol 2013; 33:1233-43. [PMID: 23319046 DOI: 10.1128/mcb.01604-12] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The quaking (qkI) gene encodes 3 major alternatively spliced isoforms that contain unique sequences at their C termini dictating their cellular localization. QKI-5 is predominantly nuclear, whereas QKI-6 is distributed throughout the cell and QKI-7 is cytoplasmic. The QKI isoforms are sequence-specific RNA binding proteins expressed mainly in glial cells modulating RNA splicing, export, and stability. Herein, we identify a new role for the QKI proteins in the regulation of microRNA (miRNA) processing. We observed that small interfering RNA (siRNA)-mediated QKI depletion of U343 glioblastoma cells leads to a robust increase in miR-7 expression. The processing from primary to mature miR-7 was inhibited in the presence QKI-5 and QKI-6 but not QKI-7, suggesting that the nuclear localization plays an important role in the regulation of miR-7 expression. The primary miR-7-1 was bound by the QKI isoforms in a QKI response element (QRE)-specific manner. We observed that the pri-miR-7-1 RNA was tightly bound to Drosha in the presence of the QKI isoforms, and this association was not observed in siRNA-mediated QKI or Drosha-depleted U343 glioblastoma cells. Moreover, the presence of the QKI isoforms led to an increase presence of pri-miR-7 in nuclear foci, suggesting that pri-miR-7-1 is retained in the nucleus by the QKI isoforms. miR-7 is known to target the epidermal growth factor (EGF) receptor (EGFR) 3' untranslated region (3'-UTR), and indeed, QKI-deficient U343 cells had reduced EGFR expression and decreased ERK activation in response to EGF. Elevated levels of miR-7 are associated with cell cycle arrest, and it was observed that QKI-deficient U343 that harbor elevated levels of miR-7 exhibited defects in cell proliferation that were partially rescued by the addition of a miR-7 inhibitor. These findings suggest that the QKI isoforms regulate glial cell function and proliferation by regulating the processing of certain miRNAs.
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Abstract
Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing (16 cases), genome-wide rearrangement analyses (32 cases), and targeted analyses of specific genomic loci (40 cases) using massively parallel sequencing. On average each tumor had 19 somatic alterations in coding genes (range, 3–70). Among genes not previously known to be involved in neuroblastoma, chromosomal deletions and sequence alterations of chromatin remodeling genes, ARID1A and ARID1B, were identified in 8 of 71 tumors (11%) and were associated with early treatment failure and decreased survival. Using tumor-specific structural alterations, we developed an approach to identify rearranged DNA fragments in sera, providing personalized biomarkers for minimal residual disease detection and monitoring. These results highlight dysregulation of chromatin remodeling in pediatric tumorigenesis and provide new approaches for the management of neuroblastoma patients.
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Toma MI, Wuttig D, Kaiser S, Herr A, Weber T, Zastrow S, Koch R, Meinhardt M, Baretton GB, Wirth MP, Fuessel S. PARK2 and PACRG are commonly downregulated in clear-cell renal cell carcinoma and are associated with aggressive disease and poor clinical outcome. Genes Chromosomes Cancer 2012; 52:265-73. [PMID: 23125027 DOI: 10.1002/gcc.22026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/05/2012] [Indexed: 01/24/2023] Open
Abstract
PARK2 is an E3 ligase, known to be involved in ubiquitination of several proteins and to play a role in neuronal protection. The gene PARK2 and its potentially co-regulated gene PACRG have been previously found to be deleted in clear-cell renal cell carcinomas (ccRCCs). The aim of our study was to evaluate the mRNA and protein expression of PARK2 and PACRG in a large cohort of ccRCC, and to investigate their association with outcome. The expression of both genes was measured by quantitative PCR in 94 primary ccRCCs and autologous nonmalignant kidney tissues. PACRG and PARK2 protein expression was determined immunohistochemically using tissue microarrays comprising 133 ccRCCs. The mRNA and protein expression of PARK2 and PACRG was significantly downregulated in ccRCCs compared with nonmalignant tissues. Low levels of PARK2 mRNA were associated with high-grade ccRCC and lymph node metastasis. Patients with low PARK2 mRNA levels showed a higher tumor-specific mortality rate and a shorter overall survival (OS) than those with high PARK2 expression. Patients without PACRG mRNA expression in the tumor had a shorter disease-free survival and OS than those with tumors expressing PACRG. In multivariate analyses, neither PARK2 nor PACRG expression were independent prognostic factors. The protein expression of PARK2 and PACRG was significantly downregulated in ccRCCs (82.8, and 96.9%, respectively), but no association with clinical outcome was noticed.
