201
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Hsu CL, Chung FH, Chen CH, Hsu TT, Liu SM, Chung DS, Hsu YF, Chen CL, Ma N, Lee HC. Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions. Sci Rep 2016; 6:32523. [PMID: 27597445 PMCID: PMC5011650 DOI: 10.1038/srep32523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/08/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer stem cells (CSCs), or cancer cells with stem cell-like properties, generally exhibit drug resistance and have highly potent cancer inducing capabilities. Genome-wide expression data collected at public repositories over the last few years provide excellent material for studies that can lead to insights concerning the molecular and functional characteristics of CSCs. Here, we conducted functional genomic studies of CSC based on fourteen PCA-screened high quality public CSC whole genome gene expression datasets and, as control, four high quality non-stem-like cancer cell and non-cancerous stem cell datasets from the Gene Expression Omnibus database. A total of 6,002 molecular signatures were taken from the Molecular Signatures Database and used to characterize the datasets, which, under two-way hierarchical clustering, formed three genotypes. Type 1, consisting of mainly glia CSCs, had significantly enhanced proliferation, and significantly suppressed epithelial-mesenchymal transition (EMT), related functions. Type 2, mainly breast CSCs, had significantly enhanced EMT, but not proliferation, related functions. Type 3, composed of ovarian, prostate, and colon CSCs, had significantly suppressed proliferation related functions and mixed expressions on EMT related functions.
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Affiliation(s)
- Chueh-Lin Hsu
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Feng-Hsiang Chung
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Chih-Hao Chen
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Tzu-Ting Hsu
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Szu-Mam Liu
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Dao-Sheng Chung
- Department of Radiation Oncology, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Ya-Fen Hsu
- Department of Surgery, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Chien-Lung Chen
- Department of Nephrology, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Nianhan Ma
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan
| | - Hoong-Chien Lee
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.,Department of Physics, Chung Yuan Christian University, Zhongli, 32023, Taiwan.,Center for Dynamical Biomarkers and Translational Medicine, National Central University, Zhongli, 32001, Taiwan
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202
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Identification of Aging-Associated Gene Expression Signatures That Precede Intestinal Tumorigenesis. PLoS One 2016; 11:e0162300. [PMID: 27589228 PMCID: PMC5010213 DOI: 10.1371/journal.pone.0162300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/20/2016] [Indexed: 01/01/2023] Open
Abstract
Aging-associated alterations of cellular functions have been implicated in various disorders including cancers. Due to difficulties in identifying aging cells in living tissues, most studies have focused on aging-associated changes in whole tissues or certain cell pools. Thus, it remains unclear what kinds of alterations accumulate in each cell during aging. While analyzing several mouse lines expressing fluorescent proteins (FPs), we found that expression of FPs is gradually silenced in the intestinal epithelium during aging in units of single crypt composed of clonal stem cell progeny. The cells with low FP expression retained the wild-type Apc allele and the tissues composed of them did not exhibit any histological abnormality. Notably, the silencing of FPs was also observed in intestinal adenomas and the surrounding normal mucosae of Apc-mutant mice, and mediated by DNA methylation of the upstream promoter. Our genome-wide analysis then showed that the silencing of FPs reflects specific gene expression alterations during aging, and that these alterations occur in not only mouse adenomas but also human sporadic and hereditary (familial adenomatous polyposis) adenomas. Importantly, pharmacological inhibition of DNA methylation, which suppresses adenoma development in Apc-mutant mice, reverted the aging-associated silencing of FPs and gene expression alterations. These results identify aging-associated gene expression signatures that are heterogeneously induced by DNA methylation and precede intestinal tumorigenesis triggered by Apc inactivation, and suggest that pharmacological inhibition of the signature genes could be a novel strategy for the prevention and treatment of intestinal tumors.
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203
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Shigeyasu K, Okugawa Y, Toden S, Boland CR, Goel A. Exportin-5 Functions as an Oncogene and a Potential Therapeutic Target in Colorectal Cancer. Clin Cancer Res 2016; 23:1312-1322. [PMID: 27553833 DOI: 10.1158/1078-0432.ccr-16-1023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/13/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022]
Abstract
Purpose: Dysregulated expression of miRNAs has emerged as a hallmark feature in human cancers. Exportin-5 (XPO5), a karyopherin family member, is a key protein responsible for transporting precursor miRNAs from the nucleus to the cytoplasm. Although XPO5 is one of the key regulators of miRNA biogenesis, its functional role and potential clinical significance in colorectal cancer remains unclear.Experimental Design: The expression levels of XPO5 were initially assessed in three genomic datasets, followed by determination and validation of the relationship between XPO5 expression and clinicopathologic features in two independent colorectal cancer patient cohorts. A functional characterization of XPO5 in colorectal cancer was examined by targeted gene silencing in colorectal cancer cell lines and a xenograft animal model.Results: XPO5 is upregulated, both at mRNA and protein levels, in colorectal cancers compared with normal tissues. High XPO5 expression is associated with worse clinicopathologic features and poor survival in colorectal cancer patient cohorts. The siRNA knockdown of XPO5 resulted in reduced cellular proliferation, attenuated invasion, induction of G1-S cell-cycle arrest, and downregulation of key oncogenic miRNAs in colorectal cancer cells. These findings were confirmed in a xenograft animal model, wherein silencing of XPO5 resulted in the attenuation of tumor growth.Conclusions: XPO5 acts like an oncogene in colorectal cancer by regulating the expression of miRNAs and may be a potential therapeutic target in colorectal cancer. Clin Cancer Res; 23(5); 1312-22. ©2016 AACR.
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Affiliation(s)
- Kunitoshi Shigeyasu
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Shusuke Toden
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - C Richard Boland
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas.
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204
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Induction of KIAA1199/CEMIP is associated with colon cancer phenotype and poor patient survival. Oncotarget 2016; 6:30500-15. [PMID: 26437221 PMCID: PMC4741547 DOI: 10.18632/oncotarget.5921] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/08/2015] [Indexed: 12/23/2022] Open
Abstract
Genes induced in colon cancer provide novel candidate biomarkers of tumor phenotype and aggressiveness. We originally identified KIAA1199 (now officially called CEMIP) as a transcript highly induced in colon cancer: initially designating the transcript as Colon Cancer Secreted Protein 1. We molecularly characterized CEMIP expression both at the mRNA and protein level and found it is a secreted protein induced an average of 54-fold in colon cancer. Knockout of CEMIPreduced the ability of human colon cancer cells to form xenograft tumors in athymic mice. Tumors that did grow had increased deposition of hyaluronan, linking CEMIP participation in hyaluronan degradation to the modulation of tumor phenotype. We find CEMIP mRNA overexpression correlates with poorer patient survival. In stage III only (n = 31) or in combined stage II plus stage III colon cancer cases (n = 73), 5-year overall survival was significantly better (p = 0.004 and p = 0.0003, respectively) among patients with low CEMIP expressing tumors than those with high CEMIP expressing tumors. These results demonstrate that CEMIP directly facilitates colon tumor growth, and high CEMIP expression correlates with poor outcome in stage III and in stages II+III combined cohorts. We present CEMIP as a candidate prognostic marker for colon cancer and a potential therapeutic target.
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205
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Knockdown of CSE1L Gene in Colorectal Cancer Reduces Tumorigenesis in Vitro. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2761-8. [PMID: 27521996 DOI: 10.1016/j.ajpath.2016.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 06/03/2016] [Accepted: 06/17/2016] [Indexed: 11/21/2022]
Abstract
Human cellular apoptosis susceptibility (chromosomal segregation 1-like, CSE1L) gene plays a role in nuclear-to-cytoplasm transport and chromosome segregation during mitosis, cellular proliferation, and apoptosis. CSE1L is involved in colon carcinogenesis. CSE1L gene expression was assessed with three data sets using Affymetrix U133 + gene chips on normal human colonic mucosa (NR), adenomas (ADs), and colorectal carcinoma (CRC). CSE1L protein expression in CRC, AD, and NR from the same patients was measured by immunohistochemistry using a tissue microarray. We evaluated CSE1L expression in CRC cells (HCT116, SW480, and HT29) and its biological functions. CSE1L mRNA was significantly increased in all AD and CRC compared with NR (P < 0.001 and P = 0.02, respectivly). We observed a change in CSE1L staining intensity and cellular localization by immunohistochemistry. CSE1L was significantly increased during the transition from AD to CRC when compared with NR in a CRC tissue microarray (P = 0.01 and P < 0.001). HCT116, SW480, and HT29 cells also expressed CSE1L protein. CSE1L knockdown by shRNA inhibited protein, resulting in decreased cell proliferation, reduced colony formation in soft agar, and induction of apoptosis. CSE1L protein is expressed early and across all stages of CRC development. shRNA knockdown of CSE1L was associated with inhibition of tumorigenesis in CRC cells. CSE1L may represent a potential target for treatment of CRC.
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206
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Valcz G, Galamb O, Krenács T, Spisák S, Kalmár A, Patai ÁV, Wichmann B, Dede K, Tulassay Z, Molnár B. Exosomes in colorectal carcinoma formation: ALIX under the magnifying glass. Mod Pathol 2016; 29:928-38. [PMID: 27150162 DOI: 10.1038/modpathol.2016.72] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 02/07/2023]
Abstract
Exosomes are small membrane vesicles that have important roles in transporting a great variety of bioactive molecules between epithelial compartment and their microenvironment during tumor formation including colorectal adenoma-carcinoma sequence. We tested the mRNA expression of the top 25 exosome-related markers based on ExoCharta database in healthy (n=49), adenoma (n=49) and colorectal carcinoma (n=49) patients using Affymetrix HGU133 Plus2.0 microarrays. Most related genes showed significantly elevated expression including PGK1, PKM, ANXA5, ENO1, HSP90AB1 and MSN during adenoma-carcinoma sequence. Surprisingly, the expression of ALIX (ALG 2-interacting protein X), involved in multivesicular body (MVB) and exosome formation, was significantly reduced in normal vs adenoma (P=5.02 × 10(-13)) and in normal vs colorectal carcinoma comparisons (P=1.51 × 10(-10)). ALIX also showed significant reduction (P<0.05) at the in situ protein level in the epithelial compartment of adenoma (n=35) and colorectal carcinoma (n=37) patients compared with 27 healthy individuals. Furthermore, significantly reduced ALIX protein levels were accompanied by their gradual transition from diffuse cytoplasmic expression to granular signals, which fell into the 0.6-2 μm diameter size range of MVBs. These ALIX-positive particles were seen in the tumor nests, including tumor-stroma border, which suggest their exosome function. MVB-like structures were also detected in tumor microenvironment including α-smooth muscle actin-positive stromal cells, budding off cancer cells in the tumor front as well as in cancer cells entrapped within lymphoid vessels. In conclusion, we determined the top aberrantly expressed exosome-associated markers and revealed the transition of diffuse ALIX protein signals into a MVB-like pattern during adenoma-carcinoma sequence. These tumor-associated particles seen both in the carcinoma and the surrounding microenvironment can potentially mediate epithelial-stromal interactions involved in the regulation of tumor growth, metastatic invasion and therapy response.
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Affiliation(s)
- Gábor Valcz
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Galamb
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tibor Krenács
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University and MTA-SE Tumor Progression Research Group, Budapest, Hungary
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Barna Wichmann
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kristóf Dede
- Department of General Surgery and Surgical Oncology, Uzsoki Teaching Hospital, Budapest, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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207
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Li Z, Yu D, Gan M, Shan Q, Yin X, Tang S, Zhang S, Shi Y, Zhu Y, Lai M, Zhang D. A genome-wide assessment of rare copy number variants in colorectal cancer. Oncotarget 2016; 6:26411-23. [PMID: 26315111 PMCID: PMC4694911 DOI: 10.18632/oncotarget.4621] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/06/2015] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer (CRC) is a complex disease with an estimated heritability of approximately 35%. However, known CRC-related common single nucleotide polymorphisms (SNPs) can only explain ~0.65% of the heritability. This “missing heritability” may be explained partially by rare copy number variants (CNVs). In this study, we performed a genome-wide scan using Illumina Human-Omni Express BeadChip, 694 sporadic CRC cases and 1641 controls were eventually included in our analysis after quality control. The global burden analysis revealed a 1.53-fold excess of rare CNVs in CRC cases compared with controls (P < 1 × 10−6), and the difference being more pronounced for genic rare CNVs and CNVs overlapped with coding regions (1.65-fold and 1.84-fold, respectively, both P < 1 × 10−6). Interestingly, both the cases in the lowest and middle tertile of age carried a higher burden of rare CNVs comparing to the highest tertile. Furthermore, 639 CNV-disrupted genes exclusive to CRC cases were found to be significantly enriched in gene ontology (GO) terms concerning nucleosome assembly and olfactory receptor activity. Our study was the first to evaluate the burden of rare CNVs in sporadic CRC and suggested that rare CNVs contributed to the missing heritability of CRC.
