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Kim J, Ekstrom T, Yang W, Donahue G, Grygoryev D, Ngo TT, Muschler JL, Morgan T, Zaret KS. Longitudinal Analysis of Human Pancreatic Adenocarcinoma Development Reveals Transient Gene Expression Signatures. Mol Cancer Res 2021; 19:1854-1867. [PMID: 34330844 PMCID: PMC9398181 DOI: 10.1158/1541-7786.mcr-21-0483] [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: 06/22/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 01/07/2023]
Abstract
Previous transcriptome studies of human pancreatic ductal adenocarcinoma (PDAC) compare non-cancerous pancreatic intraepithelial neoplasias (PanIN) with late-stage PDAC obtained from different patients, thus have limited ability to discern network dynamics that contribute to the disease progression. We demonstrated previously that the 10-22 cell line, an induced pluripotent stem cell-like line reprogrammed from late-stage human PDAC cells, recapitulated the progression from PanINs to PDAC upon transplantation into NOD/LtSz-scid/IL2R-gammanull mice. Herein, we investigated the transition from precursor to PDAC using the isogenic model. We analyzed transcriptomes of genetically tagged 10-22 cells progressing from PanINs to PDAC in mice and validated the results using The Cancer Genome Atlas PDAC dataset, human clinical PanIN and PDAC tissues, and a well-established murine PDAC model. We functionally studied candidate proteins using human normal (H6C7) and cancerous (Miapaca2, Aspc1) pancreatic ductal epithelial cell lines. 10-22 cell-derived PDAC displayed the molecular signature of clinical human PDAC. Expression changes of many genes were transient during PDAC progression. Pathways for extracellular vesicle transport and neuronal cell differentiation were derepressed in the progression of PanINs to PDAC. HMG-box transcription factor 1 (HBP1) and BTB domain and CNC homolog 1 (BACH1) were implicated in regulating dynamically expressed genes during PDAC progression, and their expressions inversely correlated with PDAC patients' prognosis. Ectopic expression of HBP1 increased proliferation and migration of normal and cancerous pancreatic cells, indicating that HBP1 may confer the cell dissemination capacity in early PDAC progression. This unique longitudinal analysis provides insights into networks underlying human PDAC progression and pathogenesis. IMPLICATIONS: Manipulation of HBP1, BACH1, and RUN3 networks during PDAC progression can be harnessed to develop new targets for treating PDAC.
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Affiliation(s)
- Jungsun Kim
- Department of Molecular and Medical Genetics, Oregon Health & Science University School of Medicine, Portland, Oregon.,Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University School of Medicine, Portland, Oregon.,Knight Cancer Institute (Cancer Biology Research Program), Oregon Health & Science University School of Medicine, Portland, Oregon.,Corresponding Author: Jungsun Kim, Department of Molecular & Medical Genetics, Cancer Early Detection Advanced Research Center, Knight Cancer Institute. Oregon Health & Science University, Portland, OR 97239. Phone: 503-346-1967; E-mail:
| | - Taelor Ekstrom
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University School of Medicine, Portland, Oregon
| | - Wenli Yang
- Department of Medicine, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Greg Donahue
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Abramson Cancer Center (Tumor Biology Program), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Dmytro Grygoryev
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University School of Medicine, Portland, Oregon
| | - Thuy T.M. Ngo
- Department of Molecular and Medical Genetics, Oregon Health & Science University School of Medicine, Portland, Oregon.,Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University School of Medicine, Portland, Oregon.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - John L. Muschler
- Knight Cancer Institute (Cancer Biology Research Program), Oregon Health & Science University School of Medicine, Portland, Oregon.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Terry Morgan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University School of Medicine, Portland, Oregon.,Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Abramson Cancer Center (Tumor Biology Program), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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2
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Li M, Jin X, Li H, Yang C, Deng S, Wu G. Comprehensive Analysis of Key Genes and Regulatory Elements in Osteosarcoma Affected by Bone Matrix Mineral With Prognostic Values. Front Genet 2020; 11:533. [PMID: 32582282 PMCID: PMC7283541 DOI: 10.3389/fgene.2020.00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/04/2020] [Indexed: 01/04/2023] Open
Abstract
Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, genes involved in the mineral metabolism in the microenvironment of the bone affected by osteosarcoma are, to date, largely unknown. A public data series (GSE114237) was used to identify differentially expressed genes (DEGs) between osteosarcoma cells adhering to demineralized osseous surfaces and mineralized osseous surfaces. Functional enrichment analysis of DEGs and hub genes, protein-protein interaction network of DEGs and regulatory network (miRNA-mRNA network and transcription factor (TF)-mRNA network), survival analysis of hub genes was visualized. The prognostic hub genes were considered as candidate genes and their functional predictions were analyzed. A total of 207 DEGs were mainly enriched in extracellular space and thirteen hub genes were mainly enriched in the function of epithelial to mesenchymal transition. However, out of these, only one candidate gene was found to be suitable as a candidate gene. Besides that, 297 miRNAs and 349 TFs interacting with the hub genes were screened. In conclusion, the DEGs, hub genes, miRNAs and TFs screened out in this research could contribute to comprehend the latent mechanisms in osteosarcoma affected by matrix mineral and provide potential research molecular for further study.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Jin
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Caihong Yang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sisi Deng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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3
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MicroRNA 27a Is a Key Modulator of Cholesterol Biosynthesis. Mol Cell Biol 2020; 40:MCB.00470-19. [PMID: 32071155 DOI: 10.1128/mcb.00470-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/10/2020] [Indexed: 12/25/2022] Open
Abstract
Hypercholesterolemia is a strong predictor of cardiovascular diseases. The 3-hydroxy-3-methylglutaryl coenzyme A reductase gene (Hmgcr) coding for the rate-limiting enzyme in the cholesterol biosynthesis pathway is a crucial regulator of plasma cholesterol levels. However, the posttranscriptional regulation of Hmgcr remains poorly understood. The main objective of this study was to explore the role of microRNAs (miRNAs) in the regulation of Hmgcr expression. Systematic in silico predictions and experimental analyses reveal that miRNA 27a (miR-27a) specifically interacts with the Hmgcr 3' untranslated region in murine and human hepatocytes. Moreover, our data show that Hmgcr expression is inversely correlated with miR-27a levels in various cultured cell lines and in human and rodent tissues. Actinomycin D chase assays and relevant experiments demonstrate that miR-27a regulates Hmgcr by translational attenuation followed by mRNA degradation. Early growth response 1 (Egr1) regulates miR-27a expression under basal and cholesterol-modulated conditions. miR-27a augmentation via tail vein injection of miR-27a mimic in high-cholesterol-diet-fed Apoe -/- mice shows downregulation of hepatic Hmgcr and plasma cholesterol levels. Pathway and gene expression analyses show that miR-27a also targets several other genes (apart from Hmgcr) in the cholesterol biosynthesis pathway. Taken together, miR-27a emerges as a key regulator of cholesterol biosynthesis and has therapeutic potential for the clinical management of hypercholesterolemia.
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Li M, Jin X, Li H, Wu G, Wang S, Yang C, Deng S. Key genes with prognostic values in suppression of osteosarcoma metastasis using comprehensive analysis. BMC Cancer 2020; 20:65. [PMID: 31992246 PMCID: PMC6988291 DOI: 10.1186/s12885-020-6542-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/14/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Osteosarcoma is a primary malignant tumor originating from mesenchymal tissue, with a poor distant metastasis prognosis. The molecular mechanisms of osteosarcoma metastasis are extremely complicated. METHODS A public data series (GSE21257) was used to identify differentially expressed genes (DEGs) in osteosarcoma patients that did, or did not, develop metastases. Functional enrichment analysis, a protein-protein interaction network, and survival analysis of DEGs were performed. DEGs with a prognostic value were considered as candidate genes and their functional predictions, different expression in normal and malignant tissues, and immune infiltration were analyzed. RESULTS The DEGs were mainly enriched in the immune response. Three candidate genes (ALOX5AP, CD74, and FCGR2A) were found, all of which were expressed at higher levels in lungs and lymph nodes than in matched cancer tissues and were probably expressed in the microenvironment. CONCLUSIONS Candidate genes can help us understand the molecular mechanisms underlying osteosarcoma metastasis and provide targets for future research.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Jin
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hao Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shanshan Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Caihong Yang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Sisi Deng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Li S, Geng Q, Chen H, Zhang J, Cao C, Zhang F, Song J, Liu C, Liang W. The potential inhibitory effects of miR‑19b on vulnerable plaque formation via the suppression of STAT3 transcriptional activity. Int J Mol Med 2017; 41:859-867. [PMID: 29207010 PMCID: PMC5752162 DOI: 10.3892/ijmm.2017.3263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/06/2017] [Indexed: 02/01/2023] Open
Abstract
Atherosclerotic plaque growth requires angiogenesis, and acute coronary syndrome (ACS) is usually triggered by the rupture of unstable atherosclerotic plaques. Previous studies have identified typically circulating microRNA (miRNA/miR) profiles in patients with ACS. miRNAs serve important roles in the pathophysiology of atherosclerotic plaque progression. The present study aimed to investigate the potential role and mechanism of miR‑19b in plaque stability. miRNA array data indicated that 28 miRNAs were differentially expressed in the plasma of patients with unstable angina (UA; n=12) compared with in control individuals (n=12), and miR‑19b exhibited the most marked upregulation. Circulating miR‑19b levels were further validated in another independent cohort, which consisted of 34 patients with UA and 24 controls, by quantitative polymerase chain reaction. Gene Ontology annotations of the predicted target genes of miR‑19b suggested that miR‑19b may be involved in endothelial cell (EC) proliferation, migration and angiogenesis, which was confirmed by Cell Counting kit‑8, wound healing and tube formation assays in the present study. Finally, the present study indicated that miR‑19b may suppress signal transducer and activator of transcription 3 (STAT3) tyrosine phosphorylation and transcriptional activity in ECs, as determined by western blot analysis and luciferase reporter assay. In conclusion, the present study revealed that increased miR‑19b expression may delay unstable plaque progression in patients with UA by inhibiting EC proliferation, migration and angiogenesis via the suppression of STAT3 transcriptional activity.