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Affiliation(s)
- Marieta I Toma
- Institute of Pathology, University Hospital Carl Gustav Carus Tehnical University of Dresden, Germany.
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Bian Y, Wang L, Lu H, Yang G, Zhang Z, Fu H, Lu X, Wei M, Sun J, Zhao Q, Dong G, Lu Z. Downregulation of tumor suppressor QKI in gastric cancer and its implication in cancer prognosis. Biochem Biophys Res Commun 2012; 422:187-93. [PMID: 22569043 DOI: 10.1016/j.bbrc.2012.04.138] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 04/25/2012] [Indexed: 12/31/2022]
Abstract
Gastric cancer (GC) is the fourth most common cancer and second leading cause of cancer-related death worldwide. RNA-binding protein Quaking (QKI) is a newly identified tumor suppressor in multiple cancers, while its role in GC is largely unknown. Our study here aimed to clarify the relationship between QKI expression with the clinicopathologic characteristics and the prognosis of GC. In the 222 GC patients' specimens, QKI expression was found to be significantly decreased in most of the GC tissues, which was largely due to promoter hypermethylation. QKI overexpression reduced the proliferation ability of GC cell line in vitro study. In addition, the reduced QKI expression correlated well with poor differentiation status, depth of invasion, gastric lymph node metastasis, distant metastasis, advanced TNM stage, and poor survival. Multivariate analysis showed QKI expression was an independent prognostic factor for patient survival.
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Affiliation(s)
- Yongqian Bian
- The State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, Xi'an 710032, PR China
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Loss of p53 in quaking viable mice leads to Purkinje cell defects and reduced survival. Sci Rep 2011; 1:84. [PMID: 22355603 PMCID: PMC3239166 DOI: 10.1038/srep00084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 08/18/2011] [Indexed: 11/08/2022] Open
Abstract
The qk(v) mutation is a one megabase deletion resulting in abnormal expression of the qkI gene. qk(v) mice exhibit hypomyelination of the central nervous system and display rapid tremors and seizures as adults. The qkI locus on 6q26-27 has also been implicated as a candidate tumor suppressor gene as the qkI locus maps to a region of genetic instability in Glioblastoma Multiforme (GBM), an aggressive brain tumor of astrocytic lineage. As GBM frequently harbors mutations affecting p53, we crossbred qk(v) and p53 mutant mice to examine whether qk(v) mice on a p53(-/-) background have an increased incidence of GBM. qk(v) (/v); p53(-/-) mice had a reduced survival rate compared to p53(-/-) littermates, and the cause of death of the majority of the mice remains unknown. In addition, immunohistochemistry revealed Purkinje cell degeneration in the cerebellum. These results suggest that p53 and qkI are genetically linked for neuronal maintenance and survival.
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PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice. Proc Natl Acad Sci U S A 2010; 107:15145-50. [PMID: 20696900 DOI: 10.1073/pnas.1009941107] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In 100 primary colorectal carcinomas, we demonstrate by array comparative genomic hybridization (aCGH) that 33% show DNA copy number (DCN) loss involving PARK2, the gene encoding PARKIN, the E3 ubiquitin ligase whose deficiency is responsible for a form of autosomal recessive juvenile parkinsonism. PARK2 is located on chromosome 6 (at 6q25-27), a chromosome with one of the lowest overall frequencies of DNA copy number alterations recorded in colorectal cancers. The PARK2 deletions are mostly focal (31% approximately 0.5 Mb on average), heterozygous, and show maximum incidence in exons 3 and 4. As PARK2 lies within FRA6E, a large common fragile site, it has been argued that the observed DCN losses in PARK2 in cancer may represent merely the result of enforced replication of locally vulnerable DNA. However, we show that deficiency in expression of PARK2 is significantly associated with adenomatous polyposis coli (APC) deficiency in human colorectal cancer. Evidence of some PARK2 mutations and promoter hypermethylation is described. PARK2 overexpression inhibits cell proliferation in vitro. Moreover, interbreeding of Park2 heterozygous knockout mice with Apc(Min) mice resulted in a dramatic acceleration of intestinal adenoma development and increased polyp multiplicity. We conclude that PARK2 is a tumor suppressor gene whose haploinsufficiency cooperates with mutant APC in colorectal carcinogenesis.
