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Aiba T, Hijiya N, Akagi T, Tsukamoto Y, Hirashita Y, Kinoshita K, Uchida T, Nakada C, Kurogi S, Ueda Y, Shiroshita H, Shiraishi N, Murakami K, Inomata M, Moriyama M. Overexpression of VSNL1 Enhances Cell Proliferation in Colorectal Carcinogenesis. Pathobiology 2023; 91:121-131. [PMID: 37797604 DOI: 10.1159/000533877] [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: 05/15/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
INTRODUCTION We have previously reported that overexpression of visinin-like protein 1 (VSNL1) is frequently observed in advanced colorectal adenocarcinomas and correlates with poorer prognosis. In this study, we determined the levels of VSNL1 expression in the earlier stages of colorectal tumors including adenomas and adenocarcinomas, and attempted to clarify the functional significance of VSNL1 overexpression in colorectal carcinogenesis. METHODS Levels of VSNL expression in colorectal tumor tissues were analyzed using immunohistochemistry. The effects of VSNL1 downregulation and overexpression on cell proliferation, resistance to apoptosis, and invasiveness were determined using two VSNL1-overexpressing colorectal cancer cell lines, CW-2 and HCT-116 and VSNL1 inducibly expressing SNU-C5, respectively. Gene expression signatures in VSNL1-downregulated CW-2 and HCT-116 were identified using transcriptome and gene set enrichment analyses. RESULTS VSNL1 expression was restricted to only a few crypt cells in the non-tumorous epithelium, whereas it became enhanced in adenomas and adenocarcinomas with the progression of tumorigenesis. Downregulation of VSNL1 in CW-2 and HCT-116 cells suppressed their proliferation through induction of apoptosis. Conversely, overexpression of VSNL1 in SNU-C5 cells enhanced resistance to anoikis. Transcriptome and gene set enrichment analyses revealed that downregulation of VSNL1 altered the expression level of the apoptosis-related gene set in CW-2 and HCT-116 cells. CONCLUSION VSNL1 plays a role in both the development and progression of colorectal tumors by enhancing cell viability.
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Affiliation(s)
- Takayuki Aiba
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Naoki Hijiya
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Tomonori Akagi
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Yoshiyuki Tsukamoto
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yuka Hirashita
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Keisuke Kinoshita
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Advanced Medical Sciences, Faculty of Medicine, Oita University, Oita, Japan
| | - Chisato Nakada
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Urology, Faculty of Medicine, Oita University, Oita, Japan
| | - Shusaku Kurogi
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yoshitake Ueda
- Department of Comprehensive Surgery for Community Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Hidefumi Shiroshita
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Norio Shiraishi
- Department of Comprehensive Surgery for Community Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Masatsugu Moriyama
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
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Tage H, Yamaguchi K, Nakagawa S, Kasuga S, Takane K, Furukawa Y, Ikenoue T. Visinin-like 1, a novel target gene of the Wnt/β-catenin signaling pathway, is involved in apoptosis resistance in colorectal cancer. Cancer Med 2023. [PMID: 37096864 DOI: 10.1002/cam4.5970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/14/2023] [Accepted: 04/07/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Abnormal activation of Wnt/β-catenin signaling is associated with various aspects of cancer development. This study explored the roles of novel target genes of the Wnt/β-catenin signaling pathway in cancer cells. METHODS Using the haploid chronic myelogenous leukemia cell line HAP1, RNA sequencing (RNA-seq) was performed to identify genes whose expression was increased by APC disruption and reversed by β-catenin knockdown (KD). The regulatory mechanism and function of one of the candidate genes was investigated in colorectal cancer (CRC) cells. RESULTS In total, 64 candidate genes whose expression was regulated by Wnt/β-catenin signaling were identified. Of these candidate genes, the expression levels of six were reduced by β-catenin KD in HCT116 CRC cells in our previous microarray. One of these genes was Visinin-like 1 ( VSNL1 ), which belongs to the neuronal calcium-sensor gene family. The expression of VSNL1 was regulated by the β-catenin/TCF7L2 complex via two TCF7L2-binding elements in intron 1. VSNL1 KDinduced apoptosis in VSNL1-positive CRC cells. Additionally, forced expression of wild-type VSNL1, but not a myristoylation, Ca2+ -binding, or dimerization-defective mutant, suppressed the apoptosis induced by camptothecin and doxorubicin in VSNL1-negative CRC cells. CONCLUSION Our findings suggest that VSNL1 , a novel target gene of the Wnt/β-catenin signaling pathway, is associated with apoptosis resistance in CRC cells.