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Affiliation(s)
- Sufang Li
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Qiang Geng
- Department of Cardiology, Qingdao Municipal Hospital, Qingdao, Shandong 266011, P.R. China
| | - Hong Chen
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Jing Zhang
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Chengfu Cao
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Feng Zhang
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Junxian Song
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Chuanfen Liu
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Wenqing Liang
- Department of Cardiology, Peking University People's Hospital, Beijing 100044, P.R. China
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Wang CY, Li CY, Hsu HP, Cho CY, Yen MC, Weng TY, Chen WC, Hung YH, Lee KT, Hung JH, Chen YL, Lai MD. PSMB5 plays a dual role in cancer development and immunosuppression. Am J Cancer Res 2017; 7:2103-2120. [PMID: 29218236 PMCID: PMC5714741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023] Open
Abstract
Tumor progression and metastasis are dependent on the intrinsic properties of tumor cells and the influence of microenvironment including the immune system. It would be important to identify target drug that can inhibit cancer cell and activate immune cells. Proteasome β subunits (PSMB) family, one component of the ubiquitin-proteasome system, has been demonstrated to play an important role in tumor cells and immune cells. Therefore, we used a bioinformatics approach to examine the potential role of PSMB family. Analysis of breast TCGA and METABRIC database revealed that high expression of PSMB5 was observed in breast cancer tissue and that high expression of PSMB5 predicted worse survival. In addition, high expression of PSMB5 was observed in M2 macrophages. Based on our bioinformatics analysis, we hypothesized that PSMB5 contained immunosuppressive and oncogenic characteristics. To study the effects of PSMB5 on the cancer cell and macrophage in vitro, we silenced PSMB5 expression with shRNA in THP-1 monocytes and MDA-MB-231 cells respectively. Knockdown of PSMB5 promoted human THP-1 monocyte differentiation into M1 macrophage. On the other hand, knockdown PSMB5 gene expression inhibited MDA-MB-231 cell growth and migration by colony formation assay and boyden chamber. Collectively, our data demonstrated that delivery of PSMB5 shRNA suppressed cell growth and activated defensive M1 macrophages in vitro. Furthermore, lentiviral delivery of PSMB5 shRNA significantly decreased tumor growth in a subcutaneous mouse model. In conclusion, our bioinformatics study and functional experiments revealed that PSMB5 served as novel cancer therapeutic targets. These results also demonstrated a novel translational approach to improve cancer immunotherapy.
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Affiliation(s)
- Chih-Yang Wang
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
- Institute of Basic Medical Sciences, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Chung-Yen Li
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Hui-Ping Hsu
- Department of Surgery, College of Medicine, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Chien-Yu Cho
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
- Institute of Basic Medical Sciences, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiung, Taiwan, R.O.C
| | - Tzu-Yang Weng
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
- Institute of Basic Medical Sciences, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Wei-Ching Chen
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
- Institute of Basic Medical Sciences, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Yu-Hsuan Hung
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
- Institute of Basic Medical Sciences, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Kuo-Ting Lee
- Department of Surgery, College of Medicine, National Cheng Kung UniversityTainan, Taiwan, R.O.C
| | - Jui-Hsiang Hung
- Department of Biotechnology, Chia Nan University of Pharmacy and ScienceTainan, Taiwan, R.O.C
| | - Yi-Ling Chen
- Department of Senior Citizen Service Management, Chia Nan University of Pharmacy and ScienceTainan, Taiwan, R.O.C
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, National Cheng Kung UniversityTainan, Taiwan, R.O.C
- Institute of Basic Medical Sciences, National Cheng Kung UniversityTainan, Taiwan, R.O.C
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Quayle AP, Siddiqui AS, Jones SJM. Perturbation of Interaction Networks for Application to Cancer Therapy. Cancer Inform 2017. [DOI: 10.1177/117693510700500005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a computational approach for studying the effect of potential drug combinations on the protein networks associated with tumor cells. The majority of therapeutics are designed to target single proteins, yet most diseased states are characterized by a combination of many interacting genes and proteins. Using the topology of protein-protein interaction networks, our methods can explicitly model the possible synergistic effect of targeting multiple proteins using drug combinations in different cancer types. The methodology can be conceptually split into two distinct stages. Firstly, we integrate protein interaction and gene expression data to develop network representations of different tissue types and cancer types. Secondly, we model network perturbations to search for target combinations which cause significant damage to a relevant cancer network but only minimal damage to an equivalent normal network. We have developed sets of predicted target and drug combinations for multiple cancer types, which are validated using known cancer and drug associations, and are currently in experimental testing for prostate cancer. Our methods also revealed significant bias in curated interaction data sources towards targets with associations compared with high-throughput data sources from model organisms. The approach developed can potentially be applied to many other diseased cell types.
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Increased epoxyeicosatrienoic acids and reduced soluble epoxide hydrolase expression in the preeclamptic placenta. J Hypertens 2017; 34:1364-70. [PMID: 27115337 DOI: 10.1097/hjh.0000000000000942] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Epoxyeicosatrienoic acids (EETs) derived from cytochrome P450 (CYP)-dependent metabolism of arachidonic acid are increased in the plasma of women with preeclampsia as compared with normal pregnancy and are significantly higher in fetal than in maternal plasma and erythrocytes. We hypothesized that differences in EET synthesis or metabolism in the feto-placental unit contributed to the observed differences in circulating EETs. METHOD To evaluate EETs, formation as well as the expression of relevant CYP isoforms and the metabolizing enzyme, soluble epoxide hydrolase (sEH), biopsies of placenta were collected from 19 normal pregnancy and 10 preeclampsia at the time of cesarean section delivery. EETs were extracted from tissue homogenates and analyzed by liquid chromatography coupled with tandem mass spectrometry. RESULTS Both cis-EETs and trans-EETs were detected in the placenta. Concentration of total EETs was higher in the placenta from preeclampsia compared with normal pregnancy (2.37 ± 1.42 ng/mg vs. 1.20 ± 0.72 ng/mg, mean ± SD, P < 0.01), especially the 5,6-, 8,9- and 11,12-EETs, measured in a subgroup of tissue samples (normal pregnancy = 10, preeclampsia = 5). By immunohistochemistry, sEH, CYP2J2, CYP4A11 were present in placental villi with different pattern distribution, whereas CYP2C8 was not detectable. Neither were CYP2J2, CYP4A11, and CYP2C8 detected in the umbilical cord. Western blot analysis of placenta homogenates showed reduced expression of sEH in preeclampsia as compared with normal pregnancy. CONCLUSION Increased EETs in the placenta and umbilical cord are associated with the presence of CYP2J2, whereas reduced expression of sEH in preeclampsia may be the key factor of increased EETs in the placenta.
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Znf179 induces differentiation and growth arrest of human primary glioblastoma multiforme in a p53-dependent cell cycle pathway. Sci Rep 2017; 7:4787. [PMID: 28684796 PMCID: PMC5500472 DOI: 10.1038/s41598-017-05305-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/26/2017] [Indexed: 12/29/2022] Open
Abstract
Malignant glioblastoma multiforme (GBM) is an aggressive brain tumor with strong local invasive growth and a poor prognosis. One probable way to manipulate GBM cells toward a less invasive status is to reprogram the most malignant GBM cells to a more differentiated and less oncogenic phenotype. Herein, we identified a novel role of a RING finger protein Znf179 in gliomagenesis. Znf179 overexpression induced differentiation of primary GBM cells, which were accompanied with elevated glial fibrillary acidic protein (GFAP) expression through up-regulating several cell-cycle-related factors, p53, p21, and p27, and allowed the cell-cycle arrest in the G0/G1 phase. In addition, Znf179 was highly correlated with the prognosis and survival rates of glioma patients. The expression levels of Znf179 was relatively lower in glioma patients compared to normal people, and glioma patients with lower expression levels of Znf179 mRNA had poorer prognosis and lower survival rates. In conclusion, we provide novel insight that Znf179 can reprogram GBM cells into a more-differentiated phenotype and prevent the progression of gliomas to a more-malignant state through p53-mediated cell-cycle signaling pathways. Understanding the molecular mechanism of Znf179 in gliomagenesis could help predict prognostic consequences, and targeting Znf179 could be a potential biomarker for glioma progression.
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Pfleger CM. The Hippo Pathway: A Master Regulatory Network Important in Development and Dysregulated in Disease. Curr Top Dev Biol 2017; 123:181-228. [PMID: 28236967 DOI: 10.1016/bs.ctdb.2016.12.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Hippo Pathway is a master regulatory network that regulates proliferation, cell growth, stemness, differentiation, and cell death. Coordination of these processes by the Hippo Pathway throughout development and in mature organisms in response to diverse external and internal cues plays a role in morphogenesis, in controlling organ size, and in maintaining organ homeostasis. Given the importance of these processes, the Hippo Pathway also plays an important role in organismal health and has been implicated in a variety of diseases including eye disease, cardiovascular disease, neurodegeneration, and cancer. This review will focus on Drosophila reports that identified the core components of the Hippo Pathway revealing specific downstream biological outputs of this complicated network. A brief description of mammalian reports will complement review of the Drosophila studies. This review will also survey upstream regulation of the core components with a focus on feedback mechanisms.
