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Okuda Y, Shimura T, Abe Y, Iwasaki H, Nishigaki R, Fukusada S, Sugimura N, Kitagawa M, Yamada T, Taguchi A, Kataoka H. Urinary dipeptidase 1 and trefoil factor 1 are promising biomarkers for early diagnosis of colorectal cancer. J Gastroenterol 2024; 59:572-585. [PMID: 38836911 DOI: 10.1007/s00535-024-02110-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/24/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Currently utilized serum tumor markers and fecal immunochemical tests do not have sufficient diagnostic power for colorectal cancer (CRC) due to their low sensitivities. To establish non-invasive urinary protein biomarkers for early CRC diagnosis, we performed stepwise analyses employing urine samples from CRCs and healthy controls (HCs). METHODS Among 474 urine samples, 363 age- and sex-matched participants (188 HCs, 175 stage 0-III CRCs) were randomly divided into discovery (16 HCs, 16 CRCs), training (110 HCs, 110 CRCs), and validation (62 HCs, 49 CRCs) cohorts. RESULTS Of the 23 urinary protein candidates comprehensively identified from mass spectrometry in the discovery cohort, urinary levels of dipeptidase 1 (uDPEP1) and Trefoil factor1 (uTFF1) were the two most significant diagnostic biomarkers for CRC in both training and validation cohorts using enzyme-linked immunosorbent assays. A urinary biomarker panel comprising uDPEP1 and uTFF1 significantly distinguished CRCs from HCs, showing area under the curves of 0.825-0.956 for stage 0-III CRC and 0.792-0.852 for stage 0/I CRC. uDPEP1 and uTFF1 also significantly distinguished colorectal adenoma (CRA) patients from HCs, with uDPEP1 and uTFF1 increasing significantly in the order of HCs, CRA patients, and CRC patients. Moreover, expression levels of DPEP1 and TFF1 were also significantly higher in the serum and tumor tissues of CRC, compared to HCs and normal tissues, respectively. CONCLUSIONS This study established a promising and non-invasive urinary protein biomarker panel, which enables the early detection of CRC with high sensitivity.
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Affiliation(s)
- Yusuke Okuda
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan.
| | - Yuichi Abe
- Division of Molecular Diagnostics, Aichi Cancer Center, 1-1 Kanokoden, Chikusa-Ku, Nagoya, Aichi, 464-8681, Japan
| | - Hiroyasu Iwasaki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Ruriko Nishigaki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Shigeki Fukusada
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Naomi Sugimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Mika Kitagawa
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Tamaki Yamada
- Okazaki Public Health Center, 1-3 Harusaki, Harisaki-Cho, Okazaki, 444-0827, Japan
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center, 1-1 Kanokoden, Chikusa-Ku, Nagoya, Aichi, 464-8681, Japan
- Division of Advanced Cancer Diagnostics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Hiromi Kataoka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-Cho, Mizuho-Ku, Nagoya, 467-8601, Japan
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Zhao YQ, Jin HR, Kim D, Jung SH, Liu S, Wan J, Lo HY, Fu XQ, Wang Q, Hao C, Bellail AC. SUMO1 degrader induces ER stress and ROS accumulation through deSUMOylation of TCF4 and inhibition of its transcription of StarD7 in colon cancer. Mol Carcinog 2023; 62:1249-1262. [PMID: 37191369 PMCID: PMC10524896 DOI: 10.1002/mc.23560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
Small molecule degraders of small ubiquitin-related modifier 1 (SUMO1) induce SUMO1 degradation in colon cancer cells and inhibits the cancer cell growth; however, it is unclear how SUMO1 degradation leads to the anticancer activity of the degraders. Genome-wide CRISPR-Cas9 knockout screen has identified StAR-related lipid transfer domain containing 7 (StarD7) as a critical gene for the degrader's anticancer activity. Here, we show that both StarD7 mRNA and protein are overexpressed in human colon cancer and its knockout significantly reduces colon cancer cell growth and xenograft progression. The treatment with the SUMO1 degrader lead compound HB007 reduces StarD7 mRNA and protein levels and increases endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) production in colon cancer cells and three-dimensional (3D) organoids. The study further provides a novel mechanism of the compound anticancer activity that SUMO1 degrader-induced decrease of StarD7 occur through degradation of SUMO1, deSUMOylation and degradation of T cell-specific transcription 4 (TCF4) and thereby inhibition of its transcription of StarD7 in colon cancer cells, 3D organoids and patient-derived xenografts (PDX).
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Affiliation(s)
- Yin Quan Zhao
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
- School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hong Ri Jin
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daeho Kim
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sung Han Jung
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ho-Yin Lo
- Synovel Laboratory LLC, Danbury, CT 06811, USA
| | - Xue Qi Fu
- School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China
| | - Quan Wang
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Chunhai Hao
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anita C. Bellail
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- HB Therapeutics Inc. Indianapolis, IN 46202, USA
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3
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Ha YJ, Shin YJ, Tak KH, Park JL, Kim JH, Lee JL, Yoon YS, Kim CW, Kim SY, Kim JC. Reduced expression of alanyl aminopeptidase is a robust biomarker of non-familial adenomatous polyposis and non-hereditary nonpolyposis colorectal cancer syndrome early-onset colorectal cancer. Cancer Med 2023; 12:10091-10104. [PMID: 36748835 PMCID: PMC10166950 DOI: 10.1002/cam4.5675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Early-onset colorectal cancer (EOCRC) has been increasing in incidence worldwide but its genomic pathogenesis is mostly undetermined. This study aimed to identify robust EOCRC-specific gene expression patterns in non-familial adenomatous polyposis (FAP) and non-hereditary nonpolyposis colorectal cancer syndrome (HNPCC) EOCRC. METHOD We first performed gene expression profiling analysis using RNA sequencing of discovery cohort comprised of 49 EOCRC (age <50) and 50 late-onset colorectal cancer (LOCRC) (age >70) specimens. To obtain robust gene expression data from this analysis, we validated differentially expressed genes (DEGs) through TCGA cohort (EOCRC:59 samples, LOCRC:229 samples) and our validation cohort (EOCRC:72 samples, LOCRC:43 samples) using real-time RT-PCR. After the validation of DEGs, we validated the selected gene at protein levels using Western blotting. To identify whether genomic methylation regulates the expression of a particular gene, we selected methylation sites using The Cancer Genome Atlas (TCGA) datasets and validated them by pyrosequencing in our validation cohort. RESULTS The EOCRC patients included in this study had significantly more prominent family history of cancer than the LOCRC patients (23 [46.9%] vs. 13 [26%], p = 0.050). Alanyl aminopeptidase (ANPEP) was significantly downregulated in the EOCRC tissues (FC = 1.78, p = 0.0007) and was also commonly downregulated in the TCGA cohort (FC = -1.08, p = 0.0021). Moreover, the ANPEP mRNA and protein expression levels were significantly downregulated in the EOCRC tissues of our validation cohort (p = 0.037 and 0.027). In comparisons of the normal and tumor tissues in public datasets, the ANPEP level was significantly lower in the tumor tissue in the TCGA dataset (p < 2.2 × 10-16 ) and GSE196006 dataset (p = 0.0005). Furthermore, the ANPEP expression level did not show a decreasing tendency at a young age in the normal colon tissue of the GTEx dataset. Lastly, the hypermethylation of cg26222247 in ANPEP was identified to be weakly associated with reduced ANPEP expression in our EOCRC cohort. CONCLUSION The reduced expression of ANPEP was identified as a novel biomarker of non-FAP and non-HNPCC EOCRC.
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Affiliation(s)
- Ye Jin Ha
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Yun Jae Shin
- Personalized Genomic Medicine Research Center, Daejeon, South Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, University of Science and Technology (UST), Daejeon, South Korea
| | - Ka Hee Tak
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Jong Lyul Park
- Personalized Genomic Medicine Research Center, Daejeon, South Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jeong Hwan Kim
- Personalized Genomic Medicine Research Center, Daejeon, South Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jong Lyul Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yong Sik Yoon
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Chan Wook Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Seon Young Kim
- Personalized Genomic Medicine Research Center, Daejeon, South Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, University of Science and Technology (UST), Daejeon, South Korea
| | - Jin Cheon Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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Zhang L, Huang Z, Cai Q, Zhao C, Xiao Y, Quan X, Tang C, Gao J. Inhibition of Transketolase Improves the Prognosis of Colorectal Cancer. Front Med (Lausanne) 2022; 9:837143. [PMID: 35280908 PMCID: PMC8905541 DOI: 10.3389/fmed.2022.837143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) remains a heavy health burden worldwide. Transketolase (TKT) is a crucial enzyme in the non-oxidative phase of the Pentose Phosphate Pathway (PPP), and is up-regulated in multiple cancer types. However, the role of TKT in the prognosis of CRC remains unclear. We aimed to explore whether TKT expression is altered in CRC, how TKT is associated with the prognosis of CRC, and whether the regulation of TKT might have an impact on CRC. Differentially expressed genes (DEGs) were identified using bioinformatics analysis. TKT expression was examined in the human colon adenocarcinoma tissue microarray and xenografts. Cell viability, proliferation, migration, and apoptosis assays in vitro were applied to evaluate the protumoral effects of TKT on CRC. TKT was found to be a risk factor for the poor prognosis of CRC by bioinformatics analysis among the DEGs. TKT was significantly up-regulated in colon adenocarcinoma tissues compared with normal colon tissues in patients. Moreover, similar results were found in HCT116 and RKO human colon adenocarcinoma xenografts in nude mice. TKT expression was positively associated with advanced TNM stage, positive lymph nodes, and poor 5 or 10-year overall survival of CRC patients. In vitro, inhibition of TKT reduced cell viability, proliferation, and migration, and induced cell apoptosis. In addition, inhibition of TKT decreased the protein levels of NICD and Hes1. In conclusion, high TKT expression was associated with the poor prognosis of CRC patients. The protumoral effects of downregulating TKT may be realized by suppressing the Notch signaling pathway. TKT may be a new prognostic biomarker and therapeutic target for CRC.
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Affiliation(s)
- Linhao Zhang
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyin Huang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Qiuyu Cai
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chong Zhao
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Xiao
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Quan
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengwei Tang
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinhang Gao
- Lab of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China.,Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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5
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Asif K, Memeo L, Palazzolo S, Frión-Herrera Y, Parisi S, Caligiuri I, Canzonieri V, Granchi C, Tuccinardi T, Rizzolio F. STARD3: A Prospective Target for Cancer Therapy. Cancers (Basel) 2021; 13:4693. [PMID: 34572920 PMCID: PMC8472075 DOI: 10.3390/cancers13184693] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the major causes of death in developed countries and current therapies are based on surgery, chemotherapeutic agents, and radiation. To overcome side effects induced by chemo- and radiotherapy, in recent decades, targeted therapies have been proposed in second and even first lines. Targeted drugs act on the essential pathways involved in tumor induction, progression, and metastasis, basically all the hallmark of cancers. Among emerging pathways, the cholesterol metabolic pathway is a strong candidate for this purpose. Cancer cells have an accelerated metabolic rate and require a continuous supply of cholesterol for cell division and membrane renewal. Steroidogenic acute regulatory related lipid transfer (START) proteins are a family of proteins involved in the transfer of lipids and some of them are important in non-vesicular cholesterol transportation within the cell. The alteration of their expression levels is implicated in several diseases, including cancers. In this review, we report the latest discoveries on StAR-related lipid transfer protein domain 3 (STARD3), a member of the START family, which has a potential role in cancer, focusing on the structural and biochemical characteristics and mechanisms that regulate its activity. The role of the STARD3 protein as a molecular target for the development of cancer therapies is also discussed. As STARD3 is a key protein in the cholesterol movement in cancer cells, it is of interest to identify inhibitors able to block its activity.
