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Wu Y, Shi Z, Zhou X, Zhang P, Yang X, Ding J, Wu H. scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information. Commun Biol 2024; 7:923. [PMID: 39085477 PMCID: PMC11291681 DOI: 10.1038/s42003-024-06626-3] [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: 10/30/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and the three-dimensional (3D) structure of chromatin. However, accurately predicting cell cycle phases based on scHi-C data remains a formidable challenge. Here, we present scHiCyclePred, a prediction model that integrates multiple feature sets to leverage scHi-C data for predicting cell cycle phases. scHiCyclePred extracts 3D chromatin structure features by incorporating multi-scale interaction information. The comparative analysis illustrates that scHiCyclePred surpasses existing methods such as Nagano_method and CIRCLET across various metrics including accuracy (ACC), F1 score, Precision, Recall, and balanced accuracy (BACC). In addition, we evaluate scHiCyclePred against the previously published CIRCLET using the dataset of complex tissues (Liu_dataset). Experimental results reveal significant improvements with scHiCyclePred exhibiting improvements of 0.39, 0.52, 0.52, and 0.39 over the CIRCLET in terms of ACC, F1 score, Precision, and Recall metrics, respectively. Furthermore, we conduct analyses on three-dimensional chromatin dynamics and gene features during the cell cycle, providing a more comprehensive understanding of cell cycle dynamics through chromatin structure. scHiCyclePred not only offers insights into cell biology but also holds promise for catalyzing breakthroughs in disease research. Access scHiCyclePred on GitHub at https:// github.com/HaoWuLab-Bioinformatics/ scHiCyclePred .
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Affiliation(s)
- Yingfu Wu
- School of Software, Shandong University, Jinan, Shandong, China
- Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong, China
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhenqi Shi
- School of Software, Shandong University, Jinan, Shandong, China
| | - Xiangfei Zhou
- School of Software, Shandong University, Jinan, Shandong, China
| | - Pengyu Zhang
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiuhui Yang
- School of Software, Shandong University, Jinan, Shandong, China
| | - Jun Ding
- Department of Medicine, Meakins-Christie Laboratories, McGill University, Montreal, QC, Canada.
| | - Hao Wu
- School of Software, Shandong University, Jinan, Shandong, China.
- Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong, China.
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Bu F, Nie H, Zhu X, Wu T, Lin K, Zhao J, Huang J. A signature of 18 immune-related gene pairs to predict the prognosis of pancreatic cancer patients. IMMUNITY INFLAMMATION AND DISEASE 2020; 8:713-726. [PMID: 33128857 PMCID: PMC7654420 DOI: 10.1002/iid3.363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/25/2022]
Abstract
Pancreatic cancer is one of the most lethal malignancies. With the promising prospects conveyed by immunotherapy in cancers, we aimed to construct an immune‐related gene pairs (IRGPs) signature to predict the prognosis of pancreatic cancer patients. We downloaded clinical and transcriptional data of pancreatic cancer patients from The Cancer Genome Atlas data set as the training group and GSE57495 data set as the verification group. We filtered immune‐related transcriptional data by IMMPORT. With the assistance of lasso penalized Cox regression, we constructed our prognostic IRGPs signature and divided all samples into high‐/low‐risk groups by receiver operating characteristic curve for further comparisons. The comparisons between high‐ and low‐risk groups including survival rate, multivariate, and univariate Cox proportional‐hazards analysis, infiltration of immune cells, and Gene Set Enrichment Analysis (GSEA). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) are facilitated to analyze the proceedings in which our IRGPs signature may involve in. The results revealed that 18 IRGPs were defined as our prognostic signature. The prognostic value of this IRGPs signature was verified from the GSE57495 data set. We further demonstrated the independent prognostic value of this IRGPs signature. The contents of six immune cells between high‐/low‐risk groups were different, which was associated with the progression of diverse cancers. Results from GO, KEGG, and GSEA revealed that this IRGPs signature was involved in extracellular space, immune response, cancer pathways, cation channel, and gated channel activities. Evidently, this IRGPs signature will provide remarkable value for the therapy of pancreatic cancer patients.
