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Hosseini-Abgir A, Naghizadeh MM, Igder S, Miladpour B. Insilco prediction of the role of the FriZZled5 gene in colorectal cancer. Cancer Treat Res Commun 2023; 36:100751. [PMID: 37595345 DOI: 10.1016/j.ctarc.2023.100751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION In this study, we aimed to elucidate the crosstalk between the Wnt/β-catenin signaling pathway and colorectal cancer (CRC) associated with inflammatory bowel disease (IBD) using a bioinformatics analysis of putative common biomarkers and a systems biology approach. MATERIALS AND METHODS The following criteria were used to search the GEO and ArrayExpress databases for terms related to CRC and IBD: 1. The dataset containing the transcriptomic data, and 2. Untreated samples by medications or drugs. A total of 42 datasets were selected for additional analysis. The GEO2R identified the differentially expressed genes. The genes involved in the Wnt signaling pathway were extracted from the KEGG database. Enrichment analysis and miRNA target prediction were conducted through the ToppGene online tool. RESULTS In CRC datasets, there were 1168 up- and 998 down-regulated probes, whereas, in IBD datasets, there were 256 up- and 200 down-regulated probes. There were 65 upregulated and 57 downregulated genes shared by CRC and IBD. According to KEGG, there were 166 genes in the Wnt pathway. FriZZled5 (FZD5) was a down-regulated gene in both CRC and IBD, as determined by the intersection of CRC- and IBD-related DEGs with the Wnt pathway. It was also demonstrated that miR-191, miR-885-5p, miR-378a-3p, and miR-396-3p affect the FriZZled5 gene expression. CONCLUSION It is possible that increased expression of miR-191 and miR-885-5p, or decreased expression of miR-378a -3p and miR396-3, in IBD and CRC results in decreased expression of the FZD5 gene. Based on the function of this gene, FZD5 may be a potential therapeutic target in IBD that progresses to CRC.
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Affiliation(s)
| | | | - Somayeh Igder
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Behnoosh Miladpour
- Department of Clinical Biochemistry, Fasa University of Medical Sciences, Fasa, Iran.
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Kothalawala WJ, Győrffy B. Transcriptomic and Cellular Content Analysis of Colorectal Cancer by Combining Multiple Independent Cohorts. Clin Transl Gastroenterol 2023; 14:e00517. [PMID: 35858620 PMCID: PMC9945259 DOI: 10.14309/ctg.0000000000000517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION By linking cellular content and molecular subtypes of colorectal cancer (CRC), we aim to uncover novel features useful for targeted therapy. Our first goal was to evaluate gene expression alterations linked to CRC pathogenesis, and then, we aimed to evaluate the cellular composition differences between normal colon mucosa and tumor and between different colon cancer molecular subtypes. METHODS We collected microarray and RNA sequencing data of patients with CRC from the Genome Expression Omnibus and The Cancer Genome Atlas. We combined all cases and performed quantile normalization. Genes with a fold change of >2 were further investigated. We used xCell for cellular decomposition and CMScaller for molecular subtyping. For statistical analyses, the Kruskal-Wallis H test and Mann-Whitney U tests were performed with Bonferroni correction. RESULTS We established an integrated database of normal colon and CRC using transcriptomic data of 1,082 samples. By using this data set, we identified genes showing the highest differential expression in colon tumors. The top genes were linked to calcium signaling, matrix metalloproteinases, and transcription factors. When compared with normal samples, CD4+ memory T cells, CD8+ naive T cells, CD8+ T cells, Th1 cells, Th2 cells, and regulatory T cells were enriched in tumor tissues. The ImmuneScore was decreased in tumor samples compared with normal samples. The CMS1 and CMS4 molecular subtypes were the most immunogenic, with the highest ImmuneScore but also high infiltration by CD8+ T cells, Th1 cells, and Th2 cells in CMS1 and B-cell subtypes and CD8+ T cells in CMS4. DISCUSSION Our analysis uncovers features enabling advanced treatment selection and the development of novel therapies in CRC.
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Affiliation(s)
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- TTK Cancer Biomarker Research Group, Budapest, Hungary
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Wang B, Zhang J, Wang X, Zhao L, Wang Y, Fan Z, Liu L, Gao W. Identification and clinical validation of key genes as the potential biomarkers in colorectal adenoma. BMC Cancer 2023; 23:39. [PMID: 36631756 PMCID: PMC9832797 DOI: 10.1186/s12885-022-10422-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 12/07/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC), ranking third in cancer prevalence and second in mortality worldwide, is mainly derived from colorectal adenoma (CRA). CRA is a common benign disease in the intestine with rapidly increasing incidence and malignant potential. Therefore, this study aimed to recognize significant biomarkers and original pathogenesis in CRA. METHODS Transcriptome data of GSE8671, GSE37364, and GSE15960 were downloaded from the Gene Expression Omnibus (GEO) datasets, and differentially expressed genes (DEGs) were screened. Functional pathways enrichment, protein-protein interaction (PPI) network, stem-correlation analysis, CIBERSORT, risk score and survival analyses were performed. RT-qPCR and immunohistochemical staining were applied to verify our results. RESULTS: Screening for significant DEGs in each dataset, we identified 230 robust DEGs, including 127 upregulated and 103 downregulated genes. Functional pathways enrichment showed that these DEGs were distinctly enriched in various tumor-associated pathways, such as growth factor activity, extracellular structure organization, neutrophil activation, and inflammatory response. We filtered out two hub genes via STRING and Modules analysis, including CA2 and HSD11B2. Stem-correlation analysis displayed that hub genes were negatively associated with stem-related genes (Olfm4, CD44, CCND1 and MYC). The CIBERSORT algorithm indicated that Macrophage2, activated mast cells, and Neutrophils promoted CRA progression through inflammation. Survival analysis showed that CA2 and HSD11B2 were positively associated with survival outcomes in CRC. CONCLUSION Our study has successfully identified the critical role of two core genes in the development and oncogenesis of CRA, which provides novel insight into the underlying pathogenesis, potential biomarkers and therapeutic targets.
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Affiliation(s)
- Bangting Wang
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Jiting Zhang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Wang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Lili Zhao
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Yan Wang
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Zhining Fan
- grid.412676.00000 0004 1799 0784Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu China
| | - Li Liu
- Digestive Endoscopy Department, The First Affiliated Hospital With Nanjing Medical University and Jiangsu Province Hospital, Nanjing, Jiangsu, China.
| | - Wenqing Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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Santo SGE, da Silva TC, Vinken M, Cogliati B, Barbisan LF, Romualdo GR. The Implications of Connexin 43 Deficiency during the Early Stages of Chemically Induced Mouse Colon Carcinogenesis. Antioxidants (Basel) 2022; 11:antiox11122368. [PMID: 36552579 PMCID: PMC9774636 DOI: 10.3390/antiox11122368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Colorectal cancer (CRC), associated with an increased intake of processed red meats, saturated fats, and simple carbohydrates accompanied by low dietary fiber, fruits, and vegetables consumption, presents a high epidemiological burden. Connexin43 (Cx43) protein, which forms gap junctions or hemichannels, has tumor suppressor or oncogenic activities in a cancer type- and stage-dependent manner. Cx43 expression varies during colon carcinogenesis, and its functional role is not fully understood. Thus, we evaluated the implications of Cx43 heterologous deletion (Cx43+/-) during the early stages of a chemically induced model of colon carcinogenesis. Female C57BL/6J mice (wild-type or Cx43+/-) were submitted to a colon carcinogenesis model induced by 1,2 dimethylhydrazine (DMH). Mice were euthanized eight hours (week 7) or 30 weeks (week 37) after the last DMH administration to evaluate subacute colon toxicity outcomes or the burden of (pre)neoplastic lesions, respectively. At week 7, Cx43 deficiency inferred no alterations in the DMH-induced increase in systemic (peripheral blood), in situ (colonocytes) DNA damage, and apoptosis in the colonocytes. At week 30, Cx43+/- mice presented an increase in preneoplastic aberrant crypt foci (ACF) multiplicity, while no alterations were observed in colorectal adenoma (CRA) occurrence, multiplicity, volume, proliferation, growth, and β-catenin immunoexpression. Similarly, an in silico analysis of human CRA showed decreased mRNA expression of Cx43 with no correlation with proliferation, apoptosis, and β-catenin markers. These findings indicate the discrete role of Cx43 in the early stages of chemically induced mouse colon carcinogenesis.
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Affiliation(s)
- Sara Gomes Espírito Santo
- Department of Pathology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, São Paulo, Brazil
| | - Tereza Cristina da Silva
- School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508-270, São Paulo, Brazil
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Bruno Cogliati
- School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508-270, São Paulo, Brazil
| | - Luís Fernando Barbisan
- Department of Structural and Functional Biology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil
| | - Guilherme Ribeiro Romualdo
- Department of Pathology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, São Paulo, Brazil
- Department of Structural and Functional Biology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil
- Correspondence: ; Tel.: +55-1438800469
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Wang Q, Huang X, Zhou S, Ding Y, Wang H, Jiang W, Xu M. IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis. Int J Genomics 2022; 2022:2723264. [PMID: 36483329 PMCID: PMC9726255 DOI: 10.1155/2022/2723264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 09/01/2023] Open
Abstract
The extensive morbidity of colorectal cancer (CRC) and the inferior prognosis of terminal CRC urgently call for reliable prognostic biomarkers. For this, we identified 704 differentially expressed genes (DEGs) by intersecting three datasets, GSE41328, GSE37364, and GSE15960 from Gene Expression Omnibus database, to maximize the accuracy of the results. Preliminary analysis of the DEGs was then performed using online gene analysis datasets, such as DAVID, UCSC Cancer Genome Browser, CBioPortal, STRING, and UCSC Cancer Genome Browser. Cytoscape was utilized to visualize the protein perception interaction network of DEGs, and the bubble map of GO and KEGG enrichment function was demonstrated using the R package. The Molecular Complex Detection (MCODE), Biological Network Gene Oncology (BiNGO) plug-in in Cytoscape, was applied to further screen the DEGs to obtain 15 seed genes, which were IL1RN, GALNT12, ADH6, SCN7A, CXCL1, FGF18, SOX9, ACACB, PRRX1, MZB1, SLC22A3, CNNM4, LY6E, IFITM2, and GDPD3. Among them, IL1RN, ADH6, SCN7A, ACACB, MZB1, and GDPD3 exhibited statistically significant survival differences, whereas limited studies were conducted in CRC. Based on the enrichment results of the "Gene Ontology"(GO) and "Kyoto Encyclopedia of Genes and genomes "(KEGG) as well as documented findings of key genes, we further emphasized the potential of IL1RN and PRRX1 as markers of immune infiltrates in CRC and confirmed our hypothesis by compiling data from the UALCAN, Tumor Immune Estimation Resource, and TISIDB databases for these two genes. The above-mentioned genes might offer a valuable insight into the diagnosis, immunotherapeutic targets, and prognosis of CRC.
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Affiliation(s)
- Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Shujing Zhou
- Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Yuntao Ding
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Huizhi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Weiye Jiang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
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Domanegg K, Sleeman JP, Schmaus A. CEMIP, a Promising Biomarker That Promotes the Progression and Metastasis of Colorectal and Other Types of Cancer. Cancers (Basel) 2022; 14:cancers14205093. [PMID: 36291875 PMCID: PMC9600181 DOI: 10.3390/cancers14205093] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary CEMIP (cell migration-inducing and hyaluronan-binding protein) has been implicated in the pathogenesis of numerous diseases, including colorectal and other forms of cancer. The molecular functions of CEMIP are currently under investigation and include the degradation of the extracellular matrix component hyaluronic acid (HA), as well as the regulation of a number of signaling pathways. In this review, we survey our current understanding of how CEMIP contributes to tumor growth and metastasis, focusing particularly on colorectal cancer, for which it serves as a promising biomarker. Abstract Originally discovered as a hypothetical protein with unknown function, CEMIP (cell migration-inducing and hyaluronan-binding protein) has been implicated in the pathogenesis of numerous diseases, including deafness, arthritis, atherosclerosis, idiopathic pulmonary fibrosis, and cancer. Although a comprehensive definition of its molecular functions is still in progress, major functions ascribed to CEMIP include the depolymerization of the extracellular matrix component hyaluronic acid (HA) and the regulation of a number of signaling pathways. CEMIP is a promising biomarker for colorectal cancer. Its expression is associated with poor prognosis for patients suffering from colorectal and other types of cancer and functionally contributes to tumor progression and metastasis. Here, we review our current understanding of how CEMIP is able to foster the process of tumor growth and metastasis, focusing particularly on colorectal cancer. Studies in cancer cells suggest that CEMIP exerts its pro-tumorigenic and pro-metastatic activities through stimulating migration and invasion, suppressing cell death and promoting survival, degrading HA, regulating pro-metastatic signaling pathways, inducing the epithelial–mesenchymal transition (EMT) program, and contributing to the metabolic reprogramming and pre-metastatic conditioning of future metastatic microenvironments. There is also increasing evidence indicating that CEMIP may be expressed in cells within the tumor microenvironment that promote tumorigenesis and metastasis formation, although this remains in an early stage of investigation. CEMIP expression and activity can be therapeutically targeted at a number of levels, and preliminary findings in animal models show encouraging results in terms of reduced tumor growth and metastasis, as well as combating therapy resistance. Taken together, CEMIP represents an exciting new player in the progression of colorectal and other types of cancer that holds promise as a therapeutic target and biomarker.