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Affiliation(s)
- Hiroki Tage
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saya Nakagawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - So Kasuga
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kiyoko Takane
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Yao Q, Chen W, Gao F, Wu Y, Zhou L, Xu H, Yu J, Zhu X, Wang L, Li L, Cao H. Characteristic Analysis of Featured Genes Associated with Cholangiocarcinoma Progression. Biomedicines 2023; 11:biomedicines11030847. [PMID: 36979826 PMCID: PMC10045321 DOI: 10.3390/biomedicines11030847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
The noninvasive diagnosis of cholangiocarcinoma (CCA) is insufficiently accurate. Therefore, the discovery of new prognostic markers is vital for the understanding of the CCA mechanism and related treatment. The information on CCA patients in The Cancer Genome Atlas database was used for weighted gene co-expression network analysis. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied to analyze the modules of interest. By using receiver operating characteristic (ROC) analysis to analyze the Human Protein Atlas (HPA), the featured genes were subsequently verified. In addition, clinical samples and GSE119336 cohort data were also collected for the validation of these hub genes. Using WGCNA, we identified 61 hub genes that regulated the progression and prognosis of CCA. Eight hub genes (VSNL1, TH, PCP4, IGDCC3, RAD51AP2, MUC2, BUB1, and BUB1B) were identified which exhibited significant interactions with the tumorigenic mechanism and prognosis of CCA. In addition, GO and KEGG clarified that the blue and magenta modules were involved with chromosome segregation, mitotic and oocyte meiosis, the cell cycle, and sister chromatid segregation. Four hub genes (VSNL1, PCP4, BUB1, and BUB1B) were also verified as featured genes of progression and prognosis by the GSE119336 cohort data and five human tissue samples.
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Affiliation(s)
- Qigu Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Wenyi Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Feiqiong Gao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Yuchen Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Lingling Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Haoying Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Jong Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
| | - Xinli Zhu
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
| | - Lan Wang
- Key Laboratory of Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases of Zhejiang Province, 79 Qingchun Road, Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250117, China
| | - Hongcui Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China; (Q.Y.)
- Key Laboratory of Diagnosis and Treatment of Aging and Physic-Chemical Injury Diseases of Zhejiang Province, 79 Qingchun Road, Hangzhou 310003, China
- Correspondence: ; Tel.: +86-571-87236451; Fax: +86-571-87236459
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Lin W, Hu S, Wu Z, Xu Z, Zhong Y, Lv Z, Qiu W, Xiao X. iCancer-Pred: A tool for identifying cancer and its type using DNA methylation. Genomics 2022; 114:110486. [PMID: 36126833 DOI: 10.1016/j.ygeno.2022.110486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 01/14/2023]
Abstract
DNA methylation is an important epigenetics, which occurs in the early stages of tumor formation. And it also is of great significance to find the relationship between DNA methylation and cancer. This paper proposes a novel model, iCancer-Pred, to identify cancer and classify its types further. The datasets of DNA methylation information of 7 cancer types have been collected from The Cancer Genome Atlas (TCGA). The coefficient of variation firstly is used to reduce the number of features, and then the elastic network is applied to select important features. Finally, a fully connected neural network is constructed with these selected features. In predicting seven types of cancers, iCancer-Pred has achieved an overall accuracy of over 97% accuracy with 5-fold cross-validation. For the convenience of the application, a user-friendly web server: http://bioinfo.jcu.edu.cn/cancer or http://121.36.221.79/cancer/ is available. And the source codes are freely available for download at https://github.com/Huerhu/iCancer-Pred.
