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Ji Y, Lv J, Sun D, Huang Y. Therapeutic strategies targeting Wnt/β‑catenin signaling for colorectal cancer (Review). Int J Mol Med 2022; 49:1. [PMID: 34713301 PMCID: PMC8589460 DOI: 10.3892/ijmm.2021.5056] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common carcinomas. Although great progress has been made in recent years, CRC survival remains unsatisfactory due to high metastasis and recurrence. Understanding the underlying molecular mechanisms of CRC tumorigenesis and metastasis has become increasingly important. Recently, aberrant Wnt/β‑catenin signaling has been reported to be strongly associated with CRC tumorigenesis, metastasis and recurrence. Therefore, the Wnt/β‑catenin signaling pathway has potential value as a therapeutic target for CRC. In the present review, the dysregulation of this pathway in CRC and the promoting or suppressing function of therapeutic targets on CRC were explored. In addition, the interaction between this pathway and epithelial‑mesenchymal transition (EMT), cell stemness, mutations, metastasis‑related genes and tumor angiogenesis in CRC cells were also investigated. Numerous studies on this pathway may help identify the potential diagnostic and prognostic markers and therapeutic targets for CRC.
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Affiliation(s)
- Yong Ji
- Department of General Surgery, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
| | - Jian Lv
- Department of General Surgery, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
| | - Di Sun
- Department of General Surgery, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
| | - Yufeng Huang
- Department of Oncology, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
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2
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Fibroblast Growth Factor 9 Correlation with Lymphatic and Vascular Invasion in Colorectal Cancer. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2021. [DOI: 10.5812/ijcm.109686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background: Fibroblast growth factor 9 (FGF9) or Glia activating factor (GAF) is categorized in the paracrine class of the FGF family, which is involved in various cancer development and progressions. Interestingly, the invasion role of FGF9 in colorectal cancer (CRC) was not clarified up to now. Objectives: In the present investigation, the lymphatic and vascular invasion characteristic of FGF9 was figured out in fresh frozen (FF) tissue samples and paired Formalin-fixed, paraffin-embedded (FFPE) tissues. Methods: The present invasion study according to FGF9 expression evaluation was performed on 80 cancerous resected fresh tissues and 40 paired paraffined block specimens parallel with 80 adjacent non-tumoral tissue samples. RNA extraction and cDNA synthesis were performed; qRT-PCR at mRNA level was applied. FGF9 expression correlation with clinical parameters was defined by the Mann-Whitney U-test. ROC curve and Kaplan-Meier analyses were designed to show the value of prognostic biomarker of FGF9. Results: Accordingly, 52% of fresh tissue samples and 51% of FFPE specimens were upregulated in comparison with corresponding normal tissues. A significant correlation was seen between FGF9 expression level and tumor stage (P < 0.0017, P < 0.03), lymph node metastasis (P < 0.001, P < 0.047), and vascular invasion (P < 0.004, P < 0.047) in fresh tissue samples and paraffined blocks, respectively. ROC was created to distinguish stage I and II from III and IV in FF and FFPE samples, respectively (P < 0.002, P < 0.031). Likewise, the AUC evaluation in both fresh and paraffined samples was similar. The overall survival was lower in 3 years of follow-up in patients with CRC with overexpression of FGF9 (P < 0.02). Conclusions: Altogether, it can be deduced that lymphatic and vascular invasion correlated with FGF9 upregulation since FGF9 can be used as an effective prognostic biomarker according to pathologic results even in paraffined block samples or FF tissue specimens in CRC.
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3
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Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 2020; 74:1392-1408. [PMID: 32445281 DOI: 10.1111/evo.14023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
Abstract
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164.,Plant Biology, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Soraia Barbosa
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Menna Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Sarah Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Barbara Schönfeld
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Hamish McCallum
- School of Environment, Griffith University Nathan, Nathan, QLD, 4111, Australia
| | - Elisa Lopez-Contreras
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Samantha J Kallinen
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
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4
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Zhang Z, Zhang Y, Qin X, Wang Y, Fu J. FGF9 promotes cisplatin resistance in colorectal cancer via regulation of Wnt/β-catenin signaling pathway. Exp Ther Med 2019; 19:1711-1718. [PMID: 32104224 PMCID: PMC7026987 DOI: 10.3892/etm.2019.8399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/09/2019] [Indexed: 12/12/2022] Open
Abstract
Development of cisplatin resistance in colorectal cancer is largely caused by dysregulation of signaling pathways, including the Wnt/β-catenin signaling pathway, in cancer cells. Further investigation into the molecular mechanism of chemoresistance could improve outcomes for patients with colorectal cancer. The present study determined that fibroblast growth factor 9 (FGF9) was overexpressed in tumor tissues compared with normal tissues from patients with colorectal cancer. Using the colorectal cancer cell line LoVo, transfection of recombinant FGF9 decreased cisplatin-induced cell apoptosis whilst FGF9 silencing increased cisplatin-induced apoptosis. Western blot analysis and reverse transcription-quantitative polymerase chain reaction demonstrated that FGF9 decreased adenomatous polyposis coli (APC) mRNA and protein expression and contributed to activation of the Wnt/β-catenin signaling pathway. Notably, an increase in FGF9 and β-catenin protein expression and a decrease in APC protein expression was observed in the established LoVo cisplatin resistant cell line (LoVo/cisplatin). Silencing of FGF9 reversed cisplatin resistance of LoVo/cisplatin cells. In conclusion, the present findings suggested that FGF9 activated the Wnt signaling pathway and was a mediator of cisplatin resistance in colorectal cancer.