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Affiliation(s)
- Kevin Domanegg
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Jonathan P. Sleeman
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of Technology (KIT) Campus Nord, 76344 Eggenstein-Leopoldshafen, Germany
- Correspondence:
| | - Anja Schmaus
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of Technology (KIT) Campus Nord, 76344 Eggenstein-Leopoldshafen, Germany
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Tao W, Li L, Hu J, Xu S, Wang B, Ding J, Zhang M, Meng X, Wei X, Shan X, Peng K, Liu H, Ji F. Interaction between COX-2 and ER stress is involved in the apoptosis-induced myocardial ischemia/reperfusion injury. Am J Transl Res 2022; 14:3360-3371. [PMID: 35702111 PMCID: PMC9185046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
PURPOSE Apoptosis induced by excessive endoplasmic reticulum (ER) stress is accompanied by the occurrence and progression of myocardial ischemia/reperfusion (I/R) injury. COX-2 is also known to affect the development of I/R damage in myocardium. However, the interaction between COX-2 and ER stress in aggravating myocardial I/R lesion is not well characterized. Therefore, the purpose of our research was to explore the interaction between COX-2 and ER stress on myocardial apoptosis. METHODS The left anterior descending (LAD) coronary artery was ligatured with a 6-0# suture for 0.5 hours and subsequently subjected to reperfusion for 3 hours to simulate myocardial I/R in mice. Oxygen glucose deprivation/reoxygenation (OGD/R) was performed on H9c2 cells to construct an in vitro model of this experiment. NS398 (COX-2 specific inhibitor) and Salubrinal (Sal, ER stress inhibitor) were administered to assess the function of COX-2 and ER stress in myocardial I/R impairment. CCK-8 assay was used to evaluate the viability of H9c2 cells under different treatment conditions. TUNEL and Hoechst staining were used to detect the occurrence of apoptosis. Infarct area/area at risk and Hematoxylin-eosin stained sections were assessed after I/R. Protein expressions of glucose-regulated protein 78 (GRP78), COX-2, phosphorylation of eukaryotic translation initiation factor 2 alpha (p-eIF2α), CCAAT/enhancer-binding protein homologous protein (CHOP), and Cleaved caspase 3 in the myocardium were examined using Western blotting. Changes in Cleaved caspase 3 expression in myocardial slices were measured by immunohistochemistry. RESULTS Sal or NS398 partly reduced I/R-induced damage as testified by the apparent decrease in infarct size after I/R and reduced cell viability following OGD/R. Sal distinctly increased p-eIF2α, but caused decreased expression of COX-2, Cleaved caspase 3, and ER stress-associated proteins after I/R, suggesting that Sal effectively inhibited ER stress, apoptosis, and COX-2. Pretreatment with NS398 blocked I/R or OGD/R-induced upregulation of COX-2, Cleaved caspase 3, and ER stress-related marker proteins. CONCLUSIONS Interaction of COX-2 and ER stress regulates apoptosis and contributes to Myocardial lesion induced by I/R.
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Affiliation(s)
- Wenhui Tao
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Lingui Li
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Junkai Hu
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Shangxian Xu
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
| | - Biying Wang
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
| | - Jun Ding
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
| | - Mian Zhang
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Xiaowen Meng
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Xiang Wei
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
| | - Xisheng Shan
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Ke Peng
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Huayue Liu
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
| | - Fuhai Ji
- Department of Anesthesiology, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, China
- Institute of Anesthesiology, Soochow UniversitySuzhou, Jiangsu, China
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Rohr M, Beardsley J, Nakkina SP, Zhu X, Aljabban J, Hadley D, Altomare D. A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression. Sci Data 2021; 8:214. [PMID: 34381057 PMCID: PMC8358057 DOI: 10.1038/s41597-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Transcriptional profiling of pre- and post-malignant colorectal cancer (CRC) lesions enable temporal monitoring of molecular events underlying neoplastic progression. However, the most widely used transcriptomic dataset for CRC, TCGA-COAD, is devoid of adenoma samples, which increases reliance on an assortment of disparate microarray studies and hinders consensus building. To address this, we developed a microarray meta-dataset comprising 231 healthy, 132 adenoma, and 342 CRC tissue samples from twelve independent studies. Utilizing a stringent analytic framework, select datasets were downloaded from the Gene Expression Omnibus, normalized by frozen robust multiarray averaging and subsequently merged. Batch effects were then identified and removed by empirical Bayes estimation (ComBat). Finally, the meta-dataset was filtered for low variant probes, enabling downstream differential expression as well as quantitative and functional validation through cross-platform correlation and enrichment analyses, respectively. Overall, our meta-dataset provides a robust tool for investigating colorectal adenoma formation and malignant transformation at the transcriptional level with a pipeline that is modular and readily adaptable for similar analyses in other cancer types.
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Affiliation(s)
- Michael Rohr
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Jordan Beardsley
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Sai Preethi Nakkina
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Xiang Zhu
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Jihad Aljabban
- Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Dexter Hadley
- Department of Clinical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Deborah Altomare
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
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Youns M, Askoura M, Abbas HA, Attia GH, Khayyat AN, Goda RM, Almalki AJ, Khafagy ES, Hegazy WAH. Celastrol Modulates Multiple Signaling Pathways to Inhibit Proliferation of Pancreatic Cancer via DDIT3 and ATF3 Up-Regulation and RRM2 and MCM4 Down-Regulation. Onco Targets Ther 2021; 14:3849-3860. [PMID: 34194230 PMCID: PMC8238076 DOI: 10.2147/ott.s313933] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/13/2021] [Indexed: 12/17/2022] Open
Abstract
Background Pancreatic cancer is one of the most serious and lethal human cancers with a snowballing incidence around the world. The natural product celastrol has also been widely documented as a potent anti-inflammatory, anti-angiogenic, and anti-oxidant. Purpose To elucidate the antitumor effect of celastrol on pancreatic cancer cells and its modulatory role on whole genome expression. Methods The antitumor activity of celastrol on a panel of pancreatic cancer cells has been evaluated by Sulforhodamine B assay. Caspase 3/7 and histone-associated DNA fragments assays were done for apoptosis measurement. Additionally, prostaglandin (PGE2) inhibition was evaluated. Moreover, a microarray gene expression profiling was carried out to detect possible key players that modulate the antitumor effects of celastrol on cells of pancreatic cancer. Results Our findings indicated that celastrol suppresses the cellular growth of pancreatic cancer cells, induces apoptosis, and inhibits PGE2 production. Celastrol modulated many signaling genes and its cytotoxic effect was mainly mediated via over-expression of ATF3 and DDIT3, and down-expression of RRM2 and MCM4. Conclusion The current study aims to be a starting point to generate a hypothesis on the most significant regulatory genes and for a full dissection of the celastrol possible effects on each single gene to prevent the pancreatic cancer growth.
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Affiliation(s)
- Mahmoud Youns
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt.,Department of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Momen Askoura
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Hisham A Abbas
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Gouda H Attia
- Department of Pharmacognosy, Faculty of Pharmacy, Kafr El-Shiekh University, Kafr El-Shiekh, Egypt.,Department of Pharmacognosy, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Ahdab N Khayyat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Reham M Goda
- Department of Microbiology and Biotechnology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Mansoura, Egypt
| | - Ahmad J Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, 11942, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia, 41552, Egypt
| | - Wael A H Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
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10
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Po A, Citarella A, Catanzaro G, Besharat ZM, Trocchianesi S, Gianno F, Sabato C, Moretti M, De Smaele E, Vacca A, Fiori ME, Ferretti E. Hedgehog-GLI signalling promotes chemoresistance through the regulation of ABC transporters in colorectal cancer cells. Sci Rep 2020; 10:13988. [PMID: 32814794 PMCID: PMC7438531 DOI: 10.1038/s41598-020-70871-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/28/2020] [Indexed: 01/20/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer death. Chemoresistance is a pivotal feature of cancer cells leading to treatment failure and ATP-binding cassette (ABC) transporters are responsible for the efflux of several molecules, including anticancer drugs. The Hedgehog-GLI (HH-GLI) pathway is a major signalling in CRC, however its role in chemoresistance has not been fully elucidated. Here we show that the HH-GLI pathway favours resistance to 5-fluorouracil and Oxaliplatin in CRC cells. We identified potential GLI1 binding sites in the promoter region of six ABC transporters, namely ABCA2, ABCB1, ABCB4, ABCB7, ABCC2 and ABCG1. Next, we investigated the binding of GLI1 using chromatin immunoprecipitation experiments and we demonstrate that GLI1 transcriptionally regulates the identified ABC transporters. We show that chemoresistant cells express high levels of GLI1 and of the ABC transporters and that GLI1 inhibition disrupts the transporters up-regulation. Moreover, we report that human CRC tumours express high levels of the ABCG1 transporter and that its expression correlates with worse patients' prognosis. This study identifies a new mechanism where HH-GLI signalling regulates CRC chemoresistance features. Our results indicate that the inhibition of Gli1 regulates the ABC transporters expression and therefore should be considered as a therapeutic option in chemoresistant patients.
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Affiliation(s)
- Agnese Po
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Anna Citarella
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Giuseppina Catanzaro
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Sofia Trocchianesi
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Francesca Gianno
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Claudia Sabato
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Marta Moretti
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alessandra Vacca
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Micol Eleonora Fiori
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161, Rome, Italy.
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11
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Promoter Hypomethylation and Increased Expression of the Long Non-coding RNA LINC00152 Support Colorectal Carcinogenesis. Pathol Oncol Res 2020; 26:2209-2223. [PMID: 32307642 PMCID: PMC7471146 DOI: 10.1007/s12253-020-00800-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/27/2020] [Indexed: 12/27/2022]
Abstract
Up-regulation of the long non-coding RNA LINC00152 can contribute to cancer development, proliferation and invasion, including colorectal cancer, however, its mechanism of action in colorectal carcinogenesis and progression is only insufficiently understood. In this work we correlated LINC00152 expression with promoter DNA methylation changes in colorectal tissues along the normal-adenoma-carcinoma sequence and studied the effects of LINC00152 silencing on the cell cycle regulation and on the whole transcriptome in colon carcinoma cells using cell and molecular biology techniques. LINC00152 was significantly up-regulated in adenoma and colorectal cancer (p < 0.001) compared to normal samples, which was confirmed by real-time PCR and in situ hybridization. LINC00152 promoter hypomethylation detected in colorectal cancer (p < 0.01) was strongly correlated with increased LINC00152 expression (r=-0.90). Silencing of LINC00152 significantly suppressed cell growth, induced apoptosis and decreased cyclin D1 expression (p < 0.05). Whole transcriptome analysis of LINC00152-silenced cells revealed significant down-regulation of oncogenic and metastasis promoting genes (e.g. YES proto-oncogene 1, PORCN porcupine O-acyltransferase), and up-regulation of tumour suppressor genes (e.g. DKK1 dickkopf WNT signalling pathway inhibitor 1, PERP p53 apoptosis effector) (adjusted p < 0.05). Pathway analysis confirmed the LINC00152-related activation of oncogenic molecular pathways including those driven by PI3K/Akt, Ras, WNT, TP53, Notch and ErbB. Our results suggest that promoter hypomethylation related overexpression of LINC00152 can contribute to the pathogenesis of colorectal cancer by facilitating cell progression through the up-regulation of several oncogenic and metastasis promoting pathway elements.