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Affiliation(s)
- Kanwal Asif
- Department of Molecular Sciences and Nanosystems, PhD School in Science and Technology of Bio and Nanomaterials, Ca’ Foscari University of Venice, 30172 Venice, Italy;
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, 33081 Aviano, Italy; (S.P.); (S.P.); (V.C.)
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy;
| | - Stefano Palazzolo
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, 33081 Aviano, Italy; (S.P.); (S.P.); (V.C.)
| | - Yahima Frión-Herrera
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, 30172 Venice, Italy; or
| | - Salvatore Parisi
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, 33081 Aviano, Italy; (S.P.); (S.P.); (V.C.)
| | - Isabella Caligiuri
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, 33081 Aviano, Italy; (S.P.); (S.P.); (V.C.)
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, 33081 Aviano, Italy; (S.P.); (S.P.); (V.C.)
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Carlotta Granchi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (C.G.); (T.T.)
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (C.G.); (T.T.)
| | - Flavio Rizzolio
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (C.R.O.) IRCCS, 33081 Aviano, Italy; (S.P.); (S.P.); (V.C.)
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, 30172 Venice, Italy; or
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Carriere P, Calvo N, Novoa Díaz MB, Lopez-Moncada F, Herrera A, Torres MJ, Alonso E, Gandini NA, Gigola G, Contreras HR, Gentili C. Role of SPARC in the epithelial-mesenchymal transition induced by PTHrP in human colon cancer cells. Mol Cell Endocrinol 2021; 530:111253. [PMID: 33781836 DOI: 10.1016/j.mce.2021.111253] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/27/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Parathyroid hormone-related peptide (PTHrP) exerts its effects on cells derived from colorectal cancer (CRC) and tumor microenvironment and is involved in processes requiring the epithelial-mesenchymal transition (EMT). Here, we report that PTHrP modulates factors expression and morphological changes associated with EMT in HCT116 cells from CRC. PTHrP increased the protein expression of SPARC, a factor involved in EMT, in HCT116 cells but not in Caco-2 cells also from CRC but with less aggressiveness. PTHrP also increased SPARC expression and its subsequent release from endothelial HMEC-1 cells. The conditioned media of PTHrP-treated HMEC-1 cells induced early changes related to EMT in HCT116 cells. Moreover, SPARC treatment on HCT116 cells potentiated PTHrP modulation in E-cadherin expression and cell migration. In vivo PTHrP also increased SPARC expression and decreased E-cadherin expression. These results suggest a novel PTHrP action on CRC progression involving the microenvironment in the modulation of events associated with EMT.
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Affiliation(s)
- Pedro Carriere
- Department of Biology, Biochemistry and Pharmacy-INBIOSUR, National University of the South, Bahía Blanca, Argentina
| | - Natalia Calvo
- Department of Biology, Biochemistry and Pharmacy-INBIOSUR, National University of the South, Bahía Blanca, Argentina
| | - María Belén Novoa Díaz
- Department of Biology, Biochemistry and Pharmacy-INBIOSUR, National University of the South, Bahía Blanca, Argentina
| | - Fernanda Lopez-Moncada
- Department of Basic and Clinic Oncology. Faculty of Medicine, University of Chile, Chile
| | - Alexander Herrera
- Department of Basic and Clinic Oncology. Faculty of Medicine, University of Chile, Chile
| | - María José Torres
- Department of Basic and Clinic Oncology. Faculty of Medicine, University of Chile, Chile
| | | | | | - Graciela Gigola
- Department of Biology, Biochemistry and Pharmacy-INBIOSUR, National University of the South, Bahía Blanca, Argentina
| | - Hector R Contreras
- Department of Basic and Clinic Oncology. Faculty of Medicine, University of Chile, Chile
| | - Claudia Gentili
- Department of Biology, Biochemistry and Pharmacy-INBIOSUR, National University of the South, Bahía Blanca, Argentina.
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7
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Chen DW, Miao R, Deng ZY, Lu YY, Liang Y, Huang L. Sparse Logistic Regression With L 1/2 Penalty for Emotion Recognition in Electroencephalography Classification. Front Neuroinform 2020; 14:29. [PMID: 32848688 PMCID: PMC7427509 DOI: 10.3389/fninf.2020.00029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/28/2020] [Indexed: 01/12/2023] Open
Abstract
Emotion recognition based on electroencephalography (EEG) signals is a current focus in brain-computer interface research. However, the classification of EEG is difficult owing to large amounts of data and high levels of noise. Therefore, it is important to determine how to effectively extract features that include important information. Regularization, one of the effective methods for EEG signal processing, can effectively extract important features from the signal and has potential applications in EEG emotion recognition. Currently, the most popular regularization technique is Lasso (L 1) and Ridge Regression (L 2). In recent years, researchers have proposed many other regularization terms. In theory, L q -type regularization has a lower q value, which means that it can be used to find solutions with better sparsity. L 1/2 regularization is of L q type (0 < q < 1) and has been shown to have many attractive properties. In this work, we studied the L 1/2 penalty in sparse logistic regression for three-classification EEG emotion recognition, and used a coordinate descent algorithm and a univariate semi-threshold operator to implement L 1/2 penalty logistic regression. The experimental results on simulation and real data demonstrate that our proposed method is better than other existing regularization methods. Sparse logistic regression with L 1/2 penalty achieves higher classification accuracy than the conventional L 1, Ridge Regression, and Elastic Net regularization methods, using fewer but more informative EEG signals. This is very important for high-dimensional small-sample EEG data and can help researchers to reduce computational complexity and improve computational accuracy. Therefore, we propose that sparse logistic regression with the L 1/2 penalty is an effective technique for emotion recognition in practical classification problems.
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Affiliation(s)
- Dong-Wei Chen
- School of Electronic Information Engineering, University of Electronic Science and Technology of China, Zhongshan, China
| | - Rui Miao
- Faculty of Information Technology, Macau University of Science and Technology, Macau, China
| | - Zhao-Yong Deng
- School of Electronic Information Engineering, University of Electronic Science and Technology of China, Zhongshan, China
| | - Yue-Yue Lu
- School of Electronic Information Engineering, University of Electronic Science and Technology of China, Zhongshan, China
| | - Yong Liang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
| | - Lan Huang
- School of Electronic Information Engineering, University of Electronic Science and Technology of China, Zhongshan, China
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8
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Nakazawa Y, Nakazawa S, Kurozumi S, Ogino M, Koibuchi Y, Odawara H, Oyama T, Horiguchi J, Fujii T, Shirabe K. The pathological complete response and secreted protein acidic and rich in cysteine expression in patients with breast cancer receiving neoadjuvant nab-paclitaxel chemotherapy. Oncol Lett 2020; 19:2705-2712. [PMID: 32218821 PMCID: PMC7068243 DOI: 10.3892/ol.2020.11354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Biomarkers that can accurately predict treatment response are required for indicating optimal neoadjuvant treatments. The current study assessed the predictive value of secreted protein acidic and rich in cysteine (SPARC) mRNA expression for the response to neoadjuvant nab-paclitaxel (nab-PTX) therapy in patients with breast cancer. It was hypothesized that SPARC expression can affect the response to albumin-bound taxanes, including nab-PTX since SPARC binds albumin with a high affinity. Pre-therapeutic specimens of core needle biopsies were analyzed from 50 patients in a phase II trial of neoadjuvant nab-PTX and the factors that were associated with a pathological complete response (pCR) were assessed. The pre-therapeutic tumor mRNA levels of chemotherapy-related proteins were quantified, including SPARC, and the correlations with post-therapeutic clinicopathological factors were assessed, including with pCR. The results demonstrated that pre-therapeutic SPARC mRNA expression was significantly higher in non-pCR patients compared with patients with pCR (92.37±55.33 vs. 56.53±30.19; P=0.027). A cutoff point of 48.5 was determined using receiver operating characteristic (ROC) curve analysis (sensitivity, 83.3%; specificity, 50.0%), and patients were classified into low and high SPARC expression groups. High SPARC expression was associated with histological grade (P=0.035), estrogen receptor expression (P=0.037), and progesterone receptor expression (P=0.002) but not with HER2 (P=0.895), and Ki-67 LI (P=0.743) expression. The results of the current study indicated that a high SPARC mRNA expression was a negative predictor of pCR following neoadjuvant nab-PTX therapy regardless of breast cancer subtype. The phase II study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of the National Hospital Organization Takasaki General Medical Center (Registration nos. H23-9 and H23-33).
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Affiliation(s)
- Yuko Nakazawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan.,Department of Breast and Endocrine Surgery, National Hospital Organization Takasaki General Medical Center, Takasaki, Gunma 370-0829, Japan.,Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Seshiru Nakazawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Sasagu Kurozumi
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Misato Ogino
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan.,Department of Breast and Endocrine Surgery, National Hospital Organization Takasaki General Medical Center, Takasaki, Gunma 370-0829, Japan
| | - Yukio Koibuchi
- Department of Breast and Endocrine Surgery, National Hospital Organization Takasaki General Medical Center, Takasaki, Gunma 370-0829, Japan
| | - Hiroki Odawara
- Department of Surgery, Toho Hospital, Midori, Gunma 376-0121, Japan
| | - Tetsunari Oyama
- Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Jun Horiguchi
- Department of Breast Surgery, International University of Health and Welfare, Chiba 286-8686, Japan
| | - Takaaki Fujii
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Ken Shirabe
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
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9
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Ast V, Kordaß T, Oswald M, Kolte A, Eisel D, Osen W, Eichmüller SB, Berndt A, König R. MiR-192, miR-200c and miR-17 are fibroblast-mediated inhibitors of colorectal cancer invasion. Oncotarget 2018; 9:35559-35580. [PMID: 30473751 PMCID: PMC6238973 DOI: 10.18632/oncotarget.26263] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/06/2018] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer remains a leading cause of cancer-related death worldwide. A previous transcriptomics based study characterized molecular subgroups of which the stromal subgroup was associated with the worst clinical outcome. Micro-RNAs (miRNAs) are well-known regulators of gene expression and can follow a non-linear repression mechanism. We set up a model combining piecewise linear and linear regression and applied this combined regression model to a comprehensive colon adenocarcinoma dataset. We identified miRNAs involved in regulating characteristic gene sets, particularly extracellular matrix remodeling in the stromal subgroup. Comparison of expression data from separated (epithelial) cancer cells and stroma cells or fibroblasts associate these regulatory interactions with infiltrating stromal or tumor-associated fibroblasts. MiR-200c, miR-17 and miR-192 were identified as the most promising candidates regulating genes crucial for extracellular matrix remodeling. We validated our computational findings by in vitro assays. Enforced expression of either miR-200c, miR-17 or miR-192 in untransformed human colon fibroblasts down-regulated 85% of all predicted target genes. Expressing these miRNAs singly or in combination in human colon fibroblasts co-cultured with colon cancer cells considerably reduced cancer cell invasion validating these miRNAs as cancer cell infiltration suppressors in tumor associated fibroblasts.