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Affiliation(s)
- Weizhong Lin
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China.
| | - Siqin Hu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Zhicheng Wu
- Wuhan Ammunition Life Science & Technology Co., Ltd., Wuhan 430000, China
| | - Zhaochun Xu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Yu Zhong
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Zhe Lv
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Wangren Qiu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Xuan Xiao
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
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Lee IS, Sahu D, Hur H, Yook JH, Kim BS, Goel A. Discovery and validation of an expression signature for recurrence prediction in high-risk diffuse-type gastric cancer. Gastric Cancer 2021; 24:655-665. [PMID: 33523340 DOI: 10.1007/s10120-021-01155-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Diffuse type gastric cancer (DGC), represented by low sensitivity to chemotherapy and poor prognosis, is a heterogenous malignancy in which patient subsets exhibit diverse oncological risk-profiles. This study aimed to develop molecular biomarkers for robust prognostic risk-stratification and improve survival outcomes in patients with diffuse type gastric cancer (DGC). METHODS We undertook a systematic and comprehensive discovery and validation effort to identify recurrence prediction biomarkers by analyzing genome-wide transcriptomic profiling data from 157 patients with DGC, followed by their validation in 254 patients from 2 clinical cohorts. RESULTS Genome-wide transcriptomic profiling identified a 7-gene panel for robust prediction of recurrence in DGC patients (AUC = 0.91), which was successfully validated in an independent dataset (AUC = 0.86). Examination of 180 specimens from a training cohort allowed us to establish a gene-based risk prediction model (AUC = 0.78; 95% CI 0.71-0.84), which was subsequently validated in an independent cohort of 74 GC patients (AUC = 0.83; 95% CI 0.72-0.90). The Kaplan-Meier analyses exhibited a consistently superior performance of our risk-prediction model in the identification of high- and low-risk patient subgroups, which was significantly improved when we combined our gene signature with the tumor stage in both clinical cohorts (AUC of 0.83 in the training cohort and 0.89 in the validation cohort). Finally, for an easier clinical translation, we established a nomogram that robustly predicted prognosis in patients with DGC. CONCLUSIONS Our novel transcriptomic signature for risk-stratification and identification of high-risk patients with recurrence could serve as an important clinical decision-making tool in patients with DGC.
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Affiliation(s)
- In-Seob Lee
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Biomedical Research Center, 1218 S. Fifth Avenue, Monrovia, CA, 91016, USA.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Divya Sahu
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Biomedical Research Center, 1218 S. Fifth Avenue, Monrovia, CA, 91016, USA
| | - Hoon Hur
- Department of Surgery, Ajou University of School of Medicine, Suwon, South Korea.,Cancer Biology Graduate Program, Ajou University Graduate School of Medicine, Suwon, South Korea
| | - Jeong-Hwan Yook
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Byung-Sik Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Biomedical Research Center, 1218 S. Fifth Avenue, Monrovia, CA, 91016, USA.
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VSNL1 Promotes Gastric Cancer Cell Proliferation and Migration by Regulating P2X3/P2Y2 Receptors and Is a Clinical Indicator of Poor Prognosis in Gastric Cancer Patients. Gastroenterol Res Pract 2020; 2020:7241942. [PMID: 33376484 PMCID: PMC7744243 DOI: 10.1155/2020/7241942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/21/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022] Open
Abstract
Purpose The aim of this study was to investigate the role of Visinin Like 1 (VSNL1) in the proliferation and migration of gastric cancer (GC) cells as well as its clinical prognostic significance. Methods To this end, we evaluated VSNL1 expression in GC tissues and cell lines by real-time PCR and immunohistochemistry. To further explore the effects of VSNL1, a lentiviral vector expressing a short hairpin RNA (shRNA) against VSNL1 was constructed and transduced into the GC cell lines BGC-823 and SGC-7901. The interference efficiency of VSNL1-shRNA was determined by western blot. The effects of VSNL1 on the migration and invasion of GC cells as well as the expression of P2X3/P2Y2 were explored using MTS, colony formation, migration, and western blot assays. Results VSNL1 mRNA and protein levels were increased in GC tissues and cell lines. Furthermore, VSNL1 expression was positively correlated with Lauren's classification, lymph node metastasis, distant metastasis, TNM stage, and prognosis. VSNL1 expression was inversely correlated with the 5-year survival rate of GC patients. VSNL1 expression was markedly reduced in cells transduced with lentivirus expressing shRNA against VSNL1, and inhibiting VSNL1 expression significantly suppressed cell growth, migration, and colony formation and reduced the expression of P2X3/P2Y2. Conclusion VSNL1 may promote the proliferation and migration of GC cells by regulating P2X3 and P2Y2 expression. VSNL1 plays important roles in GC development and metastasis and may be correlated with patient prognosis.