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Yang G, Fu H, Zhang J, Lu X, Yu F, Jin L, Bai L, Huang B, Shen L, Feng Y, Yao L, Lu Z. RNA-binding protein quaking, a critical regulator of colon epithelial differentiation and a suppressor of colon cancer. Gastroenterology 2010; 138:231-40.e1-5. [PMID: 19686745 PMCID: PMC2847771 DOI: 10.1053/j.gastro.2009.08.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 06/20/2009] [Accepted: 08/06/2009] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Colon cancer is one of the best understood neoplasms from a genetic perspective, yet it remains the second most common cause of cancer-related death. Post-transcriptional regulation mediated by RNA-binding proteins or microRNAs coordinately targets multiple genes, holding promise involved in colon cancer initiation and development. Here we studied the role of RNA-binding protein quaking (QKI) in colon cancer. METHODS We observed the expression pattern of QKI in normal colon and colon cancers through reverse-transcription polymerase chain reaction and Western blot. Bisulfite sequencing and methylation-specific PCR were applied for QKI promoter methylation analysis. We used enterocyte differentiation markers and soft agar assay to test the role of QKI in colon differentiation and colon cancer development. 3' Untranslated region (UTR) reporter assay and RNA-immunoprecipitation were used to confirm the interaction between QKI and beta-catenin or p27. RESULTS QKI is significantly down-regulated and even absent in some colon cancers, which is at least partially because of the promoter hypermethylation. Forced expression of QKI in the colon cancer cells increased the expression of enterocyte differentiation marker intestinal alkaline phosphatase and lactase, together with the enhancement of p27Kip1 protein level, and membrane localized beta-catenin. Finally, QKI overexpression reduced the proliferation and tumorigenesis ability. CONCLUSIONS Our study establishes that QKI functions as a principal regulator in the differentiation of colon epithelium and a suppressor of carcinogenesis through coordinately targeting multiple genes associated with cell growth and differentiation, whose deregulation by methylation is involved in colon cancer onset and progress.
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Affiliation(s)
- Guodong Yang
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Haiyan Fu
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Jie Zhang
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Xiaozhao Lu
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Fang Yu
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Liang Jin
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Liyuan Bai
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Bo Huang
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Lan Shen
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University
| | - Yue Feng
- Department of Pharmacology, Emory University, Atlanta, GA, 30322
| | - Libo Yao
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University,To whom correspondence should be addressed: Z Lu, NO.17 Changlexi Road, the Fourth Military Medical University, 710032 Xi’an PR China, , tel: 86-29-84774513, fax 86-29-84773947. L Yao, NO.17 Changlexi Road, the Fourth Military Medical University, 710032 Xi’an PR China, , tel: 86-29-84774513, fax 86-29-84773947
| | - Zifan Lu
- Department of Biochemistry and Molecular Biology, the State Key Laboratory of Cancer Biology, the Fourth Military Medical University,To whom correspondence should be addressed: Z Lu, NO.17 Changlexi Road, the Fourth Military Medical University, 710032 Xi’an PR China, , tel: 86-29-84774513, fax 86-29-84773947. L Yao, NO.17 Changlexi Road, the Fourth Military Medical University, 710032 Xi’an PR China, , tel: 86-29-84774513, fax 86-29-84773947
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Thelander EF, Ichimura K, Corcoran M, Barbany G, Nordgren A, Heyman M, Berglund M, Mungall A, Rosenquist R, Collins VP, Grandér D, Larsson C, Lagercrantz S. Characterization of 6q deletions in mature B cell lymphomas and childhood acute lymphoblastic leukemia. Leuk Lymphoma 2009; 49:477-87. [DOI: 10.1080/10428190701817282] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Idbaih A, Crinière E, Ligon KL, Delattre O, Delattre JY. Array-based genomics in glioma research. Brain Pathol 2009; 20:28-38. [PMID: 19298630 DOI: 10.1111/j.1750-3639.2009.00274.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the years, several relevant biomarkers with a potential clinical interest have been identified in gliomas using various techniques, such as karyotype, microsatellite analysis, fluorescent in situ hybridization and chromosome comparative genomic hybridization. Despite their pivotal contribution to our understanding of gliomas biology, clinical application of these approaches has been limited by technological and clinical complexities. In contrast, genomic arrays (array-based comparative genomic hybridization and single nucleotide polymorphisms array) have emerged as promising technologies for clinical use in the setting of gliomas. Indeed, their feasibility and reliability have been rigorously assessed in gliomas and are discussed in this review. The well-known genomic biomarkers in gliomas are in fact readily and reliably identified using genomic arrays. Moreover, it detects a multitude of new cryptic genomic markers, with potential biological and/or clinical significances. The main studies dedicated to genomic characterization of gliomas using genomic arrays are reviewed here. Interestingly, several recurrent genomic signatures have been reported by different teams, suggesting the validity of these genomic patterns. In light of this, genomic arrays are relatively simple and cost-effective techniques whose implementation in molecular diagnostic laboratories should be encouraged as a valuable clinical tool for management of glioma patients.