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Affiliation(s)
- Cathie M Pfleger
- The Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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Jahanshahi M, Hsiao K, Jenny A, Pfleger CM. The Hippo Pathway Targets Rae1 to Regulate Mitosis and Organ Size and to Feed Back to Regulate Upstream Components Merlin, Hippo, and Warts. PLoS Genet 2016; 12:e1006198. [PMID: 27494403 PMCID: PMC4975479 DOI: 10.1371/journal.pgen.1006198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/24/2016] [Indexed: 12/31/2022] Open
Abstract
Hippo signaling acts as a master regulatory pathway controlling growth, proliferation, and apoptosis and also ensures that variations in proliferation do not alter organ size. How the pathway coordinates restricting proliferation with organ size control remains a major unanswered question. Here we identify Rae1 as a highly-conserved target of the Hippo Pathway integrating proliferation and organ size. Genetic and biochemical studies in Drosophila cells and tissues and in mammalian cells indicate that Hippo signaling promotes Rae1 degradation downstream of Warts/Lats. In proliferating cells, Rae1 loss restricts cyclin B levels and organ size while Rae1 over-expression increases cyclin B levels and organ size, similar to Hippo Pathway over-activation or loss-of-function, respectively. Importantly, Rae1 regulation by the Hippo Pathway is crucial for its regulation of cyclin B and organ size; reducing Rae1 blocks cyclin B accumulation and suppresses overgrowth caused by Hippo Pathway loss. Surprisingly, in addition to suppressing overgrowth, reducing Rae1 also compromises survival of epithelial tissue overgrowing due to loss of Hippo signaling leading to a tissue “synthetic lethality” phenotype. Excitingly, Rae1 plays a highly conserved role to reduce the levels and activity of the Yki/YAP oncogene. Rae1 increases activation of the core kinases Hippo and Warts and plays a post-transcriptional role to increase the protein levels of the Merlin, Hippo, and Warts components of the pathway; therefore, in addition to Rae1 coordinating organ size regulation with proliferative control, we propose that Rae1 also acts in a feedback circuit to regulate pathway homeostasis. Exquisite control of organ size is critical during animal development and its loss results in pathological conditions. The Hippo Tumor Suppressor Pathway coordinates regulation of proliferation, growth, apoptosis, and autophagy to determine and maintain precise control of organ size. However, the genes responsible for Hippo-mediated regulation of mitosis or coordination of proliferation within organ size control have evaded characterization. Here, we describe Rae1, an essential WD-repeat containing protein, as a new organ size regulator. By genetic analysis, we show that Rae1 acts downstream of the Hippo Pathway to regulate mitotic cyclins and organ size. In contexts where organ size control is lost by compromised Hippo signaling, we show that there is a requirement for Rae1 that is distinct from the requriement for Yki: reducing Yki levels causes suppression of overgrowth, while reducing Rae1 levels dramatically compromises the survival of Hippo-deficient tissue. Lastly, our studies of Rae1 uncovered a potential post-transcriptional feedback loop that reinforces Yorkie-mediated transcriptional feedback for the Hippo Pathway.
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Affiliation(s)
- Maryam Jahanshahi
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kuangfu Hsiao
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andreas Jenny
- Department of Developmental and Molecular Biology and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Cathie M. Pfleger
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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12
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Gasser RB, Schwarz EM, Korhonen PK, Young ND. Understanding Haemonchus contortus Better Through Genomics and Transcriptomics. ADVANCES IN PARASITOLOGY 2016; 93:519-67. [PMID: 27238012 DOI: 10.1016/bs.apar.2016.02.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Parasitic roundworms (nematodes) cause substantial mortality and morbidity in animals globally. The barber's pole worm, Haemonchus contortus, is one of the most economically significant parasitic nematodes of small ruminants worldwide. Although this and related nematodes can be controlled relatively well using anthelmintics, resistance against most drugs in common use has become a major problem. Until recently, almost nothing was known about the molecular biology of H. contortus on a global scale. This chapter gives a brief background on H. contortus and haemonchosis, immune responses, vaccine research, chemotherapeutics and current problems associated with drug resistance. It also describes progress in transcriptomics before the availability of H. contortus genomes and the challenges associated with such work. It then reviews major progress on the two draft genomes and developmental transcriptomes of H. contortus, and summarizes their implications for the molecular biology of this worm in both the free-living and the parasitic stages of its life cycle. The chapter concludes by considering how genomics and transcriptomics can accelerate research on Haemonchus and related parasites, and can enable the development of new interventions against haemonchosis.
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Affiliation(s)
- R B Gasser
- The University of Melbourne, Parkville, VIC, Australia
| | - E M Schwarz
- The University of Melbourne, Parkville, VIC, Australia; Cornell University, Ithaca, NY, United States
| | - P K Korhonen
- The University of Melbourne, Parkville, VIC, Australia
| | - N D Young
- The University of Melbourne, Parkville, VIC, Australia
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Guo C, Cao X, Wang Q, Wang G, An L, Du M, Qiu Y, Yang Y, Li H, Wang Y, Wang S, Wang X, Ma X. Contribution of TIMP3 polymorphisms to the development of preeclampsia in Han Chinese women. J Assist Reprod Genet 2015; 32:1525-30. [PMID: 26304100 PMCID: PMC4615926 DOI: 10.1007/s10815-015-0529-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/30/2015] [Indexed: 01/24/2023] Open
Abstract
PURPOSE The aim of this study was to investigate whether polymorphisms in the tissue inhibitor of metalloproteinase 3 gene (TIMP3) are associated with the risk of preeclampsia (PE) in Han Chinese women. METHODS Nine single TIMP3 tag-single nucleotide polymorphisms were selected by Haploview and genotyped using the Sequenom method in 181 preeclamptic and 203 healthy pregnant women from eastern China. RESULTS The allele frequencies of the tag-single nucleotide polymorphisms were not significantly different between groups (P > 0.05). However, the genotype distribution of rs135025 was shown to differ between the multigravidity PE subgroup (>3) and controls under additive (P = 0.018) and recessive models (P = 0.008), while the genotype distribution of rs80272 differed significantly between the severe PE subgroup and controls under additive (P = 0.014) and dominant models (P = 0.041). Moreover, the H2 haplotype (A-C-G-T-A-A-G-C-G) was found to be associated with the risk of PE (P = 0.035). CONCLUSIONS Genotypes of rs135025 and rs80272 in TIMP3 may therefore influence susceptibility to PE, and pregnant women carrying the H2 haplotype might be more prone to developing PE.
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Affiliation(s)
- Changlong Guo
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Xiaofang Cao
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Qidi Wang
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Guangyu Wang
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Lisha An
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Meng Du
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Yue Qiu
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Ying Yang
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China
| | - Hui Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yuting Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuo Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xingyu Wang
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China.
| | - Xu Ma
- National Research Institute for Family Planning, 12 Dahuisi Road, Haidian, Beijing, 100081, China.
- Graduate School of Peking Union Medical College, Beijing, China.
- World Health Organization Collaborating Centre for Research in Human Reproduction, Beijing, China.
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Li J, Chen H, Ren J, Song J, Zhang F, Zhang J, Lee C, Li S, Geng Q, Cao C, Xu N. Effects of statin on circulating microRNAome and predicted function regulatory network in patients with unstable angina. BMC Med Genomics 2015; 8:12. [PMID: 25889164 PMCID: PMC4364658 DOI: 10.1186/s12920-015-0082-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/06/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Statin therapy plays a pivotal role in stabilizing the plaque for unstable angina (UA) patients although its mechanism(s) remains largely unexplored. Here we aim to identify microRNAs (miRNAs) mediating the protective effect of statins in UA patients. METHODS MiRNAs Array was carried out to compare the circulating whole blood miRNA profile of UA patients treated with (n = 10) and without statin (n = 10) and plasma miRNA profile UA patients treated with (n = 5) and without statin (n = 5). 22 whole blood miRNAs and 19 plasma miRNAs were found significantly upregulated in statin group. Targets of these miRNAs were predicted by algoritms: Targetscan, Miranda and Diana microT, then clustered according to functions and cell types by using the Database for Annotation, Visualization and Integrated Discovery (DAVID). To reveal the enriched function pathways in human atherosclerotic plaque, we analyzed microarray data from GEO database, Coronary atherosclerotic plaque (n = 80); macrophages in ruptured plaque (n = 11); carotid atheroma plaque (n = 64); advanced carotid atherosclerotic plaque (n = 29) using Reactome database. Integrated analysis indicated that statin induced miRNAs mainly regulate the signaling pathways of Rho GTPase and hemostasis in human atherosclerotic lesion. In vulnerable plaque, additional immune system signaling was also targeted. RESULTS The data showed target genes regulated by these statin induced miRNAs majorly expressed in i) plaque macrophage and platelet, where they were involved in hemostasis process; ii) in monocyte to regulate NGF apoptosis; iii) and in endothelial cell function in Rho GTPase pathway. Integrate analysis indicated that statin induced miRNAs mainly regulate the signaling pathways of Rho GTPase and hemostasis in human atherosclerotic lesion. CONCLUSIONS Our study suggest that statin induces the expression of multiple miRNAs in the circulation of UA patient, which play important roles by regulating signal pathways critical for the pathogenesis of UA.
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Affiliation(s)
- Jingjin Li
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Hong Chen
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Jingyi Ren
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Junxian Song
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Feng Zhang
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Jing Zhang
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Chongyou Lee
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Sufang Li
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Qiang Geng
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Chengfu Cao
- Department of Cardiology, Peking University People's hospital, No. 11 Xizhimen South Street, Beijing, 100044, China.
| | - Ning Xu
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
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Sailem HZ, Sero JE, Bakal C. Visualizing cellular imaging data using PhenoPlot. Nat Commun 2015; 6:5825. [PMID: 25569359 PMCID: PMC4354266 DOI: 10.1038/ncomms6825] [Citation(s) in RCA: 24] [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: 10/15/2014] [Accepted: 11/11/2014] [Indexed: 11/24/2022] Open
Abstract
Visualization is essential for data interpretation, hypothesis formulation and communication of results. However, there is a paucity of visualization methods for image-derived data sets generated by high-content analysis in which complex cellular phenotypes are described as high-dimensional vectors of features. Here we present a visualization tool, PhenoPlot, which represents quantitative high-content imaging data as easily interpretable glyphs, and we illustrate how PhenoPlot can be used to improve the exploration and interpretation of complex breast cancer cell phenotypes.
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Affiliation(s)
- Heba Z. Sailem
- Dynamical Cell Systems, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Julia E. Sero
- Dynamical Cell Systems, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Chris Bakal
- Dynamical Cell Systems, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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16
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Cantacessi C, Hofmann A, Campbell BE, Gasser RB. Impact of next-generation technologies on exploring socioeconomically important parasites and developing new interventions. Methods Mol Biol 2015; 1247:437-474. [PMID: 25399114 DOI: 10.1007/978-1-4939-2004-4_31] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High-throughput molecular and computer technologies have become instrumental for systems biological explorations of pathogens, including parasites. For instance, investigations of the transcriptomes of different developmental stages of parasitic nematodes give insights into gene expression, regulation and function in a parasite, which is a significant step to understanding their biology, as well as interactions with their host(s) and disease. This chapter (1) gives a background on some key parasitic nematodes of socioeconomic importance, (2) describes sequencing and bioinformatic technologies for large-scale studies of the transcriptomes and genomes of these parasites, (3) provides some recent examples of applications and (4) emphasizes the prospects of fundamental biological explorations of parasites using these technologies for the development of new interventions to combat parasitic diseases.