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Affiliation(s)
- Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
| | - Theresa Kordaß
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
| | - Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
| | - David Eisel
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Wolfram Osen
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Stefan B. Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Alexander Berndt
- Institute of Forensic Medicine, Section Pathology, Jena University Hospital, 07747 Jena, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, 07745 Jena, Germany
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10
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Bioinformatics Analysis Reveals Most Prominent Gene Candidates to Distinguish Colorectal Adenoma from Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9416515. [PMID: 30175151 PMCID: PMC6106857 DOI: 10.1155/2018/9416515] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of death by cancer worldwide. Bowel cancer screening programs enable us to detect early lesions and improve the prognosis of patients with CRC. However, they also generate a significant number of problematic polyps, e.g., adenomas with epithelial misplacement (pseudoinvasion) which can mimic early adenocarcinoma. Therefore, biomarkers that would enable us to distinguish between adenoma with epithelial misplacement (pseudoinvasion) and adenoma with early adenocarcinomas (true invasion) are needed. We hypothesized that the former are genetically similar to adenoma and the latter to adenocarcinoma and we used bioinformatics approach to search for candidate genes that might be potentially used to distinguish between the two lesions. We used publicly available data from Gene Expression Omnibus database and we analyzed gene expression profiles of 252 samples of normal mucosa, colorectal adenoma, and carcinoma. In total, we analyzed 122 colorectal adenomas, 59 colorectal carcinomas, and 62 normal mucosa samples. We have identified 16 genes with differential expression in carcinoma compared to adenoma: COL12A1, COL1A2, COL3A1, DCN, PLAU, SPARC, SPON2, SPP1, SULF1, FADS1, G0S2, EPHA4, KIAA1324, L1TD1, PCKS1, and C11orf96. In conclusion, our in silico analysis revealed 16 candidate genes with different expression patterns in adenoma compared to carcinoma, which might be used to discriminate between these two lesions.
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11
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Ponzio G, Rezzonico R, Bourget I, Allan R, Nottet N, Popa A, Magnone V, Rios G, Mari B, Barbry P. A new long noncoding RNA (lncRNA) is induced in cutaneous squamous cell carcinoma and down-regulates several anticancer and cell differentiation genes in mouse. J Biol Chem 2017; 292:12483-12495. [PMID: 28596382 DOI: 10.1074/jbc.m117.776260] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/05/2017] [Indexed: 01/17/2023] Open
Abstract
Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer. Although some of the early events involved in this pathology have been identified, the subsequent steps leading to tumor development are poorly defined. We demonstrate here that the development of mouse tumors induced by the concomitant application of a carcinogen and a tumor promoter (7,12-dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate (TPA), respectively) is associated with the up-regulation of a previously uncharacterized long noncoding RNA (lncRNA), termed AK144841. We found that AK144841 expression was absent from normal skin and was specifically stimulated in tumors and highly tumorigenic cells. We also found that AK144841 exists in two variants, one consisting of a large 2-kb transcript composed of four exons and one consisting of a 1.8-kb transcript lacking the second exon. Gain- and loss-of-function studies indicated that AK144841 mainly inhibited gene expression, specifically down-regulating the expression of genes of the late cornified envelope-1 (Lce1) family involved in epidermal terminal differentiation and of anticancer genes such as Cgref1, Brsk1, Basp1, Dusp5, Btg2, Anpep, Dhrs9, Stfa2, Tpm1, SerpinB2, Cpa4, Crct1, Cryab, Il24, Csf2, and Rgs16 Interestingly, the lack of the second exon significantly decreased AK144841's inhibitory effect on gene expression. We also noted that high AK144841 expression correlated with a low expression of the aforementioned genes and with the tumorigenic potential of cell lines. These findings suggest that AK144841 could contribute to the dedifferentiation program of tumor-forming keratinocytes and to molecular cascades leading to tumor development.
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Affiliation(s)
- Gilles Ponzio
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and.
| | - Roger Rezzonico
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Isabelle Bourget
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, 06000 Nice, France
| | - Richard Allan
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Nicolas Nottet
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Alexandra Popa
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Virginie Magnone
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Géraldine Rios
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Bernard Mari
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
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12
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Ianaro A, Cirino G, Wallace JL. Hydrogen sulfide-releasing anti-inflammatory drugs for chemoprevention and treatment of cancer. Pharmacol Res 2016; 111:652-658. [PMID: 27475881 DOI: 10.1016/j.phrs.2016.07.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/05/2016] [Accepted: 07/26/2016] [Indexed: 02/07/2023]
Abstract
For many years it has been recognized that inhibition of cyclooxygenase enzymes is effective in reducing the incidence of many types of cancer, but the adverse effects of these drug, particularly in the gastrointestinal and cardiovascular systems, limits their utility. Recently developed hydrogen sulfide-releasing anti-inflammatory drugs may be a promising option for cancer chemoprevention. In this paper we review evidence suggesting that these novel compounds are effective in a range of animal models of various types of cancer, while exhibiting greatly reduced toxicity relative to currently marketed non-steroidal anti-inflammatory drugs. Some of the possible mechanisms of action of hydrogen sulfide-releasing anti-inflammatory drugs are also discussed.
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Affiliation(s)
- Angela Ianaro
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy; Faculty of Medicine, Universidade Camilo Castelo Branco, São Paulo, SP, Brazil
| | - John L Wallace
- Faculty of Medicine, Universidade Camilo Castelo Branco, São Paulo, SP, Brazil; Department of Physiology & Pharmacology, University of Calgary, Calgary, AB, Canada.
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13
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Profound Chemopreventative Effects of a Hydrogen Sulfide-Releasing NSAID in the APCMin/+ Mouse Model of Intestinal Tumorigenesis. PLoS One 2016; 11:e0147289. [PMID: 26910063 PMCID: PMC4766010 DOI: 10.1371/journal.pone.0147289] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 01/02/2016] [Indexed: 12/21/2022] Open
Abstract
Nonsteroidal anti-inflammatory drugs have been shown to reduce the incidence of gastrointestinal cancers, but the propensity of these drugs to cause ulcers and bleeding limits their use. H2S has been shown to be a powerful cytoprotective and anti-inflammatory substance in the digestive system. This study explored the possibility that a H2S-releasing nonsteroidal anti-inflammatory drug (ATB-346) would be effective in a murine model of hereditary intestinal cancer (APCMin+ mouse) and investigated potential mechanisms of action via transcriptomics analysis. Daily treatment with ATB-346 was significantly more effective at preventing intestinal polyp formation than naproxen. Significant beneficial effects were seen with a treatment period of only 3–7 days, and reversal of existing polyps was observed in the colon. ATB-346, but not naproxen, significantly decreased expression of intestinal cancer-associated signaling molecules (cMyc, β-catenin). Transcriptomic analysis identified 20 genes that were up-regulated in APCMin+ mice, 18 of which were reduced to wild-type levels by one week of treatment with ATB-346. ATB-346 is a novel, gastrointestinal-sparing anti-inflammatory drug that potently and rapidly prevents and reverses the development of pre-cancerous lesions in a mouse model of hereditary intestinal tumorigenesis. These effects may be related to the combined effects of suppression of cyclooxygenase and release of H2S, and correction of most of the APCMin+-associated alterations in the transcriptome. ATB-346 may represent a promising agent for chemoprevention of tumorigenesis in the GI tract and elsewhere.
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14
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Nian Q, Zhang Z, Wei C, Kuang X, Wang X, Wang L. Gene expression profiling in myelodysplastic syndrome after SPARC overexpression associated with Ara-C. Oncol Rep 2015; 34:2072-82. [PMID: 26238482 DOI: 10.3892/or.2015.4139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 12/11/2022] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC) is involved in many biological processes, including erythropoiesis and cell proliferation. However, the role of SPARC in myelodysplastic syndrome (MDS) remains to be elucidated. Pyrimidine analogue cytosine arabinoside (Ara-C) is among the most effective agents used in the treatment of acute leukemia. The aim of the present study was to determine whether the chemotherapeutic activity of Ara-C was enhanced by the overexpression of SPARC. DNA microarray technology and RNA sequencing were employed to examine differential gene expression in the apoptosis signaling pathway after gene change occurred in cells following drug treatment. The results showed that upregulation of the expression of SPARC induced SKM-1 cell death and inhibited proliferation. Additionally, the apoptotic rate of SPARC overexpression combined with Ara-C increased significantly. Transcription factors CPBP and ZNF333 regulated the 69 genes and long non-coding RNA (lncRNA). Moreover, the mRNA and protein expression of apoptosis-related genes in the DNA microarray results were increased. These results suggest that SPARC expression changes with Ara-C, revealing a possible application in the treatment of MDS.
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Affiliation(s)
- Qing Nian
- Department of Emergency, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Zhiqiang Zhang
- Department of Emergency, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Chunmei Wei
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Xingyi Kuang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Xingyong Wang
- Department of Emergency, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong, Chongqing 400016, P.R. China
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15
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Nian Q, Chi J, Xiao Q, Wei C, Costeas P, Yang Z, Liu L, Wang L. SPARC ectopic overexpression inhibits growth and promotes programmed cell death in acute myeloid leukemia transformed from myelodysplastic syndrome cells, alone and in combination with Ara-C treatment. Oncol Rep 2015; 34:1406-14. [PMID: 26165695 DOI: 10.3892/or.2015.4114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/05/2022] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC) has a complex and pleiotropic biological role in cell life during disease. The role of SPARC in myelodysplastic syndrome (MDS) is not yet fully understood. In the present study, we investigated the role of SPARC protein overproduction in the proliferation and apoptosis of SKM-1 cells, an acute myeloid leukemia cell line transformed from MDS. SKM-1 cells were infected with the pGC-GV-SPARC vector. The cells were then assessed for proliferation and cell death following treatment with low-dose cytosine arabinoside (Ara‑C). The microarray analysis results revealed that samples from SPARC‑overexpressed cells compared to SPARC protein, in SKM-1 cells led to proliferation inhibition and promoted programmed cell death and these effects were greater when treated with Ara-C. The mRNA and protein expression levels of SPARC were detected by SPARC overexpression in cells treated with Ara-C resulting in a significant upregulation of the mixed lineage kinase domain-like (MLKL) gene expression and five other genes. The results showed that the necrotic signaling pathway may play a role when the two conditions were combined via the upregulation of the MLKL protein. MLKL upregulation in SPARC overexpressed cells treated with Ara-C, indicates necrosis as a possible cell death process for the SKM-1 cells under these stringent conditions.
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Affiliation(s)
- Qing Nian
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jianxiang Chi
- The Center for the Study of Haematological Malignancies, Nicosia 2032, Cyprus
| | - Qing Xiao
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Chunmei Wei
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Paul Costeas
- The Center for the Study of Haematological Malignancies, Nicosia 2032, Cyprus
| | - Zesong Yang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lin Liu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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16
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del Rincón SV, Widschwendter M, Sun D, Ekholm-Reed S, Tat J, Teixeira LK, Ellederova Z, Grolieres E, Reed SI, Spruck C. Cks overexpression enhances chemotherapeutic efficacy by overriding DNA damage checkpoints. Oncogene 2015; 34:1961-7. [PMID: 24858038 PMCID: PMC4245389 DOI: 10.1038/onc.2014.137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 12/12/2022]
Abstract
Cdc kinase subunit (Cks) proteins Cks1 and Cks2 are adaptor-like proteins that bind many cyclin-dependent kinases. A wealth of clinical data has shown that Cks proteins are overexpressed in many types of human cancers and this often correlates with increased tumor aggressiveness. Previously, we showed that Cks overexpression abrogates the intra-S-phase checkpoint, a major barrier to oncogene-mediated transformation. Interestingly, the intra-S-phase checkpoint is crucial for the cellular response to replication stress, a major pathway of apoptosis induction by many chemotherapeutic agents. Here, we demonstrate cancer cells that overexpress Cks1 or Cks2 override the intra-S-phase checkpoint in the presence of replication stress-inducing chemotherapies such as 5-Fluorouracil (5-FU) and methotrexate (MTX) leading to enhanced sensitivity in vitro and in vivo. Furthermore, enforced expression of Cks1 in an MTX-resistant breast cancer cell line was found to restore drug sensitivity. Our results suggest that Cks proteins are important determinants of apoptosis induction of replication stress-inducing chemotherapies such as 5-FU.