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Chanudet E, Ye H, Ferry J, Bacon CM, Adam P, Müller-Hermelink HK, Radford J, Pileri SA, Ichimura K, Collins VP, Hamoudi RA, Nicholson AG, Wotherspoon AC, Isaacson PG, Du MQ. A20 deletion is associated with copy number gain at the TNFA/B/C locus and occurs preferentially in translocation-negative MALT lymphoma of the ocular adnexa and salivary glands. J Pathol 2009; 217:420-30. [PMID: 19006194 DOI: 10.1002/path.2466] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The genetic basis of MALT lymphoma is largely unknown. Characteristic chromosomal translocations are frequently associated with gastric and pulmonary cases, but are rare at other sites. We compared the genetic profiles of 33 ocular adnexal and 25 pulmonary MALT lymphomas by 1 Mb array-comparative genomic hybridization (CGH) and revealed recurrent 6q23 losses and 6p21.2-6p22.1 gains exclusive to ocular cases. High-resolution chromosome 6 tile-path array-CGH identified NF-kappaB inhibitor A20 as the target of 6q23.3 deletion and TNFA/B/C locus as a putative target of 6p21.2-22.1 gain. Interphase fluorescence in situ hybridization showed that A20 deletion occurred in MALT lymphoma of the ocular adnexa (8/42=19%), salivary gland (2/24=8%), thyroid (1/9=11%) and liver (1/2), but not in the lung (26), stomach (45) and skin (13). Homozygous deletion was observed in three cases. A20 deletion and TNFA/B/C gain were significantly associated (p<0.001) and exclusively found in cases without characteristic translocation. In ocular cases, A20 deletion was associated with concurrent involvement of different adnexal tissues or extraocular sites at diagnosis (p=0.007), a higher proportion of relapse (67% versus 37%) and a shorter relapse-free survival (p=0.033). A20 deletion and gain at TNFA/B/C locus may thus play an important role in the development of translocation-negative MALT lymphoma.
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Affiliation(s)
- E Chanudet
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, UK
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McCabe MG, Ichimura K, Pearson DM, Liu L, Clifford SC, Ellison DW, Collins VP. Novel mechanisms of gene disruption at the medulloblastoma isodicentric 17p11 breakpoint. Genes Chromosomes Cancer 2009; 48:121-31. [DOI: 10.1002/gcc.20625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Bockbrader K, Feng Y. Essential function, sophisticated regulation and pathological impact of the selective RNA-binding protein QKI in CNS myelin development. FUTURE NEUROLOGY 2008; 3:655-668. [PMID: 19727426 DOI: 10.2217/14796708.3.6.655] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The selective RNA-binding protein QKI play a key role in advancing oligodendrocyte-dependent myelination, which is essential for the function and development of the CNS. The emerging evidence that QKI abnormalities are associated with schizophrenia and may underlie myelin impairment in this devastating disease has greatly increased interest in understanding the function of QKI. Despite the discovery of the biochemical basis for QKI-RNA interaction, a comprehensive model is currently missing regarding how QKI regulates its mRNA ligands to promote normal myelinogenesis and how deficiency of the QKI pathway is involved in the pathogenesis of human diseases that affect CNS myelin. In this review, we will focus on the role of QKI in regulating distinct mRNA targets at critical developmental steps to promote oligodendrocyte differentiation and myelin formation. In addition, we will discuss molecular mechanisms that control QKI expression and activity during normal myelinogenesis as well as the pathological impact of QKI deficiency in dysmyelination mutant animals and in human myelin disorders.
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Affiliation(s)
- Katrina Bockbrader
- Department of Pharmacology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA, Tel.: +1 404 727 0351, ,
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Howarth KD, Blood KA, Ng BL, Beavis JC, Chua Y, Cooke SL, Raby S, Ichimura K, Collins VP, Carter NP, Edwards PAW. Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene 2008; 27:3345-59. [PMID: 18084325 PMCID: PMC2423006 DOI: 10.1038/sj.onc.1210993] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 11/13/2007] [Accepted: 11/15/2007] [Indexed: 12/21/2022]
Abstract
Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1 Mb resolution on bacterial artificial chromosome (BAC) arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2 kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1 Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Second, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300 and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer.