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Affiliation(s)
- Zhenli Li
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Dan Yu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Meifu Gan
- Department of Pathology, Taizhou Hospital, Linhai, Zhejiang, 317000, China
| | - Qiaonan Shan
- Zhejiang University School of Clinical Medicine, Hangzhou, Zhejiang, 310058, China
| | - Xiaoyang Yin
- Zhejiang University School of Clinical Medicine, Hangzhou, Zhejiang, 310058, China
| | - Shunli Tang
- Zhejiang University School of Clinical Medicine, Hangzhou, Zhejiang, 310058, China
| | - Shuai Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for The Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200000, China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Dandan Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
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208
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Feasibility of Unbiased RNA Profiling of Colorectal Tumors: A Proof of Principle. PLoS One 2016; 11:e0159522. [PMID: 27441409 PMCID: PMC4956030 DOI: 10.1371/journal.pone.0159522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/04/2016] [Indexed: 12/24/2022] Open
Abstract
Despite recent advances in molecular profiling of colorectal cancer (CRC), as of yet this has not translated into an unbiased molecular liquid biopsy profile which can accurately screen for early CRC. In this study we depict the profile of early stage CRC as well as for advanced adenomas (AA) by combination of current molecular knowledge with microarray technology, using efficient circulating free plasma RNA purification from blood and RNA amplification technologies. We joined literature search with Affymetrix gene chip experimental procedure to draw the circulating free plasma RNA profile of colorectal cancer disease reflected in blood. The RNA panel was tested by two datasets comparing patients with CRC with healthy subjects and patients with AA to healthy subjects. For the CRC patient cohort (28 CRC cases vs. 41 healthy controls), the ROC analysis of the selected biomarker panel generated a sensitivity of 75% and a specificity of 93% for the detection of CRC using 8-gene classification model. For the AA patient cohort (28 subjects vs. 46 healthy controls), a sensitivity of 60% and a specificity of 87% were calculated using a 2-gene classification model. We have identified a panel of 8 plasma RNA markers as a preliminary panel for CRC detection and subset markers suitable for AA detection. Subjected to extensive clinical validation we suggest that this panel represents a feasible approach and a potential strategy for noninvasive early diagnosis, as a first-line screening test for asymptomatic, average-risk population before colonoscopy.
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209
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Przygodzka P, Papiewska-Pajak I, Bogusz H, Kryczka J, Sobierajska K, Kowalska MA, Boncela J. Neuromedin U is upregulated by Snail at early stages of EMT in HT29 colon cancer cells. Biochim Biophys Acta Gen Subj 2016; 1860:2445-2453. [PMID: 27450890 DOI: 10.1016/j.bbagen.2016.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/07/2016] [Accepted: 07/15/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND The epithelial-mesenchymal transition (EMT) is considered a core process that facilitates the escape of cancer cells from the primary tumor site. The transcription factor Snail was identified as a key regulator of EMT; however, the cascade of regulatory events leading to metastasis remains unknown and new predictive markers of the process are awaited. METHODS Gene expressions were analysed using real-time PCR, protein level by Western immunoblotting and confocal imaging. The motility of the cells was examined using time-lapse microscopy. Affymetrix GeneChip Human Genome U133 Plus 2.0 analysis was performed to identify transcriptomic changes upon Snail. Snail silencing was performed using siRNA nucleofection. NMU detection was performed by ELISA. RESULTS HT29 cells overexpressing Snail showed changed morphology, functions and transcriptomic profile indicating EMT induction. Changes in expression of 324 genes previously correlated with cell motility were observed. Neuromedin U was the second highest upregulated gene in HT29-Snail cells. This increase was validated by real-time PCR. Additionally elevated NMU protein was detected by ELISA in cell media. CONCLUSIONS These results show that Snail in HT29 cells regulates early phenotype conversion towards an intermediate epithelial state. We provided the first evidence that neuromedin U is associated with Snail regulatory function of metastatic induction in colon cancer cells. GENERAL SIGNIFICANCE We described the global, early transcriptomic changes induced through Snail in HT29 colon cancer cells and suggested NMU involvement in this process.
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Affiliation(s)
| | | | - Helena Bogusz
- Institute of Medical Biology, PAS, 106 Lodowa Street, 93232 Lodz, Poland.
| | - Jakub Kryczka
- Institute of Medical Biology, PAS, 106 Lodowa Street, 93232 Lodz, Poland.
| | - Katarzyna Sobierajska
- Department of Molecular Cell Mechanisms, Medical University, 6/8 Mazowiecka Street, 92215 Lodz, Poland.
| | - M Anna Kowalska
- Institute of Medical Biology, PAS, 106 Lodowa Street, 93232 Lodz, Poland; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Joanna Boncela
- Institute of Medical Biology, PAS, 106 Lodowa Street, 93232 Lodz, Poland.
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210
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Evensen NA, Li Y, Kuscu C, Liu J, Cathcart J, Banach A, Zhang Q, Li E, Joshi S, Yang J, Denoya PI, Pastorekova S, Zucker S, Shroyer KR, Cao J. Hypoxia promotes colon cancer dissemination through up-regulation of cell migration-inducing protein (CEMIP). Oncotarget 2016; 6:20723-39. [PMID: 26009875 PMCID: PMC4653038 DOI: 10.18632/oncotarget.3978] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Hypoxic stress drives cancer progression by causing a transcriptional reprogramming. Recently, KIAA1199 was discovered to be a cell-migration inducing protein (renamed CEMIP) that is upregulated in human cancers. However, the mechanism of induction of CEMIP in cancer was hitherto unknown. Here we demonstrate that hypoxia induces CEMIP expression leading to enhanced cell migration. Immunohistochemistry of human colon cancer tissues revealed that CEMIP is upregulated in cancer cells located at the invasive front or in the submucosa. CEMIP localization inversely correlated with E-cadherin expression, which is characteristic of the epithelial-to-mesenchymal transition. Mechanistically, hypoxia-inducible-factor-2α (HIF-2α), but not HIF-1α binds directly to the hypoxia response element within the CEMIP promoter region resulting in increased CEMIP expression. Functional characterization reveals that CEMIP is a downstream effector of HIF-2α-mediated cell migration. Expression of CEMIP was demonstrated to negatively correlate with the expression of Jarid1A, a histone demethylase that removes methyl groups from H3K4me3 (an activation marker for transcription), resulting in altered gene repression. Low oxygen tension inhibits the function of Jarid1A, leading to increased presence of H3K4me3 within the CEMIP promoter. These results provide insight into the upregulation of CEMIP within cancer and can lead to novel treatment strategies targeting this cancer cell migration-promoting gene.
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Affiliation(s)
- Nikki A Evensen
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA.,Department of Pediatrics, NYU Medical School, New York, NY 10016, USA
| | - Yiyi Li
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA.,Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Cem Kuscu
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jingxuan Liu
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jillian Cathcart
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA
| | - Anna Banach
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA
| | - Qian Zhang
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ellen Li
- Department of Medicine/Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sonia Joshi
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jie Yang
- Department of Preventative Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Paula I Denoya
- Department of Surgery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Silvia Pastorekova
- Department of Molecular Medicine, Institute of Virology, Slovak Academy of Sciences, Bratislava 84505, Slovak Republic
| | - Stanley Zucker
- Veterans Affairs Medical Center, Northport, NY 11768, USA
| | - Kenneth R Shroyer
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jian Cao
- Department of Medicine/Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794, USA.,Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
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211
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Vučković F, Theodoratou E, Thaçi K, Timofeeva M, Vojta A, Štambuk J, Pučić-Baković M, Rudd PM, Đerek L, Servis D, Wennerström A, Farrington SM, Perola M, Aulchenko Y, Dunlop MG, Campbell H, Lauc G. IgG Glycome in Colorectal Cancer. Clin Cancer Res 2016; 22:3078-86. [PMID: 26831718 PMCID: PMC5860729 DOI: 10.1158/1078-0432.ccr-15-1867] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/31/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Alternative glycosylation has significant structural and functional consequences on IgG and consequently also on cancer immunosurveillance. Because of technological limitations, the effects of highly heritable individual variations and the differences in the dynamics of changes in IgG glycosylation on colorectal cancer were never investigated before. EXPERIMENTAL DESIGN Using recently developed high-throughput UPLC technology for IgG glycosylation analysis, we analyzed IgG glycome composition in 760 patients with colorectal cancer and 538 matching controls. Effects of surgery were evaluated in 28 patients sampled before and three times after surgery. A predictive model was built using regularized logistic regression and evaluated using a 10-cross validation procedure. Furthermore, IgG glycome composition was analyzed in 39 plasma samples collected before initial diagnosis of colorectal cancer. RESULTS We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. Although a model based on age and sex did not show discriminative power (AUC = 0.499), the addition of glycan variables into the model considerably increased the discriminative power of the model (AUC = 0.755). However, none of these differences were significant in the small set of samples collected before the initial diagnosis. CONCLUSIONS Considering the functional relevance of IgG glycosylation for both tumor immunosurveillance and clinical efficacy of therapy with mAbs, individual variation in IgG glycosylation may turn out to be important for prediction of disease course or the choice of therapy, thus warranting further, more detailed studies of IgG glycosylation in colorectal cancer. Clin Cancer Res; 22(12); 3078-86. ©2016 AACR.
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Affiliation(s)
| | - Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom. Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Kujtim Thaçi
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | | | - Jerko Štambuk
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | | | - Pauline M Rudd
- National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Lovorka Đerek
- Department of Medical Biochemistry and Laboratory Medicine, Clinical Hospital Merkur, Zagreb, Croatia
| | - Dražen Servis
- Allgemein- und Viszeralchirurgie, St. Anna Krankenhaus, Herne, Germany
| | - Annika Wennerström
- Department of Health, The National Institute for Health and Welfare, Helsinki, Finland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Markus Perola
- Department of Health, The National Institute for Health and Welfare, Helsinki, Finland
| | | | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom. Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia. Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia.
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212
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Distinct Expression Pattern of a Deafness Gene, KIAA1199, in a Primate Cochlea. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1781894. [PMID: 27403418 PMCID: PMC4923552 DOI: 10.1155/2016/1781894] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/12/2016] [Accepted: 05/23/2016] [Indexed: 11/17/2022]
Abstract
Deafness is one of the most common types of congenital impairments, and at least half of the cases are caused by hereditary mutations. Mutations of the gene KIAA1199 are associated with progressive hearing loss. Its expression is abundant in human cochlea, but interestingly the spatial expression patterns are different between mouse and rat cochleae; the pattern in humans has not been fully investigated. We performed immunohistochemical analysis of a nonhuman primate, common marmoset (Callithrix jacchus), cochlea with a KIAA1199-specific antibody. In the common marmoset cochlea, KIAA1199 protein expression was more widespread than in rodents, with all epithelial cells, including hair cells, expressing KIAA1199. Our results suggest that the primate pattern of KIAA1199 expression is wider in comparison with rodents and may play an essential role in the maintenance of cochlear epithelial cells.
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213
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Galamb O, Kalmár A, Péterfia B, Csabai I, Bodor A, Ribli D, Krenács T, Patai ÁV, Wichmann B, Barták BK, Tóth K, Valcz G, Spisák S, Tulassay Z, Molnár B. Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. Epigenetics 2016; 11:588-602. [PMID: 27245242 DOI: 10.1080/15592294.2016.1190894] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis in 9 colorectal cancer, 15 adenoma, and 6 normal tumor adjacent tissue (NAT) samples by methyl capture sequencing. Functional methylation was confirmed on 5-aza-2'-deoxycytidine-treated colorectal cancer cell line datasets. In parallel with the DNA methylation analysis, mutations of WNT pathway genes (APC, β-catenin/CTNNB1) were analyzed by 454 sequencing on GS Junior platform. Most differentially methylated CpG sites were localized in gene body regions (95% of WNT pathway genes). In the promoter regions, 33 of the 160 analyzed WNT pathway genes were differentially methylated in colorectal cancer vs. normal, including hypermethylated AXIN2, CHP1, PRICKLE1, SFRP1, SFRP2, SOX17, and hypomethylated CACYBP, CTNNB1, MYC; 44 genes in adenoma vs. NAT; and 41 genes in colorectal cancer vs. adenoma comparisons. Hypermethylation of AXIN2, DKK1, VANGL1, and WNT5A gene promoters was higher, while those of SOX17, PRICKLE1, DAAM2, and MYC was lower in colon carcinoma compared to adenoma. Inverse correlation between expression and methylation was confirmed in 23 genes, including APC, CHP1, PRICKLE1, PSEN1, and SFRP1. Differential methylation affected both canonical and noncanonical WNT pathway genes in colorectal normal-adenoma-carcinoma sequence. Aberrant DNA methylation appears already in adenomas as an early event of colorectal carcinogenesis.