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Affiliation(s)
- Zhijin Zhang
- Department of Gastroenterological Surgery, Shanghai Eighth People's Hospital, Shanghai 200235, P.R. China
| | - Yuhao Zhang
- Department of Gastroenterological Surgery, Shanghai Eighth People's Hospital, Shanghai 200235, P.R. China
| | - Xinju Qin
- Department of Gastroenterological Surgery, Shanghai Eighth People's Hospital, Shanghai 200235, P.R. China
| | - Yuexia Wang
- Department of Gastroenterological Surgery, Shanghai Eighth People's Hospital, Shanghai 200235, P.R. China
| | - Jun Fu
- Department of Gastroenterological Surgery, Shanghai Eighth People's Hospital, Shanghai 200235, P.R. China
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5
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Asakawa M, Itoh M, Suganami T, Sakai T, Kanai S, Shirakawa I, Yuan X, Hatayama T, Shimada S, Akiyama Y, Fujiu K, Inagaki Y, Manabe I, Yamaoka S, Yamada T, Tanaka S, Ogawa Y. Upregulation of cancer-associated gene expression in activated fibroblasts in a mouse model of non-alcoholic steatohepatitis. Sci Rep 2019; 9:19601. [PMID: 31862949 PMCID: PMC6925281 DOI: 10.1038/s41598-019-56039-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Non-alcoholic steatohepatitis (NASH), characterized by chronic inflammation and fibrosis, is predicted to be the leading cause of cirrhosis and hepatocellular carcinoma (HCC) in the next decade. Although recent evidence suggests the importance of fibrosis as the strongest determinant of HCC development, the molecular mechanisms underlying NASH-induced carcinogenesis still remain unclear. Here we performed RNA sequencing analysis to compare gene expression profiles of activated fibroblasts prepared from two distinct liver fibrosis models: carbon tetrachloride–induced fibrosis as a model without obesity and HCC and genetically obese melanocortin 4 receptor–deficient (MC4R-KO) mice fed Western diet, which develop steatosis, NASH, and eventually HCC. Our data showed that activated fibroblasts exhibited distinct gene expression patterns in each etiology, and that the ‘pathways in cancer’ were selectively upregulated in the activated fibroblasts from MC4R-KO mice. The most upregulated gene in these pathways was fibroblast growth factor 9 (FGF9), which was induced by metabolic stress such as palmitate. FGF9 exerted anti-apoptotic and pro-migratory effects in fibroblasts and hepatoma cells in vitro and accelerated tumor growth in a subcutaneous xenograft model. This study reveals upregulation of cancer-associated gene expression in activated fibroblasts in NASH, which would contribute to the progression from NASH to HCC.
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Affiliation(s)
- Masahiro Asakawa
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michiko Itoh
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. .,Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan. .,Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.
| | - Takayoshi Suganami
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan. .,Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Takeru Sakai
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Kanai
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ibuki Shirakawa
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Xunmei Yuan
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomomi Hatayama
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shu Shimada
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Katsuhito Fujiu
- Department of Advanced Cardiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Inagaki
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Japan
| | - Ichiro Manabe
- Department of Disease Biology and Molecular Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shoji Yamaoka
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tetsuya Yamada
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shinji Tanaka
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshihiro Ogawa
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan. .,Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan. .,Department of Molecular and Cellular Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. .,Japan Agency for Medical Research and Development, CREST, Tokyo, Japan.