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Affiliation(s)
- Cinzia Cantacessi
- Department of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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Liao WY, Ho CC, Hou HH, Hsu TH, Tsai MF, Chen KY, Chen HY, Lee YC, Yu CJ, Lee CH, Yang PC. Heparin co-factor II enhances cell motility and promotes metastasis in non-small cell lung cancer. J Pathol 2014; 235:50-64. [PMID: 25130770 DOI: 10.1002/path.4421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 08/06/2014] [Indexed: 12/20/2022]
Abstract
Using the Serial Analysis of Gene Expression (SAGE) database from the Cancer Genome Anatomy Project, we identified heparin co-factor II (HCII), which is over-expressed in non-small cell lung cancer (NSCLC). Here, we investigated the clinical significance of HCII and provided molecular evidence to support the suggestion that HCII could enhance cancer metastasis in NSCLC. We found that high HCII expression in tumour tissue was associated with increased cancer recurrence and shorter overall survival times in 75 clinically operable NSCLC patients. High pretreatment plasma concentration of HCII was associated with reduced overall survival in 57 consecutive NSCLC patients. We over-expressed and knocked down HCII expression in lung cancer cell lines and confirmed that HCII could promote cell motility, invasion ability and filopodium dynamics in NSCLC cells in vitro and increased metastatic colonization in an in vivo mouse model. Exogenous treatment of HCII promoted cancer cell migration, and this promigratory effect of HCII was independent of thrombin. We further showed that HCII could up-regulate cancer cell migration through the activation of PI3K, which acts upstream of Rac1 and Cdc42, and this effect could be blocked by heparin. We suggest that HCII is a novel metastasis enhancer and may be used as a prognostic predictor for heparin treatment in NSCLC.
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Affiliation(s)
- Wei-Yu Liao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
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18
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Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. PLoS One 2014; 9:e107156. [PMID: 25198066 PMCID: PMC4157845 DOI: 10.1371/journal.pone.0107156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/06/2014] [Indexed: 12/01/2022] Open
Abstract
Despite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes.
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Affiliation(s)
- Matthew Wortham
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Changcun Guo
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Monica Zhang
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lingyun Song
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Vishwanath R. Iyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Terrence S. Furey
- Department of Genetics, Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory E. Crawford
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hai Yan
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (YH); (HY)
| | - Yiping He
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (YH); (HY)
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A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity. BMC Genomics 2014; 15:725. [PMID: 25163811 PMCID: PMC4156628 DOI: 10.1186/1471-2164-15-725] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/15/2014] [Indexed: 02/07/2023] Open
Abstract
Background Large scale transcript analysis of human glomerular microvascular endothelial cells (HGMEC) has never been accomplished. We designed this study to define the transcriptome of HGMEC and facilitate a better characterization of these endothelial cells with unique features. Serial analysis of gene expression (SAGE) was used for its unbiased approach to quantitative acquisition of transcripts. Results We generated a HGMEC SAGE library consisting of 68,987 transcript tags. Then taking advantage of large public databases and advanced bioinformatics we compared the HGMEC SAGE library with a SAGE library of non-cultured ex vivo human glomeruli (44,334 tags) which contained endothelial cells. The 823 tags common to both which would have the potential to be expressed in vivo were subsequently checked against 822,008 tags from 16 non-glomerular endothelial SAGE libraries. This resulted in 268 transcript tags differentially overexpressed in HGMEC compared to non-glomerular endothelia. These tags were filtered using a set of criteria: never before shown in kidney or any type of endothelial cell, absent in all nephron regions except the glomerulus, more highly expressed than statistically expected in HGMEC. Neurogranin, a direct target of thyroid hormone action which had been thought to be brain specific and never shown in endothelial cells before, fulfilled these criteria. Its expression in glomerular endothelium in vitro and in vivo was then verified by real-time-PCR, sequencing and immunohistochemistry. Conclusions Our results represent an extensive molecular characterization of HGMEC beyond a mere database, underline the endothelial heterogeneity, and propose neurogranin as a potential link in the kidney-thyroid axis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-725) contains supplementary material, which is available to authorized users.
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20
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Zhang R, Song C. Loss of CSMD1 or 2 may contribute to the poor prognosis of colorectal cancer patients. Tumour Biol 2014; 35:4419-23. [DOI: 10.1007/s13277-013-1581-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022] Open
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Ilanges A, Jahanshahi M, Balobin DM, Pfleger CM. Alcohol interacts with genetic alteration of the Hippo tumor suppressor pathway to modulate tissue growth in Drosophila. PLoS One 2013; 8:e78880. [PMID: 24205337 PMCID: PMC3804493 DOI: 10.1371/journal.pone.0078880] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/16/2013] [Indexed: 12/27/2022] Open
Abstract
Alcohol-mediated cancers represent more than 3.5% of cancer-related deaths, yet how alcohol promotes cancer is a major open question. Using Drosophila, we identified novel interactions between dietary ethanol and loss of tumor suppressor components of the Hippo Pathway. The Hippo Pathway suppresses tumors in flies and mammals by inactivating transcriptional co-activator Yorkie, and the spectrum of cancers associated with impaired Hippo signaling overlaps strikingly with those associated with alcohol. Therefore, our findings may implicate loss of Hippo Pathway tumor suppression in alcohol-mediated cancers. Ethanol enhanced overgrowth from loss of the expanded, hippo, or warts tumor suppressors but, surprisingly, not from over-expressing the yorkie oncogene. We propose that in parallel to Yorkie-dependent overgrowth, impairing Hippo signaling in the presence of alcohol may promote overgrowth via additional alcohol-relevant targets. We also identified interactions between alcohol and Hippo Pathway over-activation. We propose that exceeding certain thresholds of alcohol exposure activates Hippo signaling to maintain proper growth control and prevent alcohol-mediated mis-patterning and tissue overgrowth.
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Affiliation(s)
- Anoj Ilanges
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Yale University, New Haven, Connecticut, United States of America
| | - Maryam Jahanshahi
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Denis M. Balobin
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Columbia University, New York, New York, United States of America
| | - Cathie M. Pfleger
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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22
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Binder ZA, Siu IM, Eberhart CG, ap Rhys C, Bai RY, Staedtke V, Zhang H, Smoll NR, Piantadosi S, Piccirillo SG, DiMeco F, Weingart JD, Vescovi A, Olivi A, Riggins GJ, Gallia GL. Podocalyxin-like protein is expressed in glioblastoma multiforme stem-like cells and is associated with poor outcome. PLoS One 2013; 8:e75945. [PMID: 24146797 PMCID: PMC3797817 DOI: 10.1371/journal.pone.0075945] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/23/2013] [Indexed: 11/19/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common primary malignant adult brain tumor and is associated with poor survival. Recently, stem-like cell populations have been identified in numerous malignancies including GBM. To identify genes whose expression is changed with differentiation, we compared transcript profiles from a GBM oncosphere line before and after differentiation. Bioinformatic analysis of the gene expression profiles identified podocalyxin-like protein (PODXL), a protein highly expressed in human embryonic stem cells, as a potential marker of undifferentiated GBM stem-like cells. The loss of PODXL expression upon differentiation of GBM stem-like cell lines was confirmed by quantitative real-time PCR and flow cytometry. Analytical flow cytometry of numerous GBM oncosphere lines demonstrated PODXL expression in all lines examined. Knockdown studies and flow cytometric cell sorting experiments demonstrated that PODXL is involved in GBM stem-like cell proliferation and oncosphere formation. Compared to PODXL-negative cells, PODXL-positive cells had increased expression of the progenitor/stem cell markers Musashi1, SOX2, and BMI1. Finally, PODXL expression directly correlated with increasing glioma grade and was a marker for poor outcome in patients with GBM. In summary, we have demonstrated that PODXL is expressed in GBM stem-like cells and is involved in cell proliferation and oncosphere formation. Moreover, high PODXL expression correlates with increasing glioma grade and decreased overall survival in patients with GBM.
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Affiliation(s)
- Zev A. Binder
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Johns Hopkins Physical Science Oncology Center and Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - I-Mei Siu
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Charles G. Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Colette ap Rhys
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ren-Yuan Bai
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Verena Staedtke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, Maryland, United States of America
| | - Nicolas R. Smoll
- Gippsland Medical School, Monash University, Churchill, Victoria, Australia
| | - Steven Piantadosi
- Department of Oncology Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | | | - Francesco DiMeco
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurosurgery, Istituto Nazionale Neurologico C. Besta, Milan, Italy
| | - Jon D. Weingart
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Angelo Vescovi
- Department of Biotechnology and Biosciences, University of Milano Biocca, Milan, Italy
| | - Alessandro Olivi
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory J. Riggins
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gary L. Gallia
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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23
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Liu Y, Hauser MA, Akafo SK, Qin X, Miura S, Gibson JR, Wheeler J, Gaasterland DE, Challa P, Herndon LW, Ritch R, Moroi SE, Pasquale LR, Girkin CA, Budenz DL, Wiggs JL, Richards JE, Ashley-Koch AE, Allingham RR. Investigation of known genetic risk factors for primary open angle glaucoma in two populations of African ancestry. Invest Ophthalmol Vis Sci 2013; 54:6248-54. [PMID: 23963167 PMCID: PMC3776712 DOI: 10.1167/iovs.13-12779] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Multiple genes have been associated with primary open angle glaucoma (POAG) in Caucasian populations. We now examine the association of these loci in populations of African ancestry, populations at particularly high risk for POAG. METHODS We genotyped DNA samples from two populations: African American (1150 cases and 999 controls) and those from Ghana, West Africa (483 cases and 593 controls). Our analysis included 57 single nucleotide polymorphisms (SNPs) in five loci previously associated with POAG at the genome-wide level, including CDKN2B-AS1, TMCO1, CAV1/CAV2, chromosome 8q22 intergenic region, and SIX1/SIX6. We evaluated association in the full datasets, as well as subgroups with normal pressure glaucoma (NPG, maximum IOP ≤21 mm Hg) and high pressure glaucoma (HPG, IOP >21 mm Hg). RESULTS In African Americans, we identified an association of rs10120688 in the CDNK2B-AS1 region with POAG (P = 0.0020). Several other SNPs were nominally associated, but did not survive correction for multiple testing. In the subgroup analyses, significant associations were identified for rs10965245 (P = 0.0005) in the CDKN2B-AS1 region with HPG and rs11849906 in the SIX1/SIX6 region with NPG (P = 0.006). No significant association was identified with any loci in the Ghanaian samples. CONCLUSIONS POAG genetic susceptibility alleles associated in Caucasians appear to play a greatly reduced role in populations of African ancestry. Thus, the major genetic components of POAG of African origin remain to be identified. This finding underscores the critical need to pursue large-scale genome-wide association studies in this understudied, yet disproportionately affected population.