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Affiliation(s)
- Fanqin Bu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Han Nie
- Department of Vascular Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaojian Zhu
- Zhongshan School of Medicine, Research Center of the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Ting Wu
- Infection Department of Guixi Traditional Chinese Medicine Hospital, Guixi, Jiangxi, China
| | - Kang Lin
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jiefeng Zhao
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jun Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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3
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Sriram K, Salmerón C, Wiley SZ, Insel PA. GPCRs in pancreatic adenocarcinoma: Contributors to tumour biology and novel therapeutic targets. Br J Pharmacol 2020; 177:2434-2455. [PMID: 32060895 DOI: 10.1111/bph.15028] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/06/2020] [Accepted: 01/20/2020] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer has one of the highest mortality rates (5-year survival ~9%) among cancers. Pancreatic adenocarcinoma (PAAD) is the most common (>80%) and the most lethal type of pancreatic cancer. A need exists for new approaches to treat pancreatic adenocarcinoma. GPCRs, the largest family of cell-surface receptors and drug targets, account for ~35% of approved drugs. Recent studies have revealed roles for GPCRs in PAAD cells and cells in the tumour micro-environment. This review assesses current information regarding GPCRs in PAAD by summarizing omics data for GPCRs expression in PAAD. The PAAD "GPCRome" includes GPCRs with approved agents, thereby offering potential for their repurposing/repositioning. We then reviewed the evidence for functional roles of specific GPCRs in PAAD. We also highlight gaps in understanding the contribution of GPCRs to PAAD biology and identify several GPCRs that may be novel therapeutic targets for future work in search of GPCR-targeted drugs to treat PAAD tumours.
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Affiliation(s)
- Krishna Sriram
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Cristina Salmerón
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Shu Z Wiley
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Paul A Insel
- Department of Pharmacology, University of California San Diego, La Jolla, California.,Department of Medicine, University of California San Diego, La Jolla, California
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Hara M, Takeba Y, Iiri T, Ohta Y, Ootaki M, Watanabe M, Watanabe D, Koizumi S, Otsubo T, Matsumoto N. Vasoactive intestinal peptide increases apoptosis of hepatocellular carcinoma by inhibiting the cAMP/Bcl-xL pathway. Cancer Sci 2018; 110:235-244. [PMID: 30390393 PMCID: PMC6317926 DOI: 10.1111/cas.13861] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
Vasoactive intestinal peptide (VIP) is a modulator of inflammatory responses. VIP receptors are expressed in several tumor types, such as colorectal carcinoma. The study described herein was conducted to confirm the presence of VIP and its receptors (VPAC1 and VPAC2) in surgically resected hepatocellular carcinoma (HCC) tissues and in the HCC cell line Huh7. The mechanism responsible for apoptosis of HCC cells was then examined because VIP treatment (10-10 M) significantly suppressed proliferation of Huh7 cells. In examining apoptosis-related proteins, we found caspase-3 to be significantly increased and Bcl-xL and cyclic AMP (cAMP) response element-binding protein (CREB) to be significantly decreased in Huh7 cells cultured with VIP. Furthermore, the CREB level and phosphorylation were reduced. These effects were reversed by the addition of VIP receptor antagonist or cAMP antagonist Rp-cAMPS. Pretreatment with cAMP analogue blocked the increased apoptosis, suggesting that VIP induces apoptosis via a PKA-independent signaling mechanism. Our data indicate that VIP prevents the progression of HCC by apoptosis through the cAMP/Bcl-xL pathway.