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Affiliation(s)
- Sonia V. del Rincón
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | | | - Dahui Sun
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Susanna Ekholm-Reed
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - John Tat
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Leonardo K. Teixeira
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Zdenka Ellederova
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Elise Grolieres
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Steven I. Reed
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Charles Spruck
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California, USA
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17
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Azevedo H, Fujita A, Bando SY, Iamashita P, Moreira-Filho CA. Transcriptional network analysis reveals that AT1 and AT2 angiotensin II receptors are both involved in the regulation of genes essential for glioma progression. PLoS One 2014; 9:e110934. [PMID: 25365520 PMCID: PMC4217762 DOI: 10.1371/journal.pone.0110934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/26/2014] [Indexed: 01/25/2023] Open
Abstract
Gliomas are aggressive primary brain tumors with high infiltrative potential. The expression of Angiotensin II (Ang II) receptors has been associated with poor prognosis in human astrocytomas, the most common type of glioma. In this study, we investigated the role of Angiotensin II in glioma malignancy through transcriptional profiling and network analysis of cultured C6 rat glioma cells exposed to Ang II and to inhibitors of its membrane receptor subtypes. C6 cells were treated with Ang II and specific antagonists of AT1 and AT2 receptors. Total RNA was isolated after three and six hours of Ang II treatment and analyzed by oligonucleotide microarray technology. Gene expression data was evaluated through transcriptional network modeling to identify how differentially expressed (DE) genes are connected to each other. Moreover, other genes co-expressing with the DE genes were considered in these analyses in order to support the identification of enriched functions and pathways. A hub-based network analysis showed that the most connected nodes in Ang II-related networks exert functions associated with cell proliferation, migration and invasion, key aspects for glioma progression. The subsequent functional enrichment analysis of these central genes highlighted their participation in signaling pathways that are frequently deregulated in gliomas such as ErbB, MAPK and p53. Noteworthy, either AT1 or AT2 inhibitions were able to down-regulate different sets of hub genes involved in protumoral functions, suggesting that both Ang II receptors could be therapeutic targets for intervention in glioma. Taken together, our results point out multiple actions of Ang II in glioma pathogenesis and reveal the participation of both Ang II receptors in the regulation of genes relevant for glioma progression. This study is the first one to provide systems-level molecular data for better understanding the protumoral effects of Ang II in the proliferative and infiltrative behavior of gliomas.
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Affiliation(s)
- Hátylas Azevedo
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - André Fujita
- Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
- * E-mail:
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18
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Qiu Y, Cai G, Zhou B, Li D, Zhao A, Xie G, Li H, Cai S, Xie D, Huang C, Ge W, Zhou Z, Xu LX, Jia W, Zheng S, Yen Y, Jia W. A distinct metabolic signature of human colorectal cancer with prognostic potential. Clin Cancer Res 2014; 20:2136-46. [PMID: 24526730 DOI: 10.1158/1078-0432.ccr-13-1939] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Metabolic phenotyping has provided important biomarker findings, which, unfortunately, are rarely replicated across different sample sets due to the variations from different analytical and clinical protocols used in the studies. To date, very few metabolic hallmarks in a given cancer type have been confirmed and validated by use of a metabolomic approach and other clinical modalities. Here, we report a metabolomics study to identify potential metabolite biomarkers of colorectal cancer with potential theranostic value. EXPERIMENTAL DESIGN Gas chromatography-time-of-flight mass spectrometry (GC-TOFMS)-based metabolomics was used to analyze 376 surgical specimens, which were collected from four independent cohorts of patients with colorectal cancer at three hospitals located in China and City of Hope Comprehensive Cancer Center in the United States. Differential metabolites were identified and evaluated as potential prognostic markers. A targeted transcriptomic analysis of 29 colorectal cancer and 27 adjacent nontumor tissues was applied to analyze the gene expression levels for key enzymes associated with these shared metabolites. RESULTS A panel of 15 significantly altered metabolites was identified, which demonstrates the ability to predict the rate of recurrence and survival for patients after surgery and chemotherapy. The targeted transcriptomic analysis suggests that the differential expression of these metabolites is due to robust metabolic adaptations in cancer cells to increased oxidative stress as well as demand for energy, and macromolecular substrates for cell growth and proliferation. CONCLUSIONS These patients with colorectal cancer, despite their varied genetic background, mutations, pathologic stages, and geographic locations, shared a metabolic signature that is of great prognostic and therapeutic potential.
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Affiliation(s)
- Yunping Qiu
- Authors' Affiliations: Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University; Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Med-X Institutes, Shanghai Jiao Tong University, Shanghai; State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing; Cancer Institute, 2nd Hospital Affiliated to School of Medicine, Zhejiang University, Hangzhou, PR China; Center for translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, North Carolina; Department of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, California; and Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
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19
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Nian Q, Xiao Q, Wang L, Luo J, Chen LP, Yang ZS, Liu L. SPARC silencing inhibits the growth of acute myeloid leukemia transformed from myelodysplastic syndrome via induction of cell cycle arrest and apoptosis. Int J Mol Med 2014; 33:856-62. [PMID: 24535175 PMCID: PMC3976133 DOI: 10.3892/ijmm.2014.1648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/29/2014] [Indexed: 12/23/2022] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC) plays key roles in erythropoiesis; haploinsufficiency of SPARC is implicated in the progression of the 5q- syndrome. However, the role of SPARC in other subtypes of myelodysplastic syndrome (MDS) is not fully understood, particularly in the del(5q) type with a complex karyotype, which has a high risk to transform into acute myeloid leukemia (AML). In the present study, we investigated the role of SPARC in the proliferation and apoptosis of SKM-1 cells, an acute myeloid leukemia cell line transformed from an MDS cell line. SKM-1 cells were infected with SPARC-RNAi-LV or NC-GFP-LV lentivirus. Apoptosis and cell cycle profiling were assessed by flow cytometry, and cell proliferation was evaluated by MTS assay. The mRNA and protein expression levels of SPARC, p53, caspase-3, caspase-9 and Fas were detected by RT-PCR, real-time PCR and western blot assay. The SPARC shRNA constructed by us led to a significant reduction in SPARC expression in SKM-1 cells. SPARC knockdown inhibited the proliferation of SKM-1 cells by inducing cell cycle arrest at the G1/G0 phase and apoptosis. SPARC knockdown elevated the expression of p53, caspase-9, caspase-3 and Fas at both the mRNA and protein levels. SPARC silencing inhibited the growth of AML transformed from MDS by activating p53-induced apoptosis and cell cycle arrest. These data indicate that SPARC acts as an oncogene in transformed MDS/AML and is a potential therapeutic target in MDS/AML.
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Affiliation(s)
- Qing Nian
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Qing Xiao
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jing Luo
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Li-Ping Chen
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ze-Song Yang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lin Liu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Sato T, Oshima T, Yamamoto N, Yamada T, Hasegawa S, Yukawa N, Numata K, Kunisaki C, Tanaka K, Shiozawa M, Yoshikawa T, Akaike M, Rino Y, Imada T, Masuda M. Clinical significance of SPARC gene expression in patients with gastric cancer. J Surg Oncol 2013; 108:364-8. [PMID: 24018911 DOI: 10.1002/jso.23425] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/06/2013] [Indexed: 12/22/2022]
Abstract
PURPOSE Secreted protein acidic and rich in cysteine (SPARC) is one of the first known matricellular proteins that modulates interactions between cells and extracellular matrix. Recent studies investigated the clinical significance of SPARC gene expression in the development, progression, and metastasis of cancer. The present study examined the relations of the relative expression of the SPARC gene to clinicopathological factors and overall survival in patients with gastric cancer. METHODS We studied surgical specimens of cancer tissue and adjacent normal mucosa obtained from 227 patients with previously untreated gastric cancer. The relative expression levels of SPARC mRNA in cancer tissue and in adjacent normal mucosa were measured by quantitative real-time, reverse-transcription polymerase chain reaction. RESULTS The relative expression level of the SPARC gene was higher in cancer tissue than in adjacent normal mucosa. High expression levels of the SPARC gene were related to serosal invasion (P = 0.046). Overall survival at 5 years differed significantly between patients with high SPARC gene expression and those with low expression (P = 0.006). CONCLUSIONS Overexpression of the SPARC gene may be a useful independent predictor of outcomes in patients with gastric cancer.
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Affiliation(s)
- Tsutomu Sato
- Department of Surgery, Yokohama City University, Yokohama-shi, Kanagawa-ken, Japan
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21
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Herrera VL, Ponce LR, Ruiz-Opazo N. Multiple susceptibility loci for radiation-induced mammary tumorigenesis in F2[Dahl S x R]-intercross rats. PLoS One 2013; 8:e72143. [PMID: 23967281 PMCID: PMC3743793 DOI: 10.1371/journal.pone.0072143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/06/2013] [Indexed: 02/07/2023] Open
Abstract
Although two major breast cancer susceptibility genes, BRCA1 and BRCA2, have been identified accounting for 20% of breast cancer genetic risk, identification of other susceptibility genes accounting for 80% risk remains a challenge due to the complex, multi-factorial nature of breast cancer. Complexity derives from multiple genetic determinants, permutations of gene-environment interactions, along with presumptive low-penetrance of breast cancer predisposing genes, and genetic heterogeneity of human populations. As with other complex diseases, dissection of genetic determinants in animal models provides key insight since genetic heterogeneity and environmental factors can be experimentally controlled, thus facilitating the detection of quantitative trait loci (QTL). We therefore, performed the first genome-wide scan for loci contributing to radiation-induced mammary tumorigenesis in female F2-(Dahl S x R)-intercross rats. Tumorigenesis was measured as tumor burden index (TBI) after induction of rat mammary tumors at forty days of age via 127Cs-radiation. We observed a spectrum of tumor latency, size-progression, and pathology from poorly differentiated ductal adenocarcinoma to fibroadenoma, indicating major effects of gene-environment interactions. We identified two mammary tumorigenesis susceptibility quantitative trait loci (Mts-QTLs) with significant linkage: Mts-1 on chromosome-9 (LOD-2.98) and Mts-2 on chromosome-1 (LOD-2.61), as well as two Mts-QTLs with suggestive linkage: Mts-3 on chromosome-5 (LOD-1.93) and Mts-4 on chromosome-18 (LOD-1.54). Interestingly, Chr9-Mts-1, Chr5-Mts-3 and Chr18-Mts-4 QTLs are unique to irradiation-induced mammary tumorigenesis, while Chr1-Mts-2 QTL overlaps with a mammary cancer susceptibility QTL (Mcs 3) reported for 7,12-dimethylbenz-[α]antracene (DMBA)-induced mammary tumorigenesis in F2[COP x Wistar-Furth]-intercross rats. Altogether, our results suggest at least three distinct susceptibility QTLs for irradiation-induced mammary tumorigenesis not detected in genetic studies of chemically-induced and hormone-induced mammary tumorigenesis. While more study is needed to identify the specific Mts-gene variants, elucidation of specific variant(s) could establish causal gene pathways involved in mammary tumorigenesis in humans, and hence novel pathways for therapy.
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Affiliation(s)
- Victoria L Herrera
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
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22
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Liang Y, Liu C, Luan XZ, Leung KS, Chan TM, Xu ZB, Zhang H. Sparse logistic regression with a L1/2 penalty for gene selection in cancer classification. BMC Bioinformatics 2013; 14:198. [PMID: 23777239 PMCID: PMC3718705 DOI: 10.1186/1471-2105-14-198] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 05/30/2013] [Indexed: 11/21/2022] Open
Abstract
Background Microarray technology is widely used in cancer diagnosis. Successfully identifying gene biomarkers will significantly help to classify different cancer types and improve the prediction accuracy. The regularization approach is one of the effective methods for gene selection in microarray data, which generally contain a large number of genes and have a small number of samples. In recent years, various approaches have been developed for gene selection of microarray data. Generally, they are divided into three categories: filter, wrapper and embedded methods. Regularization methods are an important embedded technique and perform both continuous shrinkage and automatic gene selection simultaneously. Recently, there is growing interest in applying the regularization techniques in gene selection. The popular regularization technique is Lasso (L1), and many L1 type regularization terms have been proposed in the recent years. Theoretically, the Lq type regularization with the lower value of q would lead to better solutions with more sparsity. Moreover, the L1/2 regularization can be taken as a representative of Lq (0 <q < 1) regularizations and has been demonstrated many attractive properties. Results In this work, we investigate a sparse logistic regression with the L1/2 penalty for gene selection in cancer classification problems, and propose a coordinate descent algorithm with a new univariate half thresholding operator to solve the L1/2 penalized logistic regression. Experimental results on artificial and microarray data demonstrate the effectiveness of our proposed approach compared with other regularization methods. Especially, for 4 publicly available gene expression datasets, the L1/2 regularization method achieved its success using only about 2 to 14 predictors (genes), compared to about 6 to 38 genes for ordinary L1 and elastic net regularization approaches. Conclusions From our evaluations, it is clear that the sparse logistic regression with the L1/2 penalty achieves higher classification accuracy than those of ordinary L1 and elastic net regularization approaches, while fewer but informative genes are selected. This is an important consideration for screening and diagnostic applications, where the goal is often to develop an accurate test using as few features as possible in order to control cost. Therefore, the sparse logistic regression with the L1/2 penalty is effective technique for gene selection in real classification problems.