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Affiliation(s)
- Yutao Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Michael A. Hauser
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Stephen K. Akafo
- Unit of Ophthalmology, Department of Surgery, University of Ghana Medical School, Accra, Ghana
| | - Xuejun Qin
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Shiroh Miura
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jason R. Gibson
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Joshua Wheeler
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Pratap Challa
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Leon W. Herndon
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | | | - Robert Ritch
- Einhorn Clinical Research Center, Department of Ophthalmology, New York Eye and Ear Infirmary, New York, New York
| | - Sayoko E. Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Louis R. Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Christopher A. Girkin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Donald L. Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Julia E. Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | | | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
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Xiang Y, Zhang X, Li Q, Xu J, Zhou X, Wang T, Xing Q, Liu Y, Wang L, He L, Zhao X. Promoter hypomethylation of TIMP3 is associated with pre-eclampsia in a Chinese population. Mol Hum Reprod 2012; 19:153-9. [PMID: 23172037 DOI: 10.1093/molehr/gas054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A study by Yuen RK, Penaherrera MS, von Dadelszen P, McFadden DE, Robinson WP. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. Eur J Hum Genet 2010;18:1006-1012 based on a Canadian population found the tissue inhibitor of the metalloproteinase 3 (TIMP3) gene to be hypomethylated in pre-eclampsia (PE) placentas and to be a potential prenatal marker for early onset PE. To further explore the role of TIMP3 in PE and to investigate whether the TIMP3 promoter shows the same methylation pattern in the Han Chinese population, we analyzed a complete methylation assay of TIMP3 including the promoter region studied in the Canadian report and the neighboring CpG island in placentas (cases n = 41, controls n = 22) maternal peripheral blood (cases n = 3; controls n = 6) and umbilical cord blood (cases n = 7; controls n = 8) using MassArray EpiTyper (Sequenom, San Diego, CA, USA). Our results confirmed the finding of aberrant TIMP3 promoter methylation in PE placentas (mean = 0.405) compared with those in controls (mean = 0.534, P = 9.40 × 10(-7)). A tissue-specific methylation pattern between placentas (mean = 0.459) and bloods (mean = 0.961, P = 6.91 × 10(-13)) was also demonstrated in our clinical samples. Furthermore, a nearly 2-fold increase in TIMP3 expression for the hypomethylated promoter was found in PE placentas (P = 0.007), pointing to a negative relationship between TIMP3 methylation and the expression (R = -0.758, P = 0.029). In conclusion, we replicated the findings of Yuen et al. in our Han Chinese-based study, confirming that TIMP3 is likely to be involved in the etiology of PE and that hypomethylated and placenta-specific TIMP3 may be a potential marker for early diagnosis of PE in maternal plasma.
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Affiliation(s)
- Yuqian Xiang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, China
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Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P. Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome Med 2012; 4:76. [PMID: 23046790 PMCID: PMC3556652 DOI: 10.1186/gm377] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/20/2012] [Accepted: 10/09/2012] [Indexed: 02/07/2023] Open
Abstract
Background Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation. Here, we analyzed GNS and NS cell transcriptomes to identify gene expression alterations underlying the disease phenotype. Methods Sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (Tag-seq) on adherent GNS cell lines from three glioblastoma cases and two normal NS cell lines. Validation by quantitative real-time PCR was performed on 82 differentially expressed genes across a panel of 16 GNS and 6 NS cell lines. The molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of GNS cells and comparison with public data for 867 glioma biopsies. Results Transcriptome analysis revealed major differences correlated with glioma histological grade, and identified misregulated genes of known significance in glioblastoma as well as novel candidates, including genes associated with other malignancies or glioma-related pathways. This analysis further detected several long non-coding RNAs with expression profiles similar to neighboring genes implicated in cancer. Quantitative PCR validation showed excellent agreement with Tag-seq data (median Pearson r = 0.91) and discerned a gene set robustly distinguishing GNS from NS cells across the 22 lines. These expression alterations include oncogene and tumor suppressor changes not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a GNS expression signature strongly associated with patient survival (P = 1e-6, Cox model). Conclusions These results support the utility of GNS cell cultures as a model system for studying the molecular processes driving glioblastoma and the use of NS cells as reference controls. The association between a GNS expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumor growth. We anticipate that analysis of normal and malignant stem cells will be an important complement to large-scale profiling of primary tumors.
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Affiliation(s)
- Pär G Engström
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Diva Tommei
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stefan H Stricker
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Christine Ender
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Steven M Pollard
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Paul Bertone
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK ; Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany ; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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A Prevalence of Imprinted Genes within the Total Transcriptomes of Human Tissues and Cells. Mol Biol Int 2012; 2012:793506. [PMID: 22997578 PMCID: PMC3446743 DOI: 10.1155/2012/793506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 06/23/2012] [Accepted: 06/28/2012] [Indexed: 11/30/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon that causes a differential expression of paternally and maternally inherited alleles of a subset of genes (the so-called imprinted genes). Imprinted genes are distributed throughout the genome and it is predicted that about 1% of the human genes may be imprinted. It is recognized that the allelic expression of imprinted genes varies between tissues and developmental stages. The current study represents the first attempt to estimate a prevalence of imprinted genes within the total human transcriptome. In silico analysis of the normalized expression profiles of a comprehensive panel of 173 established and candidate human imprinted genes was performed, in 492 publicly available SAGE libraries. The latter represent human cell and tissue samples in a variety of physiological and pathological conditions. Variations in the prevalence of imprinted genes within the total transcriptomes (ranging from 0.08% to 4.36%) and expression profiles of the individual imprinted genes are assessed. This paper thus provides a useful reference on the size of the imprinted transcriptome and expression of the individual imprinted genes.
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Cerutti JM. Employing genetic markers to improve diagnosis of thyroid tumor fine needle biopsy. Curr Genomics 2012; 12:589-96. [PMID: 22654558 PMCID: PMC3271311 DOI: 10.2174/138920211798120781] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 12/18/2022] Open
Abstract
Fine-Needle Aspiration (FNA) is the most widely used and cost-effective preoperative test for the initial evaluation of a thyroid nodule, although it has limited diagnostic accuracy for several types of tumors. Patients will often receive cytological report of indeterminate cytology and are referred to surgery for a more accurate diagnosis. An improved test would help physicians rapidly focus treatment on true malignancies and avoid some unnecessary treatment of benign tumors. This review will discuss current molecular markers that may improve thyroid nodule diagnosis.
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Affiliation(s)
- Janete M Cerutti
- Genetic Bases of Thyroid Tumor Laboratory, Division of Genetics, Department of Morphology and Genetics and Division of Endocrinology, Department of Medicine, Federal University of São Paulo, SP, Brazil
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Hui L, Slonim DK, Wick HC, Johnson KL, Koide K, Bianchi DW. Novel neurodevelopmental information revealed in amniotic fluid supernatant transcripts from fetuses with trisomies 18 and 21. Hum Genet 2012; 131:1751-9. [PMID: 22752091 DOI: 10.1007/s00439-012-1195-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/19/2012] [Indexed: 01/15/2023]
Abstract
Trisomies 18 and 21 are the two most common live born autosomal aneuploidies in humans. While the anatomic abnormalities in affected fetuses are well documented, the dysregulated biological pathways associated with the development of the aneuploid phenotype are less clear. Amniotic fluid (AF) cell-free RNA is a valuable source of biological information obtainable from live fetuses. In this study, we mined gene expression data previously produced by our group from mid-trimester AF supernatant samples. We identified the euploid, trisomy 18 and trisomy 21 AF transcriptomes, and analyzed them with a particular focus on the nervous system. We used multiple bioinformatics resources, including DAVID, Ingenuity Pathway Analysis, and the BioGPS Gene Expression Atlas. Our analyses confirmed that AF supernatant from aneuploid fetuses is enriched for nervous system gene expression and neurological disease pathways. Tissue analysis showed that fetal brain cortex and Cajal-Retzius cells were significantly enriched for genes contained in the AF transcriptomes. We also examined AF transcripts known to be dysregulated in aneuploid fetuses compared with euploid controls and identified several brain-specific transcripts among them. Many of these genes play critical roles in nervous system development. NEUROD2, which was downregulated in trisomy 18, induces neurogenic differentiation. SOX11, downregulated in trisomy 21, is a transcription factor that is essential for pan-neuronal protein expression and axonal growth of sensory neurons. Our results show that whole transcriptome analysis of cell-free RNA in AF from live pregnancies permits discovery of biomarkers of abnormal human neurodevelopment and advances our understanding of the pathophysiology of aneuploidy.
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Affiliation(s)
- Lisa Hui
- Mother Infant Research Institute and the Division of Genetics, Department of Pediatrics, The Floating Hospital for Children at Tufts Medical Center, 800 Washington St, Boston, MA 02111, USA.