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Transcriptional profiling of medulloblastoma with extensive nodularity (MBEN) reveals two clinically relevant tumor subsets with VSNL1 as potent prognostic marker. Acta Neuropathol 2020; 139:583-596. [PMID: 31781912 DOI: 10.1007/s00401-019-02102-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023]
Abstract
Medulloblastoma with extensive nodularity (MBEN) is one of the few central nervous system (CNS) tumor entities occurring in infants which is traditionally associated with good to excellent prognosis. Some MBEN, however, have been reported with an unfavorable clinical course. We performed an integrated DNA/RNA-based molecular analysis of a multi-institutional MBEN cohort (n = 41) to identify molecular events which might be responsible for variability in patients' clinical outcomes. RNA sequencing analysis of this MBEN cohort disclosed two clear transcriptome clusters (TCL) of these CNS tumors: "TCL1 MBEN" and "TCL2 MBEN" which were associated with various gene expression signatures, mutational landscapes and, importantly, prognosis. Thus, the clinically unfavorable "TCL1 MBEN" subset revealed transcriptome signatures composed of cancer-associated signaling pathways and disclosed a high frequency of clinically relevant germline PTCH1/SUFU alterations. In contrast, gene expression profiles of tumors from the clinically favorable "TCL2 MBEN" subgroup were associated with activation of various neurometabolic and neurotransmission signaling pathways, and germline SHH-pathway gene mutations were extremely rare in this transcriptome cluster. "TCL2 MBEN" also revealed strong and ubiquitous expression of VSNL1 (visinin-like protein 1) both at the mRNA and protein level, which was correlated with a favorable clinical course. Thus, combining mutational and epigenetic profiling with transcriptome analysis including VSNL1 immunohistochemistry, MBEN patients could be stratified into clinical risk groups of potential value for subsequent treatment planning.
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Chen G, Han N, Li G, Li X, Li G, Li Z, Li Q. Time course analysis based on gene expression profile and identification of target molecules for colorectal cancer. Cancer Cell Int 2016; 16:22. [PMID: 27013928 PMCID: PMC4806509 DOI: 10.1186/s12935-016-0296-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/09/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The study aimed to investigate the expression changes of genes in colorectal cancer (CRC) and screen the potential molecular targets. METHODS The GSE37178 of mRNA expression profile including the CRC samples extracted by surgical resection and the paired normal samples was downloaded from Gene Expression Omnibus database. The genes whose expressions were changed at four different time points were screened and clustered using Mfuzz package. Then DAVID was used to perform the functional and pathway enrichment analysis for genes in different clusters. The protein-protein interaction (PPI) networks were constructed for genes in the clusters according to the STRING database. Furthermore, the related-transcription factors (TFs) and microRNAs (miRNAs) were obtained based on the resources in databases and then were combined with the PPI networks in each cluster to construct the integrated network containing genes, TFs and miRNAs. RESULTS As a result, 314 genes were clustered into four groups. Genes in cluster 1 and cluster 2 showed a decreasing trend, while genes in cluster 3 and cluster 4 presented an increasing trend. Then 18 TFs (e.g., TCF4, MEF2C and FOS) and 18 miRNAs (e.g., miR-382, miR-217, miR-1184, miR-326 and miR-330-5p) were identified and three integrated networks for cluster 1, 3, and 4 were constructed. CONCLUSIONS The results implied that expression of PITX2, VSNL1, TCF4, MEF2C and FOS are time-related and associated with CRC development, accompanied by several miRNAs including miR-382, miR-217, miR-21, miR-1184, miR-326 and miR-330-5p. All of them might be used as potential diagnostic or therapeutic target molecules for CRC.