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12
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Yoshida H, Okada Y. Role of HYBID (Hyaluronan Binding Protein Involved in Hyaluronan Depolymerization), Alias KIAA1199/CEMIP, in Hyaluronan Degradation in Normal and Photoaged Skin. Int J Mol Sci 2019; 20:ijms20225804. [PMID: 31752258 PMCID: PMC6888145 DOI: 10.3390/ijms20225804] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/13/2019] [Accepted: 11/17/2019] [Indexed: 01/22/2023] Open
Abstract
Photoaged skin is characterized clinically by apparent manifestations such as wrinkles and sagging, and histologically by an accumulation of abnormal elastin and a severe loss of collagen fibers in the dermis. Quantitative and qualitative alterations in elastin and collagens are considered to be responsible for the formation of wrinkles and sagging. However, since the integrity of elastin and collagen fibers in the dermis is maintained by their interactions with hyaluronan (HA) and a proteoglycan network structure, HA degradation may be the initial process, prior to the breakdown of the fibrillary components, leading to wrinkles and sagging in photoaged skin. We have recently discovered a new HA-degrading mechanism mediated by HYBID (hyaluronan binding protein involved in hyaluronan depolymerization), alias KIAA1199/CEMIP, in human skin fibroblasts, and examined the implication of HYBID for skin photoaging. In this review, we give an overview of the characteristics of HYBID and its prospective roles in HA turnover in normal skin and excessive HA degradation in photoaged skin. In addition, we describe our data on the inhibition of HYBID activity and expression by plant extracts in skin fibroblasts; and propose novel strategies to prevent or improve photoaging symptoms, such as skin wrinkling, by inhibition of HYBID-mediated HA degradation.
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Affiliation(s)
- Hiroyuki Yoshida
- Biological Science Research, Kao Corporation, 3-28, 5-chome, Kotobuki-cho, Odawara-shi, Kanagawa 250-0002, Japan
- Correspondence: (H.Y.); (Y.O.); Tel.: +81-465-34-6116 (H.Y.); +81-3-5800-7531 (Y.O.); Fax: +81-465-34-3037 (H.Y.); +81-3-5800-7532 (Y.O.)
| | - Yasunori Okada
- Department of Pathophysiology for Locomotive and Neoplastic Diseases, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Correspondence: (H.Y.); (Y.O.); Tel.: +81-465-34-6116 (H.Y.); +81-3-5800-7531 (Y.O.); Fax: +81-465-34-3037 (H.Y.); +81-3-5800-7532 (Y.O.)
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13
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Marchiori C, Scarpa M, Kotsafti A, Morgan S, Fassan M, Guzzardo V, Porzionato A, Angriman I, Ruffolo C, Sut S, Dall'Acqua S, Bardini R, De Caro R, Castoro C, Scarpa M, Castagliuolo I. Epithelial CD80 promotes immune surveillance of colonic preneoplastic lesions and its expression is increased by oxidative stress through STAT3 in colon cancer cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:190. [PMID: 31072360 PMCID: PMC6509793 DOI: 10.1186/s13046-019-1205-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/01/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND One of the most potent costimulatory molecules involved in the recognition and killing of tumor cells is CD80. However, its role and the molecular mechanisms regulating its expression in sporadic colorectal carcinogenesis remain elusive. Here, we provide evidence for CD80 overexpression in human colon epithelial cells derived from preneoplastic mucosa. METHODS Expression of CD80 on colonic epithelial cells isolated from normal human colonic mucosa, preneoplastic and neoplastic specimens was assessed by flow cytometry. WT and CD80KO mice received azoxymethane to induce colon preneoplastic lesions and sacrificed to perform histology, flow cytometry analysis and immunohistochemistry of colonic mucosa. Some WT mice were treated with a monoclonal anti-CD80 antibody following AOM administration. Primary colon epithelial cells and CT26 cell line were used to quantify the expression of CD80 in response to pro-oxidant stimuli. Specific pharmacological inhibitors and siRNA silencing were used to inhibit MAPK pathways and STAT3. RESULTS CD80 expression was significantly increased in colon epithelial cells of human preneoplastic lesions. In the AOM model, CD80 impairment by administration of neutralizing antibodies or use of CD80 knockout mice enhanced dysplasia development. In vitro, CD80 upregulation was induced by oxidative stress in colon cancer cells and primary colon epithelial cells. In addition, reactive oxygen species could induce CD80 expression via the JNK and p38 MAPK pathways, that activated STAT3 transcription factor in colon cancer epithelial cells. CONCLUSION This study provide evidence for a major role of CD80 in orchestrating immune surveillance of colon preneoplastic lesions and might help to develop novel approaches that exploit anti-tumor immunity to prevent and control colon cancer.
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Affiliation(s)
- Chiara Marchiori
- Department of Molecular Medicine DMM, University of Padua, Padua, Italy
| | - Melania Scarpa
- Laboratory of Advanced Translational Research, Veneto Institute of Oncology IOV - IRCCS, via Gattamelata 64, 35128, Padua, Italy.
| | - Andromachi Kotsafti
- Laboratory of Advanced Translational Research, Veneto Institute of Oncology IOV - IRCCS, via Gattamelata 64, 35128, Padua, Italy
| | - Susan Morgan
- Pathology Unit, Sheffield Teaching Hospitals, Sheffield, UK
| | - Matteo Fassan
- Surgical Pathology Unit from the Department of Medicine DIMED, University of Padua, Padua, Italy
| | - Vincenza Guzzardo
- Surgical Pathology Unit from the Department of Medicine DIMED, University of Padua, Padua, Italy
| | | | - Imerio Angriman
- General Surgery Unit from the Department of Surgery, Oncology and Gastroenterology DISCOG, University of Padua, Padua, Italy
| | - Cesare Ruffolo
- General Surgery Unit (IV), Ca' Foncello Hospital, Treviso, Italy
| | - Stefania Sut
- Department of Pharmaceutical and Pharmacological Sciences DSF, University of Padua, Padua, Italy
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences DSF, University of Padua, Padua, Italy
| | - Romeo Bardini
- General Surgery Unit from the Department of Surgery, Oncology and Gastroenterology DISCOG, University of Padua, Padua, Italy
| | | | - Carlo Castoro
- Laboratory of Advanced Translational Research, Veneto Institute of Oncology IOV - IRCCS, via Gattamelata 64, 35128, Padua, Italy
| | - Marco Scarpa
- Laboratory of Advanced Translational Research, Veneto Institute of Oncology IOV - IRCCS, via Gattamelata 64, 35128, Padua, Italy
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14
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Maroni P, Bendinelli P, Matteucci E, Desiderio MA. The therapeutic effect of miR-125b is enhanced by the prostaglandin endoperoxide synthase 2/cyclooxygenase 2 blockade and hampers ETS1 in the context of the microenvironment of bone metastasis. Cell Death Dis 2018; 9:472. [PMID: 29700305 PMCID: PMC5920088 DOI: 10.1038/s41419-018-0499-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 02/07/2023]
Abstract
Bone is the most common site for breast cancer spread. In the pro-metastatic cell line 1833, derived from MDA-MB-231 breast adenocarcinoma cells, both hypoxia and hepatocyte growth factor (HGF) influence the effect of miR-125b on ETS proto-oncogene 1 transcription factor (ETS1). The effect of hypoxia inducible factor 1 alpha subunit (HIF1A), known to promote metastatic spread by upregulating prostaglandin endoperoxide synthase 2 (PTGS2), may be dampened by miR-125b targeting PTGS2. Here, we investigated whether miR-125b plays a role in breast cancer metastasis by measuring its activity in response to the chemotherapeutic agent NS-398 in a xenograft model. NS-398 is typically used in the clinic to target PTGS2. We also aimed to describe the molecular mechanisms in vitro, since the enhancement of epithelial properties may favor the efficacy of therapies. We report that in the xenograft model, miR-125b reduced metastasis to the bone. We also report suppression of PTGS2 enhanced survival by decreasing HIF1A in cells within the bone marrow. In 1833 cells transfected with a miR-125b mimic we observed several phenotypic changes including enhancement of the epithelial marker E-cadherin, a reduction of mesenchymal-associated genes and a reduction of WNT-associated stem cell signaling. Our findings suggest that in vivo, key players of the bone microenvironment promoting breast cancer spread are regulated by miR-125b. In future, biological molecules imitating miR-125b may enhance the sensitivity of chemotherapeutic agents used to counteract bone metastases.
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Affiliation(s)
- Paola Maroni
- Istituto Ortopedico Galeazzi IRCCS, Via R. Galeazzi 4, 20161, Milano, Italy
| | - Paola Bendinelli
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Via L. Mangiagalli 31, 20133, Milano, Italy
| | - Emanuela Matteucci
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Via L. Mangiagalli 31, 20133, Milano, Italy
| | - Maria Alfonsina Desiderio
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Via L. Mangiagalli 31, 20133, Milano, Italy.
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15
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Youns M, ElKhoely A, Kamel R. The growth inhibitory effect of gambogic acid on pancreatic cancer cells. Naunyn Schmiedebergs Arch Pharmacol 2018; 391:551-560. [PMID: 29546614 DOI: 10.1007/s00210-018-1485-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/06/2018] [Indexed: 02/08/2023]
Abstract
Pancreatic cancer, the fourth most common cause of cancer-related deaths, is one of the most aggressive and devastating human malignancies with increasing incidence worldwide. To date, surgical resection is the only potentially curative therapy available for pancreatic cancer patients. Early diagnosis of pancreatic tumors is difficult, and hence, nearly 80% of patients cannot receive surgical resection. Natural products have always been a vital source for novel compounds for cancer treatment. The naturally occurring prenylated xanthone, gambogic acid, has been previously shown to exert potent anticancer, anti-inflammatory, apoptotic, antiangiogenic, and antioxidant activities. However, to our knowledge, there have been no specific studies showing its effect on the whole-genome expression in pancreatic cancer cells. Here, the anticancer activity of gambogic acid toward a panel of pancreatic cancer cells with different differentiation stages has been evaluated. Additionally, a whole-genome transcription profiling study was performed in order to identify possible candidate players modulating the antitumor effect of gambogic acid on pancreatic cancer cells. Expression analysis results showed that the pancreatic adenocarcinoma signaling pathway was specifically affected upon gambogic acid treatment. Moreover, the growth inhibitory effect of gambogic acid on pancreatic cancer cells was modulated through up-regulation of DDIT3, DUSP1, and DUSP5 and down-regulation of ALDOA, TOP2A, and ATG4B. The present work is a starting point for the generation of hypotheses on significantly regulated candidate key player genes and for a detailed dissection of the potential role of each individual gene for the activity of gambogic acid on pancreatic cancer.
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Affiliation(s)
- Mаhmoud Youns
- Department of Functional Genome analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. .,Oman Pharmacy Institute, Muscat, Sultanate of Oman. .,Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt.
| | - Abeer ElKhoely
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Rehab Kamel
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
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16
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Loss of Myosin Vb in colorectal cancer is a strong prognostic factor for disease recurrence. Br J Cancer 2017; 117:1689-1701. [PMID: 29024942 PMCID: PMC5729446 DOI: 10.1038/bjc.2017.352] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/24/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023] Open
Abstract
Background: Selecting the most beneficial treatment regimens for colorectal cancer (CRC) patients remains challenging due to a lack of prognostic markers. Members of the Myosin family, proteins recognised to have a major role in trafficking and polarisation of cells, have recently been reported to be closely associated with several types of cancer and might thus serve as potential prognostic markers in the context of CRC. Methods: We used a previously established meta-analysis of publicly available gene expression data to analyse the expression of different members of the Myosin V family, namely MYO5A, 5B, and 5C, in CRC. Using laser-microdissected material as well as tissue microarrays from paired human CRC samples, we validated both RNA and protein expression of Myosin Vb (MYO5B) and its known adapter proteins (RAB8A and RAB25) in an independent patient cohort. Finally, we assessed the prognostic value of both MYO5B and its adapter-coupled combinatorial gene expression signatures. Results: The meta-analysis as well as an independent patient cohort study revealed a methylation-independent loss of MYO5B expression in CRC that matched disease progression. Although MYO5B mutations were identified in a small number of patients, these cannot be solely responsible for the common downregulation observed in CRC patients. Significantly, CRC patients with low MYO5B expression displayed shorter overall, disease-, and metastasis-free survival, a trend that was further reinforced when RAB8A expression was also taken into account. Conclusions: Our data identify MYO5B as a powerful prognostic biomarker in CRC, especially in early stages (stages I and II), which might help stratifying patients with stage II for adjuvant chemotherapy.