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Cantacessi C, Campbell BE, Gasser RB. Key strongylid nematodes of animals — Impact of next-generation transcriptomics on systems biology and biotechnology. Biotechnol Adv 2012; 30:469-88. [DOI: 10.1016/j.biotechadv.2011.08.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/09/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
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Wortham M, Jin G, Sun JL, Bigner DD, He Y, Yan H. Aberrant Otx2 expression enhances migration and induces ectopic proliferation of hindbrain neuronal progenitor cells. PLoS One 2012; 7:e36211. [PMID: 22558385 PMCID: PMC3338642 DOI: 10.1371/journal.pone.0036211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/28/2012] [Indexed: 11/18/2022] Open
Abstract
Dysregulation of Otx2 is a hallmark of the pediatric brain tumor medulloblastoma, yet its functional significance in the establishment of these tumors is unknown. Here we have sought to determine the functional consequences of Otx2 overexpression in the mouse hindbrain to characterize its potential role in medulloblastoma tumorigenesis and identify the cell types responsive to this lineage-specific oncogene. Expression of Otx2 broadly in the mouse hindbrain resulted in the accumulation of proliferative clusters of cells in the cerebellar white matter and dorsal brainstem of postnatal mice. We found that brainstem ectopia were derived from neuronal progenitors of the rhombic lip and that cerebellar ectopia were derived from granule neuron precursors (GNPs) that had migrated inwards from the external granule layer (EGL). These hyperplasias exhibited various characteristics of medulloblastoma precursor cells identified in animal models of Shh or Wnt group tumors, including aberrant localization and altered spatiotemporal control of proliferation. However, ectopia induced by Otx2 differentiated and dispersed as the animals reached adulthood, indicating that factors restricting proliferative lifespan were a limiting factor to full transformation of these cells. These studies implicate a role for Otx2 in altering the dynamics of neuronal progenitor cell proliferation.
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Affiliation(s)
- Matthew Wortham
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Genglin Jin
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Julia Lailai Sun
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Darell D. Bigner
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Yiping He
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hai Yan
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Putative multifunctional signature of lung metastases in dedifferentiated chondrosarcoma. Sarcoma 2012; 2012:820254. [PMID: 22448124 PMCID: PMC3289931 DOI: 10.1155/2012/820254] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 10/21/2011] [Accepted: 11/03/2011] [Indexed: 12/22/2022] Open
Abstract
Chondrosarcomas are among the most malignant skeletal tumors. Dedifferentiated chondrosarcoma is a highly aggressive subtype of chondrosarcoma, with lung metastases developing within a few months of diagnosis in 90% of patients. In this paper we performed comparative analyses of the transcriptomes of five individual metastatic lung lesions that were surgically resected from a patient with dedifferentiated chondrosarcoma. We document for the first time a high heterogeneity of gene expression profiles among the individual lung metastases. Moreover, we reveal a signature of “multifunctional” genes that are expressed in all metastatic lung lesions. Also, for the first time, we document the occurrence of massive macrophage infiltration in dedifferentiated chondrosarcoma lung metastases.
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Ante M, Wingender E, Fuchs M. Integration of gene expression data with prior knowledge for network analysis and validation. BMC Res Notes 2011; 4:520. [PMID: 22123172 PMCID: PMC3298547 DOI: 10.1186/1756-0500-4-520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 11/28/2011] [Indexed: 01/17/2023] Open
Abstract
Background Reconstruction of protein-protein interaction or metabolic networks based on expression data often involves in silico predictions, while on the other hand, there are unspecific networks of in vivo interactions derived from knowledge bases. We analyze networks designed to come as close as possible to data measured in vivo, both with respect to the set of nodes which were taken to be expressed in experiment as well as with respect to the interactions between them which were taken from manually curated databases Results A signaling network derived from the TRANSPATH database and a metabolic network derived from KEGG LIGAND are each filtered onto expression data from breast cancer (SAGE) considering different levels of restrictiveness in edge and vertex selection. We perform several validation steps, in particular we define pathway over-representation tests based on refined null models to recover functional modules. The prominent role of the spindle checkpoint-related pathways in breast cancer is exhibited. High-ranking key nodes cluster in functional groups retrieved from literature. Results are consistent between several functional and topological analyses and between signaling and metabolic aspects. Conclusions This construction involved as a crucial step the passage to a mammalian protein identifier format as well as to a reaction-based semantics of metabolism. This yielded good connectivity but also led to the need to perform benchmark tests to exclude loss of essential information. Such validation, albeit tedious due to limitations of existing methods, turned out to be informative, and in particular provided biological insights as well as information on the degrees of coherence of the networks despite fragmentation of experimental data. Key node analysis exploited the networks for potentially interesting proteins in view of drug target prediction.
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Affiliation(s)
- Michael Ante
- Department of Bioinformatics, Medical School, Georg-August-University Goettingen, Goldschmidtstr, 1, 37077 Goettingen, Germany.
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O’Connor MD, Wederell E, Robertson G, Delaney A, Morozova O, Poon SS, Yap D, Fee J, Zhao Y, McDonald H, Zeng T, Hirst M, Marra MA, Aparicio SA, Eaves CJ. Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance. Exp Hematol 2011; 39:866-79.e1. [DOI: 10.1016/j.exphem.2011.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/13/2011] [Accepted: 05/20/2011] [Indexed: 12/24/2022]
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Abstract
The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor initiation and progression remain largely unknown. Unfortunately, most of these data are scattered in multiple databases and supplementary materials of publications, thus making their retrieval, evaluation, comparison and visualization a rather arduous task. Here we report the development and implementation of an open access database (BTECH), a community resource for the deposition of a wide range of molecular data derived from brain tumor studies. This comprehensive database integrates multiple datasets, including transcript profiles, epigenomic CpG methylation data, DNA copy number alterations and structural chromosomal rearrangements, tumor-associated gene lists, SNPs, genomic features concerning Alu repeats and general genomic annotations. A genome browser has also been developed that allows for the simultaneous visualization of the different datasets and the various annotated features. Besides enabling an integrative view of diverse datasets through the genome browser, we also provide links to the original references for users to have a more accurate understanding of each specific dataset. This integrated platform will facilitate uncovering interactions among genetic and epigenetic factors associated with brain tumor development. BTECH is freely available at http://cmbteg.childrensmemorial.org/.
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Vidal DO, de Souza JES, Pires LC, Masotti C, Salim ACM, Costa MCF, Galante PAF, de Souza SJ, Camargo AA. Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags. Genome 2011; 54:120-7. [PMID: 21326368 DOI: 10.1139/g10-103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recent reports have demonstrated that a significant proportion of human genes display allelic differential expression (ADE). ADE is associated with phenotypic variability and may contribute to complex genetic diseases. Here, we present a computational analysis of ADE using allele-specific serial analysis of gene expression (SAGE) tags representing 1295 human genes. We identified 472 genes for which unequal representation (>3-fold) of allele-specific SAGE tags was observed in at least one SAGE library, suggesting the occurrence of ADE. For 235 out of these 472 genes, the difference in the expression level between both allele-specific SAGE tags was statistically significant (p < 0.05). Eleven candidate genes were then subjected to experimental validation and ADE was confirmed for 8 out of these 11 genes. Our results suggest that at least 25% of the human genes display ADE and that allele-specific SAGE tags can be efficiently used for the identification of such genes.
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Affiliation(s)
- Daniel Onofre Vidal
- Ludwig Institute for Cancer Research, São Paulo Branch, Rua João Julião, 245 - 1°Andar, 01323-903, São Paulo, SP, Brazil
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Wong JCT, Chan SK, Schaeffer DF, Sagaert X, Lim HJ, Kennecke H, Owen DA, Suh KW, Kim YB, Tai IT. Absence of MMP2 expression correlates with poor clinical outcomes in rectal cancer, and is distinct from MMP1-related outcomes in colon cancer. Clin Cancer Res 2011; 17:4167-76. [PMID: 21531813 DOI: 10.1158/1078-0432.ccr-10-1224] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE Treatments for colorectal cancer (CRC) are primarily disease stage based. However, heterogeneity in outcome within even a single stage highlights its limitations in predicting disease behavior. Recently, the role of gene expression as predictive and prognostic markers has been explored. Our objectives were to identify consistently differentially expressed genes through meta-analysis of high-throughput gene-expression studies, and evaluate their predictive and prognostic significance in colon (CC) and rectal (RC) cancers. EXPERIMENTAL DESIGN Publications applying high-throughput gene- expression technologies to specific CRC stages were identified. A vote counting strategy was used to identify the most significant differentially expressed genes. Their predictive and prognostic values were independently assessed in a tissue microarray of 191 cases of stage II-IV CC/RC from two tertiary care centers. Their biological effects were also examined in vitro. RESULTS MMP1 and MMP2 were identified as consistently underexpressed in liver metastasis compared with primary CRC. Shorter time to distant metastasis and overall survival occurred in stage III CC lacking MMP1 expression, and in stage III RC lacking MMP2. MMP1 levels in stage II and III CC were associated with increased likelihood of distant metastasis, whereas the risk of local recurrence in stage III RC could be stratified by MMP2. Promotion of cell invasion of CRC cell lines exposed to MMP1/2 inhibitors were confirmed in vitro. CONCLUSIONS MMP1 and MMP2 may be useful biomarkers that can help stratify patients at higher risk of developing recurrence in colorectal cancer, and guide individualized treatment decisions to achieve better outcomes.
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Affiliation(s)
- John C T Wong
- Division of Gastroenterology, Department of Medicine, and Department of Pathology, University of British Columbia, 2775 Laurel Street, Vancouver, British Columbia, Canada, V5Z 1M9
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Milnthorpe AT, Soloviev M. Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms. BMC Bioinformatics 2011; 12:97. [PMID: 21496233 PMCID: PMC3094240 DOI: 10.1186/1471-2105-12-97] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 04/15/2011] [Indexed: 12/03/2022] Open
Abstract
Background The Cancer Genome Anatomy Project (CGAP) xProfiler and cDNA Digital Gene Expression Displayer (DGED) have been made available to the scientific community over a decade ago and since then were used widely to find genes which are differentially expressed between cancer and normal tissues. The tissue types are usually chosen according to the ontology hierarchy developed by NCBI. The xProfiler uses an internally available flat file database to determine the presence or absence of genes in the chosen libraries, while cDNA DGED uses the publicly available UniGene Expression and Gene relational databases to count the sequences found for each gene in the presented libraries. Results We discovered that the CGAP approach often includes libraries from dependent or irrelevant tissues (one third of libraries were incorrect on average, with some tissue searches no correct libraries being selected at all). We also discovered that the CGAP approach reported genes from outside the selected libraries and may omit genes found within the libraries. Other errors include the incorrect estimation of the significance values and inaccurate settings for the library size cut-off values. We advocated a revised approach to finding libraries associated with tissues. In doing so, libraries from dependent or irrelevant tissues do not get included in the final library pool. We also revised the method for determining the presence or absence of a gene by searching the UniGene relational database, revised calculation of statistical significance and sorted the library cut-off filter. Conclusion Our results justify re-evaluation of all previously reported results where NCBI CGAP expression data and tools were used.