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Affiliation(s)
- KD Howarth
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - KA Blood
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - BL Ng
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - JC Beavis
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - Y Chua
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - SL Cooke
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - S Raby
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - K Ichimura
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231 Addenbrookes Hospital, Hills Road, Cambridge, U.K
| | - VP Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231 Addenbrookes Hospital, Hills Road, Cambridge, U.K
| | - NP Carter
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - PAW Edwards
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
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Monoranu CM, Huang B, Zangen ILV, Rutkowski S, Vince GH, Gerber NU, Puppe B, Roggendorf W. Correlation between 6q25.3 deletion status and survival in pediatric intracranial ependymomas. ACTA ACUST UNITED AC 2008; 182:18-26. [PMID: 18328946 DOI: 10.1016/j.cancergencyto.2007.12.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Revised: 11/29/2007] [Accepted: 12/10/2007] [Indexed: 02/08/2023]
Abstract
Losses and rearrangements of genetic material on chromosome 6q are frequently found in several human malignancies, including primary central nervous system tumors. We previously used microsatellite analysis of ependymomas to identify frequent deletions in regions 6q15 approximately q16, 6q21 approximately q22.1, and 6q24.3 approximately q25.3. To refine our preliminary analysis of potential prognostic regions, we used a panel of 25 microsatellite markers located between 6q15 and 6qter in 49 pairs of matched normal and tumor specimens from 28 children and 21 adults with ependymoma. Allelic deletions were detected in 34 of 49 patients (69%), and two common regions of deletions (6q24.3 and 6q25.2 approximately q25.3) were identified. A short segment of approximately 0.4 Mb between D6S1612 and D6S363 on 6q25.3, containing the SNX9 and SYNJ2 genes, exhibited the highest number of aberrations (n = 38). Pediatric tumors showed slightly fewer aberrations (64%) than adult tumors (76%) and also predominantly exhibited small interstitial deletions, in contrast to the extensive losses of genetic material in adults. Pediatric anaplastic intracranial (supra- and infratentorial) ependymomas harboring the 6q25.3 deletion (n = 9) showed significantly longer overall survival than did patients of the same group without the aberration (n = 6), independent of the extent of resection (P = 0.013). This supports the identified deletion on 6q25.3 as a candidate favorable prognostic parameter and warrants further investigation.
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Affiliation(s)
- Camelia-Maria Monoranu
- Department of Neuropathology, Institute of Pathology, Julius-Maximilian-University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany.
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40
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Kurian KM, Jones DTW, Marsden F, Openshaw SWS, Pearson DM, Ichimura K, Collins VP. Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases. Brain Pathol 2008; 18:469-73. [PMID: 18397339 PMCID: PMC2659379 DOI: 10.1111/j.1750-3639.2008.00148.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Subependymomas (SE) are slow-growing brain tumors that tend to occur within the ventricles of middle-aged and elderly adults. The World Health Organization classifies these tumors within the ependymoma group. Previous limited analysis of this tumor type had not revealed significant underlying cytogenetic abnormalities. We have used microarray comparative genomic hybridization to study a series of SE (n = 12). A whole-genome array at 0.97-Mb resolution showed copy number abnormalities in five of 12 cases (42%). Two cases (17%) showed regions of loss on chromosome 6. More detailed analysis of all cases using a chromosome 6 tile-path array confirmed the presence of overlapping regions of loss in only these two cases. One of these cases also showed trisomy chromosome 7. Monosomy of chromosome 8 was seen in a further two cases (17%), and a partial loss on chromosome 14 was observed in one additional case. This is the first array-based, genome-wide study of SE. The observation that five of 12 cases examined (42%) at 0.97-Mb resolution showed chromosomal copy number abnormalities is a novel finding in this tumor type.
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Affiliation(s)
- Kathreena M Kurian
- Department of Pathology, Division of Molecular Histopathology, Cambridge University, Cambridge, UK.