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17
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West NR, Hegazy AN, Owens BMJ, Bullers SJ, Linggi B, Buonocore S, Coccia M, Görtz D, This S, Stockenhuber K, Pott J, Friedrich M, Ryzhakov G, Baribaud F, Brodmerkel C, Cieluch C, Rahman N, Müller-Newen G, Owens RJ, Kühl AA, Maloy KJ, Plevy SE, Keshav S, Travis SPL, Powrie F. Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease. Nat Med 2017; 23:579-589. [PMID: 28368383 PMCID: PMC5420447 DOI: 10.1038/nm.4307] [Citation(s) in RCA: 492] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/17/2017] [Indexed: 02/08/2023]
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are complex chronic inflammatory conditions of the gastrointestinal tract that are driven by perturbed cytokine pathways. Anti-tumor necrosis factor-α (TNF) antibodies are mainstay therapies for IBD. However, up to 40% of patients are nonresponsive to anti-TNF agents, which makes the identification of alternative therapeutic targets a priority. Here we show that, relative to healthy controls, inflamed intestinal tissues from patients with IBD express high amounts of the cytokine oncostatin M (OSM) and its receptor (OSMR), which correlate closely with histopathological disease severity. The OSMR is expressed in nonhematopoietic, nonepithelial intestinal stromal cells, which respond to OSM by producing various proinflammatory molecules, including interleukin (IL)-6, the leukocyte adhesion factor ICAM1, and chemokines that attract neutrophils, monocytes, and T cells. In an animal model of anti-TNF-resistant intestinal inflammation, genetic deletion or pharmacological blockade of OSM significantly attenuates colitis. Furthermore, according to an analysis of more than 200 patients with IBD, including two cohorts from phase 3 clinical trials of infliximab and golimumab, high pretreatment expression of OSM is strongly associated with failure of anti-TNF therapy. OSM is thus a potential biomarker and therapeutic target for IBD, and has particular relevance for anti-TNF-resistant patients.
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Affiliation(s)
- Nathaniel R. West
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ahmed N. Hegazy
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Bryan Linggi
- Janssen Research and Development LLC, Raritan, NJ, USA
| | - Sofia Buonocore
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Margherita Coccia
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Dieter Görtz
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Sébastien This
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Krista Stockenhuber
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Johanna Pott
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Grigory Ryzhakov
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | | | | - Constanze Cieluch
- Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité–Universitätsmedizin Berlin, Germany
| | - Nahid Rahman
- OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford, UK
| | - Gerhard Müller-Newen
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Raymond J. Owens
- OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anja A. Kühl
- Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité–Universitätsmedizin Berlin, Germany
| | - Kevin J. Maloy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | | | - Satish Keshav
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon P. L. Travis
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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18
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Nagy ZB, Wichmann B, Kalmár A, Galamb O, Barták BK, Spisák S, Tulassay Z, Molnár B. Colorectal adenoma and carcinoma specific miRNA profiles in biopsy and their expression in plasma specimens. Clin Epigenetics 2017; 9:22. [PMID: 28289479 PMCID: PMC5310023 DOI: 10.1186/s13148-016-0305-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/19/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND MiRNA expression markers are well characterized in colorectal cancer (CRC), but less is known about miRNA expression profiles in colorectal adenomas. Genome-wide miRNA and mRNA expression analyses were conducted through the colorectal adenoma dysplasia sequence. Furthermore, analysis of the expression levels of miRNAs in matched plasma samples was performed, focusing on biomarker candidates; miRNA and mRNA expression analyses were performed on colorectal biopsies and plasma samples (20 normals; 11 tubular and 9 tubulovillous adenomas; 20 colorectal carcinomas) by miRNA 3.0 and Human Transcriptome Array (Affymetrix) and validated by RT-qPCR. Microarray data were analyzed using Expression Console and mRNA targets were predicted using miRWALK 2.0. RESULTS Based on microarray analysis, 447 miRNAs were expressed in tissue and 320 in plasma. Twelve were upregulated (miR-31, 8-fold p < 0.001) and 11 were downregulated (miR-10b 3-fold p < 0.001) in neoplastic lesions compared to normal group. Eleven miRNAs showed altered expression between adenoma subtypes (miR-183 2.8-fold change, p < 0.007). Expression level of 24 miRNAs differed between adenoma and CRC groups (including miR-196a, 3.5-fold). Three miRNAs (miR-31, miR-4506, miR-452*) were differentially expressed in adenoma compared to normal both in tissue and plasma samples. miRNA expression data were confirmed by RT-PCR both in plasma and matched tissue samples. CONCLUSIONS MiRNAs showed characteristic expression changes during CRC development in tissue. miRNAs were also presented in plasma and positively correlated with matched tissue expression levels. The identified miRNA expression changes could be verified RT-PCR methods facilitating routine application.
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Affiliation(s)
- Zsófia Brigitta Nagy
- Molecular Gastroenterology Laboratory, 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi Str. 46, Budapest, 1088 Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Alexandra Kalmár
- Molecular Gastroenterology Laboratory, 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi Str. 46, Budapest, 1088 Hungary
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barbara Kinga Barták
- Molecular Gastroenterology Laboratory, 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi Str. 46, Budapest, 1088 Hungary
| | - Sándor Spisák
- Current Address: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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19
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Galamb O, Kalmár A, Barták BK, Patai &AV, Leiszter K, Péterfia B, Wichmann B, Valcz G, Veres G, Tulassay Z, Molnár B. Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma. World J Gastroenterol 2016; 22:10325-10340. [PMID: 28058013 PMCID: PMC5175245 DOI: 10.3748/wjg.v22.i47.10325] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/20/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites.
METHODS In silico DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]. Among the differentially methylated age-related genes, secreted frizzled related protein 1 (SFRP1) promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting (MS-HRM) analysis. mRNA expression of age-related “epigenetic clock” genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylation-gene expression data was performed on 30 colonic samples using methyl capture sequencing.
RESULTS Fifty-seven age-related CpG sites including hypermethylated PPP1R16B, SFRP1, SYNE1 and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues (P < 0.05, Δβ≥ 10%). In the adenoma vs normal comparison, 70 CpG sites differed significantly, including hypermethylated DKK3, SDC2, SFRP1, SYNE1 and hypomethylated CEMIP, SPATA18 (P < 0.05, Δβ≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC (55.0% ± 8.4 %) and adenoma tissue samples (49.9% ± 18.1%) compared to normal adult (5.2% ± 2.7%) and young (2.2% ± 0.7%) colonic tissue (P < 0.0001). DNA methylation of SFRP1 promoter was slightly, but significantly increased in healthy adults compared to normal young samples (P < 0.02). This correlated with significantly increased SFRP1 mRNA levels in children compared to normal adult samples (P < 0.05). In CRC tissue the mRNA expression of 117 age-related genes were changed, while in adenoma samples 102 genes showed differential expression compared with normal colonic tissue (P < 0.05, logFC > 0.5). The change of expression for several genes including SYNE1, CLEC3B, LTBP3 and SFRP1, followed the same pattern in aging and carcinogenesis, though not for all genes (e.g., MGP).
CONCLUSION Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the mRNA expression of certain CRC- and adenoma-related key control genes.
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Identification of KIAA1199 as a Biomarker for Pancreatic Intraepithelial Neoplasia. Sci Rep 2016; 6:38273. [PMID: 27922049 PMCID: PMC5138641 DOI: 10.1038/srep38273] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 10/06/2016] [Indexed: 02/03/2023] Open
Abstract
Pancreatic cancer is one of the most aggressive cancers and has an extremely poor prognosis. Despite recent progress in both basic and clinical research, most pancreatic cancers are detected at an incurable stage owing to the absence of disease-specific symptoms. Thus, developing novel approaches for detecting pancreatic cancer at an early stage is imperative. Our in silico and immunohistochemical analyses showed that KIAA1199 is specifically expressed in human pancreatic cancer cells and pancreatic intraepithelial neoplasia, the early lesion of pancreatic cancer, in a genetically engineered mouse model and in human patient samples. We also detected secreted KIAA1199 protein in blood samples obtained from pancreatic cancer mouse models, but not in normal mice. Furthermore, we found that assessing KIAA1199 autoantibody increased the sensitivity of detecting pancreatic cancer. These results indicate the potential benefits of using KIAA1199 as a biomarker for early-stage pancreatic cancer.
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Cui ML, Zhang MX, Zhang C, Wang JJ. Role of cancer-related inflammation in colon cancer. Shijie Huaren Xiaohua Zazhi 2016; 24:4343-4353. [DOI: 10.11569/wcjd.v24.i32.4343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chronic inflammation is one of the important mechanisms for the development of colon cancer, and the role of cancer-related inflammation (CRI) in tumor development is a hot research topic in recent years. Therefore, it is very important to clarify the effect and regulation of CRI in colon cancer. Accumulating evidence indicates that transcription factors, cytokines, chemokines, cyclooxygenase-2 and microRNAs play key roles in CRI. This review focuses on the research progress about these molecules in colon cancer.
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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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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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Meng WJ, Yang L, Ma Q, Zhang H, Adell G, Arbman G, Wang ZQ, Li Y, Zhou ZG, Sun XF. MicroRNA Expression Profile Reveals miR-17-92 and miR-143-145 Cluster in Synchronous Colorectal Cancer. Medicine (Baltimore) 2015; 94:e1297. [PMID: 26266366 PMCID: PMC4616700 DOI: 10.1097/md.0000000000001297] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The expression of abnormal microRNA (miRNA, miR) is a ubiquitous feature of colorectal cancer (CRC). The pathological features and clinical behaviors of synchronous CRC have been comprehensively described; however, the expression profile of miRNA and small nucleolar RNA (snoRNA) in synchronous CRC has not been elucidated. In the present study, the expression profile of miRNA and snoRNA in 5 synchronous CRCs, along with the matched normal colorectal tissue was evaluated by microarray. Function and pathway analyses of putative targets, predicted from miRNA-mRNA interaction, were performed. Moreover, we analyzed clinicopathological and molecular characteristics of 22 patients with synchronous CRC and 579 solitary CRCs in a retrospective cohort study. We found a global dysregulation of miRNAs, including an oncogenic miR-17-92 cluster and oncosuppressive miR-143-145 cluster, and snoRNAs in synchronous CRC. Differential miRNA rather than snoRNA expression was robust enough to distinguish synchronous cancer from normal mucosa. Function analysis of putative targets suggested that miRNA clusters may modulate multiple effectors of oncogenic pathways involved in the pathogenesis of synchronous CRC. A comparison of normal mucosa between synchronous and solitary CRC suggested a differential genetic background of synchronous CRC from solitary CRC during carcinogenesis. Compared with solitary cancer patients, synchronous cases exhibited multiple extra-colonic cancers (P = 0.012), coexistence of adenoma (P = 0.012), microsatellite instability (P = 0.024), and less glucose transporter 1 (P = 0.037). Aberrant miRNA expression profiles could potentially be used as a diagnostic tool for synchronous CRC. Our findings represent the first comprehensive miRNA and snoRNA expression signatures for synchronous CRC, implicating that the miRNAs and snoRNAs may present therapeutic targets for synchronous CRC.