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Affiliation(s)
- Guoting Chen
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
| | - Ning Han
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
| | - Guofeng Li
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
| | - Xin Li
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
| | - Guang Li
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
| | - Zengchun Li
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
| | - Qinchuan Li
- Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai, 200120 China
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Estevez-Garcia P, Rivera F, Molina-Pinelo S, Benavent M, Gómez J, Limón ML, Pastor MD, Martinez-Perez J, Paz-Ares L, Carnero A, Garcia-Carbonero R. Gene expression profile predictive of response to chemotherapy in metastatic colorectal cancer. Oncotarget 2016; 6:6151-9. [PMID: 25730906 PMCID: PMC4467428 DOI: 10.18632/oncotarget.3152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/15/2015] [Indexed: 01/24/2023] Open
Abstract
Fluoropyrimidine-based chemotherapy (CT) has been the mainstay of care of metastatic colorectal cancer (mCRC) for years. Response rates are only observed, however, in about half of treated patients, and there are no reliable tools to prospectively identify patients more likely to benefit from therapy. The purpose of our study was to identify a gene expression profile predictive of CT response in mCRC. Whole genome expression analyses (Affymetrix GeneChip® HG-U133 Plus 2.0) were performed in fresh frozen tumor samples of 37 mCRC patients (training cohort). Differential gene expression profiles among the two study conditions (responders versus non-responders) were assessed using supervised class prediction algorithms. A set of 161 differentially expressed genes in responders (23 patients; 62%) versus non-responders (14 patients; 38%) was selected for further assessment and validation by RT-qPCR (TaqMan®Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards) in an independent multi-institutional cohort (53 mCRC patients). Seven of these genes were confirmed as significant predictors of response. Patients with a favorable predictive signature had significantly greater response rate (58% vs 13%, p = 0.024), progression-free survival (61% vs 13% at 1 year, HR = 0.32, p = 0.009) and overall survival (32 vs 16 months, HR = 0.21, p = 0.003) than patients with an unfavorable gene signature. This is the first study to validate a gene-expression profile predictive of response to CT in mCRC patients. Larger and prospective confirmatory studies are required, however, in order to successfully provide oncologists with adequate tools to optimize treatment selection in routine clinical practice.
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Affiliation(s)
- Purificacion Estevez-Garcia
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain.,Medical Oncology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Fernando Rivera
- Medical Oncology Department, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Sonia Molina-Pinelo
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
| | - Marta Benavent
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain.,Medical Oncology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Javier Gómez
- Pathology Department, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Maria Luisa Limón
- Medical Oncology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Maria Dolores Pastor
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
| | - Julia Martinez-Perez
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain.,Medical Oncology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Luis Paz-Ares
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain.,Medical Oncology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Amancio Carnero
- Laboratorio de Biología Molecular del Cáncer, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain
| | - Rocio Garcia-Carbonero
- Laboratorio de Oncología Molecular y Nuevas Terapias, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain.,Medical Oncology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
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Shao LN, Zhu BS, Xing CG, Yang XD, Young W, Cao JP. Effects of autophagy regulation of tumor-associated macrophages on radiosensitivity of colorectal cancer cells. Mol Med Rep 2016; 13:2661-70. [PMID: 26821367 DOI: 10.3892/mmr.2016.4820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 01/04/2016] [Indexed: 11/05/2022] Open
Abstract