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6
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Secretome Screening Reveals Fibroblast Growth Factors as Novel Inhibitors of Viral Replication. J Virol 2018; 92:JVI.00260-18. [PMID: 29899088 DOI: 10.1128/jvi.00260-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Cellular antiviral programs can efficiently inhibit viral infection. These programs are often initiated through signaling cascades induced by secreted proteins, such as type I interferons, interleukin-6 (IL-6), or tumor necrosis factor alpha (TNF-α). In the present study, we generated an arrayed library of 756 human secreted proteins to perform a secretome screen focused on the discovery of novel modulators of viral entry and/or replication. The individual secreted proteins were tested for the capacity to inhibit infection by two replication-competent recombinant vesicular stomatitis viruses (VSVs) with distinct glycoproteins utilizing different entry pathways. Fibroblast growth factor 16 (FGF16) was identified and confirmed as the most prominent novel inhibitor of both VSVs and therefore of viral replication, not entry. Importantly, an antiviral interferon signature was completely absent in FGF16-treated cells. Nevertheless, the antiviral effect of FGF16 is broad, as it was evident on multiple cell types and also on infection by coxsackievirus. In addition, other members of the FGF family also inhibited viral infection. Thus, our unbiased secretome screen revealed a novel protein family capable of inducing a cellular antiviral state. This previously unappreciated role of the FGF family may have implications for the development of new antivirals and the efficacy of oncolytic virus therapy.IMPORTANCE Viruses infect human cells in order to replicate, while human cells aim to resist infection. Several cellular antiviral programs have therefore evolved to resist infection. Knowledge of these programs is essential for the design of antiviral therapeutics in the future. The induction of antiviral programs is often initiated by secreted proteins, such as interferons. We hypothesized that other secreted proteins may also promote resistance to viral infection. Thus, we tested 756 human secreted proteins for the capacity to inhibit two pseudotypes of vesicular stomatitis virus (VSV). In this secretome screen on viral infection, we identified fibroblast growth factor 16 (FGF16) as a novel antiviral against multiple VSV pseudotypes as well as coxsackievirus. Subsequent testing of other FGF family members revealed that FGF signaling generally inhibits viral infection. This finding may lead to the development of new antivirals and may also be applicable for enhancing oncolytic virus therapy.
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7
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Sinha S. Hilbert-Schmidt and Sobol sensitivity indices for static and time series Wnt signaling measurements in colorectal cancer - part A. BMC SYSTEMS BIOLOGY 2017; 11:120. [PMID: 29202761 PMCID: PMC5716378 DOI: 10.1186/s12918-017-0488-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022]
Abstract
Background Ever since the accidental discovery of Wingless [Sharma R.P., Drosophila information service, 1973, 50, p 134], research in the field of Wnt signaling pathway has taken significant strides in wet lab experiments and various cancer clinical trials, augmented by recent developments in advanced computational modeling of the pathway. Information rich gene expression profiles reveal various aspects of the signaling pathway and help in studying different issues simultaneously. Hitherto, not many computational studies exist which incorporate the simultaneous study of these issues. Results This manuscript ∙ explores the strength of contributing factors in the signaling pathway, ∙ analyzes the existing causal relations among the inter/extracellular factors effecting the pathway based on prior biological knowledge and ∙ investigates the deviations in fold changes in the recently found prevalence of psychophysical laws working in the pathway. To achieve this goal, local and global sensitivity analysis is conducted on the (non)linear responses between the factors obtained from static and time series expression profiles using the density (Hilbert-Schmidt Information Criterion) and variance (Sobol) based sensitivity indices. Conclusion The results show the advantage of using density based indices over variance based indices mainly due to the former’s employment of distance measures & the kernel trick via Reproducing kernel Hilbert space (RKHS) that capture nonlinear relations among various intra/extracellular factors of the pathway in a higher dimensional space. In time series data, using these indices it is now possible to observe where in time, which factors get influenced & contribute to the pathway, as changes in concentration of the other factors are made. This synergy of prior biological knowledge, sensitivity analysis & representations in higher dimensional spaces can facilitate in time based administration of target therapeutic drugs & reveal hidden biological information within colorectal cancer samples.
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Affiliation(s)
- Shriprakash Sinha
- Faculty of Maths & IT, Royal Thimphu College, Nagbiphu, Thimphu, 1122, Bhutan.