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Affiliation(s)
- Wen-Jian Meng
- From the Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China (W-JM, LY, QM, Z-QW, Z-GZ); School of Medicine, Örebro University, Örebro (HZ); Department of Oncology, County Council of Östergötland, Linköping (GA); Department of Surgery, Vrinnevi Hospital, University of Linköping, Norrköping, Sweden (GA); Institute of Digestive Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China (YL, Z-GZ, X-FS); and Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden (X-FS)
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Dai Y, Jiang JB, Wang YL, Jin ZT, Hu SY. Functional and protein‑protein interaction network analysis of colorectal cancer induced by ulcerative colitis. Mol Med Rep 2015; 12:4947-58. [PMID: 26239378 PMCID: PMC4581825 DOI: 10.3892/mmr.2015.4102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 06/17/2015] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is a well‑recognized complication of ulcerative colitis (UC), and patients with UC have a higher incidence of CRC, compared with the general population. However, the properties of CRC induced by UC have not been clarified using an interaction network to analyze and compare gene sets. In the present study, six microarray datasets of CRC and UC were extracted from the Array Express database, and gene signatures were identified using the genome‑wide relative significance (GWRS) method. Functional analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Prediction of the genes and microRNA were performed using a hypergeometric method. A protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/proteins, and clusters were obtained through the Molecular Complex Detection algorithm. Topological centrality and a novel analyzing method, based on the rank value of GWGS, were used to characterize the biological importance of the clusters. A total of 217 differentially expressed (DE) genes of CRC were identified, 341 DE genes were identified in UC, and 62 common genes existed in the two. Several KEGG pathways were the same in CRC and UC. Collagenase, progesterone, heparin, urokinase, nadh and adenosine drugs demonstrated potential for use in treatment of CRC and UC. In the PPI network of CRC, 210 nodes and 752 edges were observed, wheras 314 nodes and 882 edges were identified in UC. Cluster 3 in UC had the highest GWGS, while the topological centrality of Cluster 3 in UC had the lowest degree and betweenness. PPI network analysis provided an effective way to estimate and understand the likelihood of the potential connections between proteins/genes. The results obtained following the use of GWGS to analyze differences between clusters did not agree with the topological degree and betweenness centrality, which indicated that gene fold change based GWGS was controversial with degree here in CRC and UC.
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Affiliation(s)
- Yong Dai
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Jin-Bo Jiang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yan-Lei Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Zu-Tao Jin
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - San-Yuan Hu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
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Ciarloni L, Hosseinian S, Monnier-Benoit S, Imaizumi N, Dorta G, Ruegg C. Discovery of a 29-gene panel in peripheral blood mononuclear cells for the detection of colorectal cancer and adenomas using high throughput real-time PCR. PLoS One 2015; 10:e0123904. [PMID: 25876024 PMCID: PMC4395254 DOI: 10.1371/journal.pone.0123904] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related death in developed countries. Early detection of CRC leads to decreased CRC mortality. A blood-based CRC screening test is highly desirable due to limited invasiveness and high acceptance rate among patients compared to currently used fecal occult blood testing and colonoscopy. Here we describe the discovery and validation of a 29-gene panel in peripheral blood mononuclear cells (PBMC) for the detection of CRC and adenomatous polyps (AP). Blood samples were prospectively collected from a multicenter, case-control clinical study. First, we profiled 93 samples with 667 candidate and 3 reference genes by high throughput real-time PCR (OpenArray system). After analysis, 160 genes were retained and tested again on 51 additional samples. Low expressed and unstable genes were discarded resulting in a final dataset of 144 samples profiled with 140 genes. To define which genes, alone or in combinations had the highest potential to discriminate AP and/or CRC from controls, data were analyzed by a combination of univariate and multivariate methods. A list of 29 potentially discriminant genes was compiled and evaluated for its predictive accuracy by penalized logistic regression and bootstrap. This method discriminated AP >1cm and CRC from controls with a sensitivity of 59% and 75%, respectively, with 91% specificity. The behavior of the 29-gene panel was validated with a LightCycler 480 real-time PCR platform, commonly adopted by clinical laboratories. In this work we identified a 29-gene panel expressed in PBMC that can be used for developing a novel minimally-invasive test for accurate detection of AP and CRC using a standard real-time PCR platform.
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Affiliation(s)
- Laura Ciarloni
- Diagnoplex SA, Epalinges, Switzerland
- Novigenix SA, Epalinges, Switzerland
| | - Sahar Hosseinian
- Diagnoplex SA, Epalinges, Switzerland
- Novigenix SA, Epalinges, Switzerland
| | | | - Natsuko Imaizumi
- Diagnoplex SA, Epalinges, Switzerland
- National Center for Competence in Research (NCCR), Molecular Oncology, Swiss Institute for Experimental Cancer Research (ISREC)-Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gian Dorta
- Department of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Curzio Ruegg
- Novigenix SA, Epalinges, Switzerland
- National Center for Competence in Research (NCCR), Molecular Oncology, Swiss Institute for Experimental Cancer Research (ISREC)-Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland
- * E-mail:
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Leiszter K, Sipos F, Galamb O, Krenács T, Veres G, Wichmann B, Fűri I, Kalmár A, Patai ÁV, Tóth K, Valcz G, Tulassay Z, Molnár B. Promoter hypermethylation-related reduced somatostatin production promotes uncontrolled cell proliferation in colorectal cancer. PLoS One 2015; 10:e0118332. [PMID: 25723531 PMCID: PMC4344335 DOI: 10.1371/journal.pone.0118332] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/13/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Somatostatin (SST) has anti-proliferative and pro-apoptotic effects. Our aims were to analyze and compare the SST expression during normal aging and colorectal carcinogenesis at mRNA and protein levels. Furthermore, we tested the methylation status of SST in biopsy samples, and the cell growth inhibitory effect of the SST analogue octreotide in human colorectal adenocarcinoma cell line. METHODS Colonic samples were collected from healthy children (n1 = 6), healthy adults (n2 = 41) and colorectal cancer patients (CRCs) (n3 = 34) for SST mRNA expression analysis, using HGU133 Plus2.0 microarrays. Results were validated both on original (n1 = 6; n2 = 6; n3 = 6) and independent samples ((n1 = 6; n2 = 6; n3 = 6) by real-time PCR. SST expressing cells were detected by immunohistochemistry on colonic biopsy samples (n1 = 14; n2 = 20; n3 = 23). The effect of octreotide on cell growth was tested on Caco-2 cell line. SST methylation percentage in biopsy samples (n1 = 5; n2 = 5; n3 = 9) was defined using methylation-sensitive restriction enzyme digestion. RESULTS In case of normal aging SST mRNA expression did not alter, but decreased in cancer (p < 0.05). The ratio of SST immunoreactive cells was significantly higher in children (0.70% ± 0.79%) compared to CRC (0% ± 0%) (p < 0.05). Octreotide significantly increased the proportion of apoptotic Caco-2 cells. SST showed significantly higher methylation level in tumor samples (30.2% ± 11.6%) compared to healthy young individuals (3.5% ± 1.9%) (p < 0.05). CONCLUSIONS In cancerous colonic mucosa the reduced SST production may contribute to the uncontrolled cell proliferation. Our observation that in colon cancer cells octreotide significantly enhanced cell death and attenuated cell proliferation suggests that SST may act as a regulator of epithelial cell kinetics. The inhibition of SST expression in CRC can be epigenetically regulated by promoter hypermethylation.
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Affiliation(s)
- Katalin Leiszter
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, 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, Budapest, Hungary
| | - Gábor Veres
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Barna Wichmann
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Fűri
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Árpád V. Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Kinga Tóth
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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28
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Patai ÁV, Valcz G, Hollósi P, Kalmár A, Péterfia B, Patai Á, Wichmann B, Spisák S, Barták BK, Leiszter K, Tóth K, Sipos F, Kovalszky I, Péter Z, Miheller P, Tulassay Z, Molnár B. Comprehensive DNA Methylation Analysis Reveals a Common Ten-Gene Methylation Signature in Colorectal Adenomas and Carcinomas. PLoS One 2015; 10:e0133836. [PMID: 26291085 PMCID: PMC4546193 DOI: 10.1371/journal.pone.0133836] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/02/2015] [Indexed: 02/06/2023] Open
Abstract
Microarray analysis of promoter hypermethylation provides insight into the role and extent of DNA methylation in the development of colorectal cancer (CRC) and may be co-monitored with the appearance of driver mutations. Colonic biopsy samples were obtained endoscopically from 10 normal, 23 adenoma (17 low-grade (LGD) and 6 high-grade dysplasia (HGD)), and 8 ulcerative colitis (UC) patients (4 active and 4 inactive). CRC samples were obtained from 24 patients (17 primary, 7 metastatic (MCRC)), 7 of them with synchronous LGD. Field effects were analyzed in tissues 1 cm (n = 5) and 10 cm (n = 5) from the margin of CRC. Tissue materials were studied for DNA methylation status using a 96 gene panel and for KRAS and BRAF mutations. Expression levels were assayed using whole genomic mRNA arrays. SFRP1 was further examined by immunohistochemistry. HT29 cells were treated with 5-aza-2' deoxycytidine to analyze the reversal possibility of DNA methylation. More than 85% of tumor samples showed hypermethylation in 10 genes (SFRP1, SST, BNC1, MAL, SLIT2, SFRP2, SLIT3, ALDH1A3, TMEFF2, WIF1), whereas the frequency of examined mutations were below 25%. These genes distinguished precancerous and cancerous lesions from inflamed and healthy tissue. The mRNA alterations that might be caused by systematic methylation could be partly reversed by demethylation treatment. Systematic changes in methylation patterns were observed early in CRC carcinogenesis, occuring in precursor lesions and CRC. Thus we conclude that DNA hypermethylation is an early and systematic event in colorectal carcinogenesis, and it could be potentially reversed by systematic demethylation therapy, but it would need more in vitro and in vivo experiments to support this theory.
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Affiliation(s)
- Árpád V. Patai
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Tumor Progression Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Patai
- Department of Gastroenterology and Medicine, Markusovszky University Teaching Hospital, Szombathely, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Sándor Spisák
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Katalin Leiszter
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Kinga Tóth
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Ferenc Sipos
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltán Péter
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Pál Miheller
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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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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Nogueira RB, Pires ARC, Soares TMS, Rodrigues SRDS, Campos MAM, Toloi GC, Waisberg J. Immunoexpression of the COX-2, p53, and caspase-3 proteins in colorectal adenoma and non-neoplastic mucosa. EINSTEIN-SAO PAULO 2014; 11:456-61. [PMID: 24488384 PMCID: PMC4880382 DOI: 10.1590/s1679-45082013000400009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 10/10/2013] [Indexed: 12/02/2022] Open
Abstract
Objective: To analyze the immunoexpression of the COX-2, p53, and caspase-3 proteins in colorectal adenomas and non-neoplastic mucosa. Methods: 72 individuals were subjected to colonoscopy, which provided 50 samples of adenomas and 45 samples of non-neoplastic colorectal mucosa. The tissue samples were obtained via the tissue microarray technique and subjected to immunohistochemical analysis using primary anti-p53, anti-COX-2, and anti-caspase-3 antibodies. The positivity and intensity of the immunoreaction were classified. The analyzed variables were as follows: site of the adenomas in the colon, degree of dysplasia, size, and score of positivity and intensity of immunoexpression of the p-53, caspase-3, and COX-2 proteins. Results: The immunoexpression of mutated protein p53 was positive in 30 (60%) adenoma samples and negative in 20 (40%) adenoma samples. The immunoexpression of mutated protein p53 was negative in 39 (86.6%) samples and positive in 6 (13.3%) samples of the non-neoplastic colorectal mucosa (p<0.0001). Significant differences were seen between both the largest size (p=0.006) and the highest degree of dysplasia (p<0.0001) of the adenomas and the intensity of immunoexpression of mutated protein p53. The positivity and intensity of immunoexpression of COX-2 (p=0.14) and caspase-3 (p=0.23) showed no significant differences between the adenomas and the non-neoplastic colorectal mucosa. Conclusion: Mutated protein p53 was hyperexpressed in the adenomas compared with the non-neoplastic mucosa. Greater size and greater degree of dysplasia in the adenomas were associated with higher expression of mutated protein p53. The immunoexpression of COX-2 and caspase-3 in the adenomas did not exhibit a correlation with the anatomical-pathological features of the tumors and did not differ from the corresponding expression levels in the non-neoplastic mucosa.