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Affiliation(s)
- Orsolya Galamb
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Alexandra Kalmár
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Bálint Péterfia
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - István Csabai
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - András Bodor
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Dezső Ribli
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Tibor Krenács
- d 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary.,e Tumor Progression Research Group , Hungarian Academy of Sciences - Semmelweis University , Budapest , Hungary
| | - Árpád V Patai
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Barnabás Wichmann
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Barbara Kinga Barták
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Kinga Tóth
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Gábor Valcz
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Sándor Spisák
- f Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Zsolt Tulassay
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.,b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Béla Molnár
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
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214
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Hoekstra E, Kodach LL, Das AM, Ruela-de-Sousa RR, Ferreira CV, Hardwick JC, van der Woude CJ, Peppelenbosch MP, Ten Hagen TLM, Fuhler GM. Low molecular weight protein tyrosine phosphatase (LMWPTP) upregulation mediates malignant potential in colorectal cancer. Oncotarget 2016; 6:8300-12. [PMID: 25811796 PMCID: PMC4480753 DOI: 10.18632/oncotarget.3224] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/26/2015] [Indexed: 12/27/2022] Open
Abstract
Phosphatases have long been regarded as tumor suppressors, however there is emerging evidence for a tumor initiating role for some phosphatases in several forms of cancer. Low Molecular Weight Protein Tyrosine Phosphatase (LMWPTP; acid phosphatase 1 [ACP1]) is an 18 kDa enzyme that influences the phosphorylation of signaling pathway mediators involved in cancer and is thus postulated to be a tumor-promoting enzyme, but neither unequivocal clinical evidence nor convincing mechanistic actions for a role of LMWPTP have been identified. In the present study, we show that LMWPTP expression is not only significantly increased in colorectal cancer (CRC), but also follows a step-wise increase in different levels of dysplasia. Chemical inhibition of LMWPTP significantly reduces CRC growth. Furthermore, downregulation of LMWPTP in CRC leads to a reduced migration ability in both 2D- and 3D-migration assays, and sensitizes tumor cells to the chemotherapeutic agent 5-FU. In conclusion, this study shows that LMWPTP is not only overexpressed in colorectal cancer, but it is correlated with the malignant potential of this cancer, suggesting that this phosphatase may act as a predictive biomaker of CRC stage and represents a rational novel target in the treatment of this disease.
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Affiliation(s)
- Elmer Hoekstra
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwa, Rotterdam, The Netherlands
| | - Liudmila L Kodach
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Asha M Das
- Department of Surgery, Section Surgical Oncology, Laboratory Experimental Surgical Oncology, Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwal, Rotterdam, The Netherlands
| | - Roberta R Ruela-de-Sousa
- Department of Biochemistry, Institute of Biology, University of Campinas, Brazil (UNICAMP), Campinas, Sao Paulo, Brazil
| | - Carmen V Ferreira
- Department of Biochemistry, Institute of Biology, University of Campinas, Brazil (UNICAMP), Campinas, Sao Paulo, Brazil
| | - James C Hardwick
- Department of Gastroenterology and Hepatology, Cancer Genomics Centre Netherlands and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwa, Rotterdam, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwa, Rotterdam, The Netherlands
| | - Timo L M Ten Hagen
- Department of Surgery, Section Surgical Oncology, Laboratory Experimental Surgical Oncology, Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwal, Rotterdam, The Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, 's Gravendijkwa, Rotterdam, The Netherlands
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215
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Bokanizad B, Tagett R, Ansari S, Helmi BH, Draghici S. SPATIAL: A System-level PAThway Impact AnaLysis approach. Nucleic Acids Res 2016; 44:5034-44. [PMID: 27193997 PMCID: PMC4914126 DOI: 10.1093/nar/gkw429] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 05/05/2016] [Indexed: 11/13/2022] Open
Abstract
The goal of pathway analysis is to identify the pathways that are significantly impacted when a biological system is perturbed, e.g. by a disease or drug. Current methods treat pathways as independent entities. However, many signals are constantly sent from one pathway to another, essentially linking all pathways into a global, system-wide complex. In this work, we propose a set of three pathway analysis methods based on the impact analysis, that performs a system-level analysis by considering all signals between pathways, as well as their overlaps. Briefly, the global system is modeled in two ways: (i) considering the inter-pathway interaction exchange for each individual pathways, and (ii) combining all individual pathways to form a global, system-wide graph. The third analysis method is a hybrid of these two models. The new methods were compared with DAVID, GSEA, GSA, PathNet, Crosstalk and SPIA on 23 GEO data sets involving 19 tissues investigated in 12 conditions. The results show that both the ranking and the P-values of the target pathways are substantially improved when the analysis considers the system-wide dependencies and interactions between pathways.
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Affiliation(s)
- Behzad Bokanizad
- Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
| | - Rebecca Tagett
- Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
| | - Sahar Ansari
- Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
| | - B Hoda Helmi
- Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI 48202, USA
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216
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WANG PEI, ZHUANG CHUNBO, HUANG DA, XU KESHU. Downregulation of miR-377 contributes to IRX3 deregulation in hepatocellular carcinoma. Oncol Rep 2016; 36:247-52. [DOI: 10.3892/or.2016.4815] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/26/2016] [Indexed: 11/06/2022] Open
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217
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Repositioning of a cyclin-dependent kinase inhibitor GW8510 as a ribonucleotide reductase M2 inhibitor to treat human colorectal cancer. Cell Death Discov 2016; 2:16027. [PMID: 27551518 PMCID: PMC4979501 DOI: 10.1038/cddiscovery.2016.27] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/03/2016] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related death in males and females in the world. It is of immediate importance to develop novel therapeutics. Human ribonucleotide reductase (RRM1/RRM2) has an essential role in converting ribonucleoside diphosphate to 2'-deoxyribonucleoside diphosphate to maintain the homeostasis of nucleotide pools. RRM2 is a prognostic biomarker and predicts poor survival of CRC. In addition, increased RRM2 activity is associated with malignant transformation and tumor cell growth. Bioinformatics analyses show that RRM2 was overexpressed in CRC and might be an attractive target for treating CRC. Therefore, we attempted to search novel RRM2 inhibitors by using a gene expression signature-based approach, connectivity MAP (CMAP). The result predicted GW8510, a cyclin-dependent kinase inhibitor, as a potential RRM2 inhibitor. Western blot analysis indicated that GW8510 inhibited RRM2 expression through promoting its proteasomal degradation. In addition, GW8510 induced autophagic cell death. In addition, the sensitivities of CRC cells to GW8510 were associated with the levels of RRM2 and endogenous autophagic flux. Taken together, our study indicates that GW8510 could be a potential anti-CRC agent through targeting RRM2.
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218
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You W, Tan G, Sheng N, Gong J, Yan J, Chen D, Zhang H, Wang Z. Downregulation of myosin VI reduced cell growth and increased apoptosis in human colorectal cancer. Acta Biochim Biophys Sin (Shanghai) 2016; 48:430-6. [PMID: 27044563 DOI: 10.1093/abbs/gmw020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/25/2016] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide, with the mortality increasing steadily over the last decade. Myosin VI (MYO6) expression is found to be elevated in some types of human carcinoma cell types, suggesting that it may be a sensitive biomarker for the diagnosis and follow-up. In this study, we first used the Oncomine database to explore the expression of MYO6 in CRC tissues, and then constructed a plasmid of RNA interference targeting MYO6 gene. After transfection of lentivirus targeting MYO6 into SW1116 cells, cell viability and proliferation were measured with 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and colony formation assay. Cell cycle distribution was assayed by flow cytometry and apoptosis was evaluated by Annexin V. MYO6 expression was detected by quantitative real-time polymerase chain reaction and western blot analysis. It was found that MYO6 mRNA was upregulated in CRC tissues using data mining of public Oncomine microarray datasets. Depletion of MYO6 significantly inhibited cell proliferation and colony formation. In addition, knockdown of MYO6 slightly arrested cell cycle in G0/G1 phase, but remarkably increased the proportion of the sub-G1 phase of cell with the increase of apoptotic cells. These results suggest that MYO6 may promote cell growth and may be used as a potential target for anticancer therapy of CRC.
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Affiliation(s)
- Weiqiang You
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Gewen Tan
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Nengquan Sheng
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jianfeng Gong
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jun Yan
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Di Chen
- National Key Laboratory of Science and Technology on Nano/Micro Fabrication Technology, Research Institute Micro/Nano Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huizhen Zhang
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Zhigang Wang
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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219
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Engchuan W, Meechai A, Tongsima S, Doungpan N, Chan JH. Gene-set activity toolbox (GAT): A platform for microarray-based cancer diagnosis using an integrative gene-set analysis approach. J Bioinform Comput Biol 2016; 14:1650015. [PMID: 27102089 DOI: 10.1142/s0219720016500153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cancer is a complex disease that cannot be diagnosed reliably using only single gene expression analysis. Using gene-set analysis on high throughput gene expression profiling controlled by various environmental factors is a commonly adopted technique used by the cancer research community. This work develops a comprehensive gene expression analysis tool (gene-set activity toolbox: (GAT)) that is implemented with data retriever, traditional data pre-processing, several gene-set analysis methods, network visualization and data mining tools. The gene-set analysis methods are used to identify subsets of phenotype-relevant genes that will be used to build a classification model. To evaluate GAT performance, we performed a cross-dataset validation study on three common cancers namely colorectal, breast and lung cancers. The results show that GAT can be used to build a reasonable disease diagnostic model and the predicted markers have biological relevance. GAT can be accessed from http://gat.sit.kmutt.ac.th where GAT's java library for gene-set analysis, simple classification and a database with three cancer benchmark datasets can be downloaded.
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Affiliation(s)
- Worrawat Engchuan
- 1 Data and Knowledge Engineering Laboratory, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Asawin Meechai
- 2 Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sissades Tongsima
- 3 Biostatistics and Informatics Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology
| | - Narumol Doungpan
- 4 Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jonathan H Chan
- 1 Data and Knowledge Engineering Laboratory, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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220
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Kap EJ, Seibold P, Scherer D, Habermann N, Balavarca Y, Jansen L, Zucknick M, Becker N, Hoffmeister M, Ulrich A, Benner A, Ulrich CM, Burwinkel B, Brenner H, Chang-Claude J. SNPs in transporter and metabolizing genes as predictive markers for oxaliplatin treatment in colorectal cancer patients. Int J Cancer 2016; 138:2993-3001. [PMID: 26835885 DOI: 10.1002/ijc.30026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 01/15/2023]
Abstract
Oxaliplatin is frequently used as part of a chemotherapeutic regimen with 5-fluorouracil in the treatment of colorectal cancer (CRC). The cellular availability of oxaliplatin is dependent on metabolic and transporter enzymes. Variants in genes encoding these enzymes may cause variation in response to oxaliplatin and could be potential predictive markers. Therefore, we used a two-step procedure to comprehensively investigate 1,444 single nucleotide polymorphisms (SNPs) from these pathways for their potential as predictive markers for oxaliplatin treatment, using 623 stage II-IV CRC patients (of whom 201 patients received oxaliplatin) from a German prospective patient cohort treated with adjuvant or palliative chemotherapy. First, all genes were screened using the global test that evaluated SNP*oxaliplatin interaction terms per gene. Second, one model was created by backward elimination on all SNP*oxaliplatin interactions of the selected genes. The statistical procedure was evaluated using bootstrap analyses. Nine genes differentially associated with overall survival according to oxaliplatin treatment (unadjusted p values < 0.05) were selected. Model selection resulted in the inclusion of 14 SNPs from eight genes (six transporter genes, ABCA9, ABCB11, ABCC10, ATP1A1, ATP1B2, ATP8B3, and two metabolism genes GSTM5, GRHPR), which significantly improved model fit. Using bootstrap analysis we show an improvement of the prediction error of 3.7% in patients treated with oxaliplatin. Several variants in genes involved in metabolism and transport could thus be potential predictive markers for oxaliplatin treatment in CRC patients. If confirmed, inclusion of these variants in a predictive test could identify patients who are more likely to benefit from treatment with oxaliplatin.