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8
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Wang Q, Liu S, Zhao X, Wang Y, Tian D, Jiang W. MiR-372-3p promotes cell growth and metastasis by targeting FGF9 in lung squamous cell carcinoma. Cancer Med 2017; 6:1323-1330. [PMID: 28440022 PMCID: PMC5463061 DOI: 10.1002/cam4.1026] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/26/2016] [Accepted: 01/06/2017] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to study the role of miR‐372‐3p in lung squamous cell carcinoma (LSCC) cell proliferation and invasion by suppressing FGF9. RT‐PCR was used to determine miR‐372‐3p and FGF9 mRNA expression in tissues and cells. Western blot was used to determine FGF9 expression in tissues and NCI‐H520 cell line. Dual luciferase reporter gene assay was conducted to confirm that FGF9 can be directly targeted by miR‐372‐3p. MTT, colony formation assays were conducted to investigate the effects of ectopic miR‐372‐3p and FGF9 expression on NCI‐H520 cell growth. Flow cytometry was used to analyze the influence of miR‐372‐3p and FGF9 expression on cell cycle distribution and apoptosis. Transwell assay was also conducted to see the effects of miR‐372‐3p and FGF9 expression on NCI‐H520 cell invasiveness. MiR‐372‐3p was found significantly overexpressed in both LSCC tissues and cell lines, whereas FGF9 mRNA was found underexpressed in LSCC tissues. MiR‐372‐3p directly bound to wild‐type FGF9 mRNA 3′UTR, therefore led to the reduction in FGF9 expression. The upregulation of FGF9 or the downregulation of miR‐372‐3p substantially retarded LSCC cell growth, mitosis, and invasion. MiR‐372‐3p enhanced LSCC cell proliferation and invasion through inhibiting FGF9.
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Affiliation(s)
- Qing Wang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
| | - Siyang Liu
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
| | - Xitong Zhao
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
| | - Yuan Wang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
| | - Dali Tian
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
| | - Wenjun Jiang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
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9
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Yin Y, Ren X, Smith C, Guo Q, Malabunga M, Guernah I, Zhang Y, Shen J, Sun H, Chehab N, Loizos N, Ludwig DL, Ornitz DM. Inhibition of fibroblast growth factor receptor 3-dependent lung adenocarcinoma with a human monoclonal antibody. Dis Model Mech 2016; 9:563-71. [PMID: 27056048 PMCID: PMC4892666 DOI: 10.1242/dmm.024760] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 03/30/2016] [Indexed: 12/20/2022] Open
Abstract
Activating mutations in fibroblast growth factor receptor 3 (FGFR3) have been identified in multiple types of human cancer and in congenital birth defects. In human lung cancer, fibroblast growth factor 9 (FGF9), a high-affinity ligand for FGFR3, is overexpressed in 10% of primary resected non-small cell lung cancer (NSCLC) specimens. Furthermore, in a mouse model where FGF9 can be induced in lung epithelial cells, epithelial proliferation and ensuing tumorigenesis is dependent on FGFR3. To develop new customized therapies for cancers that are dependent on FGFR3 activation, we have used this mouse model to evaluate a human monoclonal antibody (D11) with specificity for the extracellular ligand-binding domain of FGFR3, that recognizes both human and mouse forms of the receptor. Here, we show that D11 effectively inhibits signaling through FGFR3 in vitro, inhibits the growth of FGFR3-dependent FGF9-induced lung adenocarcinoma in mice, and reduces tumor-associated morbidity. Given the potency of FGF9 in this mouse model and the absolute requirement for signaling through FGFR3, this study validates the D11 antibody as a potentially useful and effective reagent for treating human cancers or other pathologies that are dependent on activation of FGFR3. Summary: This study validates the FGF9 lung adenocarcinoma mouse model as a tool to screen and evaluate potential therapeutics that are designed to inhibit FGF9 or its target receptor, FGFR3.