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Affiliation(s)
- Masaki Hara
- Division of Gastroenterology and Hepatology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yuko Takeba
- Department of Pharmacology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Taroh Iiri
- Department of Pharmacology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yuki Ohta
- Department of Pharmacology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masanori Ootaki
- Department of Pharmacology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Minoru Watanabe
- Experimental Animals Institution, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Daiki Watanabe
- Department of Pharmacology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Satoshi Koizumi
- Division of Gastroenterological Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Takehito Otsubo
- Division of Gastroenterological Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Matsumoto
- Department of Pharmacology, St. Marianna University School of Medicine, Kawasaki, Japan
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Xi T, Zhang G. Integrated analysis of tumor differentiation genes in pancreatic adenocarcinoma. PLoS One 2018; 13:e0193427. [PMID: 29596435 PMCID: PMC5875763 DOI: 10.1371/journal.pone.0193427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/09/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tumor differentiation is an important process in the development of cancer. It is valuable to identify key differentiation related genes in the prognosis and therapy of pancreatic adenocarcinoma. METHODS The mRNA expression data were downloaded from the Cancer Genome Atlas database. Then, differentially expressed tumor differentiation related genes were identified. Additionally, Gene Ontology functional categories and Kyoto Encyclopedia of Genes and Genomes biochemical pathway was used to explore the function. In addition, receiver operating characteristic and survival analysis were carried out to assess the diagnosis and prognosis value. Finally, the electronic validation of selected tumor differentiation related genes was performed. RESULTS A total of 932 genes were identified. Among which, 8 genes including JUB, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, TCTA and SSTR1 were differentially expressed in all different tumor differentiation grades. Functional analysis revealed those genes between highly differentiated and other differentiation were remarkably enriched in pancreatic adenocarcinoma and cell cycle pathway. Finally, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, BCL2L1, E2F1 and RAC1 were associated with the survival time of pancreatic adenocarcinoma patient. Among these genes, JUB, ERLIN1, FAM110B, MCM2 and BCL2L1 also had a diagnosis value for pancreatic adenocarcinoma. Additionally, the expression trend of JUB, HMGA2 and MCM2 was increased along with the tumor differentiation grades. And the expression trend of FAM110B was decreased along with the tumor differentiation grades. The electronic validation result was consistent with the bioinformatics analysis. CONCLUSIONS 12 tumor differentiation related genes including JUB, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, TCTA, SSTR1, BCL2L1, E2F1, RAC1 and STAT1 played crucial roles in the differentiation of pancreatic adenocarcinoma.
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Affiliation(s)
- Ting Xi
- Department of Gastroenterology, First People’s Hospital of Liaocheng, Liaocheng, Shandong Province, China
- * E-mail:
| | - Guizhi Zhang
- Department of Gastroenterology, Second People’s Hospital of Liaocheng, Liaocheng, Shandong Province, China
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Wiley SZ, Sriram K, Liang W, Chang SE, French R, McCann T, Sicklick J, Nishihara H, Lowy AM, Insel PA. GPR68, a proton-sensing GPCR, mediates interaction of cancer-associated fibroblasts and cancer cells. FASEB J 2018; 32:1170-1183. [PMID: 29092903 PMCID: PMC5892729 DOI: 10.1096/fj.201700834r] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022]
Abstract
The microenvironment of pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense fibrotic stroma (desmoplasia) generated by pancreatic cancer-associated fibroblasts (CAFs) derived from pancreatic stellate cells (PSCs) and pancreatic fibroblasts (PFs). Using an unbiased GPCRomic array approach, we identified 82 G-protein-coupled receptors (GPCRs) commonly expressed by CAFs derived from 5 primary PDAC tumors. Compared with PSCs and PFs, CAFs have increased expression of GPR68 (a proton-sensing GPCR), with the results confirmed by immunoblotting, The Cancer Genome Atlas data, and immunohistochemistry of PDAC tumors. Co-culture of PSCs with PDAC cells, or incubation with TNF-α, induced GPR68 expression. GPR68 activation (by decreasing the extracellular pH) enhanced IL-6 expression via a cAMP/PKA/cAMP response element binding protein signaling pathway. Knockdown of GPR68 by short interfering RNA diminished low pH-induced production of IL-6 and enhancement of PDAC cell proliferation by CAF conditioned media. CAFs from other gastrointestinal cancers also express GPR68. PDAC cells thus induce expression by CAFs of GPR68, which senses the acidic microenvironment, thereby increasing production of fibrotic markers and IL-6 and promoting PDAC cell proliferation. CAF-expressed GPR68 is a mediator of low-pH-promoted regulation of the tumor microenvironments, in particular to PDAC cell-CAF interaction and may be a novel therapeutic target for pancreatic and perhaps other types of cancers.-Wiley, S. Z., Sriram, K., Liang, W., Chang, S. E., French, R., McCann, T., Sicklick, J., Nishihara, H., Lowy, A. M., Insel, P. A. GPR68, a proton-sensing GPCR, mediates interaction of cancer-associated fibroblasts and cancer cells.