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41
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Wiedemeyer R, Brennan C, Heffernan TP, Xiao Y, Mahoney J, Protopopov A, Zheng H, Bignell G, Furnari F, Cavenee WK, Hahn WC, Ichimura K, Collins VP, Chu GC, Stratton MR, Ligon KL, Futreal PA, Chin L. Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development. Cancer Cell 2008; 13:355-64. [PMID: 18394558 PMCID: PMC2292238 DOI: 10.1016/j.ccr.2008.02.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 12/18/2007] [Accepted: 02/12/2008] [Indexed: 11/11/2022]
Abstract
We have developed a nonheuristic genome topography scan (GTS) algorithm to characterize the patterns of genomic alterations in human glioblastoma (GBM), identifying frequent p18(INK4C) and p16(INK4A) codeletion. Functional reconstitution of p18(INK4C) in GBM cells null for both p16(INK4A) and p18(INK4C) resulted in impaired cell-cycle progression and tumorigenic potential. Conversely, RNAi-mediated depletion of p18(INK4C) in p16(INK4A)-deficient primary astrocytes or established GBM cells enhanced tumorigenicity in vitro and in vivo. Furthermore, acute suppression of p16(INK4A) in primary astrocytes induced a concomitant increase in p18(INK4C). Together, these findings uncover a feedback regulatory circuit in the astrocytic lineage and demonstrate a bona fide tumor suppressor role for p18(INK4C) in human GBM wherein it functions cooperatively with other INK4 family members to constrain inappropriate proliferation.
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Affiliation(s)
- Ruprecht Wiedemeyer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Cameron Brennan
- Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Department of Neurosurgery, Weill-Cornell Medical College, New York, NY 10065, USA
- Corresponding author
| | - Timothy P. Heffernan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Yonghong Xiao
- Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - John Mahoney
- Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alexei Protopopov
- Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hongwu Zheng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Graham Bignell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Frank Furnari
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Webster K. Cavenee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Koichi Ichimura
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - V. Peter Collins
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Gerald C. Chu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
- Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Keith L. Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - P. Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lynda Chin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
- Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Corresponding author
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42
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Costa JL, Meijer G, Ylstra B, Caldas C. Array Comparative Genomic Hybridization Copy Number Profiling: A New Tool for Translational Research in Solid Malignancies. Semin Radiat Oncol 2008; 18:98-104. [DOI: 10.1016/j.semradonc.2007.10.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Ichimura K, Vogazianou AP, Liu L, Pearson DM, Bäcklund LM, Plant K, Baird K, Langford CF, Gregory SG, Collins VP. 1p36 is a preferential target of chromosome 1 deletions in astrocytic tumours and homozygously deleted in a subset of glioblastomas. Oncogene 2008; 27:2097-108. [PMID: 17934521 PMCID: PMC2650419 DOI: 10.1038/sj.onc.1210848] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 09/05/2007] [Accepted: 09/17/2007] [Indexed: 11/08/2022]
Abstract
Astrocytic, oligodendroglial and mixed gliomas are the commonest gliomas in adults. They have distinct phenotypes and clinical courses, but as they exist as a continuous histological spectrum, differentiating them can be difficult. Co-deletions of total 1p and 19q are found in the majority of oligodendrogliomas and considered as a diagnostic marker and a prognostic indicator. The 1p status of astrocytomas has not yet been thoroughly examined. Using a chromosome 1 tile path array, we investigated 108 adult astrocytic tumours for copy number alterations. Total 1p deletions were rare (2%), however partial deletions involving 1p36 were frequently identified in anaplastic astrocytomas (22%) and glioblastomas (34%). Multivariate analysis showed that patients with total 1p deletions had significantly longer survival (P=0.005). In nine glioblastomas homozygous deletions at 1p36 were identified. No somatic mutations were found among the five genes located in the homozygously deleted region. However, the CpG island of TNFRSF9 was hypermethylated in 19% of astrocytic tumours and 87% of glioma cell lines. TNFRSF9 expression was upregulated after demethylation of glioma cell lines. Akt3 amplifications were found in four glioblastomas. Our results indicate that 1p deletions are common anaplastic astrocytomas and glioblastomas but are distinct from the 1p abnormalities in oligodendrogliomas.
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Affiliation(s)
- K Ichimura
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge, UK.