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Affiliation(s)
- Yongjun Yin
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Xiaodi Ren
- Department of Quantitative Biology, Eli Lilly and Company, New York, NY 10016, USA
| | - Craig Smith
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qianxu Guo
- Department of Cancer Angiogenesis, Eli Lilly and Company, New York, NY 10016, USA
| | - Maria Malabunga
- Department of Immunology, Eli Lilly and Company, New York, NY 10016, USA
| | - Ilhem Guernah
- Department of Immunology, Eli Lilly and Company, New York, NY 10016, USA
| | - Yiwei Zhang
- Department of Antibody Technology, Eli Lilly and Company, New York, NY 10016, USA
| | - Juqun Shen
- Department of Antibody Technology, Eli Lilly and Company, New York, NY 10016, USA
| | - Haijun Sun
- Department of Bioprocess Sciences, Eli Lilly and Company, New York, NY 10016, USA
| | - Nabil Chehab
- Department of Immunology, Eli Lilly and Company, New York, NY 10016, USA
| | - Nick Loizos
- Department of Immunology, Eli Lilly and Company, New York, NY 10016, USA
| | - Dale L Ludwig
- Department of Bioprocess Sciences, Eli Lilly and Company, New York, NY 10016, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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10
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Mizukami T, Togashi Y, Naruki S, Banno E, Terashima M, de Velasco MA, Sakai K, Yoneshige A, Hayashi H, Fujita Y, Tomida S, Nakajima TE, Fujino T, Boku N, Ito A, Nakagawa K, Nishio K. Significance of FGF9 gene in resistance to anti-EGFR therapies targeting colorectal cancer: A subset of colorectal cancer patients with FGF9 upregulation may be resistant to anti-EGFR therapies. Mol Carcinog 2016; 56:106-117. [PMID: 26916220 DOI: 10.1002/mc.22476] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/31/2016] [Accepted: 02/06/2016] [Indexed: 01/04/2023]
Abstract
Although fibroblast growth factor (FGF) signals are strongly associated with malignancy, limited information is available regarding the role of the FGF9 signal in colorectal cancer (CRC). In this study, we investigated the frequency of FGF9 amplification in CRC clinical specimens and the association between the FGF9 gene and resistance to anti-EGFR therapies. In clinical samples, an FGF9 copy number gain of >5 copies was observed at a frequency of 8/145 (5.5%) and tended to be related to wild-type KRAS (7/96, 7.3%). Furthermore, FGF9 amplification was not observed in any of the samples from the 15 responders to anti-EGFR therapies but was observed in one sample from the seven non-responders with wild-type KRAS, and two samples from non-responders also had high FGF9 mRNA expression levels. FGF9 amplification was validated using a fluorescence in situ hybridization (FISH) analysis, and FGF9-amplified sections showed readily detectable signals originating from FGF9 protein when examined using immunohistochemistry. In both the in vitro and in vivo experiments using FGF9-overexpressing CRC cell lines, FGF9 overexpression induced strong resistance to anti-EGFR therapies via the enforced FGFR signal, and this resistance was cancelled by the application of an FGFR inhibitor. Considering these results, the FGF9 gene may play an important role in resistance to anti-EGFR therapies in patients with CRC, and such resistance might be overcome by combined treatment with an anti-FGFR inhibitor. These findings strongly encourage the development of FGFR-targeted therapy for CRC patients with FGF9 gene upregulation. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Takuro Mizukami
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan.,Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Yosuke Togashi
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Saeko Naruki
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Eri Banno
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Masato Terashima
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Marco A de Velasco
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Azusa Yoneshige
- Department of Pathology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Hidetoshi Hayashi
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan.,Department of Medical Oncology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Yoshihiko Fujita
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Shuta Tomida
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Takako Eguchi Nakajima
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Takashi Fujino
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Narikazu Boku
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Akihiko Ito
- Department of Pathology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University School of Medicine, Osaka-Sayama, Osaka, Japan
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11
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Liu R, Huang S, Lei Y, Zhang T, Wang K, Liu B, Nice EC, Xiang R, Xie K, Li J, Huang C. FGF8 promotes colorectal cancer growth and metastasis by activating YAP1. Oncotarget 2015; 6:935-52. [PMID: 25473897 PMCID: PMC4359266 DOI: 10.18632/oncotarget.2822] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/25/2014] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) is a major cause of cancer-related death worldwide. The poor prognosis of CRC is mainly due to uncontrolled tumor growth and distant metastases. In this study, we found that the level of FGF8 was elevated in the great majority of CRC cases and high FGF8 expression was significantly correlated with lymph nodes metastasis and worse overall survival. Functional studies showed that FGF8 can induce a more aggressive phenotype displaying epithelial-to-mesenchymal transition (EMT) and enhanced invasion and growth in CRC cells. Consistent with this, FGF8 can also promote tumor growth and metastasis in mouse models. Bioinformatics and pathological analysis suggested that YAP1 is a potential downstream target of FGF8 in CRC cells. Molecular validation demonstrated that FGF8 fully induced nuclear localization of YAP1 and enhanced transcriptional outcomes such as the expression of CTGF and CYR61, while decreasing YAP1 expression impeded FGF-8–induced cell growth, EMT, migration and invasion, revealing that YAP1 is required for FGF8-mediated CRC growth and metastasis. Taken together, these results demonstrate that FGF8 contributes to the proliferative and metastatic capacity of CRC cells and may represent a novel candidate for intervention in tumor growth and metastasis formation.