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Affiliation(s)
- Shu Z. Wiley
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Krishna Sriram
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Wenjing Liang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Qilu Hospital of Shandong University, Jinan, China
| | - Sarah E. Chang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Randall French
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Thalia McCann
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Jason Sicklick
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
- Division of Surgical Oncology, Department of Surgery, University of California, San Diego, La Jolla, California, USA
| | - Hiroshi Nishihara
- Division of Clinical Cancer Genomics, Hokkaido Cancer Center, Shiroishi-ku, Sapporo, Japan
| | - Andrew M. Lowy
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
- Division of Surgical Oncology, Department of Surgery, University of California, San Diego, La Jolla, California, USA
| | - Paul A. Insel
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
- Department of Medicine, University of California, San Diego, La Jolla, USA
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7
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Pedraza-Arévalo S, Hormaechea-Agulla D, Gómez-Gómez E, Requena MJ, Selth LA, Gahete MD, Castaño JP, Luque RM. Somatostatin receptor subtype 1 as a potential diagnostic marker and therapeutic target in prostate cancer. Prostate 2017; 77:1499-1511. [PMID: 28905400 DOI: 10.1002/pros.23426] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/23/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is a highly prevalent neoplasia that is strongly influenced by the endocrine system. Somatostatin (SST) and its five receptors (sst1-5 encoded by SSTR1-5 genes) comprise a pleiotropic system present in most endocrine-related cancers, some of which are successfully treated with SST analogs. Interestingly, it has been reported that SSTR1 is overexpressed in PCa, but its regulation, functional role, and clinical implications are still poorly known. METHODS PCa specimens (n = 52) from biopsies and control prostates from cystoprostatectomies (n = 12), as well as in silico databases were used to evaluate SSTR1 and miRNAs expression. In vitro studies in 22Rv1 PCa cells were implemented to explore the regulation of SSTR1/sst1 by different miRNAs, and to evaluate the consequences of SSTR1/sst1 overexpression, silencing and/or activation [with the specific BIM-23926 sst1 agonist (IPSEN)] on cell-proliferation, migration, signaling-pathways, and androgen-signaling. RESULTS We found that SSTR1 is overexpressed in multiple cohorts of PCa samples, as compared with normal prostate tissues, wherein it correlates with androgen receptor (AR) expression, and appears to be associated with aggressiveness (metastasis). Furthermore, our data revealed that SSTR1/sst1 expression might be regulated by specific miRNAs in PCa, including miR-24, which is downregulated in PCa samples and correlates inversely with SSTR1 expression. In vitro studies indicated that treatment with the BIM-23926 sst1 agonist, as well as SSTR1 overexpression, decreased, whereas SSTR1 silencing increased, cell-proliferation in 22Rv1 cells, likely through the regulation of PI3K/AKT-CCND3 signaling-pathway. Importantly, sst1 action was also able to modulate androgen/AR activity, and reduced PSA secretion from PCa cell lines. CONCLUSIONS Altogether, our results indicate that SSTR1 is overexpressed in PCa, where it can exert a relevant pathophysiological role by decreasing cell-proliferation and PSA secretion. Therefore, sst1, possibly in combination with miR-24, could be used as a novel tool to explore therapeutic targets in PCa.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Cell Line, Tumor
- Humans
- Male
- Middle Aged
- Molecular Targeted Therapy
- Prostatic Neoplasms, Castration-Resistant/diagnosis
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/therapy
- Receptors, Somatostatin/biosynthesis
- Receptors, Somatostatin/genetics
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Affiliation(s)
- Sergio Pedraza-Arévalo
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Daniel Hormaechea-Agulla
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Urology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - María J Requena
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Urology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, SA, 5005, Australia
| | - Manuel D Gahete
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Justo P Castaño
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Raul M Luque
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, Universidad de Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
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Yu J, Wilson J, Taylor L, Polgar P. DNA microarray and signal transduction analysis in pulmonary artery smooth muscle cells from heritable and idiopathic pulmonary arterial hypertension subjects. J Cell Biochem 2015; 116:386-97. [PMID: 25290246 PMCID: PMC4391824 DOI: 10.1002/jcb.24987] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/22/2014] [Indexed: 12/22/2022]
Abstract
Pulmonary arterial hypertension (PAH) is characterized by increased pulmonary vascular smooth muscle contraction and proliferation. Here, we analyze genome-wide mRNA expression in human pulmonary arterial smooth muscle cells (HPASMC) isolated from three control, three hereditary (HPAH), and three idiopathic PAH (IPAH) subjects using the Affymetrix Human Gene ST 1.0 chip. The microarray analysis reveals the expression of 537 genes in HPAH and 1024 genes in IPAH changed compared with control HPASMC. Among those genes, 227 genes show similar directionality of expression in both HPAH and IPAH HPASMC. Ingenuity™ Pathway Analysis (IPA) suggests that many of those genes are involved in cellular growth/proliferation and cell cycle regulation and that signaling pathways such as the mitotic activators, polo-like kinases, ATM signaling are activated under PAH conditions. Furthermore, the analysis demonstrates downregulated mRNA expression of certain vasoactive receptors such as bradykinin receptor B2 (BKB2R). Using real time PCR, we verified the downregulated BKB2R expression in the PAH cells. Bradykinin-stimulated calcium influx is also decreased in PAH PASMC. IPA also identified transcriptional factors such p53 and Rb as downregulated, and FoxM1 and Myc as upregulated in both HPAH and IPAH HPASMC. The decreased level of phospho-p53 in PAH cells was confirmed with a phospho-protein array; and we experimentally show a dysregulated proliferation of both HPAH and IPAH PASMC. Together, the microarray experiments and bioinformatics analysis highlight an aberrant proliferation and cell cycle regulation in HPASMC from PAH subjects. These newly identified pathways may provide new targets for the treatment of both hereditary and idiopathic PAH.