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Affiliation(s)
- Elisabeth J Kap
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Scherer
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and DKFZ, Heidelberg, Germany
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and DKFZ, Heidelberg, Germany
| | - Yesilda Balavarca
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and DKFZ, Heidelberg, Germany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Manuela Zucknick
- Division of Biostatistics, DKFZ, Heidelberg, Germany.,Oslo Center for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, DKFZ, Heidelberg, Germany
| | - Cornelia M Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and DKFZ, Heidelberg, Germany.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, DKFZ, Heidelberg, Germany.,Division of Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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221
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Wang G, Huang J, Zhu H, Ju S, Wang H, Wang X. Overexpression of GRO-β is associated with an unfavorable outcome in colorectal cancer. Oncol Lett 2016; 11:2391-2397. [PMID: 27073485 PMCID: PMC4812449 DOI: 10.3892/ol.2016.4222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 01/18/2016] [Indexed: 01/28/2023] Open
Abstract
Growth-related oncogene (GRO)-β, or chemokine (C-X-C motif) ligand 2 (CXCL2), is a member of the CXC chemokine family that may mediate various functions, including attracting neutrophils to sites of inflammation, and participating in tumorigenesis and progression. However, the expression of GRO-β in colorectal cancer (CRC) and the association with the clinical outcome of the disease remains poorly understood. In the present study, CXCL2 mRNA expression in CRC was analyzed using six independent datasets from the Oncomine microarray database. The immunohistochemical analysis of tissue microarrays (TMA) was used to characterize the expression of the GRO-β protein in CRC. The association between GRO-β expression and the clinicopathological features and prognosis of patients was determined by statistical analysis. The results indicated that GRO-β was highly expressed in CRC tissues, and that high GRO-β cytoplasmic expression was associated with the tumor location, extent of the primary tumor, and lymph node metastasis. Kaplan-Meier survival and Cox regression analysis revealed that high GRO-β expression was an independent indicator of poor prognosis for CRC patients. The results indicate that high GRO-β expression in CRC may correlate with an unfavorable outcome and facilitate cancer cell invasion and metastasis.
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Affiliation(s)
- Guihua Wang
- Center of Clinical Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jianfei Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Huijun Zhu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Shaoqing Ju
- Center of Clinical Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Huimin Wang
- Center of Clinical Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xudong Wang
- Center of Clinical Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
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222
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Liu TH, Guo K, Liu RQ, Zhang S, Huang ZH, Liu YK. The high expressed serum soluble neural cell adhesion molecule, a high risk factor indicating hepatic encephalopathy in hepatocelular carcinoma patients. Asian Pac J Cancer Prev 2016; 16:3131-5. [PMID: 25921109 DOI: 10.7314/apjcp.2015.16.8.3131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To investigate whether the expression of serum soluble neural cell adhesion molecule (sNCAM) is associated with hepatic encephalopathy (HE) in hepatocelular carcinoma (HCC) patients. MATERIALS AND METHODS The Oncomine Cancer Microarray database was used to determine the clinical relevance of NCAM expression in different kinds of human cancers. Sera from 75 HCC cases enrolled in this study were assessed for expression of sNCAM by enzyme linked immunosorbent assay (ELISA). RESULTS Dependent on the Oncomine Cancer Microarray database analysis, NCAM was down regulated in 10 different kinds of cancer, like bladder cancer, brain and central nervous system cancer, while up-regulated in lung cancer, uterine corpus leiomyoma and sarcoma, compared to normal groups. Puzzlingly, NCAM expression demonstrated no significant difference between normal and HCC groups. However, we found by quantitative ELISA that the level of sNCAM in sera from HCC patients with HE (347.4±151.9 ng/ml) was significantly more up-regulated than that in HCC patients without HE (260.3±104.2 ng/ml), the p-value being 0.008. sNCAM may be an important risk factor of HE in HCC patients, the correlation coefficients was 0.278 (P< 0.05) on rank correlation analysis. CONCLUSIONS This study highlights that up-regulated level of serum sNCAM is associated with HE in HCC patients and suggests that the high expression can be used as an indicator.
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Affiliation(s)
- Tian-Hua Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China E-mail :
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223
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The MAP3K ZAK, a novel modulator of ERK-dependent migration, is upregulated in colorectal cancer. Oncogene 2015; 35:3190-200. [PMID: 26522728 DOI: 10.1038/onc.2015.379] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/30/2015] [Accepted: 09/04/2015] [Indexed: 12/22/2022]
Abstract
Often described as a mediator of cell cycle arrest or as a pro-apoptotic factor in stressful conditions, the MAP3K ZAK (Sterile alpha motif and leucine zipper-containing kinase) has also been proven to positively regulate epidermal growth factor receptor (EGFR) and WNT signaling pathways, cancer cell proliferation and cellular neoplastic transformation. Here, we show that both isoforms of ZAK, ZAK-α and ZAK-β are key factors in cancer cell migration. While ZAK depletion reduced cell motility of HeLa and HCT116 cells, its overexpression triggered the activation of all three mitogen-activated protein kinases (MAPKs), extracellular signal-regulated kinase (ERK), c-JUN N-terminal kinase (JNK) and p38, as well as an increase in cell motion. On the contrary, the kinase-dead mutants, ZAK-α K45M and ZAK-β K45M, were not able to provoke such events, and instead exerted a dominant-negative effect on MAPK activation and cell migration. Pharmacological inhibition of ZAK by nilotinib, preventing ZAK-autophosphorylation and thereby auto-activation, led to the same results. Activated by epidermal growth factor (EGF), we further showed that ZAK constitutes an essential element of the EGF/ERK-dependent cell migration pathway. Using public transcriptomic databases and tissue microarrays, we finally established that, as strong factors of the EGFR signaling pathway, ZAK-α and/or ZAK-β transcripts and protein(s) are frequently upregulated in colorectal adenoma and carcinoma patients. Notably, gene set enrichment analysis disclosed a significant correlation between ZAK+ colorectal premalignant lesions and gene sets belonging to the MAPK/ERK and motility-related signaling pathways of the reactome database, strongly suggesting that ZAK induces such pro-tumoral reaction cascades in human cancers.
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Bayerlová M, Jung K, Kramer F, Klemm F, Bleckmann A, Beißbarth T. Comparative study on gene set and pathway topology-based enrichment methods. BMC Bioinformatics 2015; 16:334. [PMID: 26489510 PMCID: PMC4618947 DOI: 10.1186/s12859-015-0751-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/29/2015] [Indexed: 01/08/2023] Open
Abstract
Background Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. Methods We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. Results In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. Conclusions We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both types of methods for enrichment analysis require further improvements in order to deal with the problem of pathway overlaps. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0751-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michaela Bayerlová
- Department of Medical Statistics, University Medical Center Göttingen, 37099, Göttingen, Germany.
| | - Klaus Jung
- Department of Medical Statistics, University Medical Center Göttingen, 37099, Göttingen, Germany.
| | - Frank Kramer
- Department of Medical Statistics, University Medical Center Göttingen, 37099, Göttingen, Germany.
| | - Florian Klemm
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, 37099, Göttingen, Germany.
| | - Annalen Bleckmann
- Department of Medical Statistics, University Medical Center Göttingen, 37099, Göttingen, Germany. .,Department of Hematology and Medical Oncology, University Medical Center Göttingen, 37099, Göttingen, Germany.
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen, 37099, Göttingen, Germany.
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225
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Dow LE, O'Rourke KP, Simon J, Tschaharganeh DF, van Es JH, Clevers H, Lowe SW. Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer. Cell 2015; 161:1539-1552. [PMID: 26091037 DOI: 10.1016/j.cell.2015.05.033] [Citation(s) in RCA: 379] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/27/2015] [Accepted: 04/10/2015] [Indexed: 12/15/2022]
Abstract
The adenomatous polyposis coli (APC) tumor suppressor is mutated in the vast majority of human colorectal cancers (CRC) and leads to deregulated Wnt signaling. To determine whether Apc disruption is required for tumor maintenance, we developed a mouse model of CRC whereby Apc can be conditionally suppressed using a doxycycline-regulated shRNA. Apc suppression produces adenomas in both the small intestine and colon that, in the presence of Kras and p53 mutations, can progress to invasive carcinoma. In established tumors, Apc restoration drives rapid and widespread tumor-cell differentiation and sustained regression without relapse. Tumor regression is accompanied by the re-establishment of normal crypt-villus homeostasis, such that once aberrantly proliferating cells reacquire self-renewal and multi-lineage differentiation capability. Our study reveals that CRC cells can revert to functioning normal cells given appropriate signals and provide compelling in vivo validation of the Wnt pathway as a therapeutic target for treatment of CRC.
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Affiliation(s)
- Lukas E Dow
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kevin P O'Rourke
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program
| | - Janelle Simon
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darjus F Tschaharganeh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Johan H van Es
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY
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Torres-Ayuso P, Tello-Lafoz M, Mérida I, Ávila-Flores A. Diacylglycerol kinase-ζ regulates mTORC1 and lipogenic metabolism in cancer cells through SREBP-1. Oncogenesis 2015; 4:e164. [PMID: 26302180 PMCID: PMC4632073 DOI: 10.1038/oncsis.2015.22] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/26/2015] [Accepted: 07/07/2015] [Indexed: 01/03/2023] Open
Abstract
Diacylglycerol kinases (DGKs) transform diacylglycerol (DAG) into phosphatidic acid (PA), balancing the levels of these key metabolic and signaling lipids. We previously showed that PA derived from the DGKζ isoform promotes mammalian target of rapamycin complex 1 (mTORC1) activation. This function might be crucial for the growth and survival of cancer cells, especially for those resistant to the allosteric mTOR inhibitor rapamycin. How this positive function of DGKζ coordinates with DAG metabolism and signaling is unknown. In this study, we used a rapamycin-resistant colon cancer cell line as a model to address the role of DGKζ in tumor cells. We found that DGKζ predominated over other PA sources such as DGKα or phospholipase D to activate mTORC1, and that its activity was a component of the rapamycin-induced feedback loops. We show that the DGKζ DAG-consuming function is central to cell homeostasis, as DAG negatively regulates levels of the lipogenic transcription factor SREBP-1. Our findings suggest a model in which simultaneous regulation of DAG and PA levels by DGKζ is integrated with mTOR function to maintain tumor cell homeostasis; we provide new evidence of the crosstalk between mTOR and lipid metabolism that will be advantageous in the design of drug therapies.
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Affiliation(s)
- P Torres-Ayuso
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - M Tello-Lafoz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - I Mérida
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - A Ávila-Flores
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
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227
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Long Non-Coding RNAs: The Key Players in Glioma Pathogenesis. Cancers (Basel) 2015; 7:1406-24. [PMID: 26230711 PMCID: PMC4586776 DOI: 10.3390/cancers7030843] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) represent a novel class of RNAs with no functional protein-coding ability, yet it has become increasingly clear that interactions between lncRNAs with other molecules are responsible for important gene regulatory functions in various contexts. Given their relatively high expressions in the brain, lncRNAs are now thought to play important roles in normal brain development as well as diverse disease processes including gliomagenesis. Intriguingly, certain lncRNAs are closely associated with the initiation, differentiation, progression, recurrence and stem-like characteristics in glioma, and may therefore be exploited for the purposes of sub-classification, diagnosis and prognosis. LncRNAs may also serve as potential therapeutic targets as well as a novel biomarkers in the treatment of glioma. In this article, the functional aspects of lncRNAs, particularly within the central nervous system (CNS), will be briefly discussed, followed by highlights of the important roles of lncRNAs in mediating critical steps during glioma development. In addition, the key lncRNA players and their possible mechanistic pathways associated with gliomagenesis will be addressed.