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Affiliation(s)
- Yong Liang
- Faculty of Information Technology & State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China.
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Guijarro-Muñoz I, Sánchez A, Martínez-Martínez E, García JM, Salas C, Provencio M, Alvarez-Vallina L, Sanz L. Gene expression profiling identifies EPHB4 as a potential predictive biomarker in colorectal cancer patients treated with bevacizumab. Med Oncol 2013; 30:572. [PMID: 23579861 DOI: 10.1007/s12032-013-0572-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/04/2013] [Indexed: 12/21/2022]
Abstract
The anti-VEGF monoclonal antibody bevacizumab was approved in 2004 as a first-line treatment for metastatic colorectal cancer (CRC) in combination with chemotherapy and provided proof of principle for antiangiogenic therapy. However, there is no biomarker that can help to select patients who may benefit from bevacizumab in order to improve cost-effectiveness and therapeutic outcomes. The aim of this study was to compare gene expression profiles in CRC patients treated with bevacizumab who responded to the treatment with those that did not respond, in an effort to identify potential predictive biomarkers. RNA isolated from formalin-fixed paraffin-embedded tumor specimens of patients treated with bevacizumab was subjected to gene expression analysis with quantitative RT-PCR arrays profiling 84 genes implicated in the angiogenic process. Data were validated at the protein level using immunohistochemistry. We identified a gene, EPHB4, whose expression was significantly increased in nonresponders (p = 0.048, Mann-Whitney test). Furthermore, high EPHB4 tumor levels were associated with decreased median overall survival (16 months vs 48, Log-rank p = 0.012). This was not observed in a control group of CRC patients treated only with chemotherapy, suggesting that EPHB4 constitutes a potential predictive biomarker and not a mere prognostic one. These data support the notion of a potential synergy between EPHB4-EFNB2 and VEGF-VEGFR pathways, making patients with high EPHB4 expression more resistant to VEGF blocking. Therefore, determination of EPHB4 levels in CRC samples could be useful for the prediction of response to bevacizumab.
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Affiliation(s)
- Irene Guijarro-Muñoz
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro Majadahonda, Joaquin Rodrigo 2, 28222 Madrid, Spain
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24
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The Lipid Transfer Protein StarD7: Structure, Function, and Regulation. Int J Mol Sci 2013; 14:6170-86. [PMID: 23507753 PMCID: PMC3634439 DOI: 10.3390/ijms14036170] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/17/2013] [Accepted: 02/22/2013] [Indexed: 02/06/2023] Open
Abstract
The steroidogenic acute regulatory (StAR) protein-related lipid transfer (START) domain proteins constitute a family of evolutionarily conserved and widely expressed proteins that have been implicated in lipid transport, metabolism, and signaling. The 15 well-characterized mammalian START domain-containing proteins are grouped into six subfamilies. The START domain containing 7 mRNA encodes StarD7, a member of the StarD2/phosphatidylcholine transfer protein (PCTP) subfamily, which was first identified as a gene overexpressed in a choriocarcinoma cell line. Recent studies show that the StarD7 protein facilitates the delivery of phosphatidylcholine to the mitochondria. This review summarizes the latest advances in StarD7 research, focusing on the structural and biochemical features, protein-lipid interactions, and mechanisms that regulate StarD7 expression. The implications of the role of StarD7 in cell proliferation, migration, and differentiation are also discussed.
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25
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Wang JJ, Fang ZX, Ye HM, You P, Cai MJ, Duan HB, Wang F, Zhang ZY. Clinical significance of overexpressed cyclin-dependent kinase subunits 1 and 2 in esophageal carcinoma. Dis Esophagus 2013; 26:729-36. [PMID: 23301842 PMCID: PMC4797631 DOI: 10.1111/dote.12013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mammalian cyclin-dependent kinase subunit (Cks) family has two members, Cks1 and Cks2. Overexpression of Cks1 and Cks2 has been reported to be associated with high aggressiveness and poor prognosis in several malignancies, including prostate and hepatocellular carcinomas. However, whether Cks1 and Cks2 are overexpressed in esophageal carcinoma remains uncharacterized. To investigate whether overexpression of the Cks family is clinically relevant in esophageal carcinoma, and whether expression patterns of Cks1 and Cks2 can serve as biomarkers for esophageal carcinoma. Real-time quantitative reverse transcription polymerase chain reaction, immunohistochemistry, and Western blot analyses were applied to detect the expression of Cks1 and Cks2 at the mRNA and protein levels, respectively. The associations between Cks1 or Cks2 expressions and clinical features and p27(kip1) expressions in esophageal carcinoma were analyzed. Comparing with the adjacent noncancerous tissues, esophageal carcinoma exhibited elevated expression of Cks1 in 58% cases at the mRNA level and 54% cases at the protein level, and elevated expression of Cks2 in 65% cases at the mRNA level and 61% cases at the protein level, respectively. The expressions of both Cks1 and Cks2 were negatively associated with the p27(kip1) protein level in the tumor tissues. Furthermore, overexpression of Cks1 and Cks2 in esophageal carcinoma was closely associated with poor pathological features of esophageal carcinoma, including higher histologic grade of tumor, regional lymph nodes invasion, and neoplastic embolus. Overexpression of Cks1 and Cks2 is associated with the aggressive tumor behaviors of esophageal carcinoma. Further efforts are needed to determine whether overexpression of Cks1 and Cks2 can serve as novel biomarkers for esophageal carcinoma.
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Affiliation(s)
- Jia-Jia Wang
- Center for Clinical Laboratory, Zhongshan Hospital, Fujian Medical University, Xiamen University, Xiamen, China
| | - Zan-Xi Fang
- Center for Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Hui-Ming Ye
- Center for Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Pan You
- Center for Clinical Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Min-Jing Cai
- Center for Clinical Laboratory, Zhongshan Hospital, Fujian Medical University, Xiamen University, Xiamen, China
| | - Hong-Bing Duan
- Department of Chest Surgery, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Fen Wang
- Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Zhong-Ying Zhang
- Center for Clinical Laboratory, Zhongshan Hospital, Fujian Medical University, Xiamen University, Xiamen, China
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Chen J, Shi D, Liu X, Fang S, Zhang J, Zhao Y. Targeting SPARC by lentivirus-mediated RNA interference inhibits cervical cancer cell growth and metastasis. BMC Cancer 2012; 12:464. [PMID: 23050783 PMCID: PMC3488331 DOI: 10.1186/1471-2407-12-464] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/08/2012] [Indexed: 12/20/2022] Open
Abstract
Background Secreted protein acidic and rich in cysteine (SPARC), a calcium-binding matricellular glycoprotein, is implicated in the progressions of some cancers. However, no information has been available to date regarding the function of SPARC in cervical cancer cell growth and metastasis. Methods In this study, we isolated and established high invasive subclones and low invasive subclones from human cervical cancer cell lines HeLa and SiHa by the limited dilution method. Real-time q-RT-PCR, Western Blot and ICC were performed to investigate SPARC mRNA and protein expressions in high invasive subclones and low invasive subclones. Then lentivirus vector with SPARC shRNA was constructed and infected the highly invasive subclones. Real-time q-RT-PCR, Western Blot and ICC were also performed to investigate the changes of SPARC expression after viral infection. In functional assays, effects of SPARC knockdown on the biological behaviors of cervical cancer cells were investigated. The mechanisms of SPARC in cervical cancer proliferation, apoptosis and invasion were also researched. Results SPARC was over-expressed in the highly invasive subclones compared with the low invasive subclones. Knockdown of SPARC significantly suppressed cervical cancer cell proliferation, and induced cell cycle arrest at the G1/G0 phase through the p53/p21 pathway, also caused cell apoptosis accompanied by the decreased ratio of Bcl-2/Bax, and inhibited cell invasion and metastasis accompanied by down-regulated MMP2 and MMP9 expressions and up-regulated E-cadherin expression. Conclusion SPARC is related to the invasive phenotype of cervical cancer cells. Knockdown of SPARC significantly suppresses cervical cancer cell proliferation, induces cell apoptosis and inhibits cell invasion and metastasis. SPARC as a promoter improves cervical cancer cell growth and metastasis.
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Affiliation(s)
- Jie Chen
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan 250012, China
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27
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Flores-Martín J, Rena V, Márquez S, Panzetta-Dutari GM, Genti-Raimondi S. StarD7 knockdown modulates ABCG2 expression, cell migration, proliferation, and differentiation of human choriocarcinoma JEG-3 cells. PLoS One 2012; 7:e44152. [PMID: 22952907 PMCID: PMC3430668 DOI: 10.1371/journal.pone.0044152] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/30/2012] [Indexed: 11/18/2022] Open
Abstract
Background StAR-related lipid transfer domain containing 7 (StarD7) is a member of the START-domain protein family whose function still remains unclear. Our data from an explorative microarray assay performed with mRNAs from StarD7 siRNA-transfected JEG-3 cells indicated that ABCG2 (ATP-binding cassette sub-family G member 2) was one of the most abundantly downregulated mRNAs. Methodology/Principal Findings Here, we have confirmed that knocking down StarD7 mRNA lead to a decrease in the xenobiotic/lipid transporter ABCG2 at both the mRNA and protein levels (−26.4% and −41%, p<0.05, at 48 h of culture, respectively). Also a concomitant reduction in phospholipid synthesis, bromodeoxyuridine (BrdU) uptake and 3H-thymidine incorporation was detected. Wound healing and transwell assays revealed that JEG-3 cell migration was significantly diminished (p<0.05). Conversely, biochemical differentiation markers such as human chorionic gonadotrophin β-subunit (βhCG) protein synthesis and secretion as well as βhCG and syncytin-1 mRNAs were increased approximately 2-fold. In addition, desmoplakin immunostaining suggested that there was a reduction of intercellular desmosomes between adjacent JEG-3 cells after knocking down StarD7. Conclusions/Significance Altogether these findings provide evidence for a role of StarD7 in cell physiology indicating that StarD7 modulates ABCG2 multidrug transporter level, cell migration, proliferation, and biochemical and morphological differentiation marker expression in a human trophoblast cell model.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 2
- ATP-Binding Cassette Transporters/genetics
- ATP-Binding Cassette Transporters/metabolism
- Biomarkers/metabolism
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation
- Choriocarcinoma/genetics
- Choriocarcinoma/pathology
- Chorionic Gonadotropin, beta Subunit, Human/genetics
- Chorionic Gonadotropin, beta Subunit, Human/metabolism
- Gene Expression Regulation, Neoplastic
- Gene Knockdown Techniques
- Gene Products, env/genetics
- Gene Products, env/metabolism
- Gene Silencing
- Giant Cells/metabolism
- Humans
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Phospholipids/biosynthesis
- Pregnancy Proteins/genetics
- Pregnancy Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Up-Regulation/genetics
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Affiliation(s)
- Jésica Flores-Martín
- Centro de Investigaciones en Bioquímica Clínica e Inmunología-Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Viviana Rena
- Centro de Investigaciones en Bioquímica Clínica e Inmunología-Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sebastián Márquez
- Centro de Investigaciones en Bioquímica Clínica e Inmunología-Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Graciela M. Panzetta-Dutari
- Centro de Investigaciones en Bioquímica Clínica e Inmunología-Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Susana Genti-Raimondi
- Centro de Investigaciones en Bioquímica Clínica e Inmunología-Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- * E-mail:
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Han X, Fang X, Lou X, Hua D, Ding W, Foltz G, Hood L, Yuan Y, Lin B. Silencing SOX2 induced mesenchymal-epithelial transition and its expression predicts liver and lymph node metastasis of CRC patients. PLoS One 2012; 7:e41335. [PMID: 22912670 PMCID: PMC3422347 DOI: 10.1371/journal.pone.0041335] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 06/25/2012] [Indexed: 12/15/2022] Open
Abstract
SOX2 is an important stem cell marker and plays important roles in development and carcinogenesis. However, the role of SOX2 in Epithelial-Mesenchymal Transition has not been investigated. We demonstrated, for the first time, that SOX2 is involved in the Epithelial-Mesenchymal Transition (EMT) process as knock downof SOX2 in colorectal cancer (CRC) SW620 cells induced a Mesenchymal-Epithelial Transition (MET) process with recognized changes in the expression of key genes involved in the EMT process including E-cadherin and vimentin. In addition, we provided a link between SOX2 activity and the WNT pathway by showing that knock down of SOX2 reduced the WNT pathway activity in colorectal cancer (CRC) cells. We further demonstrated that SOX2 is involved in cell migration and invasion in vitro and in metastasis in vivo for CRC cells, and that the process might be mediated through the MMP2 activity. Finally, an IHC analysis of 44 cases of colorectal cancer patients suggested that SOX2 is a prognosis marker for metastasis of colorectal cancers.