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MESH Headings
- Antibodies, Phospho-Specific/metabolism
- Case-Control Studies
- Cell Cycle/genetics
- Cell Proliferation
- Cells, Cultured
- Familial Primary Pulmonary Hypertension/genetics
- Familial Primary Pulmonary Hypertension/pathology
- Gene Expression Profiling
- Gene Expression Regulation
- Humans
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Oligonucleotide Array Sequence Analysis
- Phenotype
- Phosphorylation
- Principal Component Analysis
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/physiopathology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Receptor, Angiotensin, Type 1/genetics
- Receptor, Angiotensin, Type 1/metabolism
- Receptor, Bradykinin B2/genetics
- Receptor, Bradykinin B2/metabolism
- Signal Transduction/genetics
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Jun Yu
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Jamie Wilson
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Linda Taylor
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Peter Polgar
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
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9
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Liu SX, Xia ZS, Zhong YQ. Gene therapy in pancreatic cancer. World J Gastroenterol 2014; 20:13343-68. [PMID: 25309069 PMCID: PMC4188890 DOI: 10.3748/wjg.v20.i37.13343] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/29/2013] [Accepted: 06/12/2014] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is a highly lethal disease and notoriously difficult to treat. Only a small proportion of PC patients are eligible for surgical resection, whilst conventional chemoradiotherapy only has a modest effect with substantial toxicity. Gene therapy has become a new widely investigated therapeutic approach for PC. This article reviews the basic rationale, gene delivery methods, therapeutic targets and developments of laboratory research and clinical trials in gene therapy of PC by searching the literature published in English using the PubMed database and analyzing clinical trials registered on the Gene Therapy Clinical Trials Worldwide website (http://www. wiley.co.uk/genmed/ clinical). Viral vectors are main gene delivery tools in gene therapy of cancer, and especially, oncolytic virus shows brighter prospect due to its tumor-targeting property. Efficient therapeutic targets for gene therapy include tumor suppressor gene p53, mutant oncogene K-ras, anti-angiogenesis gene VEGFR, suicide gene HSK-TK, cytosine deaminase and cytochrome p450, multiple cytokine genes and so on. Combining different targets or combination strategies with traditional chemoradiotherapy may be a more effective approach to improve the efficacy of cancer gene therapy. Cancer gene therapy is not yet applied in clinical practice, but basic and clinical studies have demonstrated its safety and clinical benefits. Gene therapy will be a new and promising field for the treatment of PC.