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228
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Brown AR, Simmen RCM, Raj VR, Van TT, MacLeod SL, Simmen FA. Krüppel-like factor 9 (KLF9) prevents colorectal cancer through inhibition of interferon-related signaling. Carcinogenesis 2015. [PMID: 26210742 DOI: 10.1093/carcin/bgv104] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Expression of the transcription factor Krüppel-like factor 9 (KLF9) is frequently reduced in colorectal cancers, although a tumor suppressive role has not been established. To determine if KLF9 suppresses intestinal adenoma formation, we generated mice of distinct Klf9 genotypes in the background of the Apc (Min/+) mouse and compared their adenoma burdens at 16 weeks of age. While small intestine adenoma burden remained unchanged among Klf9 genotypes, male and female Apc(Min/+)/Klf9(-/-) and Apc(Min/+)/Klf9(+/-) mice exhibited significantly more colon adenomas than their Apc(Min/+)/Klf9(+/+) counterparts. Microarray analysis showed significant increases in the expression of interferon-induced genes in the colon mucosa of female Apc (Min/+)/Klf9(+/-) and Apc(Min/+)/Klf9(-/-) compared to Apc(Min/+)/Klf9(+/+) mice, prior to overt adenoma occurrence. Gene upregulation was confirmed by qPCR of colon mucosa and by siRNA knockdown of KLF9 in human HT29 colorectal cancer cells. Increases in expression of these genes were further augmented by supplementation with Interferon β1. Circulating levels of the cytokine, interferon-stimulated gene 15 (ISG15) were increased in Apc(Min/+)/Klf9(+/-) and Apc(Min/+)/Klf9(-/-) mice relative to Apc(Min/+)/Klf9(+/+). Additionally, colon mucosal levels of ISG15 were increased in Apc(Min/+)/Klf9(+/-) mice. Chromatin immunoprecipitation demonstrated KLF9 recruitment to the ISG15 promoter. Lastly, treatment with ISG15 suppressed apoptosis in HT29 cells, in the presence and absence of 5-fluorouracil (5FU). Results show KLF9 to be a haploinsufficient suppressor of colon tumorigenesis in Apc(Min/+) mice in part, by repression of ISG15 and the latter's antiapoptotic function. SUMMARY Krüppel-like factor 9 (KLF9) is a haploinsufficient tumor suppressor in the ApcMin/+ mouse colon by suppressing expression of ISG15, an apoptosis-inhibiting cytokine.
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Affiliation(s)
- Adam R Brown
- Interdisciplinary Biomedical Sciences Program, Department of Physiology and Biophysics
| | - Rosalia C M Simmen
- Interdisciplinary Biomedical Sciences Program, Department of Physiology and Biophysics
| | | | - Trang T Van
- Interdisciplinary Biomedical Sciences Program
| | - Stewart L MacLeod
- Department of Pediatrics, University of Arkansas for Medical Sciences, Slot #505, 4301 West Markham Street, Little Rock, AR 72205, USA
| | - Frank A Simmen
- Interdisciplinary Biomedical Sciences Program, Department of Physiology and Biophysics,
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Pan Y, Cao F, Guo A, Chang W, Chen X, Ma W, Gao X, Guo S, Fu C, Zhu J. Endoplasmic reticulum ribosome-binding protein 1, RRBP1, promotes progression of colorectal cancer and predicts an unfavourable prognosis. Br J Cancer 2015. [PMID: 26196185 PMCID: PMC4559827 DOI: 10.1038/bjc.2015.260] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Ribosome-binding protein 1 (RRBP1) has been implicated in the regulation of unfolded protein response, which is involved in almost every aspect of cancer development. We aimed to explore the significance of RRBP1 in the progression and prognosis of colorectal cancer (CRC). METHODS The study population consisted of 856 patients with stage I-III CRC from two hospitals. RRBP1 expression was examined by immunohistochemistry (IHC) in colorectal tissues. The correlation of RRBP1 expression and CRC occurrence was assessed in paired cancer-adjacent tissues. Factors contributing to prognosis were evaluated in a training-validation design with univariate and multivariate Cox analysis. Colorectal cancer aggressiveness caused by RRBP1 knockdown or overexpression was evaluated in CRC cells. RESULTS RRBP1 was aberrantly overexpressed in CRC. Compared with low-RRBP1 patients, high-RRBP1 patients had shorter disease-specific survival in the training (hazard ratio (HR), 2.423; 95% confidence interval (CI), 1.531-3.835) and validation cohorts (HR, 3.749; 95% CI, 2.166-6.448) in multivariate Cox analysis. High-RRBP1 independently predicted a shorter disease-free survival (HR, 4.821; 95% CI, 3.220-7.218) in the validation cohort. RRBP1 knockdown reduced the aggressiveness of CRC cells in vitro and inhibited the growth of CRC xenografts in vivo. CONCLUSIONS High RRBP1 expression facilitates CRC progression and predicts an unfavourable post-operative prognosis.
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Affiliation(s)
- Y Pan
- Department of Digestive Endoscopy, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, China
| | - F Cao
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, 174 Changhai Road, Shanghai, 200433, China
| | - A Guo
- Department of Internal Medicine, Yangpu Hosptial, Tongji University School of Medicine, 450 Tengyue Road, Shanghai, 200090, China
| | - W Chang
- Department of Environmental Hygiene, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - X Chen
- Department of Environmental Hygiene, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - W Ma
- Department of Environmental Hygiene, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - X Gao
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, 174 Changhai Road, Shanghai, 200433, China
| | - S Guo
- Department of Pathology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Shanghai, 201203, China
| | - C Fu
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, 174 Changhai Road, Shanghai, 200433, China
| | - J Zhu
- Department of Environmental Hygiene, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, China
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Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients. PLoS One 2015; 10:e0125766. [PMID: 26147197 PMCID: PMC4493072 DOI: 10.1371/journal.pone.0125766] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/26/2015] [Indexed: 12/25/2022] Open
Abstract
Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation. The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type. To date, no holistic approach has been used to screen VGCC family genes in different types of cancer. We analyzed the transcript expression of VGCCs in clinical cancer tissue samples by accessing ONCOMINE (www.oncomine.org), a web-based microarray database, to perform a systematic analysis. Every member of the VGCCs was examined across 21 different types of cancer by comparing mRNA expression in cancer to that in normal tissue. A previous study showed that altered expression of mRNA in cancer tissue may play an oncogenic role and promote tumor development; therefore, in the present findings, we focus only on the overexpression of VGCCs in different types of cancer. This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer. CACNA1F only showed high expression in testis cancer, whereas CACNA1A, CACNA1C, and CACNA1D were highly expressed in most types of cancer. The current analysis revealed that specific VGCCs likely play essential roles in specific types of cancer. Collectively, we identified several VGCC targets and classified them according to different cancer subtypes for prospective studies on the underlying carcinogenic mechanisms. The present findings suggest that VGCCs are possible targets for prospective investigation in cancer treatment.
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231
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Zhao X, Fan J, Zhi F, Li A, Li C, Berger AE, Boorgula MP, Barkataki S, Courneya JP, Chen Y, Barnes KC, Cheadle C. Mobilization of epithelial mesenchymal transition genes distinguishes active from inactive lesional tissue in patients with ulcerative colitis. Hum Mol Genet 2015; 24:4615-24. [PMID: 26034135 DOI: 10.1093/hmg/ddv192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/19/2015] [Indexed: 12/13/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic, relapsing and debilitating idiopathic inflammation, with variable and complex pathophysiologies. Our objective was to elucidate patterns of gene expression underlying the progression of UC disease. Single endoscopic pinch FFPE biopsies (n = 41) were sampled at both active and inactive stages at the same site in individual UC patients and compared with each other and with non-inflammatory bowel disease healthy controls. Gene expression results were validated by quantitative reverse transcriptase-PCR (QRT-PCR), and results at the protein level were validated by immunohistochemistry and western blot. Analysis of microarray results demonstrated that UC patients in remission display an intermediate gene expression phenotype between active UC patients and controls. It is clear that UC active site recovery does not revert fully back to a healthy control phenotype. Both UC active and inactive tissue displayed evidence, at both the gene expression and protein level, of a positive precancerous state as indicated by increases in the expression of Chitinase 3-Like-1, and the colorectal cancer metastasis marker MMP1. A key distinguishing feature between active and inactive UC, however, was the mobilization of marker genes and proteins for the Epithelial Mesenchymal Transition (EMT) pathway only in active UC. Analysis of the gene expression signatures associated with UC remission identified multiple pathways which appear to be permanently dysregulated in UC patients at formerly active sites in spite of clear histological recovery. Among these pathways, the EMT pathway was specifically up-regulated only in active UC emphasizing the potential for cancer progression in these patients.
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Affiliation(s)
- Xinmei Zhao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China, Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Jinshui Fan
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China, Department of Gastroenterology and Institute of Gastroenterology, Guangzhou First Municipal People's Hospital, Guangzhou Medical University, Guangzhou 510180, China
| | - Chen Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Alan E Berger
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Meher Preethi Boorgula
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Sangjucta Barkataki
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Jean-Paul Courneya
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Yuqing Chen
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Kathleen C Barnes
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
| | - Chris Cheadle
- Division of Allergy and Clinical Immunology, the Johns Hopkins School of Medicine, Baltimore, MD 21224, USA and
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Yang X, Qiu P, Chen B, Lin Y, Zhou Z, Ge R, Zou H, Wang J, Wang J. KIAA1199 as a potential diagnostic biomarker of rheumatoid arthritis related to angiogenesis. Arthritis Res Ther 2015; 17:140. [PMID: 26022278 PMCID: PMC4448531 DOI: 10.1186/s13075-015-0637-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/22/2015] [Indexed: 01/24/2023] Open
Abstract
Introduction Our previous proteomic study on fibroblast-like synoviocytes (FLSs) derived from the synovial tissues found that the expression of KIAA1199 was higher in rheumatoid arthritis (RA) patients than in healthy controls. The aim of this study was to examine the biological function of KIAA1199 and evaluate its clinical diagnosis value in RA. Methods The over-expression of KIAA1199 was verified by quantitative real-time polymerase chain reaction (qPCR), Immunohistochemistry, Immunofluorescence and enzyme linked immunosorbent assay (ELISA) in inactive and active RA patients and healthy controls. The effect of KIAA1199 expression on FLSs proliferation, angiogenesis and related pathway were analyzed by MTT, cell migration, tube formation, chorioallantoic membrane (CAM) assay, qPCR and western-blotting after KIAA1199 knockdown and over-expression. Results The verification results show the up-regulation of KIAA1199 in RA patients at mRNA and protein level as compared to that in healthy controls. ELISA and receiver operator characteristic (ROC) analysis shows that KIAA1199 concentration in serum, synovial fluid and synovial tissues could be used as dependable biomarkers for the diagnosis of active RA, provided an area under roc curve (AUC) of 0.83, 0.92 and 0.92. Sensitivity and specificity, which were determined by cut-off points, reached 72% 84% and 80% in sensitivity and 80%, 93.3%, 93.3% in specificity, respectively. Moreover, KIAA1199 also enhance the proliferation and angiogenesis of synovial membrane, and KIAA1199/ PLXNB3/ SEMA5A/CTGF axis may be a newly found pathway enhancing cell proliferation and angiogenesis. Conclusion KIAA1199 may be a potential diagnostic biomarker of RA related to angiogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13075-015-0637-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinyu Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Pengcheng Qiu
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Bingbing Chen
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Yaoyao Lin
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Zhonghao Zhou
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Renshan Ge
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Hai Zou
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Jianmin Wang
- Department of Rheumatology, Jiamusi Central Hospital, Jiamusi, China.
| | - Jianguang Wang
- Department of Biochemistry, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
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Regenerating gene 1B silencing inhibits colon cancer cell HCT116 proliferation and invasion. Int J Biol Markers 2015; 30:e217-25. [PMID: 25768000 DOI: 10.5301/jbm.5000133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The human regenerating gene 1B (REG1B) is found to be frequently up-regulated in many types of human tumors. It is unclear whether REG1B expression may have therapeutic value in colorectal carcinoma. Additionally, how REG1B is associated with the clinical features of colorectal carcinoma is not known. To investigate the relationship between REG1B and colorectal cancer, we analyzed REG1B expression in clinical specimens and cell lines and the effect of down-regulation of REG1B by short hairpin RNA (shRNA) in HCT116 cells. METHODS Paraffin-embedded specimens from 30 pairs of colorectal cancer tissues and adjacent colon tissues were used to investigate the expression of REG1B by immunohistochemistry. We also examined whether REG1B itself may be related to cell proliferation, cell cycle arrest, apoptosis, migration and invasion in colon cancer HCT116 cells. RESULTS Our results showed that REG1B was highly expressed in colorectal carcinoma and was significantly associated with cell differentiation status. The results also illustrated that REG1B silencing with shRNA inhibited cell proliferation, migration and invasion but did not induce apoptosis. Furthermore, down-regulation of REG1B induces G1-phase cell cycle arrest in colon cancer cells. CONCLUSIONS Knockdown of REG1B can inhibit cell proliferation, migration and invasion. It may act by a mechanism regulating cell cycle progression. Thus, REG1B may be a novel candidate therapeutic target for colorectal cancer.