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Affiliation(s)
- Xu Han
- Systems Biology Division, Zhejiang–California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xuefeng Fang
- Department of Medical Oncology, The 2nd Hospital of Zhejiang University Medical College, Hangzhou, Zhejiang, China
| | - Xiaoyan Lou
- Systems Biology Division, Zhejiang–California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dasong Hua
- Systems Biology Division, Zhejiang–California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenchao Ding
- Systems Biology Division, Zhejiang–California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Gregory Foltz
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, Washington, United States of America
| | - Leroy Hood
- The Institute for Systems Biology, Seattle, Washington, United States of America
| | - Ying Yuan
- Department of Medical Oncology, The 2nd Hospital of Zhejiang University Medical College, Hangzhou, Zhejiang, China
- * E-mail: (YY); (BL)
| | - Biaoyang Lin
- Systems Biology Division, Zhejiang–California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (YY); (BL)
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Chen J, Wang M, Xi B, Xue J, He D, Zhang J, Zhao Y. SPARC is a key regulator of proliferation, apoptosis and invasion in human ovarian cancer. PLoS One 2012; 7:e42413. [PMID: 22879971 PMCID: PMC3411787 DOI: 10.1371/journal.pone.0042413] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 07/05/2012] [Indexed: 01/03/2023] Open
Abstract
Background Secreted protein acidic and rich in cysteine (SPARC), a calcium-binding matricellular glycoprotein, is implicated in the progression of many cancers. In this study, we investigated the expression and function of SPARC in ovarian cancer. Methods cDNA microarray analysis was performed to compare gene expression profiles of the highly invasive and the low invasive subclones derived from the SKOV3 human ovarian cancer cell line. Immunohistochemistry (IHC) staining was performed to investigate SPARC expression in a total of 140 ovarian tissue specimens. In functional assays, effects of SPARC knockdown on the biological behavior of ovarian cancer cells were investigated. The mechanisms of SPARC in ovarian cancer proliferation, apoptosis and invasion were also researched. Results SPARC was overexpressed in the highly invasive subclone compared with the low invasive subclone. High SPARC expression was associated with high stage, low differentiation, lymph node metastasis and poor prognosis of ovarian cancer. Knockdown of SPARC expression significantly suppressed ovarian cancer cell proliferation, induced cell apoptosis and inhibited cell invasion and metastasis. Conclusion SPARC is overexpressed in highly invasive subclone and ovarian cancer tissues and plays an important role in ovarian cancer growth, apoptosis and metastasis.
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Affiliation(s)
- Jie Chen
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan, China
| | - Mei Wang
- Pharmacy Department, Shandong Provincial Hospital affiliated to Shandong University, Jinan, China
| | - Bo Xi
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan, China
| | - Jian Xue
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan, China
| | - Dan He
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan, China
| | - Jie Zhang
- Central Laboratory, Shandong Provincial Hospital affiliated to Shandong University, Jinan, China
- * E-mail: (JZ); (YZ)
| | - Yueran Zhao
- Central Laboratory, Shandong Provincial Hospital affiliated to Shandong University, Jinan, China
- * E-mail: (JZ); (YZ)
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Meding S, Balluff B, Elsner M, Schöne C, Rauser S, Nitsche U, Maak M, Schäfer A, Hauck SM, Ueffing M, Langer R, Höfler H, Friess H, Rosenberg R, Walch A. Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer. J Pathol 2012; 228:459-70. [PMID: 22430872 DOI: 10.1002/path.4021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 03/05/2012] [Accepted: 03/09/2012] [Indexed: 01/08/2023]
Abstract
Regional lymph node metastasis negatively affects prognosis in colon cancer patients. The molecular processes leading to regional lymph node metastasis are only partially understood and proteomic markers for metastasis are still scarce. Therefore, a tissue-based proteomic approach was undertaken for identifying proteins associated with regional lymph node metastasis. Two complementary tissue-based proteomic methods have been employed. MALDI imaging was used for identifying small proteins (≤25 kDa) in situ and label-free quantitative proteomics was used for identifying larger proteins. A tissue cohort comprising primary colon tumours without metastasis (UICC II, pN0, n = 21) and with lymph node metastasis (UICC III, pN2, n = 33) was analysed. Subsequent validation of identified proteins was done by immunohistochemical staining on an independent tissue cohort consisting of primary colon tumour specimens (n = 168). MALDI imaging yielded ten discriminating m/z species, and label-free quantitative proteomics 28 proteins. Two MALDI imaging-derived candidate proteins (FXYD3 and S100A11) and one from the label-free quantitative proteomics (GSTM3) were validated on the independent tissue cohort. All three markers correlated significantly with regional lymph node metastasis: FXYD3 (p = 0.0110), S100A11 (p = 0.0071), and GSTM3 (p = 0.0173). FXYD3 and S100A11 were more highly expressed in UICC II patient tumour tissues. GSTM3 was more highly expressed in UICC III patient tumour tissues. By our tissue-based proteomic approach, we could identify a large panel of proteins which are associated with regional lymph node metastasis and which have not been described so far. Here we show that novel markers for regional lymph metastasis can be identified by MALDI imaging or label-free quantitative proteomics and subsequently validated on an independent tissue cohort.
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Affiliation(s)
- Stephan Meding
- Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
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Liu H, Zhang H, Jiang X, Ma Y, Xu Y, Feng S, Liu F. Knockdown of Secreted Protein Acidic and Rich in Cysteine (SPARC) Expression Diminishes Radiosensitivity of Glioma Cells. Cancer Biother Radiopharm 2011; 26:705-15. [DOI: 10.1089/cbr.2011.0987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Haiyan Liu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
- Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu Province, China
| | - Haowen Zhang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Xin Jiang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Yan Ma
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Yuanyuan Xu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Shuang Feng
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Fenju Liu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
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Larkin SET, Holmes S, Cree IA, Walker T, Basketter V, Bickers B, Harris S, Garbis SD, Townsend PA, Aukim-Hastie C. Identification of markers of prostate cancer progression using candidate gene expression. Br J Cancer 2011; 106:157-65. [PMID: 22075945 PMCID: PMC3251845 DOI: 10.1038/bjc.2011.490] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Metastatic prostate cancer (PCa) has no curative treatment options. Some forms of PCa are indolent and slow growing, while others metastasise quickly and may prove fatal within a very short time. The basis of this variable prognosis is poorly understood, despite considerable research. The aim of this study was to identify markers associated with the progression of PCa. METHODS Artificial neuronal network analysis combined with data from literature and previous work produced a panel of putative PCa progression markers, which were used in a transcriptomic analysis of 29 radical prostatectomy samples and correlated with clinical outcome. RESULTS Statistical analysis yielded seven putative markers of PCa progression, ANPEP, ABL1, PSCA, EFNA1, HSPB1, INMT and TRIP13. Two data transformation methods were utilised with only markers that were significant in both selected for further analysis. ANPEP and EFNA1 were significantly correlated with Gleason score. Models of progression co-utilising markers ANPEP and ABL1 or ANPEP and PSCA had the ability to correctly predict indolent or aggressive disease, based on Gleason score, in 89.7% and 86.2% of cases, respectively. Another model of TRIP13 expression in combination with preoperative PSA level and Gleason score was able to correctly predict recurrence in 85.7% of cases. CONCLUSION This proof of principle study demonstrates a novel association of carcinogenic and tumourigenic gene expression with PCa stage and prognosis.
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Affiliation(s)
- S E T Larkin
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michaels Building, White Swan Road, Portsmouth, PO1 2DT, UK.
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Menghi F, Orzan FN, Eoli M, Farinotti M, Maderna E, Pisati F, Bianchessi D, Valletta L, Lodrini S, Galli G, Anghileri E, Pellegatta S, Pollo B, Finocchiaro G. DNA microarray analysis identifies CKS2 and LEPR as potential markers of meningioma recurrence. Oncologist 2011; 16:1440-50. [PMID: 21948653 DOI: 10.1634/theoncologist.2010-0249] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Meningiomas are the most frequent intracranial tumors. Surgery can be curative, but recurrences are possible. We performed gene expression analyses and loss of heterozygosity (LOH) studies looking for new markers predicting the recurrence risk. We analyzed expression profiles of 23 meningiomas (10 grade I, 10 grade II, and 3 grade III) and validated the data using quantitative polymerase chain reaction (qPCR). We performed LOH analysis on 40 meningiomas, investigating chromosomal regions on 1p, 9p, 10q, 14q, and 22q. We found 233 and 268 probe sets to be significantly down- and upregulated, respectively, in grade II or III meningiomas. Genes downregulated in high-grade meningiomas were overrepresented on chromosomes 1, 6, 9, 10, and 14. Based on functional enrichment analysis, we selected LIM domain and actin binding 1 (LIMA1), tissue inhibitor of metalloproteinases 3 (TIMP3), cyclin-dependent kinases regulatory subunit 2 (CKS2), leptin receptor (LEPR), and baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) for validation using qPCR and confirmed their differential expression in the two groups of tumors. We calculated ΔCt values of CKS2 and LEPR and found that their differential expression (C-L index) was significantly higher in grade I than in grade II or III meningiomas (p < .0001). Interestingly, the C-L index of nine grade I meningiomas from patients who relapsed in <5 years was significantly lower than in grade I meningiomas from patients who did not relapse. These findings indicate that the C-L index may be relevant to define the progression risk in meningioma patients, helping guide their clinical management. A prospective analysis on a larger number of cases is warranted.