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44
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Idbaih A, Marie Y, Lucchesi C, Pierron G, Manié E, Raynal V, Mosseri V, Hoang-Xuan K, Kujas M, Brito I, Mokhtari K, Sanson M, Barillot E, Aurias A, Delattre JY, Delattre O. BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int J Cancer 2008; 122:1778-86. [PMID: 18076069 DOI: 10.1002/ijc.23270] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathological classification of gliomas constitutes a critical step of the clinical management of patients, yet it is frequently challenging. To assess the relationship between genetic abnormalities and clinicopathological characteristics, we have performed a genetic and clinical analysis of a series of gliomas. A total of 112 gliomas were analyzed by comparative genomic hybridization on a BAC array with a 1 megabase resolution. Altered regions were identified and correlation analysis enabled to retrieve significant associations and exclusions. Whole chromosomes (chrs) 1p and 19q losses with centromeric breakpoints and EGFR high level amplification were found to be mutually exclusive, permitting identification of 3 distinct, nonoverlapping groups of tumors with striking clinicopathological differences. Type A tumors with chrs 1p and 19q co-deletion exhibited an oligodendroglial phenotype and a longer patient survival. Type B tumors were characterized by EGFR amplification. They harbored a WHO high grade of malignancy and a short patient survival. Finally, type C tumors displayed none of the previous patterns but the presence of chr 7 gain, chr 9p deletion and/or chr 10 loss. It included astrocytic tumors in patients younger than in type B and whose prognosis was highly dependent upon the number of alterations. A multivariate analysis based on a Cox model shows that age, WHO grade and genomic type provide complementary prognostic informations. Finally, our results highlight the potential of a whole-genome analysis as an additional diagnostic in cases of unclear conventional genetic findings.
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45
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Chénard CA, Richard S. New implications for the QUAKING RNA binding protein in human disease. J Neurosci Res 2008; 86:233-42. [PMID: 17787018 DOI: 10.1002/jnr.21485] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The use of spontaneously occurring mouse models has proved to be a valuable tool throughout the years to delineate the signals required for nervous system development. This is especially true in the field of myelin biology, with a large number of different models available. The quaking viable mouse models dysmyelination in the nervous system and links the QUAKING RNA binding proteins to myelination and cell fate decisions. In this Mini-Review, we highlight the biological functions attributed to this KH-type RNA binding protein and the recent achievements linking it to human disorders.
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Affiliation(s)
- Carol Anne Chénard
- Terry Fox Molecular Oncology Group, Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Department of Oncology, McGill University, Montréal, Québec, Canada
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46
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Abstract
Genetic alterations are a key feature of cancer cells and typically target biological processes and pathways that contribute to cancer pathogenesis. Array-based comparative genomic hybridization (aCGH) has provided a wealth of new information on copy number changes in cancer on a genome-wide level and aCGH data have also been utilized in cancer classification. More importantly, aCGH analyses have allowed highly accurate localization of specific genetic alterations that, for example, are associated with tumor progression, therapy response, or patient outcome. The genes involved in these aberrations are likely to contribute to cancer pathogenesis, and the high-resolution mapping by aCGH greatly facilitates the subsequent identification of these cancer-associated genes.
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Affiliation(s)
- Anne Kallioniemi
- Laboratory of Cancer Genetics, Tampere University Hospital and Institute of Medical Technology, University of Tampere, Biokatu 6, Tampere FI-33014, Finland.
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47
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Michels E, De Preter K, Van Roy N, Speleman F. Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genet Med 2007; 9:574-84. [PMID: 17873645 DOI: 10.1097/gim.0b013e318145b25b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Over the past few years, various reliable platforms for high-resolution detection of DNA copy number changes have become widely available. Together with optimized protocols for labeling and hybridization and algorithms for data analysis and representation, this has lead to a rapid increase in the application of this technology in the study of copy number variation in the human genome in normal cells and copy number imbalances in genetic diseases, including cancer. In this review, we briefly discuss specific technical issues relevant for array comparative genomic hybridization analysis in cancer tissues. We specifically focus on recent successes of array comparative genomic hybridization technology in the progress of our understanding of oncogenesis in a variety of cancer types. A third section highlights the potential of sensitive genome-wide detection of patterns of DNA imbalances or molecular portraits for class discovery and therapeutic stratification.
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Affiliation(s)
- Evi Michels
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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48
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Fiegler H, Redon R, Carter NP. Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes. Nat Protoc 2007; 2:577-87. [PMID: 17406619 PMCID: PMC2688820 DOI: 10.1038/nprot.2007.53] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microarray-based comparative genomic hybridization has become a widespread method for the analysis of DNA copy number changes across the human genome. Initial methods for microarray construction using large-insert clones required the preparation of DNA from large-scale cultures. This rapidly became an expensive and time-consuming process when expanded to the number of clones needed for higher resolution arrays. To overcome this problem, several PCR-based strategies have been developed to enable array construction from small amounts of cloned DNA. Here, we describe the construction of microarrays composed of human-specific large-insert clones (40-200 kb) using a specific degenerate oligonucleotide PCR strategy. In addition, we also describe array hybridization using manual and automated procedures and methods for array analysis. The technology and protocols described in this article can easily be adapted for other species dependent on the availability of clone libraries. According to our protocols, the procedure will take approximately 3 days from labeling the DNA to scanning the hybridized slides.