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Hamabe A, Yamamoto H, Konno M, Uemura M, Nishimura J, Hata T, Takemasa I, Mizushima T, Nishida N, Kawamoto K, Koseki J, Doki Y, Mori M, Ishii H. Combined evaluation of hexokinase 2 and phosphorylated pyruvate dehydrogenase-E1α in invasive front lesions of colorectal tumors predicts cancer metabolism and patient prognosis. Cancer Sci 2014; 105:1100-8. [PMID: 25060325 PMCID: PMC4462394 DOI: 10.1111/cas.12487] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/22/2014] [Accepted: 07/04/2014] [Indexed: 12/31/2022] Open
Abstract
Although numerous studies have shown the significance of cancer-specific aerobic glycolysis, how glycolysis contributes to tumor invasion, a critical phenomenon in metastasis, remains unclear. With regard to colorectal cancer (CRC), we studied two critical gate enzymes, hexokinase 2 (HK2), which is involved in glycolysis, and phosphorylated pyruvate dehydrogenase-E1α (p-PDH), which is involved in oxidative phosphorylation (OxPhos). Immunohistochemical analyses using anti-HK2 and p-PDH antibodies were performed on surgically resected CRC samples (n = 104), and the expression in invasive front lesions of tumors was assessed. Positive HK2 expression correlated with extensive tumor diameter (P = 0.0460), advanced tumor depth (P = 0.0395), and presence of lymph node metastasis (P = 0.0409). Expression of p-PDH tended to be higher in right-sided CRCs than in left-sided CRCs (P = 0.0883). In survival analysis, the combined evaluation of positive HK2 and negative p-PDH was associated with reduced recurrence-free survival (RFS) (P = 0.0169 in all stages and P = 0.0238 in Stage II and III patients, respectively). This evaluation could predict RFS more precisely than the independent evaluation. The present study indicated that high HK2 expression combined with low p-PDH expression in the invasive front lesions of CRC tumors is predictive of tumor aggressiveness and survival of CRC cases.
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Affiliation(s)
- Atsushi Hamabe
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Junichi Nishimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Taishi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Ichiro Takemasa
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Naohiro Nishida
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Koichi Kawamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Jun Koseki
- Department ofCancer Profiling Discovery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
| | - Hideshi Ishii
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka UniversityOsaka, Japan
- Department ofCancer Profiling Discovery, Graduate School of Medicine, Osaka UniversityOsaka, Japan
- Correspondence Hideshi Ishii, Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan., Tel: +81-(0)6-6879-2641, 2640; Fax: +81-(0)6-6879-2639;, E-mail:
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Identification of SOCS2 and SOCS6 as biomarkers in human colorectal cancer. Br J Cancer 2014; 111:726-35. [PMID: 25025962 PMCID: PMC4134506 DOI: 10.1038/bjc.2014.377] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/05/2014] [Accepted: 06/12/2014] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Over the past years, some members of the family of suppressor of cytokine signalling (SOCS) proteins have emerged as potential tumour suppressors. This study aimed at investigating the clinical significance of SOCS proteins in colorectal carcinoma (CRC). METHODS We integrated publicly available microarray expression data on CRC in humans, analysed the expression pattern of SOCSs and assessed the predictive power of SOCS2 and SOCS6 for diagnostic purposes by generating receiver operating characteristic curves. Using laser microdissected patient material we assessed SOCS expression on RNA and protein levels as well as their methylation status in an independent CRC patient cohort. Finally, we investigated the prognostic value of SOCS2 and SOCS6. RESULTS The meta-analysis as well as the independent patient cohort analysis reveal a stage-independent downregulation of SOCS2 and SOCS6 and identify both molecules as diagnostic biomarkers for CRC. We demonstrate a different methylation pattern within the SOCS2 promoter between tumour tissue and normal control tissue in 25% of CRC patients. Furthermore, early CRC stage patients with low expression of SOCS2 display significantly shorter disease-free survival. CONCLUSIONS Our data offers evidence that SOCS2 and SOCS6 levels are reduced in CRC and may serve as diagnostic biomarkers for CRC patients.
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Filiou MD, Arefin AS, Moscato P, Graeber MB. 'Neuroinflammation' differs categorically from inflammation: transcriptomes of Alzheimer's disease, Parkinson's disease, schizophrenia and inflammatory diseases compared. Neurogenetics 2014; 15:201-12. [PMID: 24928144 DOI: 10.1007/s10048-014-0409-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 12/30/2022]
Abstract
'Neuroinflammation' has become a widely applied term in the basic and clinical neurosciences but there is no generally accepted neuropathological tissue correlate. Inflammation, which is characterized by the presence of perivascular infiltrates of cells of the adaptive immune system, is indeed seen in the central nervous system (CNS) under certain conditions. Authors who refer to microglial activation as neuroinflammation confuse this issue because autoimmune neuroinflammation serves as a synonym for multiple sclerosis, the prototypical inflammatory disease of the CNS. We have asked the question whether a data-driven, unbiased in silico approach may help to clarify the nomenclatorial confusion. Specifically, we have examined whether unsupervised analysis of microarray data obtained from human cerebral cortex of Alzheimer's, Parkinson's and schizophrenia patients would reveal a degree of relatedness between these diseases and recognized inflammatory conditions including multiple sclerosis. Our results using two different data analysis methods provide strong evidence against this hypothesis demonstrating that very different sets of genes are involved. Consequently, the designations inflammation and neuroinflammation are not interchangeable. They represent different categories not only at the histophenotypic but also at the transcriptomic level. Therefore, non-autoimmune neuroinflammation remains a term in need of definition.
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Affiliation(s)
- Michaela D Filiou
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804, Munich, Germany
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ZHANG YONGSHENG, JIA SHUQIN, JIANG WENG. KIAA1199 and its biological role in human cancer and cancer cells (Review). Oncol Rep 2014; 31:1503-8. [DOI: 10.3892/or.2014.3038] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/24/2014] [Indexed: 11/05/2022] Open
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Hatzfeld M, Wolf A, Keil R. Plakophilins in Desmosomal Adhesion and Signaling. ACTA ACUST UNITED AC 2014; 21:25-42. [DOI: 10.3109/15419061.2013.876017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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36
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Li C, Lee PS, Sun Y, Gu X, Zhang E, Guo Y, Wu CL, Auricchio N, Priolo C, Li J, Csibi A, Parkhitko A, Morrison T, Planaguma A, Kazani S, Israel E, Xu KF, Henske EP, Blenis J, Levy BD, Kwiatkowski D, Yu JJ. Estradiol and mTORC2 cooperate to enhance prostaglandin biosynthesis and tumorigenesis in TSC2-deficient LAM cells. ACTA ACUST UNITED AC 2014; 211:15-28. [PMID: 24395886 PMCID: PMC3892971 DOI: 10.1084/jem.20131080] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Lymphangioleiomyomatosis (LAM) is a progressive neoplastic disorder that leads to lung destruction and respiratory failure primarily in women. LAM is typically caused by tuberous sclerosis complex 2 (TSC2) mutations resulting in mTORC1 activation in proliferative smooth muscle-like cells in the lung. The female predominance of LAM suggests that estradiol contributes to disease development. Metabolomic profiling identified an estradiol-enhanced prostaglandin biosynthesis signature in Tsc2-deficient (TSC(-)) cells, both in vitro and in vivo. Estradiol increased the expression of cyclooxygenase-2 (COX-2), a rate-limiting enzyme in prostaglandin biosynthesis, which was also increased at baseline in TSC-deficient cells and was not affected by rapamycin treatment. However, both Torin 1 treatment and Rictor knockdown led to reduced COX-2 expression and phospho-Akt-S473. Prostaglandin production was also increased in TSC-deficient cells. In preclinical models, both Celecoxib and aspirin reduced tumor development. LAM patients had significantly higher serum prostaglandin levels than healthy women. 15-epi-lipoxin-A4 was identified in exhaled breath condensate from LAM subjects and was increased by aspirin treatment, indicative of functional COX-2 expression in the LAM airway. In vitro, 15-epi-lipoxin-A4 reduced the proliferation of LAM patient-derived cells in a dose-dependent manner. Targeting COX-2 and prostaglandin pathways may have therapeutic value in LAM and TSC-related diseases, and possibly in other conditions associated with mTOR hyperactivation.
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Affiliation(s)
- Chenggang Li
- Pulmonary and Critical Care Medicine, 2 Translational Medicine, Department of Medicine, Brigham and Women's Hospital-Harvard Medical School, Boston, MA 02115
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Budinska E, Popovici V, Tejpar S, D'Ario G, Lapique N, Sikora KO, Di Narzo AF, Yan P, Hodgson JG, Weinrich S, Bosman F, Roth A, Delorenzi M. Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. J Pathol 2013; 231:63-76. [PMID: 23836465 PMCID: PMC3840702 DOI: 10.1002/path.4212] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 02/06/2023]
Abstract
The recognition that colorectal cancer (CRC) is a heterogeneous disease in terms of clinical behaviour and response to therapy translates into an urgent need for robust molecular disease subclassifiers that can explain this heterogeneity beyond current parameters (MSI, KRAS, BRAF). Attempts to fill this gap are emerging. The Cancer Genome Atlas (TGCA) reported two main CRC groups, based on the incidence and spectrum of mutated genes, and another paper reported an EMT expression signature defined subgroup. We performed a prior free analysis of CRC heterogeneity on 1113 CRC gene expression profiles and confronted our findings to established molecular determinants and clinical, histopathological and survival data. Unsupervised clustering based on gene modules allowed us to distinguish at least five different gene expression CRC subtypes, which we call surface crypt-like, lower crypt-like, CIMP-H-like, mesenchymal and mixed. A gene set enrichment analysis combined with literature search of gene module members identified distinct biological motifs in different subtypes. The subtypes, which were not derived based on outcome, nonetheless showed differences in prognosis. Known gene copy number variations and mutations in key cancer-associated genes differed between subtypes, but the subtypes provided molecular information beyond that contained in these variables. Morphological features significantly differed between subtypes. The objective existence of the subtypes and their clinical and molecular characteristics were validated in an independent set of 720 CRC expression profiles. Our subtypes provide a novel perspective on the heterogeneity of CRC. The proposed subtypes should be further explored retrospectively on existing clinical trial datasets and, when sufficiently robust, be prospectively assessed for clinical relevance in terms of prognosis and treatment response predictive capacity. Original microarray data were uploaded to the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/) under Accession Nos E-MTAB-990 and E-MTAB-1026.
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Affiliation(s)
- Eva Budinska
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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Lu Z, Ding L, Lu Q, Chen YH. Claudins in intestines: Distribution and functional significance in health and diseases. Tissue Barriers 2013; 1:e24978. [PMID: 24478939 PMCID: PMC3879173 DOI: 10.4161/tisb.24978] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 02/08/2023] Open
Abstract
Intestines are organs that not only digest food and absorb nutrients, but also provide a defense barrier against pathogens and noxious agents ingested. Tight junctions (TJs) are the most apical component of the junctional complex, providing one form of cell-cell adhesion in enterocytes and playing a critical role in regulating paracellular barrier permeability. Alteration of TJs leads to a number of pathophysiological diseases causing malabsorption of nutrition and intestinal structure disruption, which may even contribute to systemic organ failure. Claudins are the major structural and functional components of TJs with at least 24 members in mammals. Claudins have distinct charge-selectivity, either by tightening the paracellular pathway or functioning as paracellular channels, regulating ions and small molecules passing through the paracellular pathway. In this review, we have discussed the functions of claudin family members, their distribution and localization in the intestinal tract of mammals, their alterations in intestine-related diseases and chemicals/agents that regulate the expression and localization of claudins as well as the intestinal permeability, which provide a therapeutic view for treating intestinal diseases.