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10
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Somatostatin receptor 1, a novel EBV-associated CpG hypermethylated gene, contributes to the pathogenesis of EBV-associated gastric cancer. Br J Cancer 2013; 108:2557-64. [PMID: 23722468 PMCID: PMC3694244 DOI: 10.1038/bjc.2013.263] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Somatostatin receptor 1 (SSTR1) was preferentially methylated in Epstein-Barr virus (EBV)-positive gastric cancer using promoter methylation array. We aimed to analyse the epigenetic alteration and biological function of SSTR1 in EBV-associated gastric cancer (EBVaGC). METHODS Promoter methylation was examined by combined bisulphite restriction analysis (COBRA) and pyrosequencing. The biological functions of SSTR1 were evaluated by loss- and gain-of-function assays. RESULTS Promoter hypermethylation of SSTR1 was detected in EBV-positive gastric cancer cell lines (AGS-EBV) with SSTR1 transcriptional silence, but not in EBV-negative gastric cancer cell lines with SSTR1 expression. Expression level of SSTR1 was restored in AGS-EBV by exposure to demethylating agent. Moreover, methylation level of SSTR1 was significantly higher in EBV-positive primary gastric cancers compared with EBV-negative gastric cancers (P=0.004). Knock-down of SSTR1 in gastric cancer cell lines (AGS and BGC823) increased cell proliferation and colony formation ability, and promoted G1 to S-phase transition, enhanced cell migration and invasive ability. In contrast, ectopic expression of SSTR1 in gastric cancer cell lines (MKN28 and MGC803) significantly suppressed cell growth in culture conditions and reduced tumour size in nude mice. The tumour suppressive effect of SSTR1 was associated with upregulation of cyclin-dependent kinase inhibitors (p16, p15, p27 and p21); downregulation of oncogenes (MYC and MDM2), key cell proliferation and pro-survival regulators (PI3KR1, AKT, BCL-XL and MET); and inhibition of the migration/invasion-related genes (integrins, MMP1 (matrix metallopeptidase 1), PLAUR (plasminogen activator urokinase receptor) and IL8 (interleukin 8)). CONCLUSION Somatostatin receptor 1 is a novel methylated gene driven by EBV infection in gastric cancer cells and acts as a potential tumour suppressor.
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Jiang P, Smith AD, Li R, Rao JN, Liu L, Donahue JM, Wang JY, Turner DJ. Sphingosine kinase 1 overexpression stimulates intestinal epithelial cell proliferation through increased c-Myc translation. Am J Physiol Cell Physiol 2013; 304:C1187-97. [PMID: 23576579 DOI: 10.1152/ajpcell.00271.2012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sphingosine-1-phosphate (S1P), through mechanisms that are not completely understood, is shown to modulate cellular proliferation, which is critically important for maintaining the integrity of intestinal epithelium. Here, we show that increased S1P promotes proliferation in intestinal epithelial cells. We found that overexpression of sphingosine kinase 1 (SphK1), the rate-limiting enzyme for S1P synthesis, significantly increased cell proliferation and that this occurred through enhanced expression of c-Myc. Further, we found that the increased pattern of expression of c-Myc occurred predominantly due to its increased translation. The overexpressed SphK1 led to increased checkpoint kinase 2 and enhanced HuR phosphorylation which allowed for increased translation of c-Myc mRNA through HuR binding at the 3'-untranslated regions. Our findings demonstrate that S1P modulates intestinal cell proliferation and provides new insights as to the mechanistic actions of SphK1 and S1P in maintaining intestinal epithelial homeostasis.
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Affiliation(s)
- Ping Jiang
- Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA
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The Concept of Divergent Targeting through the Activation and Inhibition of Receptors as a Novel Chemotherapeutic Strategy: Signaling Responses to Strong DNA-Reactive Combinatorial Mimicries. JOURNAL OF SIGNAL TRANSDUCTION 2012; 2012:282050. [PMID: 22523681 PMCID: PMC3317223 DOI: 10.1155/2012/282050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 12/13/2011] [Indexed: 10/28/2022]
Abstract
Recently, we reported the combination of multitargeted ErbB1 inhibitor-DNA damage combi-molecules with OCT in order to downregulate ErbB1 and activate SSTRs. Absence of translation to cell kill was believed to be partially due to insufficient ErbB1 blockage and DNA damage. In this study, we evaluated cell response to molecules that damage DNA more aggressively and induce stronger attenuation of ErbB1 phosphorylation. We used three cell lines expressing low levels (U87MG) or transfected to overexpress wildtype (U87/EGFR) or a variant (U87/EGFRvIII) of ErbB1. The results showed that Iressa ± HN2 and the combi-molecules, ZRBA4 and ZR2003, significantly blocked ErbB1 phosphorylation in U87MG cells. Addition of OCT significantly altered cell cycle distribution. Analysis of the DNA damage response pathway revealed strong upregulation of p53 by HN2 and the combi-molecules. Apoptosis was only induced by a 48 h exposure to HN2. All other treatments resulted in cell necrosis. This is in agreement with Akt-Bad pathway activation and survivin upregulation. Despite strong DNA damaging properties and downregulation of ErbB1 phosphorylation by these molecules, the strongest effect of SSTR activation was on cell cycle distribution. Therefore, any enhanced antiproliferative effects of combining ErbB1 inhibition with SSTR activation must be addressed in the context of cell cycle arrest.