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Affiliation(s)
- Francesca Menghi
- Unit of Molecular Neuro-Oncology, Fondazione Istituto Neurologico Besta, Milan, Italy
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Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW. Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. FASEB J 2011; 25:1449-60. [PMID: 21228220 DOI: 10.1096/fj.10-172205] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The connection between intestinal microbiota and host physiology is increasingly becoming recognized. The details of this dynamic interaction, however, remain to be explored. Toll-like receptor 2 (Tlr2) is important for its role in bacterial recognition, intestinal inflammation, and obesity-related metabolic changes. Therefore, we sought to determine the epigenomic and metagenomic consequences of Tlr2 deficiency in the colonic mucosa of mice to gain insights into biological pathways that shape the interface between the gut microbiota and the mammalian host. Colonic mucosa from wild type (WT) and Tlr2(-/-) C57BL/6 mice was interrogated by microarrays specific for DNA methylation and gene expression. The mucosal microbiome was studied by next-generation pyrosequencing of bacterial 16S rRNA. The expression of genes involved in immune processes was significantly modified by the absence of Tlr2, a number of which correlated with DNA methylation changes. The epigenomic and transcriptomic modifications associated with alteration in mucosal microbial composition. Several bacterial species, including members of the Firmicutes were significantly different in abundance between WT and Tlr2(-/-) animals. This manuscript highlights the intimate interrelationships between expression of immune-related genes and immunity pathways in the host with compositional and functional differences of the mammalian microbiome.
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Affiliation(s)
- Richard Kellermayer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030-2399, USA.
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Peng J, Wang Z, Chen W, Ding Y, Wang H, Huang H, Huang W, Cai S. Integration of genetic signature and TNM staging system for predicting the relapse of locally advanced colorectal cancer. Int J Colorectal Dis 2010; 25:1277-85. [PMID: 20706727 DOI: 10.1007/s00384-010-1043-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2010] [Indexed: 02/04/2023]
Abstract
PURPOSE To identify potential genetic markers in treated stage II-III colorectal cancer patients and predict 3-year tumor relapse using statistical models based on important clinical factors and significant genetic markers. METHODS Gene expression profiling by cDNA-mediated Annealing, Selection, extension and Ligation assay was performed in a prospectively collected 95 stage II-III colorectal cancer patients with Fluorouracil-based adjuvant chemotherapy. We studied the gene expression level of 502 genes for patients with different outcomes. The prognostic effect of genetic signature was evaluated in multivariate analysis. We further integrated the genetic signature to clinical Classification of Malignant Tumors (TNM) staging system for predicting of 3-year tumor relapse. RESULTS An 8-gene signature was identified to well discriminate patients with different treatment outcomes. An integrated risk factor, which including 8-gene signature and TNM staging has been developed. ROC curve revealed that our integrated risk factor was better than genetic signature or current sixth edition TNM staging system alone. CONCLUSIONS Our 8-gene signature was promising in predicting 3-year disease-free survival rate for locally advanced colorectal cancer. The integrated risk factor, which combining genetic signature with clinical TNM staging system may further improve the outcome prediction.
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Affiliation(s)
- Junjie Peng
- Department of Colorectal Surgery, Cancer Hospital, Fudan University, 270 Dong An Road, Shanghai, People's Republic of China
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Skrzypczak M, Goryca K, Rubel T, Paziewska A, Mikula M, Jarosz D, Pachlewski J, Oledzki J, Ostrowsk J. Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability. PLoS One 2010; 5. [PMID: 20957034 PMCID: PMC2948500 DOI: 10.1371/journal.pone.0013091] [Citation(s) in RCA: 276] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 09/08/2010] [Indexed: 12/16/2022] Open
Abstract
Background Clinical progression of colorectal cancers (CRC) may occur in parallel with distinctive signaling alterations. We designed multidirectional analyses integrating microarray-based data with biostatistics and bioinformatics to elucidate the signaling and metabolic alterations underlying CRC development in the adenoma-carcinoma sequence. Methodology/Principal Findings Studies were performed on normal mucosa, adenoma, and carcinoma samples obtained during surgery or colonoscopy. Collections of cryostat sections prepared from the tissue samples were evaluated by a pathologist to control the relative cell type content. The measurements were done using Affymetrix GeneChip HG-U133plus2, and probe set data was generated using two normalization algorithms: MAS5.0 and GCRMA with least-variant set (LVS). The data was evaluated using pair-wise comparisons and data decomposition into singular value decomposition (SVD) modes. The method selected for the functional analysis used the Kolmogorov-Smirnov test. Expressional profiles obtained in 105 samples of whole tissue sections were used to establish oncogenic signaling alterations in progression of CRC, while those representing 40 microdissected specimens were used to select differences in KEGG pathways between epithelium and mucosa. Based on a consensus of the results obtained by two normalization algorithms, and two probe set sorting criteria, we identified 14 and 17 KEGG signaling and metabolic pathways that are significantly altered between normal and tumor samples and between benign and malignant tumors, respectively. Several of them were also selected from the raw microarray data of 2 recently published studies (GSE4183 and GSE8671). Conclusion/Significance Although the proposed strategy is computationally complex and labor–intensive, it may reduce the number of false results.
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Affiliation(s)
- Magdalena Skrzypczak
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Tymon Rubel
- Laboratory of Bioinformatics and Systems Biology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michal Mikula
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Dorota Jarosz
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jacek Pachlewski
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Janusz Oledzki
- Department of Colorectal Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowsk
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
- * E-mail:
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Inoue M, Senju S, Hirata S, Ikuta Y, Hayashida Y, Irie A, Harao M, Imai K, Tomita Y, Tsunoda T, Furukawa Y, Ito T, Nakamura Y, Baba H, Nishimura Y. Identification of SPARC as a candidate target antigen for immunotherapy of various cancers. Int J Cancer 2010; 127:1393-403. [PMID: 20063317 DOI: 10.1002/ijc.25160] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To establish efficient anticancer immunotherary, it is important to identify tumor-associated antigens (TAAs) directing the immune system to attack cancer. A genome-wide cDNA microarray analysis identified that secreted protein acidic and rich in cysteine (SPARC) gene is overexpressed in the gastric, pancreatic and colorectal cancer tissues but not in their noncancerous counterparts. This study attempted to identify HLA-A24 (A*2402)-restricted and SPARC-derived CTL epitopes. We previously identified H-2K(d)-restricted and SPARC-derived CTL epitope peptides in BALB/c mice, of which H-2K(d)-binding peptide motif is comparable with that of HLA-A24 binding peptides. By using these peptides, we tried to induce HLA-A24 (A*2402)-restricted and SPARC-reactive human CTLs and demonstrated an antitumor immune response. The SPARC-A24-1(143-151) (DYIGPCKYI) and SPARC-A24-4(225-234) (MYIFPVHWQF) peptides-reactive CTLs were successfully induced from peripheral blood mononuclear cells by in vitro stimulation with these two peptides in HLA-A24 (A*2402) positive healthy donors and cancer patients, and these CTLs exhibited cytotoxicity specific to cancer cells expressing both SPARC and HLA-A24 (A*2402). Furthermore, the adoptive transfer of the SPARC-specific CTLs could inhibit the tumor growth in nonobese diabetic/severe combined immunodeficient mice bearing human cancer cells expressing both HLA-A24 (A*2402) and SPARC. These findings suggest that SPARC is a potentially useful target candidate for cancer immunotherapy.
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Affiliation(s)
- Mitsuhiro Inoue
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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Comparability of microarray data between amplified and non amplified RNA in colorectal carcinoma. J Biomed Biotechnol 2009; 2009:837170. [PMID: 19826639 PMCID: PMC2760353 DOI: 10.1155/2009/837170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 05/28/2009] [Accepted: 07/13/2009] [Indexed: 11/18/2022] Open
Abstract
Microarray analysis reaches increasing popularity during the investigation of prognostic gene clusters in oncology. The standardisation of technical procedures will be essential to compare various datasets produced by different research groups. In several projects the amount of available tissue is limited. In such cases the preamplification of RNA might be necessary prior to microarray hybridisation. To evaluate the comparability of microarray results generated either by amplified or non amplified RNA we isolated RNA from colorectal cancer samples (stage UICC IV) following tumour tissue enrichment by macroscopic manual dissection (CMD). One part of the RNA was directly labelled and hybridised to GeneChips (HG-U133A, Affymetrix), the other part of the RNA was amplified according to the “Eberwine” protocol and was then hybridised to the microarrays. During unsupervised hierarchical clustering the samples were divided in groups regarding the RNA pre-treatment and 5.726 differentially expressed genes were identified. Using independent microarray data of 31 amplified vs. 24 non amplified RNA samples from colon carcinomas (stage UICC III) in a set of 50 predictive genes we validated the amplification bias. In conclusion microarray data resulting from different pre-processing regarding RNA pre-amplification can not be compared within one analysis.
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Arnold SA, Brekken RA. SPARC: a matricellular regulator of tumorigenesis. J Cell Commun Signal 2009; 3:255-73. [PMID: 19809893 PMCID: PMC2778590 DOI: 10.1007/s12079-009-0072-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 09/14/2009] [Indexed: 12/11/2022] Open
Abstract
Although many clinical studies have found a correlation of SPARC expression with malignant progression and patient survival, the mechanisms for SPARC function in tumorigenesis and metastasis remain elusive. The activity of SPARC is context- and cell-type-dependent, which is highlighted by the fact that SPARC has shown seemingly contradictory effects on tumor progression in both clinical correlative studies and in animal models. The capacity of SPARC to dictate tumorigenic phenotype has been attributed to its effects on the bioavailability and signaling of integrins and growth factors/chemokines. These molecular pathways contribute to many physiological events affecting malignant progression, including extracellular matrix remodeling, angiogenesis, immune modulation and metastasis. Given that SPARC is credited with such varied activities, this review presents a comprehensive account of the divergent effects of SPARC in human cancers and mouse models, as well as a description of the potential mechanisms by which SPARC mediates these effects. We aim to provide insight into how a matricellular protein such as SPARC might generate paradoxical, yet relevant, tumor outcomes in order to unify an apparently incongruent collection of scientific literature.
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Affiliation(s)
- Shanna A Arnold
- Hamon Center for Therapeutic Oncology Research, Division of Surgical Oncology and Departments of Surgery and Pharmacology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593 USA
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Kos K, Wong S, Tan B, Gummesson A, Jernas M, Franck N, Kerrigan D, Nystrom FH, Carlsson LM, Randeva HS, Pinkney JH, Wilding JP. Regulation of the fibrosis and angiogenesis promoter SPARC/osteonectin in human adipose tissue by weight change, leptin, insulin, and glucose. Diabetes 2009; 58:1780-8. [PMID: 19509023 PMCID: PMC2712789 DOI: 10.2337/db09-0211] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Matricellular Secreted Protein, Acidic and Rich in Cysteine (SPARC), originally discovered in bone as osteonectin, is a mediator of collagen deposition and promotes fibrosis. Adipose tissue collagen has recently been found to be linked with metabolic dysregulation. Therefore, we tested the hypothesis that SPARC in human adipose tissue is influenced by glucose metabolism and adipokines. RESEARCH DESIGN AND METHODS Serum and adipose tissue biopsies were obtained from morbidly obese nondiabetic subjects undergoing bariatric surgery and lean control subjects for analysis of metabolic markers, SPARC, and various cytokines (RT-PCR). Additionally, 24 obese subjects underwent a very-low-calorie diet of 1,883 kJ (450 kcal)/day for 16 weeks and serial subcutaneous-abdominal-adipose tissue (SCAT) biopsies (weight loss: 28 +/- 3.7 kg). Another six lean subjects underwent fast-food-based hyperalimentation for 4 weeks (weight gain: 7.2 +/- 1.6 kg). Finally, visceral adipose tissue explants were cultured with recombinant leptin, insulin, and glucose, and SPARC mRNA and protein expression determined by Western blot analyses. RESULTS SPARC expression in human adipose tissue correlated with fat mass and was higher in SCAT. Weight loss induced by very-low-calorie diet lowered SPARC expression by 33% and increased by 30% in adipose tissue of subjects gaining weight after a fast-food diet. SPARC expression was correlated with leptin independent of fat mass and correlated with homeostasis model assessment-insulin resistance. In vitro experiments showed that leptin and insulin potently increased SPARC production dose dependently in visceral adipose tissue explants, while glucose decreased SPARC protein. CONCLUSIONS Our data suggest that SPARC expression is predominant in subcutaneous fat and its expression and secretion in adipose tissue are influenced by fat mass, leptin, insulin, and glucose. The profibrotic effects of SPARC may contribute to metabolic dysregulation in obesity.
