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Liu LYD, Chang LY, Kuo WH, Hwa HL, Shyu MK, Chang KJ, Hsieh FJ. In Silico Prediction for Regulation of Transcription Factors onTheir Shared Target Genes Indicates Relevant Clinical Implications in a Breast Cancer Population. Cancer Inform 2012; 11:113-37. [PMID: 22553415 PMCID: PMC3337786 DOI: 10.4137/cin.s8470] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Aberrant transcriptional activities have been documented in breast cancers. Studies often find some transcription factors to be inappropriately regulated and enriched in certain pathological states. The promoter regions of most target genes have binding sites for their transcription factors. An ample of evidence supports their combinatorial effect on their shared target gene expressions. Here, we used a new statistic method, bivariate CID, to predict combinatorial interaction activity between ERα and a transcription factor (E2F1or GATA3 or ERRα) in regulating target gene expression via four regulatory mechanisms. We identified gene sets in three signal transduction pathways perturbed in breast tumors: cell cycle, VEGF, and PDGFRB. Bivariate network analysis revealed several target genes previously implicated in tumor angiogenesis are among the predicted shared targets, including VEGFA, PDGFRB. In summary, our analysis suggests the importance for the multivariate space of an inferred ERα transcriptional regulatory network in breast cancer diagnostic and therapeutic development.
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Affiliation(s)
- Li-Yu D Liu
- Department of Agronomy, Biometry Division, National Taiwan University, Taipei, Taiwan
| | - Li-Yun Chang
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Lin Hwa
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Kwang Shyu
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - King-Jen Chang
- Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Fon-Jou Hsieh
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
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Liu LYD, Chang LY, Kuo WH, Hwa HL, Lin YS, Huang SF, Chen CN, Chang KJ, Hsieh FJ. Major Functional Transcriptome of an Inferred Center Regulator of an ER(-) Breast Cancer Model System. Cancer Inform 2012; 11:87-111. [PMID: 22553414 PMCID: PMC3337785 DOI: 10.4137/cin.s8633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We aimed to find clinically relevant gene activities ruled by the signal transducer and activator of transcription 3 (STAT3) proteins in an ER(-) breast cancer population via network approach. STAT3 is negatively associated with both lymph nodal category and stage. MYC is a component of STAT3 network. MYC and STAT3 may co-regulate gene expressions for Warburg effect, stem cell like phenotype, cell proliferation and angiogenesis. We identified a STAT3 network in silico showing its ability in predicting its target gene expressions primarily for specific tumor subtype, tumor progression, treatment options and prognostic features. The aberrant expressions of MYC and STAT3 are enriched in triple negatives (TN). They promote histological grade, vascularity, metastasis and tumor anti-apoptotic activities. VEGFA, STAT3, FOXM1 and METAP2 are druggable targets. High levels of METAP2, MMP7, IGF2 and IGF2R are unfavorable prognostic factors. STAT3 is an inferred center regulator at early cancer development predominantly in TN.