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Balentine CJ, Berger DH, Liu SH, Chen C, Nemunaitis J, Brunicardi FC. Defining the cancer master switch. World J Surg 2011; 35:1738-45. [PMID: 21286716 DOI: 10.1007/s00268-010-0941-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Recent research has focused on signaling cascades and their interactions yielding considerable insight into which genetic pathways are targeted and how they tend to be altered in tumors. Therapeutic interventions now can be designed based on the knowledge of pathways vital to tumor growth and survival. These critical targets for intervention, master switches for cancer, are termed so because the tumor attempts to "flip the switch" in a way that promotes its survival, whereas molecular therapy aims to "switch off" signals important for tumor-related processes. METHODS Literature review. CONCLUSIONS Defining useful targets for therapy depends on identifying pathways that are crucial for tumor growth, survival, and metastasis. Because not all signaling cascades are created equal, selecting master switches or targets for intervention needs to be done in a systematic fashion. This discussion proposes a set of criteria to define what it means to be a cancer master switch and provides examples to illustrate their application.
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Mutation of herpesvirus Saimiri ORF51 glycoprotein specifically targets infectivity to hepatocellular carcinoma cell lines. J Biomed Biotechnol 2010; 2011:785158. [PMID: 21197456 PMCID: PMC3004438 DOI: 10.1155/2011/785158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 10/14/2010] [Accepted: 10/14/2010] [Indexed: 11/18/2022] Open
Abstract
Herpesvirus saimiri (HVS) is a gamma herpesvirus with several properties that make it an amenable gene therapy vector; namely its large packaging capacity, its ability to persist as a nonintegrated episome, and its ability to infect numerous human cell types. We used RecA-mediated recombination to develop an HVS vector with a mutated virion protein. The heparan sulphate-binding region of HVS ORF51 was substituted for a peptide sequence which interacts with somatostatin receptors (SSTRs), overexpressed on hepatocellular carcinoma (HCC) cells. HVS mORF51 showed reduced infectivity in non-HCC human cell lines compared to wild-type virus. Strikingly, HVS mORF51 retained its ability to infect HCC cell lines efficiently. However, neutralisation assays suggest that HVS mORF51 has no enhanced binding to SSTRs. Therefore, mutation of the ORF51 glycoprotein has specifically targeted HVS to HCC cell lines by reducing the infectivity of other cell types; however, the mechanism for this targeting is unknown.
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Huang YW, Luo J, Weng YI, Mutch DG, Goodfellow PJ, Miller DS, Huang THM. Promoter hypermethylation of CIDEA, HAAO and RXFP3 associated with microsatellite instability in endometrial carcinomas. Gynecol Oncol 2010; 117:239-47. [PMID: 20211485 PMCID: PMC2849881 DOI: 10.1016/j.ygyno.2010.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 02/03/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
Abstract
OBJECTIVE DNA promoter methylation is an epigenetic phenomenon for long-term gene silencing during tumorigenesis. The purpose of this study is to identify novel hypermethylated loci associated with clinicopathologic variables in endometrioid endometrial carcinomas. METHODS To find hypermethylated promoter loci, we used differential methylation hybridization coupling with microarray and further validated by combined bisulfite restriction analysis and MassARRAY assay. Methylation levels of candidate loci were corrected with clinicopathologic factors of endometrial carcinomas. RESULTS Increased promoter methylation of CIDE, HAAO and RXFP3 was detected in endometrial carcinomas compared with adjacent normal tissues, and was associated with decreased gene expression of all three genes. In a clinical cohort, promoter hypermethylation on CIDEA, HAAO and RXFP3 was detected in 85, 63 and 71% of endometrial carcinomas, respectively (n=118, P<0.001) compared with uninvolved normal endometrium. Methylation status of CIDEA, HAAO and RXFP3 had significant association with microsatellite instability in tumors (P<0.001). Furthermore, methylation levels of HAAO were further found to relate to disease-free survivals (P=0.034). CONCLUSIONS Hypermethylation of CIDEA, HAAO and RXFP3 promoter regions appears to be a frequent event in endometrial carcinomas. Hypermethylation at these loci is strongly associated with microsatellite instability status. Moreover, HAAO methylation predicts disease-free survival in this cohort of patients with endometrioid endometrial cancer.