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Affiliation(s)
- Rui Liu
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Shan Huang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yunlong Lei
- Department of Biochemistry and Molecular Biology, and Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, P. R. China
| | - Tao Zhang
- The School of Biomedical Sciences, Chengdu Medical College, Chengdu, P. R. China
| | - Kui Wang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Bo Liu
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, P.R. China
| | - Ke Xie
- Department of Oncology, Sichuan Provincial People's Hospital, Chengdu, P. R. China
| | - Jingyi Li
- The School of Biomedical Sciences, Chengdu Medical College, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
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12
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Cohen-Kedar S, Baram L, Elad H, Brazowski E, Guzner-Gur H, Dotan I. Human intestinal epithelial cells respond to β-glucans via Dectin-1 and Syk. Eur J Immunol 2014; 44:3729-40. [PMID: 25251945 DOI: 10.1002/eji.201444876] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/04/2014] [Accepted: 09/22/2014] [Indexed: 12/14/2022]
Abstract
Intestinal epithelial cells (IECs) are the first to encounter luminal antigens and may be involved in intestinal immune responses. Fungi are important components of the intestinal microflora. The potential role of fungi, and in particular their cell wall component β-glucan, in modulating human intestinal epithelial responses is still unclear. Here we examined whether human IECs are capable of recognizing and responding to β-glucans, and the potential mechanisms of their activation. We show that human IECs freshly isolated from surgical specimens, and the human IEC lines HT-29 and SW480, express the β-glucan receptor Dectin-1. The β-glucan-consisting glycans curdlan and zymosan stimulated IL-8 and CCL2 secretion by IEC lines. This was significantly inhibited by a Dectin-1 blockade using its soluble antagonist laminarin. Spleen tyrosine kinase (Syk), a signaling mediator of Dectin-1 activation, is expressed in human IECs. β-glucans and Candida albicans induced Syk phosphorylation, and Syk inhibition significantly decreased β-glucan-induced chemokine secretion from IECs. Thus, IECs may respond to β-glucans by the secretion of pro-inflammatory chemokines in a Dectin-1- and Syk-dependent pathway, via receptors and a signaling pathway described to date only for myeloid cells. These findings highlight the importance of fungi-IEC interactions in intestinal inflammation.
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Affiliation(s)
- Sarit Cohen-Kedar
- Inflammatory Bowel Diseases Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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13
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Weygant N, Qu D, Berry WL, May R, Chandrakesan P, Owen DB, Sureban SM, Ali N, Janknecht R, Houchen CW. Small molecule kinase inhibitor LRRK2-IN-1 demonstrates potent activity against colorectal and pancreatic cancer through inhibition of doublecortin-like kinase 1. Mol Cancer 2014; 13:103. [PMID: 24885928 PMCID: PMC4030036 DOI: 10.1186/1476-4598-13-103] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/24/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Doublecortin-like kinase 1 (DCLK1) is emerging as a tumor specific stem cell marker in colorectal and pancreatic cancer. Previous in vitro and in vivo studies have demonstrated the therapeutic effects of inhibiting DCLK1 with small interfering RNA (siRNA) as well as genetically targeting the DCLK1+ cell for deletion. However, the effects of inhibiting DCLK1 kinase activity have not been studied directly. Therefore, we assessed the effects of inhibiting DCLK1 kinase activity using the novel small molecule kinase inhibitor, LRRK2-IN-1, which demonstrates significant affinity for DCLK1. RESULTS Here we report that LRRK2-IN-1 demonstrates potent anti-cancer activity including inhibition of cancer cell proliferation, migration, and invasion as well as induction of apoptosis and cell cycle arrest. Additionally we found that it regulates stemness, epithelial-mesenchymal transition, and oncogenic targets on the molecular level. Moreover, we show that LRRK2-IN-1 suppresses DCLK1 kinase activity and downstream DCLK1 effector c-MYC, and demonstrate that DCLK1 kinase activity is a significant factor in resistance to LRRK2-IN-1. CONCLUSIONS Given DCLK1's tumor stem cell marker status, a strong understanding of its biological role and interactions in gastrointestinal tumors may lead to discoveries that improve patient outcomes. The results of this study suggest that small molecule inhibitors of DCLK1 kinase should be further investigated as they may hold promise as anti-tumor stem cell drugs.