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Affiliation(s)
- Andrew T Milnthorpe
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK.
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Liu Y, Munro D, Layfield D, Dellinger A, Walter J, Peterson K, Rickman CB, Allingham RR, Hauser MA. Serial analysis of gene expression (SAGE) in normal human trabecular meshwork. Mol Vis 2011; 17:885-93. [PMID: 21528004 PMCID: PMC3081805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/29/2011] [Indexed: 11/05/2022] Open
Abstract
PURPOSE To identify the genes expressed in normal human trabecular meshwork tissue, a tissue critical to the pathogenesis of glaucoma. METHODS Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. RESULTS A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. CONCLUSIONS This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.
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Affiliation(s)
- Yutao Liu
- Center for Human Genetics, Duke University Medical Center, Durham, NC
| | - Drew Munro
- Department of Ophthalmology, Duke University Medical Center, Durham, NC
| | - David Layfield
- Center for Human Genetics, Duke University Medical Center, Durham, NC
| | - Andrew Dellinger
- Center for Human Genetics, Duke University Medical Center, Durham, NC
| | - Jeffrey Walter
- Center for Human Genetics, Duke University Medical Center, Durham, NC
| | - Katherine Peterson
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Catherine Bowes Rickman
- Department of Ophthalmology, Duke University Medical Center, Durham, NC,Department of Cell Biology, Duke University Medical Center, Durham, NC
| | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC
| | - Michael A. Hauser
- Center for Human Genetics, Duke University Medical Center, Durham, NC,Department of Ophthalmology, Duke University Medical Center, Durham, NC
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Bai RY, Staedtke V, Riggins GJ. Molecular targeting of glioblastoma: Drug discovery and therapies. Trends Mol Med 2011; 17:301-312. [PMID: 21411370 DOI: 10.1016/j.molmed.2011.01.011] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 01/10/2011] [Accepted: 01/21/2011] [Indexed: 12/19/2022]
Abstract
Despite advances in treatment for glioblastoma multiforme (GBM), patient prognosis remains poor. Although there is growing evidence that molecular targeting could translate into better survival for GBM, current clinical data show limited impact on survival. Recent progress in GBM genomics implicate several activated pathways and numerous mutated genes. This molecular diversity can partially explain therapeutic resistance and several approaches have been postulated to target molecular changes. Furthermore, most drugs are unable to reach effective concentrations within the tumor owing to elevated intratumoral pressure, restrictive vasculature and other limiting factors. Here, we describe the preclinical and clinical developments in treatment strategies of GBM. We review the current clinical trials for GBM and discuss the challenges and future directions of targeted therapies.
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Affiliation(s)
- Ren-Yuan Bai
- Departments of Neurosurgery, Johns Hopkins University School of Medicine, CRB II Rm. 257, 1550 Orleans Street, Baltimore, MD 21231, USA
| | - Verena Staedtke
- Departments of Neurosurgery, Johns Hopkins University School of Medicine, CRB II Rm. 257, 1550 Orleans Street, Baltimore, MD 21231, USA
| | - Gregory J Riggins
- Departments of Neurosurgery, Johns Hopkins University School of Medicine, CRB II Rm. 257, 1550 Orleans Street, Baltimore, MD 21231, USA
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Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon JJ, Winter P, Kahl G. The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC PLANT BIOLOGY 2011; 11:31. [PMID: 21320317 PMCID: PMC3045889 DOI: 10.1186/1471-2229-11-31] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 02/14/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. RESULTS We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. CONCLUSIONS This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.
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Affiliation(s)
- Carlos Molina
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
- Unité de Recherche en Légumineuses, INRA-URLEG, 17 Rue Sully, 21000 Dijon, France
| | | | - Faheema Khan
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard University, New Delhi, India
| | - Nadia Fatnassi
- Estación Experimental del Zaidín, CSIC, C/Profesor Albareda, 1, 18008-Granada, Spain
| | - Ralf Horres
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
| | - Björn Rotter
- GenXPro GmbH, Frankfurt Innovation Center FIZ Biotechnology, Altendörferallee 3, D-60438 Frankfurt am Main, Germany
| | - Diana Steinhauer
- GenXPro GmbH, Frankfurt Innovation Center FIZ Biotechnology, Altendörferallee 3, D-60438 Frankfurt am Main, Germany
| | - Laurie Amenc
- Soil Symbiosis and Environment, INRA, 1 place Viala, 34060 Montpellier-Cedex, France
| | - Jean-Jacques Drevon
- Soil Symbiosis and Environment, INRA, 1 place Viala, 34060 Montpellier-Cedex, France
| | - Peter Winter
- GenXPro GmbH, Frankfurt Innovation Center FIZ Biotechnology, Altendörferallee 3, D-60438 Frankfurt am Main, Germany
| | - Günter Kahl
- Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt am Main, Germany
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Shimokawa K, Mogushi K, Shoji S, Hiraishi A, Ido K, Mizushima H, Tanaka H. iCOD: an integrated clinical omics database based on the systems-pathology view of disease. BMC Genomics 2010; 11 Suppl 4:S19. [PMID: 21143802 PMCID: PMC3005924 DOI: 10.1186/1471-2164-11-s4-s19] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Variety of information relating between genome and the pathological findings in disease will yield a wealth of clues to discover new function, the role of genes and pathways, and future medicine. In addition to molecular information such as gene expression and genome copy number, detailed clinical information is essential for such systematic omics analysis. RESULTS In order to provide a basic platform to realize a future medicine based on the integration of molecular and clinico-pathological information of disease, we have developed an integrated clinical omics database (iCOD) in which comprehensive disease information of the patients is collected, including not only molecular omics data such as CGH (Comparative Genomic Hybridization) and gene expression profiles but also comprehensive clinical information such as clinical manifestations, medical images (CT, X-ray, ultrasounds, etc), laboratory tests, drug histories, pathological findings and even life-style/environmental information. The iCOD is developed to combine the molecular and clinico-pathological information of the patients to provide the holistic understanding of the disease. Furthermore, we developed several kinds of integrated view maps of disease in the iCOD, which summarize the comprehensive patient data to provide the information for the interrelation between the molecular omics data and clinico-pathological findings as well as estimation for the disease pathways, such as three layer-linked disease map, disease pathway map, and pathome-genome map. CONCLUSIONS With these utilities, our iCOD aims to contribute to provide the omics basis of the disease as well as to promote the pathway-directed disease view. The iCOD database is available online, containing 140 patient cases of hepatocellular carcinoma, with raw data of each case as supplemental data set to download. The iCOD and supplemental data can be accessed at http://omics.tmd.ac.jp/icod_pub_eng.
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Affiliation(s)
- Kazuro Shimokawa
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
| | - Kaoru Mogushi
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
| | - Satoshi Shoji
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
| | - Atsuko Hiraishi
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
| | - Keisuke Ido
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
| | - Hiroshi Mizushima
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
| | - Hiroshi Tanaka
- Information Center for Medical Sciences, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
- Department of Bioinformatics and Computational Biology School of Biomedical Science, Tokyo Medical Dental University, Yushima Bunkyo-ku, Tokyo, Japan
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Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res 2010; 39:D835-41. [PMID: 21062809 PMCID: PMC3013713 DOI: 10.1093/nar/gkq1132] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Gene Expression Database (GXD) is a community resource of mouse developmental expression information. GXD integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants. GXD places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases. Web-based query forms support simple or complex searches that take advantage of all these integrated data. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. Since the last report, the GXD data content has increased significantly, the interface and data displays have been improved, new querying capabilities were implemented, and links to other expression resources were added. GXD is available through the MGI web site (www.informatics.jax.org), or directly at www.informatics.jax.org/expression.shtml.
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Valletti A, Anselmo A, Mangiulli M, Boria I, Mignone F, Merla G, D'Angelo V, Tullo A, Sbisà E, D'Erchia AM, Pesole G. Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation. Mol Cancer 2010; 9:230. [PMID: 20813049 PMCID: PMC2941758 DOI: 10.1186/1476-4598-9-230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 09/02/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Many evidences report that alternative splicing, the mechanism which produces mRNAs and proteins with different structures and functions from the same gene, is altered in cancer cells. Thus, the identification and characterization of cancer-specific splice variants may give large impulse to the discovery of novel diagnostic and prognostic tumour biomarkers, as well as of new targets for more selective and effective therapies. RESULTS We present here a genome-wide analysis of the alternative splicing pattern of human genes through a computational analysis of normal and cancer-specific ESTs from seventeen anatomical groups, using data available in AspicDB, a database resource for the analysis of alternative splicing in human. By using a statistical methodology, normal and cancer-specific genes, splice sites and cassette exons were predicted in silico. The condition association of some of the novel normal/tumoral cassette exons was experimentally verified by RT-qPCR assays in the same anatomical system where they were predicted. Remarkably, the presence in vivo of the predicted alternative transcripts, specific for the nervous system, was confirmed in patients affected by glioblastoma. CONCLUSION This study presents a novel computational methodology for the identification of tumor-associated transcript variants to be used as cancer molecular biomarkers, provides its experimental validation, and reports specific biomarkers for glioblastoma.