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Szafron LM, Balcerak A, Grzybowska EA, Pienkowska-Grela B, Felisiak-Golabek A, Podgorska A, Kulesza M, Nowak N, Pomorski P, Wysocki J, Rubel T, Dansonka-Mieszkowska A, Konopka B, Lukasik M, Kupryjanczyk J. The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues. PLoS One 2015; 10:e0127475. [PMID: 25978564 PMCID: PMC4433331 DOI: 10.1371/journal.pone.0127475] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/15/2015] [Indexed: 12/13/2022] Open
Abstract
CRNDE, recently described as the lncRNA-coding gene, is overexpressed at RNA level in human malignancies. Its role in gametogenesis, cellular differentiation and pluripotency has been suggested as well. Herein, we aimed to verify our hypothesis that the CRNDE gene may encode a protein product, CRNDEP. By using bioinformatics methods, we identified the 84-amino acid ORF encoded by one of two CRNDE transcripts, previously described by our research team. This ORF was cloned into two expression vectors, subsequently utilized in localization studies in HeLa cells. We also developed a polyclonal antibody against CRNDEP. Its specificity was confirmed in immunohistochemical, cellular localization, Western blot and immunoprecipitation experiments, as well as by showing a statistically significant decrease of endogenous CRNDEP expression in the cells with transient shRNA-mediated knockdown of CRNDE. Endogenous CRNDEP localizes predominantly to the nucleus and its expression seems to be elevated in highly proliferating tissues, like the parabasal layer of the squamous epithelium, intestinal crypts or spermatocytes. After its artificial overexpression in HeLa cells, in a fusion with either the EGFP or DsRed Monomer fluorescent tag, CRNDEP seems to stimulate the formation of stress granules and localize to them. Although the exact role of CRNDEP is unknown, our preliminary results suggest that it may be involved in the regulation of the cell proliferation. Possibly, CRNDEP also participates in oxygen metabolism, considering our in silico results, and the correlation between its enforced overexpression and the formation of stress granules. This is the first report showing the existence of a peptide encoded by the CRNDE gene.
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Affiliation(s)
- Lukasz Michal Szafron
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
- * E-mail:
| | - Anna Balcerak
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Ewa Anna Grzybowska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Barbara Pienkowska-Grela
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Anna Felisiak-Golabek
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Agnieszka Podgorska
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Magdalena Kulesza
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Natalia Nowak
- Neurobiology Center, Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Pawel Pomorski
- Multimodal Laboratory of Cell Adhesion and Motility, NanoBioGeo Consortium, Nencki Institute of Experimental Biology, Warsaw, Poland
- Department of Biochemistry, Laboratory Of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Juliusz Wysocki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Tymon Rubel
- The Institute of Radioelectronics, Warsaw University of Technology, Warsaw, Poland
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Bozena Konopka
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Martyna Lukasik
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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235
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Abstract
Tumor epithelial cells develop within a microenvironment consisting of extracellular matrix, growth factors, and cytokines produced by nonepithelial stromal cells. In response to paracrine signals from tumor epithelia, stromal cells modify the microenvironment to promote tumor growth and metastasis. Here, we identify interleukin 33 (IL-33) as a regulator of tumor stromal cell activation and mediator of intestinal polyposis. In human colorectal cancer, IL-33 expression was induced in the tumor epithelium of adenomas and carcinomas, and expression of the IL-33 receptor, IL1RL1 (also referred to as IL1-R4 or ST2), localized predominantly to the stroma of adenoma and both the stroma and epithelium of carcinoma. Genetic and antibody abrogation of responsiveness to IL-33 in the Apc(Min/+) mouse model of intestinal tumorigenesis inhibited proliferation, induced apoptosis, and suppressed angiogenesis in adenomatous polyps, which reduced both tumor number and size. Similar to human adenomas, IL-33 expression localized to tumor epithelial cells and expression of IL1RL1 associated with two stromal cell types, subepithelial myofibroblasts and mast cells, in Apc(Min/+) polyps. In vitro, IL-33 stimulation of human subepithelial myofibroblasts induced the expression of extracellular matrix components and growth factors associated with intestinal tumor progression. IL-33 deficiency reduced mast cell accumulation in Apc(Min/+) polyps and suppressed the expression of mast cell-derived proteases and cytokines known to promote polyposis. Based on these findings, we propose that IL-33 derived from the tumor epithelium promotes polyposis through the coordinated activation of stromal cells and the formation of a protumorigenic microenvironment.
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236
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Higdon R, Kolker E. Can "normal" protein expression ranges be estimated with high-throughput proteomics? J Proteome Res 2015; 14:2398-407. [PMID: 25877823 DOI: 10.1021/acs.jproteome.5b00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although biological science discovery often involves comparing conditions to a normal state, in proteomics little is actually known about normal. Two Human Proteome studies featured in Nature offer new insights into protein expression and an opportunity to assess how high-throughput proteomics measures normal protein ranges. We use data from these studies to estimate technical and biological variability in protein expression and compare them to other expression data sets from normal tissue. Results show that measured protein expression across same-tissue replicates vary by ±4- to 10-fold for most proteins. Coefficients of variation (CV) for protein expression measurements range from 62% to 117% across different tissue experiments; however, adjusting for technical variation reduced this variability by as much as 50%. In addition, the CV could also be reduced by limiting comparisons to proteins with at least 3 or more unique peptide identifications as the CV was on average 33% lower than for proteins with 2 or fewer peptide identifications. We also selected 13 housekeeping proteins and genes that were expressed across all tissues with low variability to determine their utility as a reference set for normalization and comparative purposes. These results present the first step toward estimating normal protein ranges by determining the variability in expression measurements through combining publicly available data. They support an approach that combines standard protocols with replicates of normal tissues to estimate normal protein ranges for large numbers of proteins and tissues. This would be a tremendous resource for normal cellular physiology and comparisons of proteomics studies.
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Affiliation(s)
- Roger Higdon
- †Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.,‡CDO Analytics, Seattle Children's Hospital, Seattle, Washington 98101, United States
| | - Eugene Kolker
- †Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.,‡CDO Analytics, Seattle Children's Hospital, Seattle, Washington 98101, United States.,§Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington, Seattle, Washington 98195, United States.,∥Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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237
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Bauer C, Stec K, Glintschert A, Gruden K, Schichor C, Or-Guil M, Selbig J, Schuchhardt J. BioMiner: Paving the Way for Personalized Medicine. Cancer Inform 2015; 14:55-63. [PMID: 26005322 PMCID: PMC4406277 DOI: 10.4137/cin.s20910] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/17/2014] [Accepted: 12/25/2014] [Indexed: 01/03/2023] Open
Abstract
Personalized medicine is promising a revolution for medicine and human biology in the 21st century. The scientific foundation for this revolution is accomplished by analyzing biological high-throughput data sets from genomics, transcriptomics, proteomics, and metabolomics. Currently, access to these data has been limited to either rather simple Web-based tools, which do not grant much insight or analysis by trained specialists, without firsthand involvement of the physician. Here, we present the novel Web-based tool “BioMiner,” which was developed within the scope of an international and interdisciplinary project (SYSTHER†) and gives access to a variety of high-throughput data sets. It provides the user with convenient tools to analyze complex cross-omics data sets and grants enhanced visualization abilities. BioMiner incorporates transcriptomic and cross-omics high-throughput data sets, with a focus on cancer. A public instance of BioMiner along with the database is available at http://systherDB.microdiscovery.de/, login and password: “systher”; a tutorial detailing the usage of BioMiner can be found in the Supplementary File.
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Affiliation(s)
- Chris Bauer
- Research and Development, MicroDiscovery GmbH, Berlin, Germany
| | - Karol Stec
- Research and Development, MicroDiscovery GmbH, Berlin, Germany
| | | | - Kristina Gruden
- Department for Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Christian Schichor
- Department of Neurosurgery, Klinikum der Ludwig-Maximilian-Universität München, Munich, Germany
| | - Michal Or-Guil
- Systems Immunology Lab, Department of Biology, Humboldt University, Berlin, Germany. ; Research Center ImmunoSciences, Charité University of Medicine Berlin, Berlin, Germany
| | - Joachim Selbig
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Giardina C, Nakanishi M, Khan A, Kuratnik A, Xu W, Brenner B, Rosenberg DW. Regulation of VDR Expression in Apc-Mutant Mice, Human Colon Cancers and Adenomas. Cancer Prev Res (Phila) 2015; 8:387-99. [PMID: 25873367 DOI: 10.1158/1940-6207.capr-14-0371] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/20/2015] [Indexed: 02/06/2023]
Abstract
One variable that may affect the ability of vitamin D to reduce colon cancer risk is the expression of its high-affinity receptor, VDR. Here, we show that vitamin D does not reduce tumor formation in Apc(Δ14/+) mice and that VDR expression is lost in the majority of the colon tumor cells. The extent of VDR loss corresponded inversely to the level of β-catenin nuclear localization and could be observed in early lesions composed of just a few crypts. Analysis of reported VDR regulators showed that the repressing class I histone deacetylases (HDAC) were significantly elevated in the tumors (up to 4-fold), whereas the VDR-activating retinoid X receptors (RXR) were downregulated (∼50%). Expression of the Slug repressor was also increased, but was found primarily in stromal cells. Analysis of epigenetically active compounds on colon cell lines and intestinal organoids showed that HDAC inhibitors were particularly adept at stimulating VDR expression. Treatment of tumor-bearing Apc(Δ14/+) mice with the HDAC inhibitor panobinostat increased VDR expression in the tumors and normal mucosa. The RXR agonist bexarotene failed to activate VDR expression, indicating that RXR ligands were not limiting. Analysis of human microarray data indicated that VDR mRNA is frequently downregulated in colon adenomas, which correlated positively with RXRA expression and inversely with HDAC 2 and 8 expression. Human adenomas showed variable VDR protein expression levels, both between and within individual lesions. Determining the mechanisms of VDR regulation in colon neoplasms may significantly enhance our ability to use vitamin D as a cancer prevention agent.