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Affiliation(s)
- Nathaniel Weygant
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Dongfeng Qu
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - William L Berry
- Peggy and Charles Stephenson Oklahoma Cancer Center, Oklahoma City, OK, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Randal May
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | | | - Daniel B Owen
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sripathi M Sureban
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Naushad Ali
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
- Peggy and Charles Stephenson Oklahoma Cancer Center, Oklahoma City, OK, USA
| | - Ralf Janknecht
- Peggy and Charles Stephenson Oklahoma Cancer Center, Oklahoma City, OK, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Courtney W Houchen
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
- Peggy and Charles Stephenson Oklahoma Cancer Center, Oklahoma City, OK, USA
- COARE Biotechnology, Oklahoma City, OK, USA
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14
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Ohgino K, Soejima K, Yasuda H, Hayashi Y, Hamamoto J, Naoki K, Arai D, Ishioka K, Sato T, Terai H, Ikemura S, Yoda S, Tani T, Kuroda A, Betsuyaku T. Expression of fibroblast growth factor 9 is associated with poor prognosis in patients with resected non-small cell lung cancer. Lung Cancer 2014; 83:90-6. [DOI: 10.1016/j.lungcan.2013.10.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 01/08/2023]
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15
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Chen TM, Shih YH, Tseng JT, Lai MC, Wu CH, Li YH, Tsai SJ, Sun HS. Overexpression of FGF9 in colon cancer cells is mediated by hypoxia-induced translational activation. Nucleic Acids Res 2013; 42:2932-44. [PMID: 24334956 PMCID: PMC3950685 DOI: 10.1093/nar/gkt1286] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Human fibroblast growth factor 9 (FGF9) is a potent mitogen involved in many physiological processes. Although FGF9 messenger RNA (mRNA) is ubiquitously expressed in embryos, FGF9 protein expression is generally low and restricted to a few adult organs. Aberrant expression of FGF9 usually results in human malignancies including cancers, but the mechanism remains largely unknown. Here, we report that FGF9 protein, but not mRNA, was increased in hypoxia. Two sequence elements, the upstream open reading frame (uORF) and the internal ribosome entry site (IRES), were identified in the 5' UTR of FGF9 mRNA. Functional assays indicated that FGF9 protein synthesis was normally controlled by uORF-mediated translational repression, which kept the protein at a low level, but was upregulated in response to hypoxia through a switch to IRES-dependent translational control. Our data demonstrate that FGF9 IRES functions as a cellular switch to turn FGF9 protein synthesis ‘on’ during hypoxia, a likely mechanism underlying FGF9 overexpression in cancer cells. Finally, we provide evidence to show that hypoxia-induced translational activation promotes FGF9 protein expression in colon cancer cells. Altogether, this dynamic working model may provide a new direction in anti-tumor therapies and cancer intervention.
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Affiliation(s)
- Tsung-Ming Chen
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, Institute of Bioinformatics and Biosignaling, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan and Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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16
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JIAO FENG, JIN ZILIANG, WANG LEI, WANG LIWEI. Research and clinical applications of molecular biomarkers in gastrointestinal carcinoma (Review). Biomed Rep 2013; 1:819-827. [PMID: 24649035 PMCID: PMC3917016 DOI: 10.3892/br.2013.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 08/12/2013] [Indexed: 11/06/2022] Open
Abstract
Gastrointestinal (GI) carcinoma is a common malignant disease worldwide. Its development and progression is a multistage process involving a multifactorial etiology. Although the detailed mechanisms of the development of GI carcinoma remain controversial, the elucidation of its molecular biology over the last few years has resulted in a better perspective on its epidemiology, carcinogenesis and pathogenesis. More significantly, it is currently possible to use biological indicators or biomarkers in differential diagnosis, prognostic evaluation and specific clinical interventions. In this review, we aimed to describe the biomarkers of pathogenesis, invasion, metastasis and prognosis of GI carcinoma and discuss their potential clinical applications. The majority of these biomarkers, such as tumor-associated antigens, oncogenes and tumor suppressor genes, metastasis-associated genes, cell adhesion molecules, cytokines, growth factors and microRNAs, are currently broadly applicable.
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Affiliation(s)
- FENG JIAO
- Department of Oncology, The First People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 201620, P.R. China
| | - ZILIANG JIN
- Department of Oncology, The First People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 201620, P.R. China
| | - LEI WANG
- Department of Oncology, The First People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 201620, P.R. China
| | - LIWEI WANG
- Department of Oncology, The First People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 201620, P.R. China
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17
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Secrier M, Schneider R. PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes. PLoS One 2013; 8:e72361. [PMID: 23951317 PMCID: PMC3741141 DOI: 10.1371/journal.pone.0072361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/13/2013] [Indexed: 01/04/2023] Open
Abstract
Timing common and specific modulators of disease progression is crucial for treatment, but the understanding of the underlying complex system of interactions is limited. While attempts at elucidating this experimentally have produced enormous amounts of phenotypic data, tools that are able to visualize and analyze them are scarce and the insight obtained from the data is often unsatisfactory. Linking and visualizing processes from genes to phenotypes and back, in a temporal context, remains a challenge in systems biology. We introduce PhenoTimer, a 2D/3D visualization tool for the mapping of time-resolved phenotypic links in a genetic context. It uses a novel visualization approach for relations between morphological defects, pathways or diseases, to enable fast pattern discovery and hypothesis generation. We illustrate its capabilities of tracing dynamic motifs on cell cycle datasets that explore the phenotypic order of events upon perturbations of the system, transcriptional activity programs and their connection to disease. By using this tool we are able to fine-grain regulatory programs for individual time points of the cell cycle and better understand which patterns arise when these programs fail. We also illustrate a way to identify common mechanisms of misregulation in diseases and drug abuse.