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Affiliation(s)
- Alessio Valletti
- Dipartimento di Biochimica e Biologia Molecolare, University of Bari, Quagliariello, via Orabona 4, Bari 70126, Italy
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Morrissy S, Zhao Y, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Prabhu AL, Tam A, Hirst M, Marra M. Digital gene expression by tag sequencing on the illumina genome analyzer. ACTA ACUST UNITED AC 2010; Chapter 11:Unit 11.11.1-36. [PMID: 20373513 DOI: 10.1002/0471142905.hg1111s65] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This unit provides a protocol for performing digital gene expression profiling on the Illumina Genome Analyzer sequencing platform. Tag sequencing (Tag-seq) is an implementation of the LongSAGE protocol on the Illumina sequencing platform that increases utility while reducing both the cost and time required to generate gene expression profiles. The ultra-high-throughput sequencing capability of the Illumina platform allows the cost-effective generation of libraries containing an average of 20 million tags, a 200-fold improvement over classical LongSAGE. Tag-seq has less sequence composition bias, leading to a better representation of AT-rich tag sequences, and allows a more accurate profiling of a subset of the transcriptome characterized by AT-rich genes expressed at levels below the threshold of detection of LongSAGE (Morrissy et al., 2009).
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Affiliation(s)
- Sorana Morrissy
- BCCA Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Chari R, Lonergan KM, Pikor LA, Coe BP, Zhu CQ, Chan THW, MacAulay CE, Tsao MS, Lam S, Ng RT, Lam WL. A sequence-based approach to identify reference genes for gene expression analysis. BMC Med Genomics 2010; 3:32. [PMID: 20682026 PMCID: PMC2928167 DOI: 10.1186/1755-8794-3-32] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 08/03/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An important consideration when analyzing both microarray and quantitative PCR expression data is the selection of appropriate genes as endogenous controls or reference genes. This step is especially critical when identifying genes differentially expressed between datasets. Moreover, reference genes suitable in one context (e.g. lung cancer) may not be suitable in another (e.g. breast cancer). Currently, the main approach to identify reference genes involves the mining of expression microarray data for highly expressed and relatively constant transcripts across a sample set. A caveat here is the requirement for transcript normalization prior to analysis, and measurements obtained are relative, not absolute. Alternatively, as sequencing-based technologies provide digital quantitative output, absolute quantification ensues, and reference gene identification becomes more accurate. METHODS Serial analysis of gene expression (SAGE) profiles of non-malignant and malignant lung samples were compared using a permutation test to identify the most stably expressed genes across all samples. Subsequently, the specificity of the reference genes was evaluated across multiple tissue types, their constancy of expression was assessed using quantitative RT-PCR (qPCR), and their impact on differential expression analysis of microarray data was evaluated. RESULTS We show that (i) conventional references genes such as ACTB and GAPDH are highly variable between cancerous and non-cancerous samples, (ii) reference genes identified for lung cancer do not perform well for other cancer types (breast and brain), (iii) reference genes identified through SAGE show low variability using qPCR in a different cohort of samples, and (iv) normalization of a lung cancer gene expression microarray dataset with or without our reference genes, yields different results for differential gene expression and subsequent analyses. Specifically, key established pathways in lung cancer exhibit higher statistical significance using a dataset normalized with our reference genes relative to normalization without using our reference genes. CONCLUSIONS Our analyses found NDUFA1, RPL19, RAB5C, and RPS18 to occupy the top ranking positions among 15 suitable reference genes optimal for normalization of lung tissue expression data. Significantly, the approach used in this study can be applied to data generated using new generation sequencing platforms for the identification of reference genes optimal within diverse contexts.
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Affiliation(s)
- Raj Chari
- Department of Integrative Oncology, British Columbia Cancer Agency Research Centre, Vancouver, BC, Canada.
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hHSS1: a novel secreted factor and suppressor of glioma growth located at chromosome 19q13.33. J Neurooncol 2010; 102:197-211. [PMID: 20680400 PMCID: PMC3052511 DOI: 10.1007/s11060-010-0314-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 07/12/2010] [Indexed: 11/24/2022]
Abstract
The completion of the Human Genome Project resulted in discovery of many unknown novel genes. This feat paved the way for the future development of novel therapeutics for the treatment of human disease based on novel biological functions and pathways. Towards this aim, we undertook a bioinformatics analysis of in-house microarray data derived from purified hematopoietic stem cell populations. This effort led to the discovery of HSS1 (Hematopoietic Signal peptide-containing Secreted 1) and its splice variant HSM1 (Hematopoietic Signal peptide-containing Membrane domain-containing 1). HSS1 gene is evolutionarily conserved across species, phyla and even kingdoms, including mammals, invertebrates and plants. Structural analysis showed no homology between HSS1 and known proteins or known protein domains, indicating that it was a truly novel protein. Interestingly, the human HSS1 (hHSS1) gene is located at chromosome 19q13.33, a genomic region implicated in various cancers, including malignant glioma. Stable expression of hHSS1 in glioma-derived A172 and U87 cell lines greatly reduced their proliferation rates compared to mock-transfected cells. hHSS1 expression significantly affected the malignant phenotype of U87 cells both in vitro and in vivo. Further, preliminary immunohistochemical analysis revealed an increase in hHSS1/HSM1 immunoreactivity in two out of four high-grade astrocytomas (glioblastoma multiforme, WHO IV) as compared to low expression in all four low-grade diffuse astrocytomas (WHO grade II). High-expression of hHSS1 in high-grade gliomas was further supported by microarray data, which indicated that mesenchymal subclass gliomas exclusively up-regulated hHSS1. Our data reveal that HSS1 is a truly novel protein defining a new class of secreted factors, and that it may have an important role in cancer, particularly glioma.
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Gellert P, Jenniches K, Braun T, Uchida S. C-It: a knowledge database for tissue-enriched genes. Bioinformatics 2010; 26:2328-33. [PMID: 20628071 DOI: 10.1093/bioinformatics/btq417] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Due to the development of high-throughput technologies such as microarrays, it has become possible to determine genome-wide expression changes in a single experiment. Although much attention has been paid to identify differentially expressed genes, the functions of tens of thousands of genes in different species still remain unknown. RESULTS C-It is a knowledge database that has its focus on 'uncharacterized genes'. C-It contains expression profiles of various tissues from human, mouse, rat, chicken and zebrafish. By applying our previously introduced algorithm DGSA (Database-Dependent Gene Selection and Analysis), it is possible to screen for uncharacterized, tissue-enriched genes in the species mentioned above. C-It is designed to include further expression studies, which might provide more comprehensive coverage of gene expression patterns and tissue-enriched splicing isoforms. We propose that C-It will be an excellent starting point to study uncharacterized genes. AVAILABILITY C-It is freely available online without registration at http://C-It.mpi-bn.mpg.dehttp://C-It.mpi-bn.mpg.de.
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Affiliation(s)
- Pascal Gellert
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
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Kavak E, Unlü M, Nistér M, Koman A. Meta-analysis of cancer gene expression signatures reveals new cancer genes, SAGE tags and tumor associated regions of co-regulation. Nucleic Acids Res 2010; 38:7008-21. [PMID: 20621981 PMCID: PMC2978353 DOI: 10.1093/nar/gkq574] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cancer is among the major causes of human death and its mechanism(s) are not fully understood. We applied a novel meta-analysis approach to multiple sets of merged serial analysis of gene expression and microarray cancer data in order to analyze transcriptome alterations in human cancer. Our methodology, which we denote ‘COgnate Gene Expression patterNing in tumours’ (COGENT), unmasked numerous genes that were differentially expressed in multiple cancers. COGENT detected well-known tumor-associated (TA) genes such as TP53, EGFR and VEGF, as well as many multi-cancer, but not-yet-tumor-associated genes. In addition, we identified 81 co-regulated regions on the human genome (RIDGEs) by using expression data from all cancers. Some RIDGEs (28%) consist of paralog genes while another subset (30%) are specifically dysregulated in tumors but not in normal tissues. Furthermore, a significant number of RIDGEs are associated with GC-rich regions on the genome. All assembled data is freely available online (www.oncoreveal.org) as a tool implementing COGENT analysis of multi-cancer genes and RIDGEs. These findings engender a deeper understanding of cancer biology by demonstrating the existence of a pool of under-studied multi-cancer genes and by highlighting the cancer-specificity of some TA-RIDGEs.
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Affiliation(s)
- Ersen Kavak
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey.
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An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. PLoS Genet 2010; 6:e1000977. [PMID: 20548944 PMCID: PMC2883588 DOI: 10.1371/journal.pgen.1000977] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 05/06/2010] [Indexed: 01/14/2023] Open
Abstract
Osteoporosis is a complex disorder and commonly leads to fractures in elderly persons. Genome-wide association studies (GWAS) have become an unbiased approach to identify variations in the genome that potentially affect health. However, the genetic variants identified so far only explain a small proportion of the heritability for complex traits. Due to the modest genetic effect size and inadequate power, true association signals may not be revealed based on a stringent genome-wide significance threshold. Here, we take advantage of SNP and transcript arrays and integrate GWAS and expression signature profiling relevant to the skeletal system in cellular and animal models to prioritize the discovery of novel candidate genes for osteoporosis-related traits, including bone mineral density (BMD) at the lumbar spine (LS) and femoral neck (FN), as well as geometric indices of the hip (femoral neck-shaft angle, NSA; femoral neck length, NL; and narrow-neck width, NW). A two-stage meta-analysis of GWAS from 7,633 Caucasian women and 3,657 men, revealed three novel loci associated with osteoporosis-related traits, including chromosome 1p13.2 (RAP1A, p = 3.6x10(-8)), 2q11.2 (TBC1D8), and 18q11.2 (OSBPL1A), and confirmed a previously reported region near TNFRSF11B/OPG gene. We also prioritized 16 suggestive genome-wide significant candidate genes based on their potential involvement in skeletal metabolism. Among them, 3 candidate genes were associated with BMD in women. Notably, 2 out of these 3 genes (GPR177, p = 2.6x10(-13); SOX6, p = 6.4x10(-10)) associated with BMD in women have been successfully replicated in a large-scale meta-analysis of BMD, but none of the non-prioritized candidates (associated with BMD) did. Our results support the concept of our prioritization strategy. In the absence of direct biological support for identified genes, we highlighted the efficiency of subsequent functional characterization using publicly available expression profiling relevant to the skeletal system in cellular or whole animal models to prioritize candidate genes for further functional validation.
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