Tumor‑associated macrophages (TAMs), a major component of the tumor microenvironment, are crucial to the processes of tumor growth, infiltration and metastasis, and contribute to drug resistance. The importance of TAMs in radiation resistance of colorectal cancer remains unclear. To investigate the effects of autophagy regulation of TAMs on the radiosensitivity of colorectal cancer cells, the current study induced TAM formation from THP‑1 monocyte cells. Sequential treatment of THP‑1 cells with PMA for 72 h and human recombinant interleukin‑4 for 24 h was used to stimulate THP‑1 differentiation to TAMs. Expression of the cell surface markers CD68, CD204 and CD206, and changes to cell morphology were used to confirm successful differentiation. The TAMs were stimulated to promote or inhibit autophagy during co‑culture with LoVo colorectal adenocarcinoma cells. The cells were irradiated, with subsequent measurement of LoVo colony formation and apoptosis. Additionally, the expression of p53, Bcl‑2, survivin and Smac proteins was assessed by western blotting. Monodansylcadaverin staining was used to analyze the presence of autophagic vacuoles in TAM, and western blot analysis was used to assess the expression of Beclin‑1, LC3B I and II, ATG‑3, ‑5 and ‑7. The results demonstrated TAM autophagy to be markedly altered by rapamycin and bafilomycin A1 treatment. Following co‑culture with TAMs, the colony formation rate and survival fraction of LoVo cells were significantly higher than those in the control group (P<0.05). It was further demonstrated that the regulation of autophagy in TAMs was able to inhibit the colony formation of LoVo colorectal cancer cells. Upregulation of TAM autophagy using rapamycin exhibited more effective inhibition of LoVo colony formation than autophagy downregulation. Notably, apoptosis was significantly increased in LoVo cells when co‑cultured with TAMs only, or with rapamycin‑mediated autophagy upregulated TAMs, compared with LoVo cells cultured alone (P<0.01). Expression of Bcl‑2, survivin and p53 were reduced in LoVo cells co‑cultured with TAMs, compared with the control group (P<0.05), whereas Smac expression was increased in the co‑culture groups (P<0.01). It was demonstrated that rapamycin‑mediated autophagy stimulation in TAMs led to reduced expression levels of survivin and Bcl‑2, however, Smac expression was increased. The upregulation of autophagy in TAMs inhibited proliferation and induced apoptosis in colon cancer cells, and altered the expression of radiosensitivity‑associated proteins. This data indicated that the radiosensitivity of colorectal cancer cells is associated with autophagy of TAM, and that stimulating TAM autophagy may increase the radiosensitivity of colorectal cancer cells.
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Affiliation(s)
- Le-Ning Shao
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Bao-Song Zhu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Chun-Gen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Xiao-Dong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Wu Young
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Jian-Ping Cao
- Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu 215123, P.R. China
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Shahim P, Mattsson N, Macy EM, Crimmins DL, Ladenson JH, Zetterberg H, Blennow K, Tegner Y. Serum visinin-like protein-1 in concussed professional ice hockey players. Brain Inj 2015; 29:872-6. [DOI: 10.3109/02699052.2015.1018324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Isaksson HS, Sorbe B, Nilsson TK. Whole genome expression profiling of blood cells in ovarian cancer patients -prognostic impact of the CYP1B1, MTSS1, NCALD, and NOP14. Oncotarget 2015; 5:4040-9. [PMID: 24961659 PMCID: PMC4147304 DOI: 10.18632/oncotarget.1938] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ovarian cancer patients with different tumor stages and cell differentiation might be distinguished from each other by gene expression profiles in whole blood cell mRNA by the Affymetrix Human Gene 1.0 ST Array. We also examined if there is any association with other clinical variables, response to therapy, and residual tumor burden after surgery. Patients were divided into two groups, one with poor prognosis, advanced stage and poorly differentiated tumors (n = 22), and one group with good prognosis, early stage and well- to medium differentiated tumors (n = 11). Six genes were found to be differentially expressed: the PDIA3, LYAR, NOP14, NCALD and MTSS1 genes were down-regulated and the CYP1B1 gene expression was up-regulated in the poor prognosis group, all with p value <0.05, adjusted for mass comparison. In survival analyses, CYP1B1, MTSS1, NCALD and NOP14 remained significantly different (p<0.05). Patient groups did not differ in any transcript related to acute phase or immune responses. This minimal gene expression signature of prognostic ovarian cancer-related genes opens up an avenue for more practicable monitoring of ovarian cancer patients by simple peripheral blood tests, which may evolve into a tool to guide selection of curative and postoperative supportive therapies.
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Affiliation(s)
| | | | - Torbjörn K Nilsson
- Department of Medical Biosciences/Clinical Chemistry, Umeå University,Umeå, Sweden
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Zhang P, Ji DB, Han HB, Shi YF, Du CZ, Gu J. Downregulation of miR-193a-5p correlates with lymph node metastasis and poor prognosis in colorectal cancer. World J Gastroenterol 2014; 20:12241-12248. [PMID: 25232258 PMCID: PMC4161809 DOI: 10.3748/wjg.v20.i34.12241] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/08/2014] [Accepted: 05/29/2014] [Indexed: 02/07/2023] Open
Abstract
AIM: To investigate the correlation of miR-193a-5p with lymph node metastasis and postoperative survival of colorectal cancer (CRC) patients.