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Affiliation(s)
- Maria Secrier
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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18
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Surendranath V, Theis M, Habermann BH, Buchholz F. Designing efficient and specific endoribonuclease-prepared siRNAs. Methods Mol Biol 2013; 942:193-204. [PMID: 23027053 DOI: 10.1007/978-1-62703-119-6_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA interference (RNAi) has grown to be one of the main techniques for loss-of-function studies, leading to the elucidation of biological function of genes in various cellular systems and model organisms. While for many invertebrates such as Drosophila melanogaster (D. melanogaster) and Caenorhabditis elegans (C. elegans) long double-stranded RNA (dsRNA) can directly be used to induce a RNAi response, chemically synthesized small interfering RNAs (siRNAs) are typically employed in mammalian cells to avoid an interferon-like response triggered by long dsRNA (Reynolds et al., RNA 12:988-993, 2006). However, siRNAs are expensive and beset with unintentional gene targeting effects (off-targets) confounding the analysis of results from such studies. We, and others, have developed an alternative technology for RNAi in mammalian cells, termed endoribonuclease-prepared siRNA (esiRNA), which is based on the enzymatic generation of siRNA pools by digestion of long dsRNAs with recombinant RNase III in vitro (Yang et al., Proc Natl Acad Sci USA 99: 9942-9947, 2002; Myers et al., Nat Biotechnol 21:324-328; 2003). This technology has proven to be cost-efficient and reliable. Furthermore, several studies have demonstrated that complex pools of siRNAs, as inherent in esiRNAs, which target one transcript reduce off-target effects (Myers et al., J RNAi Gene Silencing 2:181, 2006; Kittler et al., Nat Methods 4:337-344, 2007). Within this chapter we describe design criteria for the generation of target-optimized esiRNAs.
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19
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Hsieh TH, Tsai CF, Hsu CY, Kuo PL, Hsi E, Suen JL, Hung CH, Lee JN, Chai CY, Wang SC, Tsai EM. n-Butyl benzyl phthalate promotes breast cancer progression by inducing expression of lymphoid enhancer factor 1. PLoS One 2012; 7:e42750. [PMID: 22905168 PMCID: PMC3414447 DOI: 10.1371/journal.pone.0042750] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 07/12/2012] [Indexed: 11/30/2022] Open
Abstract
Environmental hormones play important roles in regulating the expression of genes involved in cell proliferation, drug resistance, and breast cancer risk; however, their precise role in human breast cancer cells during cancer progression remains unclear. To elucidate the effect of the most widely used industrial phthalate, n-butyl benzyl phthalate (BBP), on cancer progression, we evaluated the results of BBP treatment using a whole human genome cDNA microarray and MetaCore software and selected candidate genes whose expression was changed by more than ten-fold by BBP compared with controls to analyze the signaling pathways in human breast cancer initiating cells (R2d). A total of 473 genes were upregulated, and 468 were downregulated. Most of these genes are involved in proliferation, epithelial-mesenchymal transition, and angiogenesis signaling. BBP induced the viability, invasion and migration, and tube formation in vitro, and Matrigel plug angiogenesis in vivo of R2d and MCF-7. Furthermore, the viability and invasion and migration of these cell lines following BBP treatment was reduced by transfection with a small interfering RNA targeting the mRNA for lymphoid enhancer-binding factor 1; notably, the altered expression of this gene consistently differentiated tumors expressing genes involved in proliferation, epithelial-mesenchymal transition, and angiogenesis. These findings contribute to our understanding of the molecular impact of the environmental hormone BBP and suggest possible strategies for preventing and treating human breast cancer.
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Affiliation(s)
- Tsung-Hua Hsieh
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cheng-Fang Tsai
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Yi Hsu
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Lin Kuo
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Edward Hsi
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jau-Ling Suen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hsing Hung
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jau-Nan Lee
- Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chee-Yin Chai
- Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shao-Chun Wang
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Eing-Mei Tsai
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail:
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