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Affiliation(s)
- Zhe Lu
- Department of Basic Medicine; Hangzhou Normal University, Hangzhou, PR China ; Department of Anatomy and Cell Biology; Brody School of Medicine; East Carolina University; Greenville, NC USA
| | - Lei Ding
- Department of Anatomy and Cell Biology; Brody School of Medicine; East Carolina University; Greenville, NC USA ; Department of Oncology; Beijing Shijitan Hospital; Capital Medical University; Beijing, PR China
| | - Qun Lu
- Department of Anatomy and Cell Biology; Brody School of Medicine; East Carolina University; Greenville, NC USA
| | - Yan-Hua Chen
- Department of Anatomy and Cell Biology; Brody School of Medicine; East Carolina University; Greenville, NC USA
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Mitosis is a source of potential markers for screening and survival and therapeutic targets in cervical cancer. PLoS One 2013; 8:e55975. [PMID: 23405241 PMCID: PMC3566100 DOI: 10.1371/journal.pone.0055975] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 01/04/2013] [Indexed: 01/18/2023] Open
Abstract
The effect of preventive human papillomavirus (HPV) vaccination on the reduction of the cervical cancer (CC) burden will not be known for 30 years. Therefore, it's still necessary to improve the procedures for CC screening and treatment. The objective of this study was to identify and characterize cellular targets that could be considered potential markers for screening or therapeutic targets. A pyramidal strategy was used. Initially the expression of 8,638 genes was compared between 43 HPV16-positive CCs and 12 healthy cervical epitheliums using microarrays. A total of 997 genes were deregulated, and 21 genes that showed the greatest deregulation were validated using qRT-PCR. The 6 most upregulated genes (CCNB2, CDC20, PRC1, SYCP2, NUSAP1, CDKN3) belong to the mitosis pathway. They were further explored in 29 low-grade cervical intraepithelial neoplasias (CIN1) and 21 high-grade CIN (CIN2/3) to investigate whether they could differentiate CC and CIN2/3 (CIN2+) from CIN1 and controls. CCNB2, PRC1, and SYCP2 were mostly associated with CC and CDC20, NUSAP1, and CDKN3 were also associated with CIN2/3. The sensitivity and specificity of CDKN3 and NUSAP1 to detect CIN2+ was approximately 90%. The proteins encoded by all 6 genes were shown upregulated in CC by immunohistochemistry. The association of these markers with survival was investigated in 42 CC patients followed up for at least 42 months. Only CDKN3 was associated with poor survival and it was independent from clinical stage (HR = 5.9, 95%CI = 1.4-23.8, p = 0.01). CDKN3 and NUSAP1 may be potential targets for the development of screening methods. Nevertheless, further studies with larger samples are needed to define the optimal sensitivity and specificity. Inhibition of mitosis is a well-known strategy to combat cancers. Therefore, CDKN3 may be not only a screening and survival marker but a potential therapeutic target in CC. However, whether it's indispensable for tumor growth remains to be demonstrated.
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Joudeh J, Allen JE, Das A, Prabhu V, Farbaniec M, Adler J, El-Deiry WS. Novel antineoplastics targeting genetic changes in colorectal cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 779:1-34. [PMID: 23288633 DOI: 10.1007/978-1-4614-6176-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cytotoxic chemotherapy remains the mainstay of the medical -management of colorectal cancer (CRC). Research over the last two decades has led to a molecular understanding of the oncogenic mechanisms involved in CRC and has contributed to the rational development of antineoplastics that target these mechanisms. During carcinogenesis, genetic changes often occur in molecules that play key functional roles in cancer such as cell proliferation, angiogenesis, apoptosis, cell death and immune-mediated destruction of cancer cells. Here, we review novel antineoplastics that are approved or in development for CRC that target molecules associated with genetic aberrations in CRC. Some of these targeted antineoplastics have proven effective against other solid tumors and hold promise in treating CRC whereas others are now routinely used in combination with cytotoxic agents. This article reviews antineoplastics that target genetic changes in CRC, their antitumor mechanisms, and their stage of development.
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Affiliation(s)
- Jamal Joudeh
- Penn State Hershey Medical Center, Hershey, PA, USA.
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Leiszter K, Galamb O, Sipos F, Krenács T, Veres G, Wichmann B, Kalmár A, Patai ÁV, Tóth K, Valcz G, Molnár B, Tulassay Z. Sporadic colorectal cancer development shows rejuvenescence regarding epithelial proliferation and apoptosis. PLoS One 2013; 8:e74140. [PMID: 24098334 PMCID: PMC3789736 DOI: 10.1371/journal.pone.0074140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/29/2013] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND AIMS Sporadic colorectal cancer (CRC) development is a sequential process showing age-dependency, uncontrolled epithelial proliferation and decreased apoptosis. During juvenile growth cellular proliferation and apoptosis are well balanced, which may be perturbed upon aging. Our aim was to correlate proliferative and apoptotic activities in aging human colonic epithelium and colorectal cancer. We also tested the underlying molecular biology concerning the proliferation- and apoptosis-regulating gene expression alterations. MATERIALS AND METHODS Colorectal biopsies from healthy children (n1 = 14), healthy adults (n2 = 10), adult adenomas (n3 = 10) and CRCs (n4 = 10) in adults were tested for Ki-67 immunohistochemistry and TUNEL apoptosis assay. Mitosis- and apoptosis-related gene expression was also studied in healthy children (n1 = 6), adult (n2 = 41) samples and in CRC (n3 = 34) in HGU133plus2.0 microarray platform. Measured alterations were confirmed with RT-PCR both on dependent and independent sample sets (n1 = 6, n2 = 6, n3 = 6). RESULTS Mitotic index (MI) was significantly higher (p<0.05) in intact juvenile (MI = 0.33±0.06) and CRC samples (MI = 0.42±0.10) compared to healthy adult samples (MI = 0.15±0.06). In contrast, apoptotic index (AI) was decreased in children (0.13±0.06) and significantly lower in cancer (0.06±0.03) compared to healthy adult samples (0.17±0.05). Eight proliferation- (e.g. MKI67, CCNE1) and 11 apoptosis-associated genes (e.g. TNFSF10, IFI6) had altered mRNA expression both in the course of normal aging and carcinogenesis, mainly inducing proliferation and reducing apoptosis compared to healthy adults. Eight proliferation-associated genes including CCND1, CDK1, CDK6 and 26 apoptosis-regulating genes (e.g. SOCS3) were differently expressed between juvenile and cancer groups mostly supporting the pronounced cell growth in CRC. CONCLUSION Colorectal samples from children and CRC patients can be characterized by similarly increased proliferative and decreased apoptotic activities compared to healthy colonic samples from adults. Therefore, cell kinetic alterations during colorectal cancer development show uncontrolled rejuvenescence as opposed to the controlled cell growth in juvenile colonic epithelium.
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Affiliation(s)
- Katalin Leiszter
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Orsolya Galamb
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Tibor Krenács
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Veres
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Barnabás Wichmann
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Árpád V. Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Kinga Tóth
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics 2012; 13:272. [PMID: 23088656 PMCID: PMC3487959 DOI: 10.1186/1471-2105-13-272] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/17/2012] [Indexed: 11/10/2022] Open
Abstract
Background Early screening for cancer is arguably one of the greatest public health advances over the last fifty years. However, many cancer screening tests are invasive (digital rectal exams), expensive (mammograms, imaging) or both (colonoscopies). This has spurred growing interest in developing genomic signatures that can be used for cancer diagnosis and prognosis. However, progress has been slowed by heterogeneity in cancer profiles and the lack of effective computational prediction tools for this type of data. Results We developed anti-profiles as a first step towards translating experimental findings suggesting that stochastic across-sample hyper-variability in the expression of specific genes is a stable and general property of cancer into predictive and diagnostic signatures. Using single-chip microarray normalization and quality assessment methods, we developed an anti-profile for colon cancer in tissue biopsy samples. To demonstrate the translational potential of our findings, we applied the signature developed in the tissue samples, without any further retraining or normalization, to screen patients for colon cancer based on genomic measurements from peripheral blood in an independent study (AUC of 0.89). This method achieved higher accuracy than the signature underlying commercially available peripheral blood screening tests for colon cancer (AUC of 0.81). We also confirmed the existence of hyper-variable genes across a range of cancer types and found that a significant proportion of tissue-specific genes are hyper-variable in cancer. Based on these observations, we developed a universal cancer anti-profile that accurately distinguishes cancer from normal regardless of tissue type (ten-fold cross-validation AUC > 0.92). Conclusions We have introduced anti-profiles as a new approach for developing cancer genomic signatures that specifically takes advantage of gene expression heterogeneity. We have demonstrated that anti-profiles can be successfully applied to develop peripheral-blood based diagnostics for cancer and used anti-profiles to develop a highly accurate universal cancer signature. By using single-chip normalization and quality assessment methods, no further retraining of signatures developed by the anti-profile approach would be required before their application in clinical settings. Our results suggest that anti-profiles may be used to develop inexpensive and non-invasive universal cancer screening tests.
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Affiliation(s)
- Héctor Corrada Bravo
- Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
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Kalmar A, Wichmann B, Galamb O, Spisák S, Tóth K, Leiszter K, Tulassay Z, Molnár B. Gene expression analysis of normal and colorectal cancer tissue samples from fresh frozen and matched formalin-fixed, paraffin-embedded (FFPE) specimens after manual and automated RNA isolation. Methods 2012; 59:S16-9. [PMID: 23036325 DOI: 10.1016/j.ymeth.2012.09.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Although RNA isolation is a routine process in gene expression analysis studies, the applicability of most widely available formalin-fixed, paraffin-embedded (FFPE) samples is still limited compared to fresh frozen tissue samples due to the lower quality of the isolated RNA. Recently, novel automated isolation methods were developed in order to reduce manual sample handling and increase RNA quality and quantity. Here we present a comparison of the performance of fresh frozen and matched FFPE tissue samples obtained from the same surgically removed colonic specimens (10 normal, 10 CRC) in RT-PCR experiments. RNA isolations were performed with the automated MagNA Pure 96 Cellular RNA Large Volume Kit (Roche) compared to the manual RNeasy FFPE Mini Kit (Qiagen). Gene expression analysis of a colorectal cancer-specific marker set (with 7 genes: COL12A1, CXCL1, CXCL2, GREM1, IL1B, IL8, SLC7A5) was performed with array real-time PCR using Transcriptor First Strand cDNA Synthesis Kit (Roche) and RealTime ready assays on LightCycler® 480 System (Roche). On the basis of the gene expression of the analyzed markers, fresh frozen tumorous and normal samples could be distinguished with 100% sensitivity and 100% specificity after both isolation methods. The FFPE samples could be distinguished by similarly high specificity and sensitivity with the MagNA Pure 96 isolated samples (sensitivity: 90,0%; specificity: 90,0%) and the samples isolated with manual Qiagen method (sensitivity: 85,0%; specificity: 70,0%). According to these results, FFPE samples isolated by automated methods can serve as valuable source for retrospective gene expression studies in the field of biomarker discovery and development.
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Affiliation(s)
- Alexandra Kalmar
- 2nd Department of Medicine, Semmelweis University, Szentkirályi Str. 46, 1088 Budapest, Hungary.
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Wen Z, Liu ZP, Liu Z, Zhang Y, Chen L. An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc 2012; 20:659-67. [PMID: 22967703 DOI: 10.1136/amiajnl-2012-001168] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Many methods have been developed to identify disease genes and further module biomarkers of complex diseases based on gene expression data. It is generally difficult to distinguish whether the variations in gene expression are causative or merely the effect of a disease. The limitation of relying on gene expression data alone highlights the need to develop new approaches that can explore various data to reflect the casual relationship between network modules and disease traits. METHODS In this work, we developed a novel network-based approach to identify putative causal module biomarkers of complex diseases by integrating heterogeneous information, for example, epigenomic data, gene expression data, and protein-protein interaction network. We first formulated the identification of modules as a mathematical programming problem, which can be solved efficiently and effectively in an accurate manner. Then, we applied our approach to colorectal cancer (CRC) and identified several network modules that can serve as potential module biomarkers for characterizing CRC. Further validations using three additional gene expression datasets verified their candidate biomarker properties and the effectiveness of the method. Functional enrichment analysis also revealed that the identified modules are strongly related to hallmarks of cancer, and the enriched functions, such as inflammatory response, receptor and signaling pathways, are specific to CRC. RESULTS Through constructing a transcription factor (TF)-module network, we found that aberrant DNA methylation of genes encoding TF considerably contributes to the activity change of some genes, which may function as causal genes of CRC, and that can also be exploited to develop efficient therapies or effective drugs. CONCLUSION Our method can potentially be extended to the study of other complex diseases and the multiclassification problem.