METHODS: A total of 304 formalin-fixed, paraffin-embedded specimens (69 paired cancer and normal tissues, 55 primary tumors of stage III CRC and matched lymph nodes, and 56 primary tumors of stage II CRC) were included in this study. The relative expression levels of miR-193a-5p in the normal mucosa, primary cancer, and metastatic lymph node lesions were measured by quantitative real-time reverse transcriptase polymerase chain reaction. We evaluated the association of its expression with colorectal cancer lymph node metastasis, clinicopathological factors, and patient survival.
RESULTS: The relative expression level of miR-193a-5p was significantly lower in CRC tissues than in the normal mucosa (P = 0.0060). The expression levels of miR-193a-5p were lower in primary CRC tissues with lymph node metastases than in those without metastases (P = 0.0006), and decreased expression of miR-193a-5p correlated with advanced lymph node metastatic stage (P = 0.0007). Kaplan-Meier analysis showed that patients with low miR-193a-5p expression had decreased disease-free survival (DFS) (P = 0.0026) and poor overall survival (OS) (P = 0.0003). Interestingly, for the group of patients with lymph node metastases, miR-193a-5p expression was also related to survival. Patients with low miR-193a-5p expression had decreased DFS (P = 0.0262) and poor OS (P = 0.0230). Moreover, multivariate analysis indicated that downregulation of miR-193a-5p was an independent predictor of poor OS.
CONCLUSION: Downregulation of miR-193a-5p correlates with lymph node metastasis and poor survival of CRC. miR-193a-5p may be a useful biomarker for CRC diagnosis, metastasis and prognosis prediction.
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Kawamata F, Homma S, Kamachi H, Einama T, Kato Y, Tsuda M, Tanaka S, Maeda M, Kajino K, Hino O, Takahashi N, Kamiyama T, Nishihara H, Taketomi A, Todo S. C-ERC/mesothelin provokes lymphatic invasion of colorectal adenocarcinoma. J Gastroenterol 2014; 49:81-92. [PMID: 23512344 DOI: 10.1007/s00535-013-0773-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 02/06/2013] [Indexed: 02/04/2023]
Abstract
BACKGROUND Lymph node metastasis is a key event of colorectal cancer (CRC) progression. Mesothelin is expressed in various types of malignant tumor and associated with an unfavorable prognosis. The full-length mesothelin (Full-ERC) is cleaved by protease into membrane-bound C-ERC/mesothelin and N-ERC/mesothelin which is secreted into the blood. The aim of this study was to examine the biological role of mesothelin in CRC by clinicopathological analysis and in vitro lymphatic invasion assay. METHODS Ninety-one cases of CRC specimens were immunohistochemically examined and the localization of mesothelin in luminal membrane and/or cytoplasm was also evaluated. Lymphatic invasion assay was also performed using the human CRC cell line, WiDr, which was transfected with Full-, N- and C-ERC/mesothelin expression plasmids (Full-WiDr, N-WiDr and C-WiDr). RESULTS Immunohistochemically, "luminal membrane positive" of mesothelin was identified in 37.4 %, and correlated with lymphatic permeation and lymph node metastasis, but not with patients' prognosis. Interestingly, among the patients with lymph node metastasis (N = 38), "luminal membrane positive" of mesothelin significantly correlated with unfavorable patients' outcome. In addition, lymphatic invasion assay revealed that Full-WiDr and C-WiDr more significantly invaded human lymphatic endothelial cells than the Mock-WiDr (P < 0.01). CONCLUSION The luminal membrane expression of mesothelin was associated with unfavorable prognosis of CRC patients with lymph node metastasis. Moreover, this is the first report to prove the biological function of C-ERC/mesothelin associated with lymphatic invasion of cancer in vitro.
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Affiliation(s)
- Futoshi Kawamata
- Department of General Surgery, Hokkaido University, Graduate School of Medicine, Sapporo, Japan
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