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Affiliation(s)
- Katrina Kos
- Diabetes and Endocrinology Research Unit, Clinical Sciences Centre, University Hospital Aintree, Liverpool, U.K
| | - Steve Wong
- Diabetes and Endocrinology Research Unit, Clinical Sciences Centre, University Hospital Aintree, Liverpool, U.K
| | - Bee Tan
- Endocrinology and Metabolism Group, Warwick Medical School, University of Warwick, U.K
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Jernas
- Department of Molecular and Clinical Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niclas Franck
- Department of Medical and Health Sciences, Division of Cardiovascular Medicine, Linköping University, Linköping, Sweden
| | - David Kerrigan
- Department of Surgery, University Hospital Aintree, Liverpool, U.K
| | - Fredrik H. Nystrom
- Department of Medical and Health Sciences, Division of Cardiovascular Medicine, Linköping University, Linköping, Sweden
| | - Lena M.S. Carlsson
- Department of Molecular and Clinical Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Harpal S. Randeva
- Endocrinology and Metabolism Group, Warwick Medical School, University of Warwick, U.K
| | | | - John P.H. Wilding
- Diabetes and Endocrinology Research Unit, Clinical Sciences Centre, University Hospital Aintree, Liverpool, U.K
- Corresponding author: John P.H. Wilding,
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Erickson HS, Albert PS, Gillespie JW, Rodriguez-Canales J, Marston Linehan W, Pinto PA, Chuaqui RF, Emmert-Buck MR. Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples. Nat Protoc 2009; 4:902-22. [PMID: 19478806 DOI: 10.1038/nprot.2009.61] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen-related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 h.
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Affiliation(s)
- Heidi S Erickson
- Pathogenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
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Podhajcer OL, Benedetti LG, Girotti MR, Prada F, Salvatierra E, Llera AS. The role of the matricellular protein SPARC in the dynamic interaction between the tumor and the host. Cancer Metastasis Rev 2008; 27:691-705. [PMID: 18542844 DOI: 10.1007/s10555-008-9146-7] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tumor growth is essentially the result of an evolving cross-talk between malignant and surrounding stromal cells (fibroblasts, endothelial cells and inflammatory cells). This heterogeneous mass of extracellular matrix and intermingled cells interact through cell-cell and cell-matrix contacts. Malignant cells also secrete soluble proteins that reach neighbor stromal cells, forcing them to provide the soil on which they will grow and metastasize. Different studies including expression array analysis identified the matricellular protein SPARC as a marker of poor prognosis in different cancer types. Further evidence demonstrated that high SPARC levels are often associated with the most aggressive and highly metastatic tumors. Here we describe the most recent evidence that links SPARC with human cancer progression, the controversy regarding its role in certain human cancers and the physiological processes in which SPARC is involved: epithelial-mesenchymal transition, immune surveillance and angiogenesis. Its relevance as a potential target in cancer therapy is also discussed.
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Affiliation(s)
- Osvaldo L Podhajcer
- Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir, University of Buenos Aires, National Council for Scientific and Technological Research (CONICET), Buenos Aires, Argentina.
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A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. J Mol Med (Berl) 2008; 87:211-24. [PMID: 19066834 DOI: 10.1007/s00109-008-0419-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 11/04/2008] [Accepted: 11/06/2008] [Indexed: 10/21/2022]
Abstract
We present a novel approach for microarray analysis of RNA derived from microdissected cells of routinely formalin-fixed and paraffin-embedded (FFPE) cancer resection specimens. Subsequent to RNA sample preparation and hybridization to standard GeneChips (Affymetrix), RNA samples yielded 36.43 +/- 9.60% (FFPE), 49.90 +/- 4.43% (fresh-frozen), and 53.9% (cell line) present calls. Quality control parameters and Q-RT-PCR validation demonstrated reliability of results. Microarray datasets of FFPE samples were informative and comparable to those of fresh-frozen samples. A systematic measurement difference of differentially processed tissues was eliminated by a correction step for comparative unsupervised data analysis of fresh-frozen and FFPE samples. Within FFPE samples, unsupervised clustering analyses clearly distinguished between normal and malignant tissues as well as to further separate tumor samples according to histological World Health Organization (WHO) subtypes. In summary, our approach represents a major step towards integration of microarrays into retrospective studies and enables further investigation of the relevance of microarray analysis for clinico-pathological diagnostics.
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Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S. Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC SYSTEMS BIOLOGY 2008; 2:106. [PMID: 19055846 PMCID: PMC2628381 DOI: 10.1186/1752-0509-2-106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 12/05/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND Prostate cancer is a leading cause of death in the male population, therefore, a comprehensive study about the genes and the molecular networks involved in the tumoral prostate process becomes necessary. In order to understand the biological process behind potential biomarkers, we have analyzed a set of 57 cDNA microarrays containing approximately 25,000 genes. RESULTS Principal Component Analysis (PCA) combined with the Maximum-entropy Linear Discriminant Analysis (MLDA) were applied in order to identify genes with the most discriminative information between normal and tumoral prostatic tissues. Data analysis was carried out using three different approaches, namely: (i) differences in gene expression levels between normal and tumoral conditions from an univariate point of view; (ii) in a multivariate fashion using MLDA; and (iii) with a dependence network approach. Our results show that malignant transformation in the prostatic tissue is more related to functional connectivity changes in their dependence networks than to differential gene expression. The MYLK, KLK2, KLK3, HAN11, LTF, CSRP1 and TGM4 genes presented significant changes in their functional connectivity between normal and tumoral conditions and were also classified as the top seven most informative genes for the prostate cancer genesis process by our discriminant analysis. Moreover, among the identified genes we found classically known biomarkers and genes which are closely related to tumoral prostate, such as KLK3 and KLK2 and several other potential ones. CONCLUSION We have demonstrated that changes in functional connectivity may be implicit in the biological process which renders some genes more informative to discriminate between normal and tumoral conditions. Using the proposed method, namely, MLDA, in order to analyze the multivariate characteristic of genes, it was possible to capture the changes in dependence networks which are related to cell transformation.
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Affiliation(s)
- André Fujita
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Luciana Rodrigues Gomes
- Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748, São Paulo-SP, 05508-900, Brazil
| | - João Ricardo Sato
- Mathematics, Computation and Cognition Center, Universidade Federal do ABC, Rua Santa Adélia, 166 – Santo André, 09210-170, Brazil
| | - Rui Yamaguchi
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Carlos Eduardo Thomaz
- Department of Electrical Engineering, Centro Universitário da FEI, Av. Humberto de Alencar Castelo Branco, 3972 – São Bernardo do Campo, 09850-901, Brazil
| | - Mari Cleide Sogayar
- Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748, São Paulo-SP, 05508-900, Brazil
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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Upregulation of the cycline kinase subunit CKS2 increases cell proliferation rate in gastric cancer. J Cancer Res Clin Oncol 2008; 135:761-9. [PMID: 19034516 DOI: 10.1007/s00432-008-0510-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Accepted: 10/27/2008] [Indexed: 01/25/2023]
Abstract
PURPOSE CKS2 was identified as an upregulated gene in gastric cancer via our DNA microarray. This study was to verify the upregulation of CKS2 in many gastric cancer patients and to examine the CKS2-mediated cellular response. METHODS CKS2 upregulation was analyzed using reverse transcriptase PCR, real-time PCR, and immunohistochemical and clinicopathological analyses. GFP-CKS2 or CKS2-siRNA was used to analyze the cellular localization and proliferation. RESULTS The strong upregulation of mRNA and protein levels of CKS2 was identified. In CKS2-overexpressing cells, tumor suppressor p53 and p21(cip1) were downregulated and cell growth was increased. In contrast, CKS2-siRNA-transfected cells showed an increased tumor suppressor expression and decreased cell growth. CONCLUSIONS We showed that CKS2 was significantly upregulated in gastric cancers and a high level of CKS2 was highly correlated with histologic tumor differentiation and pathological grade of the tumor size, lymph node, and metastasis stage. We suggest that the cell cycle regulator CKS2 might be deeply involved in gastric cancer progression.
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SPARC in cancer biology: its role in cancer progression and potential for therapy. Drug Resist Updat 2008; 11:231-46. [PMID: 18849185 DOI: 10.1016/j.drup.2008.08.005] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 08/25/2008] [Accepted: 08/26/2008] [Indexed: 02/06/2023]
Abstract
The ability to effectively target a tumor to achieve complete regression and cure is the ultimate goal that drives our need to better understand tumor biology. Recently, SPARC has generated considerable interest as a multi-faceted protein that belongs to a family of matricellular proteins. It functions not only to modulate cell-cell and cell-matrix interactions, but its de-adhesive and growth inhibitory properties in non-transformed cells have led to studies to assess its role in cancer. Its divergent actions reflect the complexity of this protein, because in certain types of cancers, such as melanomas and gliomas, SPARC is associated with a highly aggressive tumor phenotype, while in others, mainly ovarian, neuroblastomas and colorectal cancers, SPARC may function as a tumor suppressor. Recent studies have also demonstrated a role for SPARC in sensitizing therapy-resistant cancers. Here, the role of SPARC in cancer progression and its potential application in cancer therapy is discussed.
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Podhajcer OL, Benedetti L, Girotti MR, Prada F, Salvatierra E, Llera AS. The role of the matricellular protein SPARC in the dynamic interaction between the tumor and the host. Cancer Metastasis Rev 2008; 27:523-37. [PMID: 18459035 DOI: 10.1007/s10555-008-9135-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Tumor growth is essentially the result of an evolving cross-talk between malignant and surrounding stromal cells (fibroblasts, endothelial cells and inflammatory cells). This heterogeneous mass of extracellular matrix and intermingled cells interact through cell-cell and cell-matrix contacts. Malignant cells also secrete soluble proteins that reach neighbor stromal cells, forcing them to provide the soil on which they will grow and metastasize. Different studies including expression array analysis identified the matricellular protein SPARC as a marker of poor prognosis in different cancer types. Further evidence demonstrated that high SPARC levels are often associated with the most aggressive and highly metastatic tumors. Here we describe the most recent evidence that links SPARC with human cancer progression, the controversy regarding its role in certain human cancers and the physiological processes in which SPARC is involved: epithelial-mesenchymal transition, immune surveillance and angiogenesis. Its relevance as a potential target in cancer therapy is also discussed.
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Affiliation(s)
- Osvaldo L Podhajcer
- Laboratory of Molecular and Cellular Therapy, Fundacion Instituto Leloir, University of Buenos Aires, National Council for Scientific and Technological Research (CONICET), Buenos Aires, Argentina.
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Fabris S, Mosca L, Todoerti K, Cutrona G, Lionetti M, Intini D, Matis S, Colombo M, Agnelli L, Gentile M, Spriano M, Callea V, Festini G, Molica S, Lambertenghi Deliliers G, Morabito F, Ferrarini M, Neri A. Molecular and transcriptional characterization of 17p loss in B-cell chronic lymphocytic leukemia. Genes Chromosomes Cancer 2008; 47:781-93. [DOI: 10.1002/gcc.20579] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Bustin SA. Molecular medicine, gene-expression profiling and molecular diagnostics: putting the cart before the horse. Biomark Med 2008; 2:201-7. [DOI: 10.2217/17520363.2.3.201] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Stephen A Bustin
- Institute of Cell & Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK; 3rd Floor, Alexandra Wing Royal London Hospital, London, E1 1BB, UK
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