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Affiliation(s)
- Yi-Wen Huang
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jingqin Luo
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - Yu-I Weng
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - David G. Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - Paul J. Goodfellow
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - David S. Miller
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tim H.-M. Huang
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Yu X, Zhang Y, Chen C, Yao Q, Li M. Targeted drug delivery in pancreatic cancer. Biochim Biophys Acta Rev Cancer 2009; 1805:97-104. [PMID: 19853645 DOI: 10.1016/j.bbcan.2009.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 10/07/2009] [Accepted: 10/11/2009] [Indexed: 12/16/2022]
Abstract
Effective drug delivery in pancreatic cancer treatment remains a major challenge. Because of the high resistance to chemo and radiation therapy, the overall survival rate for pancreatic cancer is extremely low. Recent advances in drug delivery systems hold great promise for improving cancer therapy. Using liposomes, nanoparticles, and carbon nanotubes to deliver cancer drugs and other therapeutic agents such as siRNA, suicide gene, oncolytic virus, small molecule inhibitor, and antibody has been a success in recent preclinical trials. However, how to improve the specificity and stability of the delivered drug using ligand or antibody directed delivery represent a major problem. Therefore, developing novel, specific, tumor-targeted drug delivery systems is urgently needed for this terrible disease. This review summarizes the current progress on targeted drug delivery in pancreatic cancer and provides important information on potential therapeutic targets for pancreatic cancer treatment.
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Affiliation(s)
- Xianjun Yu
- Michael E. DeBakey Department of Surgery, Molecular Surgeon Research Center, Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Impact of Octreotide and SOM-230 on liver metastasis and hepatic lipidperoxidation in ductal pancreatic adenocarcinoma in Syrian Hamster. Clin Exp Metastasis 2009; 26:719-27. [PMID: 19521786 DOI: 10.1007/s10585-009-9271-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Accepted: 05/12/2009] [Indexed: 01/20/2023]
Abstract
Octreotide is a somatostatin analogue binding on two receptor subtypes. In previous trials Octreotide showed inhibitory effects on tumour growth and liver metastasis in experimental pancreatic cancer. Thus we evaluated whether the new somatostatin analogue SOM-230 binding on 4 receptor subtypes has superior effects on carcinogenesis in pancreatic carcinoma. About 120 Syrian hamsters were randomised into six groups (n = 20): Gr.1: Aqua/Aqua, Gr.2: BOP/Aqua, Gr.3: Aqua/Octreotide, Gr.4: BOP/Octreotide, Gr.5: Aqua/SOM-230, Gr.6: BOP/SOM-230. Tumour groups 2,4,6 subcutaneously received 10 mg/kg body weight N-nitrosobis-2-oxopropylamin (BOP) weekly for 10 weeks, healthy control Gr.1,3,5 were given aqua. In the 17th week therapy started with Octreotide and SOM-230 for 16 weeks, after 32 weeks animals were sacrificed. Pancreas and liver were histopathologically analysed. Hepatic lipidperoxidation was determined by activities of antioxidative enzymes gluthation-peroxidase (GSH-Px) and superoxiddismutase (SOD) as well as concentration of thiobarbituric-acid reactive substances (TBARS). Incidence of liver metastases was 88.2% in Gr.2 (BOP/Aqua), it was decreased in Gr.4 (BOP/Octreo: 40%) and Gr.6 (BOP/SOM-230: 50%) (P < 0.05). Mean number/animal and mean-2-dimensional size of liver metastases did not differ between tumour groups. Comparing GSH-Px-activity in intrametastatic and extrametastatic hepatic tissue revealed a significant increase extrametastatically in Gr.2 (BOP/Aqua) and Gr.6 (BOP/SOM-230). SOD-activity in liver metastases was decreased in Gr.2 (1,801) (P < 0.05) versus Gr.4 (8,304) and Gr.6 (7,038). Intrametastatic TBARS concentration was increased in Gr.2 compared to Gr.4 (BOP/Octreotid) and Gr.6 (BOP/SOM-230) (P < 0.05). Octreotide and SOM-230 equally reduced liver metastasis in ductal pancreatic adenocarcinoma probably by a reduction of lipidperoxidation.
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