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Affiliation(s)
- Charles Giardina
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut.
| | - Masako Nakanishi
- Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut
| | - Awaad Khan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Anton Kuratnik
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Wanli Xu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Bruce Brenner
- Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut
| | - Daniel W Rosenberg
- Center for Molecular Medicine, University of Connecticut Health Center, Farmington, Connecticut
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239
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Thomas SS, Makar KW, Li L, Zheng Y, Yang P, Levy L, Rudolph RY, Lampe PD, Yan M, Markowitz SD, Bigler J, Lampe JW, Potter JD. Tissue-specific patterns of gene expression in the epithelium and stroma of normal colon in healthy individuals in an aspirin intervention trial. BMC MEDICAL GENETICS 2015; 16:18. [PMID: 25927723 PMCID: PMC4422425 DOI: 10.1186/s12881-015-0161-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/26/2015] [Indexed: 12/21/2022]
Abstract
Background Regular aspirin use reduces colon adenoma and carcinoma incidence. UDP-glucuronosyltransferases (UGT) are involved in aspirin metabolism and clearance, and variant alleles in UGT1A6 have been shown to alter salicylic acid metabolism and risk of colon neoplasia. Methods In a randomized, cross-over, placebo-controlled trial of 44 healthy men and women, homozygous for UGT1A6*1 or UGT1A6*2, we explored differences between global epithelial and stromal expression, using Affymetrix U133 + 2.0 microarrays and tested effects of 60-day aspirin supplementation (325 mg/d) on epithelial and stromal gene expression and colon prostaglandin E2 (PGE2) levels. Results No statistically significant differences in gene expression were observed in response to aspirin or UGT1A6 genotype, but tissue PGE2 levels were lower with aspirin compared to placebo (p <0.001). Transcripts differentially expressed between epithelium and stroma (N = 4916, P <0.01, false discovery rate <0.001), included a high proportion of genes involved in cell signaling, cellular movement, and cancer. Genes preferentially expressed in epithelium were involved in drug and xenobiotic metabolism, fatty acid and lipid metabolism, apoptosis signaling, and ion transport. Genes preferentially expressed in stroma included those involved in inflammation, cellular adhesion, and extracellular matrix production. Wnt-Tcf4 pathway genes were expressed in both epithelium and stroma but differed by subcellular location. Conclusions These results suggest that, in healthy individuals, subtle effects of aspirin on gene expression in normal colon tissue are likely overwhelmed by inter-individual variability in microarray analyses. Differential expression of critical genes between colonic epithelium and stroma suggest that these tissue types need to be considered separately. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0161-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sushma S Thomas
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Karen W Makar
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Lin Li
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Yingye Zheng
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Peiying Yang
- M.D. Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Lisa Levy
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | | | - Paul D Lampe
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Min Yan
- Case Western Reserve University School of Medicine, Cincinnati, OH, 44106, USA.
| | - Sanford D Markowitz
- Case Western Reserve University School of Medicine, Cincinnati, OH, 44106, USA.
| | | | - Johanna W Lampe
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - John D Potter
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
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240
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Zhang Y, Wang X, Wang Z, Tang H, Fan H, Guo Q. miR-182 promotes cell growth and invasion by targeting forkhead box F2 transcription factor in colorectal cancer. Oncol Rep 2015; 33:2592-8. [PMID: 25738520 DOI: 10.3892/or.2015.3833] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/30/2015] [Indexed: 01/23/2023] Open
Abstract
Forkhead box F2 transcription factor (FoxF2) has been described to promote organ development, extracellular matrix (ECM) synthesis and epithelial-mesenchymal interaction. Although recent studies reported decreased FoxF2 expression in several types of cancers, indicating its potential role in carcinogenesis, the mechanistic role of FoxF2 is yet to be explored. MicroRNAs (miRNAs) are strongly implicated in carcinogenesis. The oncogenetic properties of miR-182 have been described in multiple cancers. In the present study, we aimed to investigate the role of miR-182 in colorectal cancer (CRC) and identify the regulation of FoxF2 by miR-182. Bioinformatic analyses on gene expression profiling datasets showed decreased FoxF2 expression in colorectal adenomas, primary tumors compared to normal colon epithelial and a negative association between FoxF2 and β-catenin expression. Restoration of FoxF2 in CRC cells suppressed β-catenin expression and simultaneously inhibited cell growth and invasion. Furthermore, we observed that miR-182 was aberrantly upregulated in CRC. Knockdown of miR-182 in CRC cells impeded cell growth and invasion. The direct binding of miR-182 to the 3' untranslated region (3'UTR) of FoxF2 mRNA was confirmed using a luciferase reporter gene assay. Importantly, elevated FoxF2 expression was observed in miR-182-knockdown cells with a simultaneous reduction in β-catenin. In conclusion, the present study describes a potential mechanism underlying an miR-182/FoxF2 link contributing to CRC development. miR-182-induced downregulation of FoxF2 partly accounts for increased activity of β-catenin signaling. Inhibition of miR-182 represents a potential strategy against CRC.
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Affiliation(s)
- Yu Zhang
- Yunnan Provincial Institute of Digestive Medicine, Department of Gastroenterology, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Xinying Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhongqiu Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Hui Tang
- Yunnan Provincial Institute of Digestive Medicine, Department of Gastroenterology, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Hong Fan
- Yunnan Provincial Institute of Digestive Medicine, Department of Gastroenterology, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Qiang Guo
- Yunnan Provincial Institute of Digestive Medicine, Department of Gastroenterology, The First People's Hospital of Yunnan Province, Kunming, P.R. China
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241
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Abstract
NRMT (N-terminal regulator of chromatin condensation 1 methyltransferase) was the first eukaryotic methyltransferase identified to specifically methylate the free α-amino group of proteins. Since the discovery of this N-terminal methyltransferase, many new substrates have been identified and the modification itself has been shown to regulate DNA-protein interactions. Sequence analysis predicts one close human homologue of NRMT, METTL11B (methyltransferase-like protein 11B, now renamed NRMT2). We show in the present paper for the first time that NRMT2 also has N-terminal methylation activity and recognizes the same N-terminal consensus sequences as NRMT (now NRMT1). Both enzymes have similar tissue expression and cellular localization patterns. However, enzyme assays and MS experiments indicate that they differ in their specific catalytic functions. Although NRMT1 is a distributive methyltransferase that can mono-, di- and tri-methylate its substrates, NRMT2 is primarily a monomethylase. Concurrent expression of NRMT1 and NRMT2 accelerates the production of trimethylation, and we propose that NRMT2 activates NRMT1 by priming its substrates for trimethylation.
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242
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ALEXANDER MELANNIE, BURCH JAMESB, STECK SUSANE, CHEN CHINFU, HURLEY THOMASG, CAVICCHIA PHILIP, RAY MEREDITH, SHIVAPPA NITIN, GUESS JACLYN, ZHANG HONGMEI, YOUNGSTEDT SHAWND, CREEK KIME, LLOYD STEPHEN, YANG XIAOMING, HÉBERT JAMESR. Case-control study of the PERIOD3 clock gene length polymorphism and colorectal adenoma formation. Oncol Rep 2015; 33:935-41. [PMID: 25501848 PMCID: PMC4306271 DOI: 10.3892/or.2014.3667] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 09/18/2014] [Indexed: 01/02/2023] Open
Abstract
Clock genes are expressed in a self-perpetuating, circadian pattern in virtually every tissue including the human gastrointestinal tract. They coordinate cellular processes critical for tumor development, including cell proliferation, DNA damage response and apoptosis. Circadian rhythm disturbances have been associated with an increased risk for colon cancer and other cancers. This mechanism has not been elucidated, yet may involve dysregulation of the 'period' (PER) clock genes, which have tumor suppressor properties. A variable number tandem repeat (VNTR) in the PERIOD3 (PER3) gene has been associated with sleep disorders, differences in diurnal hormone secretion, and increased premenopausal breast cancer risk. Susceptibility related to PER3 has not been examined in conjunction with adenomatous polyps. This exploratory case-control study was the first to test the hypothesis that the 5-repeat PER3 VNTR sequence is associated with increased odds of adenoma formation. Information on demographics, medical history, occupation and lifestyle was collected prior to colonoscopy. Cases (n=49) were individuals with at least one histopathologically confirmed adenoma. Controls (n=97) included patients with normal findings or hyperplastic polyps not requiring enhanced surveillance. Unconditional multiple logistic regression was used to calculate odds ratios (ORs) with 95% confidence intervals (CIs), after adjusting for potential confounding. Adenomas were detected in 34% of participants. Cases were more likely to possess the 5-repeat PER3 genotype relative to controls (4/5 OR, 2.1; 95% CI, 0.9-4.8; 5/5 OR, 5.1; 95% CI, 1.4-18.1; 4/5+5/5 OR, 2.5; 95% CI, 1.7-5.4). Examination of the Oncomine microarray database indicated lower PERIOD gene expression in adenomas relative to adjacent normal tissue. Results suggest a need for follow-up in a larger sample.
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Affiliation(s)
- MELANNIE ALEXANDER
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - JAMES B. BURCH
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Dorn Department of Veterans Affairs Medical Center, Columbia, SC, USA
| | - SUSAN E. STECK
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - CHIN-FU CHEN
- Center for Molecular Studies, Greenwood Genetic Center, Greenwood, SC, USA
| | - THOMAS G. HURLEY
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
| | - PHILIP CAVICCHIA
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - MEREDITH RAY
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - NITIN SHIVAPPA
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - JACLYN GUESS
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - HONGMEI ZHANG
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - SHAWN D. YOUNGSTEDT
- College of Nursing and Health Innovation, and College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - KIM E. CREEK
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - STEPHEN LLOYD
- South Carolina Medical Endoscopy Center, and Department of Family Medicine, University of South Carolina School of Medicine, Columbia, SC, USA
| | - XIAOMING YANG
- Medical Chronobiology Laboratory, Dorn Department of Veterans Affairs Medical Center, Columbia, SC, USA
| | - JAMES R. HÉBERT
- South Carolina Statewide Cancer Prevention and Control Program, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Department of Family and Preventive Medicine, School of Medicine, University of South Carolina, Columbia, SC, USA
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Binder H, Hopp L, Lembcke K, Wirth H. Personalized Disease Phenotypes from Massive OMICs Data. BIG DATA ANALYTICS IN BIOINFORMATICS AND HEALTHCARE 2015. [DOI: 10.4018/978-1-4666-6611-5.ch015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Application of new high-throughput technologies in molecular medicine collects massive data for hundreds to thousands of persons in large cohort studies by characterizing the phenotype of each individual on a personalized basis. The chapter aims at increasing our understanding of disease genesis and progression and to improve diagnosis and treatment. New methods are needed to handle such “big data.” Machine learning enables one to recognize and to visualize complex data patterns and to make decisions potentially relevant for diagnosis and treatment. The authors address these tasks by applying the method of self-organizing maps and present worked examples from different disease entities of the colon ranging from inflammation to cancer.
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244
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Sinha S. Reproducibility of parameter learning with missing observations in naive Wnt Bayesian network trained on colorectal cancer samples and doxycycline-treated cell lines. ACTA ACUST UNITED AC 2015; 11:1802-19. [DOI: 10.1039/c5mb00117j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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245
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Yarmishyn AA, Batagov AO, Tan JZ, Sundaram GM, Sampath P, Kuznetsov VA, Kurochkin IV. HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome. BMC Genomics 2014; 15 Suppl 9:S7. [PMID: 25522241 PMCID: PMC4290621 DOI: 10.1186/1471-2164-15-s9-s7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies. Results We developed a computational pipeline to annotate lncRNAs on popular Affymetrix U133 microarrays, creating a resource allowing measurement of expression of 1581 lncRNAs. This resource can be utilized to interrogate existing microarray datasets for various lncRNA studies. We found that these lncRNAs fall into three distinct classes according to their statistical distribution by length. Remarkably, these three classes of lncRNAs were co-localized with protein coding genes exhibiting distinct gene ontology groups. This annotation was applied to microarray analysis which identified a 159 lncRNA signature that discriminates between localized and metastatic stages of neuroblastoma. Analysis of an independent patient cohort revealed that this signature differentiates also relapsing from non-relapsing primary tumors. This is the first example of the signature developed via the analysis of expression of lncRNAs solely. One of these lncRNAs, termed HOXD-AS1, is encoded in HOXD cluster. HOXD-AS1 is evolutionary conserved among hominids and has all bona fide features of a gene. Studying retinoid acid (RA) response of SH-SY5Y cell line, a model of human metastatic neuroblastoma, we found that HOXD-AS1 is a subject to morphogenic regulation, is activated by PI3K/Akt pathway and itself is involved in control of RA-induced cell differentiation. Knock-down experiments revealed that HOXD-AS1 controls expression levels of clinically significant protein-coding genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer. Conclusions Our findings greatly extend the number of noncoding RNAs functionally implicated in tumor development and patient treatment and highlight their role as potential prognostic biomarkers of neuroblastomas.