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Affiliation(s)
- Zhenshu Wen
- Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Proteomic signatures of the desmoplastic invasion front reveal collagen type XII as a marker of myofibroblastic differentiation during colorectal cancer metastasis. Oncotarget 2012; 3:267-85. [PMID: 22408128 PMCID: PMC3359884 DOI: 10.18632/oncotarget.451] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs), represent a pivotal compartment of solid cancers (desmoplasia), and are causatively implicated in cancer development and progression. CAFs are recruited by growth factors secreted by cancer cells and they present a myofibroblastic phenotype, similar to the one obtained by resident fibroblasts during wound healing. Paracrine signaling between cancer cells and CAFs results in a unique protein expression profile in areas of desmoplastic reaction, which is speculated to drive metastasis. In an attempt to decipher large-scale proteomic profiles of the cancer invasive margins, we developed an in vitro coculture model system, based on tumor-host cell interactions between colon cancer cells and CAFs. Proteomic analysis of conditioned media derived from these cocultures coupled to mass spectrometry and bioinformatic analysis was performed to uncover myofibroblastic signatures of the cancer invasion front. Our analysis resulted in the identification and generation of a desmoplastic protein dataset (DPD), consisting of 152 candidate proteins of desmoplasia. By using monoculture exclusion datasets, a secretome algorithm and gene-expression meta-analysis in DPD, we specified a 22-protein “myofibroblastic signature” with putative importance in the regulation of colorectal cancer metastasis. Of these proteins, we investigated collagen type XII by immunohistochemistry, a fibril-associated collagen with interrupted triple helices (FACIT), whose expression has not been reported in desmoplastic lesions in any type of cancer. Collagen type XII was highly expressed in desmoplastic stroma by and around alpha-smooth muscle actin (α-SMA) positive CAFs, as well as in cancer cells lining the invasion front, in a small cohort of colon cancer patients. Other stromal markers, such as collagen type III, were also expressed in stromal collagen, but not in cancer cells. In a complementary fashion, gene expression meta-analysis revealed that COL12A1 is also an upregulated gene in colorectal cancer. Our proteomic analysis identified previously documented markers of tumor invasion fronts and our DPD could serve as a pool for future investigation of the tumor microenvironment. Collagen type XII is a novel candidate marker of myofibroblasts, and/or cancer cells undergoing dedifferentiation.
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Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J, Pujana MA. Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. Integr Biol (Camb) 2012; 4:1038-48. [PMID: 22806580 PMCID: PMC4699251 DOI: 10.1039/c2ib20052j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 07/02/2012] [Indexed: 12/21/2022]
Abstract
The products of genes mutated or differentially expressed in cancer tend to occupy central positions within the network of protein-protein interactions, or the interactome network. Integration of different types of gene and protein relationships has considerably increased the understanding of the mechanisms of carcinogenesis, while also enhancing the applicability of expression signatures. In this scenario, however, it remains unknown how cancer develops, progresses and responds to therapies in a potentially controlled manner at the systems level. Here, by applying the concepts of load transfer and cascading failures in power grids, we examine the impact and transmission of cancer-related gene expression changes in the interactome network. Relative to random perturbations, this study reveals topological robustness associated with all cancer conditions. In addition, experimental perturbation of a central cancer node, which consists of over-expression of the α-synuclein (SNCA) protein in MCF7 breast cancer cells, also reveals robustness. Conversely, a search for proteins with an opposite topological impact identifies the autophagy pathway. Mechanistically, the existence of smaller shortest paths among cancer-related proteins appears to be a topological feature that partially contributes to the restricted perturbation of the network. Together, the results of this study suggest that cancer develops, progresses and responds to therapies following controlled, restricted perturbation of the interactome network.
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Affiliation(s)
- Jordi Serra-Musach
- Translational Research Laboratory, Breast Cancer Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Gran via 199, L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain.
- ICO, IdIBGi, Girona 17007, Catalonia, Spain
| | - Helena Aguilar
- Translational Research Laboratory, Breast Cancer Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Gran via 199, L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain.
| | - Francesco Iorio
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Francesc Comellas
- Department of Applied Mathematics IV, Polytechnic University of Catalonia, Castelldefels, Barcelona 08860, Catalonia, Spain
| | - Antoni Berenguer
- Biomarkers and Susceptibility Unit, Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain
| | | | - Julio Saez-Rodriguez
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Miguel Angel Pujana
- Translational Research Laboratory, Breast Cancer Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Gran via 199, L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain.
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Kleberg K, Jensen GM, Christensen DP, Lundh M, Grunnet LG, Knuhtsen S, Poulsen SS, Hansen MB, Bindslev N. Transporter function and cyclic AMP turnover in normal colonic mucosa from patients with and without colorectal neoplasia. BMC Gastroenterol 2012; 12:78. [PMID: 22734885 PMCID: PMC3457850 DOI: 10.1186/1471-230x-12-78] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/19/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The pathogenesis of colorectal neoplasia is still unresolved but has been associated with alterations in epithelial clearance of xenobiotics and metabolic waste products. The aim of this study was to functionally characterize the transport of cyclic nucleotides in colonic biopsies from patients with and without colorectal neoplasia. METHODS Cyclic nucleotides were used as model substrates shared by some OATP- and ABC-transporters, which in part are responsible for clearance of metabolites and xenobiotics from the colonic epithelium. On colonic biopsies from patients with and without colorectal neoplasia, molecular transport was electrophysiologically registered in Ussing-chamber set-ups, mRNA level of selected transporters was quantified by rt-PCR, and subcellular location of transporters was determined by immunohistochemistry. RESULTS Of four cyclic nucleotides, dibuturyl-cAMP induced the largest short circuit current in both patient groups. The induced short circuit current was significantly lower in neoplasia-patients (p = 0.024). The observed altered transport of dibuturyl-cAMP in neoplasia-patients could not be directly translated to an observed increased mRNA expression of OATP4A1 and OATP2B1 in neoplasia patients. All other examined transporters were expressed to similar extents in both patient groups. CONCLUSIONS OATP1C1, OATP4A1, OATP4C1 seem to be involved in the excretory system of human colon. ABCC4 is likely to be involved from an endoplasmic-Golgi complex and basolateral location in goblet cells. ABCC5 might be directly involved in the turnover of intracellular cAMP at the basolateral membrane of columnar epithelial cells, while OATP2B1 is indirectly related to the excretory system. Colorectal neoplasia is associated with lower transport or sensitivity to cyclic nucleotides and increased expression of OATP2B1 and OATP4A1 transporters, known to transport PGE(2).
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Affiliation(s)
- Karen Kleberg
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Hamfjord J, Stangeland AM, Hughes T, Skrede ML, Tveit KM, Ikdahl T, Kure EH. Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing. PLoS One 2012; 7:e34150. [PMID: 22529906 PMCID: PMC3328481 DOI: 10.1371/journal.pone.0034150] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/23/2012] [Indexed: 12/19/2022] Open
Abstract
We present the results of a global study of dysregulated miRNAs in paired samples of normal mucosa and tumor from eight patients with colorectal cancer. Although there is existing data of miRNA contribution to colorectal tumorigenesis, these studies are typically small to medium scale studies of cell lines or non-paired tumor samples. The present study is to our knowledge unique in two respects. Firstly, the normal and adjacent tumor tissue samples are paired, thus taking into account the baseline differences between individuals when testing for differential expression. Secondly, we use high-throughput sequencing, thus enabling a comprehensive survey of all miRNAs expressed in the tissues. We use Illumina sequencing technology to perform sequencing and two different tools to statistically test for differences in read counts per gene between samples: edgeR when using the pair information and DESeq when ignoring this information, i.e., treating tumor and normal samples as independent groups. We identify 37 miRNAs that are significantly dysregulated in both statistical approaches, 19 down-regulated and 18 up-regulated. Some of these miRNAs are previously published as potential regulators in colorectal adenocarcinomas such as miR-1, miR-96 and miR-145. Our comprehensive survey of differentially expressed miRNAs thus confirms some existing findings. We have also discovered 16 dysregulated miRNAs, which to our knowledge have not previously been associated with colorectal carcinogenesis: the following significantly down-regulated miR-490-3p, -628-3p/-5p, -1297, -3151, -3163, -3622a-5p, -3656 and the up-regulated miR-105, -549, -1269, -1827, -3144-3p, -3177, -3180-3p, -4326. Although the study is preliminary with only eight patients included, we believe the results add to the present knowledge on miRNA dysregulation in colorectal carcinogenesis. As such the results would serve as a robust training set for validation of potential biomarkers in a larger cohort study. Finally, we also present data supporting the hypothesis that there are differences in miRNA expression between adenocarcinomas and neuroendocrine tumors of the colon.
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Affiliation(s)
- Julian Hamfjord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Astrid M. Stangeland
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Timothy Hughes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Martina L. Skrede
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Kjell M. Tveit
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tone Ikdahl
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Elin H. Kure
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
- Department of Environmental and Health Studies, Faculty of Arts and Sciences, Telemark University College, Bø, Norway
- * E-mail:
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LaPointe LC, Pedersen SK, Dunne R, Brown GS, Pimlott L, Gaur S, McEvoy A, Thomas M, Wattchow D, Molloy PL, Young GP. Discovery and validation of molecular biomarkers for colorectal adenomas and cancer with application to blood testing. PLoS One 2012; 7:e29059. [PMID: 22276102 PMCID: PMC3261845 DOI: 10.1371/journal.pone.0029059] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 11/20/2011] [Indexed: 11/24/2022] Open
Abstract
Background & Aims Colorectal cancer incidence and deaths are reduced by the detection and removal of early-stage, treatable neoplasia but we lack proven biomarkers sensitive for both cancer and pre-invasive adenomas. The aims of this study were to determine if adenomas and cancers exhibit characteristic patterns of biomarker expression and to explore whether a tissue-discovered (and validated) biomarker is differentially expressed in the plasma of patients with colorectal adenomas or cancer. Methods Candidate RNA biomarkers were identified by oligonucleotide microarray analysis of colorectal specimens (222 normal, 29 adenoma, 161 adenocarcinoma and 50 colitis) and validated in a previously untested cohort of 68 colorectal specimens using a custom-designed oligonucleotide microarray. One validated biomarker, KIAA1199, was assayed using qRT-PCR on plasma extracted RNA from 20 colonoscopy-confirmed healthy controls, 20 patients with adenoma, and 20 with cancer. Results Genome-wide analysis uncovered reproducible gene expression signatures for both adenomas and cancers compared to controls. 386/489 (79%) of the adenoma and 439/529 (83%) of the adenocarcinoma biomarkers were validated in independent tissues. We also identified genes differentially expressed in adenomas compared to cancer. KIAA1199 was selected for further analysis based on consistent up-regulation in neoplasia, previous studies and its interest as an uncharacterized gene. Plasma KIAA1199 RNA levels were significantly higher in patients with either cancer or adenoma (31/40) compared to neoplasia-free controls (6/20). Conclusions Colorectal neoplasia exhibits characteristic patterns of gene expression. KIAA1199 is differentially expressed in neoplastic tissues and KIAA1199 transcripts are more abundant in the plasma of patients with either cancer or adenoma compared to controls.
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Affiliation(s)
- Lawrence C LaPointe
- Flinders Centre for Cancer Prevention and Control, Flinders University of South Australia, Adelaide, South Australia, Australia.
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Galamb O, Wichmann B, Sipos F, Spisák S, Krenács T, Tóth K, Leiszter K, Kalmár A, Tulassay Z, Molnár B. Dysplasia-carcinoma transition specific transcripts in colonic biopsy samples. PLoS One 2012; 7:e48547. [PMID: 23155391 PMCID: PMC3498283 DOI: 10.1371/journal.pone.0048547] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/26/2012] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The early molecular detection of the dysplasia-carcinoma transition may enhance the strength of diagnosis in the case of colonic biopsies. Our aims were to identify characteristic transcript sets in order to develop diagnostic mRNA expression patterns for objective classification of benign and malignant colorectal diseases and to test the classificatory power of these markers on an independent sample set. METHODOLOGY/PRINCIPAL FINDINGS Colorectal cancer (CRC) and adenoma specific transcript sets were identified using HGU133plus2 microarrays and 53 biopsies (22 CRC, 20 adenoma and 11 normal). Ninety-four independent biopsies (27 CRC, 29 adenoma and 38 normal) were analyzed on microarrays for testing the classificatory power of the discriminatory genes. Array real-time PCR validation was done on 68 independent samples (24 CRC, 24 adenoma and 20 normal). A set of 11 transcripts (including CXCL1, CHI3L1 and GREM1) was determined which could correctly discriminate between high-grade dysplastic adenoma and CRC samples by 100% sensitivity and 88.9% specificity. The discriminatory power of the marker set was proved to be high on independent samples in both microarray and RT-PCR analyses. 95.6% of original and 94.1% of cross-validated samples was correctly classified in discriminant analysis. CONCLUSIONS/SIGNIFICANCE The identified transcripts could correctly characterize the dysplasia-carcinoma transition in biopsy samples, also on a large independent sample set. These markers can establish the basis of gene expression based diagnostic classification of colorectal cancer. Diagnostic RT-PCR cards can become part of the automated routine procedure.
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Affiliation(s)
- Orsolya Galamb
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barnabás Wichmann
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
| | - Ferenc Sipos
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Sándor Spisák
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tibor Krenács
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Kinga Tóth
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Katalin Leiszter
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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