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Affiliation(s)
- Heike Fiegler
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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49
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Jones DTW, Ichimura K, Liu L, Pearson DM, Plant K, Collins VP. Genomic analysis of pilocytic astrocytomas at 0.97 Mb resolution shows an increasing tendency toward chromosomal copy number change with age. J Neuropathol Exp Neurol 2006; 65:1049-58. [PMID: 17086101 PMCID: PMC2761618 DOI: 10.1097/01.jnen.0000240465.33628.87] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Brain tumors are the most common solid tumors of childhood, accounting for over 20% of cancers in children under 15 years of age. Pilocytic astrocytomas (PAs), World Health Organization grade I, are one of the most frequently occurring childhood brain tumors, yet little is known about genetic changes characterizing this entity. We have used microarray comparative genomic hybridization at 0.97 Mb resolution to study a series of PAs (n = 44). No copy number abnormality was seen in 64% of cases at this resolution. However, whole chromosomal gain (median 5 chromosomes affected) occurred in 32% of tumors. The most frequently affected chromosomes were 5 and 7 (11 of 44 cases each) followed by 6, 11, 15, and 20 (greater than 10% of cases each). Findings were confirmed by fluorescence in situ hybridization and microsatellite analysis in a subset of tumors. Chromosomal gain was significantly more frequent in PAs from patients over 15 years old (p = 0.03, Fisher exact test). The number of chromosomes involved was also significantly greater in the older group (p = 0.02, Mann-Whitney U test). One case (2%) showed a region of gain on chromosome 3 and one (2%) a deletion on 6q as their sole abnormalities. This is the first genomewide study to show this nonrandom pattern of genetic alteration in pilocytic astrocytomas.
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Affiliation(s)
- David T W Jones
- Department of Pathology, Division of Molecular Histopathology, Cambridge University, Cambridge, UK.
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50
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Johnson N, Hamoudi R, Ichimura K, Liu L, Pearson D, Collins VP, Du MQ. Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. J Transl Med 2006; 86:968-78. [PMID: 16751780 PMCID: PMC2815849 DOI: 10.1038/labinvest.3700441] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Array-based comparative genomic hybridisation (aCGH) has diverse applications in cancer gene discovery and translational research. Currently, aCGH is performed primarily using high molecular weight DNA samples and its application to formalin-fixed and paraffin-embedded (FFPE) tissues remains to be established. To explore how aCGH can be reliably applied to archival FFPE tissues and whether it is possible to apply aCGH to small numbers of cells microdissected from FFPE tissue sections, we have systematically performed aCGH on 15 pairs of matched frozen and FFPE astrocytic tumour tissues using a well-established in-house human 1 Mb BAC/PAC genomic array. By spiking tumour DNA with normal DNA, we demonstrated that at least 70% of tumour DNA was required for reliable aCGH analysis. Using aCGH data from frozen tissue as a reference, it was found that only FFPE astrocytic tumour tissues that supported PCR amplification of >300 bp DNA fragment provided high quality, reproducible aCGH data. The presence of necrosis in a tissue specimen had an adverse effect on the quality of aCGH, while fixation in formalin for up to 96 h of fresh tissue did not appear to affect the quality of the result. As little as 10-20 ng DNA from frozen or FFPE tissues could be readily used for aCGH analysis following whole genome amplification (WGA). Furthermore, as few as 2000 microdissected cells from haematoxylin-stained slides of archival FFPE tissues could be successfully used for aCGH investigations when WGA was used. By careful assessment of DNA integrity and review of histology, to exclude necrosis and select specimens with a high proportion of tumour cells, it is feasible to preselect archival FFPE tissues adequate for aCGH analysis. With the help of microdissection and WGA, it is also possible to apply aCGH to histologically defined lesions, such as carcinoma in situ.
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Affiliation(s)
| | | | | | | | | | | | - Ming-Qing Du
- Correspondence author: Ming-Qing Du, Professor of Oncological Pathology, Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231, Level 3 Lab Block, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ, United Kingdom, Tel: 01223 767092, Fax: 01223 586670,
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