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Özdemir BC, Hensel J, Secondini C, Wetterwald A, Schwaninger R, Fleischmann A, Raffelsberger W, Poch O, Delorenzi M, Temanni R, Mills IG, van der Pluijm G, Thalmann GN, Cecchini MG. The molecular signature of the stroma response in prostate cancer-induced osteoblastic bone metastasis highlights expansion of hematopoietic and prostate epithelial stem cell niches. PLoS One 2014; 9:e114530. [PMID: 25485970 PMCID: PMC4259356 DOI: 10.1371/journal.pone.0114530] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/10/2014] [Indexed: 01/18/2023] Open
Abstract
The reciprocal interaction between cancer cells and the tissue-specific stroma is critical for primary and metastatic tumor growth progression. Prostate cancer cells colonize preferentially bone (osteotropism), where they alter the physiological balance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption, and elicit prevalently an osteoblastic response (osteoinduction). The molecular cues provided by osteoblasts for the survival and growth of bone metastatic prostate cancer cells are largely unknown. We exploited the sufficient divergence between human and mouse RNA sequences together with redefinition of highly species-specific gene arrays by computer-aided and experimental exclusion of cross-hybridizing oligonucleotide probes. This strategy allowed the dissection of the stroma (mouse) from the cancer cell (human) transcriptome in bone metastasis xenograft models of human osteoinductive prostate cancer cells (VCaP and C4-2B). As a result, we generated the osteoblastic bone metastasis-associated stroma transcriptome (OB-BMST). Subtraction of genes shared by inflammation, wound healing and desmoplastic responses, and by the tissue type-independent stroma responses to a variety of non-osteotropic and osteotropic primary cancers generated a curated gene signature ("Core" OB-BMST) putatively representing the bone marrow/bone-specific stroma response to prostate cancer-induced, osteoblastic bone metastasis. The expression pattern of three representative Core OB-BMST genes (PTN, EPHA3 and FSCN1) seems to confirm the bone specificity of this response. A robust induction of genes involved in osteogenesis and angiogenesis dominates both the OB-BMST and Core OB-BMST. This translates in an amplification of hematopoietic and, remarkably, prostate epithelial stem cell niche components that may function as a self-reinforcing bone metastatic niche providing a growth support specific for osteoinductive prostate cancer cells. The induction of this combinatorial stem cell niche is a novel mechanism that may also explain cancer cell osteotropism and local interference with hematopoiesis (myelophthisis). Accordingly, these stem cell niche components may represent innovative therapeutic targets and/or serum biomarkers in osteoblastic bone metastasis.
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Affiliation(s)
- Berna C. Özdemir
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Janine Hensel
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Chiara Secondini
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Antoinette Wetterwald
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Ruth Schwaninger
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
| | | | | | - Olivier Poch
- ICube UMR7357, University of Strasbourg, Strasbourg, France
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, Department of Oncology, University of Lausanne and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ramzi Temanni
- Biomedical Informatics Division, Sidra Medical and Research Center, Doha, Qatar
| | - Ian G. Mills
- Prostate Cancer Research Group, Norway Centre for Molecular Medicine (NCMM), University of Oslo, Oslo, Norway
| | - Gabri van der Pluijm
- Department of Urology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - George N. Thalmann
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Marco G. Cecchini
- Urology Research Laboratory, Department of Urology and Department of Clinical Research, University of Bern, Bern, Switzerland
- * E-mail:
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Herr R, Köhler M, Andrlová H, Weinberg F, Möller Y, Halbach S, Lutz L, Mastroianni J, Klose M, Bittermann N, Kowar S, Zeiser R, Olayioye MA, Lassmann S, Busch H, Boerries M, Brummer T. B-Raf inhibitors induce epithelial differentiation in BRAF-mutant colorectal cancer cells. Cancer Res 2014; 75:216-29. [PMID: 25381152 DOI: 10.1158/0008-5472.can-13-3686] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BRAF mutations are associated with aggressive, less-differentiated and therapy-resistant colorectal carcinoma. However, the underlying mechanisms for these correlations remain unknown. To understand how oncogenic B-Raf contributes to carcinogenesis, in particular to aspects other than cellular proliferation and survival, we generated three isogenic human colorectal carcinoma cell line models in which we can dynamically modulate the expression of the B-Raf(V600E) oncoprotein. Doxycyclin-inducible knockdown of endogenous B-Raf(V600E) decreases cellular motility and invasion in conventional and three-dimensional (3D) culture, whereas it promotes cell-cell contacts and induces various hallmarks of differentiated epithelia. Importantly, all these effects are recapitulated by B-Raf (PLX4720, vemurafenib, and dabrafenib) or MEK inhibitors (trametinib). Surprisingly, loss of B-Raf(V600E) in HT29 xenografts does not only stall tumor growth, but also induces glandular structures with marked expression of CDX2, a tumor-suppressor and master transcription factor of intestinal differentiation. By performing the first transcriptome profiles of PLX4720-treated 3D cultures of HT29 and Colo-205 cells, we identify several upregulated genes linked to epithelial differentiation and effector functions, such as claudin-1, a Cdx-2 target gene encoding a critical tight junction component. Thereby, we provide a mechanism for the clinically observed correlation between mutant BRAF and the loss of Cdx-2 and claudin-1. PLX4720 also suppressed several metastasis-associated transcripts that have not been implicated as targets, effectors or potential biomarkers of oncogenic B-Raf signaling so far. Together, we identify a novel facet of clinically applied B-Raf or MEK inhibitors by showing that they promote cellular adhesion and differentiation of colorectal carcinoma cells.
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Affiliation(s)
- Ricarda Herr
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Albert-Ludwigs-University (ALU), Freiburg, Germany. Faculty of Biology, ALU, Freiburg, Germany
| | - Martin Köhler
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Albert-Ludwigs-University (ALU), Freiburg, Germany. Faculty of Biology, ALU, Freiburg, Germany. Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Hana Andrlová
- Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Florian Weinberg
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Albert-Ludwigs-University (ALU), Freiburg, Germany. Faculty of Biology, ALU, Freiburg, Germany
| | - Yvonne Möller
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Sebastian Halbach
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Albert-Ludwigs-University (ALU), Freiburg, Germany. Faculty of Biology, ALU, Freiburg, Germany. Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Lisa Lutz
- Department of Pathology, University Medical Center, ALU, Freiburg, Germany
| | - Justin Mastroianni
- Faculty of Biology, ALU, Freiburg, Germany. Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Martin Klose
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany
| | - Nicola Bittermann
- Department of Pathology, University Medical Center, ALU, Freiburg, Germany
| | - Silke Kowar
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany
| | - Robert Zeiser
- Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany. Centre for Biological Signalling Studies BIOSS, ALU Freiburg
| | - Monilola A Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Silke Lassmann
- Department of Pathology, University Medical Center, ALU, Freiburg, Germany. Centre for Biological Signalling Studies BIOSS, ALU Freiburg. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tilman Brummer
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Albert-Ludwigs-University (ALU), Freiburg, Germany. Centre for Biological Signalling Studies BIOSS, ALU Freiburg.
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Shostak K, Zhang X, Hubert P, Göktuna SI, Jiang Z, Klevernic I, Hildebrand J, Roncarati P, Hennuy B, Ladang A, Somja J, Gothot A, Close P, Delvenne P, Chariot A. NF-κB-induced KIAA1199 promotes survival through EGFR signalling. Nat Commun 2014; 5:5232. [PMID: 25366117 PMCID: PMC4241993 DOI: 10.1038/ncomms6232] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 09/09/2014] [Indexed: 12/21/2022] Open
Abstract
Constitutive activation of EGFR- and NF-κB-dependent pathways is a hallmark of cancer, yet signalling proteins that connect both oncogenic cascades are poorly characterized. Here we define KIAA1199 as a BCL-3- and p65-dependent gene in transformed keratinocytes. KIAA1199 expression is enhanced on human papillomavirus (HPV) infection and is aberrantly expressed in clinical cases of cervical (pre)neoplastic lesions. Mechanistically, KIAA1199 binds Plexin A2 and protects from Semaphorin 3A-mediated cell death by promoting EGFR stability and signalling. Moreover, KIAA1199 is an EGFR-binding protein and KIAA1199 deficiency impairs EGF-dependent Src, MEK1 and ERK1/2 phosphorylations. Therefore, EGFR stability and signalling to downstream kinases requires KIAA1199. As such, KIAA1199 promotes EGF-mediated epithelial-mesenchymal transition (EMT). Taken together, our data define KIAA1199 as an oncogenic protein induced by HPV infection and constitutive NF-κB activity that transmits pro-survival and invasive signals through EGFR signalling.
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Affiliation(s)
- Kateryna Shostak
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Xin Zhang
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Pascale Hubert
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Experimental Pathology, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Cancer, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Serkan Ismail Göktuna
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Zheshen Jiang
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Iva Klevernic
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Julien Hildebrand
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Patrick Roncarati
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Experimental Pathology, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Cancer, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Benoit Hennuy
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] GIGA Transcriptomics Facility, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Aurélie Ladang
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Joan Somja
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Experimental Pathology, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Cancer, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - André Gothot
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] GIGA-Infection, Immunity and Inflammation, Department of Medicine/Hematology, University of Liege, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Pierre Close
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Philippe Delvenne
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Experimental Pathology, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Cancer, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
| | - Alain Chariot
- 1] Interdisciplinary Cluster for Applied Genoproteomics (GIGA-Research) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [2] Laboratory of Medical Chemistry, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [3] GIGA-Signal Transduction, University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium [4] Walloon Excellence in Life Sciences and Biotechnology (WELBIO) , University of Liege, 1, Avenue de l'ho^pital, CHU, Sart-Tilman, Liege 4000, Belgium
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Martorell Ò, Barriga FM, Merlos-Suárez A, Stephan-Otto Attolini C, Casanova J, Batlle E, Sancho E, Casali A. Iro/IRX transcription factors negatively regulate Dpp/TGF-β pathway activity during intestinal tumorigenesis. EMBO Rep 2014; 15:1210-8. [PMID: 25296644 DOI: 10.15252/embr.201438622] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Activating mutations in Wnt and EGFR/Ras signaling pathways are common in colorectal cancer (CRC). Remarkably, clonal co-activation of these pathways in the adult Drosophila midgut induces "tumor-like" overgrowths. Here, we show that, in these clones and in CRC cell lines, Dpp/TGF-β acts as a tumor suppressor. Moreover, we discover that the Iroquois/IRX-family-protein Mirror downregulates the transcription of core components of the Dpp pathway, reducing its tumor suppressor activity. We also show that this genetic interaction is conserved in human CRC cells, where the Iro/IRX proteins IRX3 and IRX5 diminish the response to TGF-β. IRX3 and IRX5 are upregulated in human adenomas, and their levels correlate inversely with the gene expression signature of response to TGF-β. In addition, Irx5 expression confers a growth advantage in the presence of TGF-β, but is selected against in its absence. Together, our results identify a set of Iro/IRX proteins as conserved negative regulators of Dpp/TGF-β activity. We propose that during the characteristic adenoma-to-carcinoma transition of human CRC, the activity of IRX proteins could reduce the sensitivity to the cytostatic effect of TGF-β, conferring a growth advantage to tumor cells prior to the acquisition of mutations in TGF-β pathway components.
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Affiliation(s)
- Òscar Martorell
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | | | | | | | - Jordi Casanova
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Andreu Casali
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
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Castellone MD, Langella A, Cantara S, Laurila JP, Laatikainen LE, Bellelli R, Pacini F, Salvatore M, Laukkanen MO. Extracellular superoxide dismutase induces mouse embryonic fibroblast proliferative burst, growth arrest, immortalization, and consequent in vivo tumorigenesis. Antioxid Redox Signal 2014; 21:1460-74. [PMID: 24328532 DOI: 10.1089/ars.2013.5475] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AIMS Rat sarcoma virus (RAS)-induced tumorigenesis has been suggested to follow a three-stage model consisting of an initial RAS activation, senescence induction, and evasion of p53-dependent senescence checkpoints. While reactive oxygen species act as second messengers in RAS-induced senescence, they are also involved in oncogenic transformation by inducing proliferation and promoting mutations. In the current work, we investigated the role of extracellular superoxide dismutase (SOD3) in RAS-induced senescence and immortalization in vitro and in vivo. We used a mouse embryonic fibroblast (MEF) primary cell model along with immortalized and transformed human cell lines derived from papillary and anaplastic thyroid cancer. RESULTS Based on our data, sod3 RNA interference in H-RasV12-transduced cells markedly inhibited cell growth, while sod3 over-expression in MEFs initially caused a proliferative burst followed by the activation of DNA damage checkpoints, induction of p53-p21 signal transduction, and senescence. Subsequently, sod3-transduced MEF cells developed co-operative p21-p16 down-regulation and acquired transformed cell characteristics such as increased telomerase activity, loss of contact inhibition, growth in low-nutrient conditions, and in vivo tumorigenesis. Interestingly, as previously reported with RAS, we showed a dose-dependent response to SOD3 in vitro and in vivo involving transcriptional and non-transcriptional regulatory mechanisms. INNOVATION SOD3 may mediate H-RasV12-induced initiation of primary cell immortalization. CONCLUSIONS Our results indicate that SOD3 influences growth signaling in primary and cancer cells downstream of the ras oncogene and could serve as a therapy target at an early tumorigenesis phase.
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Affiliation(s)
- Maria Domenica Castellone
- 1 Department of Molecular Medicine and Medical Biotechnologies, Institute of Experimental Endocrinology and Oncology (CNR), University of Naples Federico II , Naples, Italy
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