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Affiliation(s)
- Li-Yu Daisy Liu
- Department of Agronomy, Biometry Division, National Taiwan University, Taipei, Taiwan
| | - Li-Yun Chang
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Lin Hwa
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | | | - Shiu-Feng Huang
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Chiung-Nien Chen
- Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - King-Jen Chang
- Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
- Cheng Ching General Hospital, Taichung, Taiwan
| | - Fon-Jou Hsieh
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
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Alcázar JL, Jurado M. Three-dimensional ultrasound for assessing women with gynecological cancer: A systematic review. Gynecol Oncol 2011; 120:340-6. [DOI: 10.1016/j.ygyno.2010.10.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 10/19/2010] [Indexed: 12/26/2022]
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Tawada K, Ishihara T, Kobayashi A, Yamaguchi T, Tsuyuguchi T, Matsuyama M, Yokosuka O. Quantitative analysis of vascular endothelial growth factor in liver metastases from pancreatic carcinoma as a predictor of chemotherapeutic effect and prognosis. Clin Cancer Res 2008; 14:7438-43. [PMID: 18974391 DOI: 10.1158/1078-0432.ccr-07-4980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE In pancreatic carcinoma, vascular endothelial growth factor (VEGF) expression at the primary site has been suggested to be a prognostic parameter. We quantitatively analyzed VEGF expression in liver metastases from pancreatic carcinoma and examined the correlation among VEGF expression in liver metastases, clinicopathologic factors, and clinical outcome. EXPERIMENTAL DESIGN The subjects consisted of 23 patients with pancreatic adenocarcinoma who had liver metastases and were treated with S-1 and gemcitabine as the first-line treatment. VEGF expression was quantitated by enzyme immunoassay in biopsy specimens of liver metastases and nontumorous liver tissue, and in plasma. In 10 of the 23 patients, VEGF expression was also quantitated in biopsy specimens of the primary pancreatic tumor. All samples were collected before treatment. RESULTS The VEGF level in nontumorous liver tissue was 36.6 +/- 10.0 pg/mg protein versus 376.8 +/- 106.1 pg/mg protein in liver metastases (P = 0.0016). Pretreatment VEGF levels in plasma and in primary pancreatic carcinoma did not correlate with VEGF levels in the corresponding liver metastases. The median VEGF level in liver metastases (138.9 pg/mg protein) was used as the cutoff value between high and low VEGF expression in liver metastases. Patients showing high VEGF expression had a significantly longer progression-free survival and overall survival than patients showing low VEGF expression in liver metastases (P = 0.0219 and P = 0.0074, respectively). CONCLUSIONS Evaluation of VEGF levels in liver metastases might be useful in assessing the prognosis of patients with metastatic pancreatic carcinoma who are under systemic chemotherapy.
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Affiliation(s)
- Katsunobu Tawada
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.
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Alcázar JL. Tumor angiogenesis assessed by three-dimensional power Doppler ultrasound in early, advanced and metastatic ovarian cancer: A preliminary study. Ultrasound Obstet Gynecol 2006; 28:325-9. [PMID: 16906635 DOI: 10.1002/uog.3804] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
OBJECTIVE To evaluate tumor vascularity by three-dimensional power Doppler ultrasound (3D-PDU) in early and advanced stage primary ovarian cancers and in metastatic tumors to the ovary. PATIENTS AND METHODS This was a retrospective analysis of clinical and sonographic data from 49 women with primary ovarian cancers or metastatic tumors to the ovary. All women underwent 3D-PDU prior to surgery. Vascularization index (VI), flow index (FI) and vascularization flow index (VFI) from solid portions or papillary projections in the tumors were calculated using the Virtual Organ Computer-aided AnaLysis (VOCAL(trade mark)) program. Definitive histological diagnosis was obtained in each case. RESULTS Among the 49 women, 10 had stage I primary cancers (five low-malignant potential tumors and five invasive tumors), 26 had advanced stage primary ovarian cancers and 13 had metastatic tumors to the ovary. Mean VI and VFI were significantly higher in advanced stage tumors and metastatic tumors as compared with early stage tumors. No differences in 3D-PDU indices were found between advanced stage and metastatic cancers. CONCLUSIONS Vascular indices derived from 3D-PDU tend to be higher in advanced stage and metastatic ovarian cancers as compared with early stage ovarian tumors.
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Affiliation(s)
- J L Alcázar
- Department of Obstetrics and Gynecology, Clínica Universitaria de Navarra, University of Navarra, Pamplona, Spain.
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Magnon C, Galaup A, Rouffiac V, Opolon P, Connault E, Rosé M, Perricaudet M, Roche A, Germain S, Griscelli F, Lassau N. Dynamic assessment of antiangiogenic therapy by monitoring both tumoral vascularization and tissue degeneration. Gene Ther 2006; 14:108-17. [PMID: 16943854 DOI: 10.1038/sj.gt.3302849] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tumor growth is dependent both on endothelial and tumor cells. The aim of this study was to investigate dynamically whether changes in tumor vasculature implicate tumor tissue degeneration during antiangiogenic therapies. In order to quantify intra-tumor vascularization and necrosis, we have used ultrasound technology. This study has identified essential parameters needed to quantify specifically and sensitively the number of microvessels and the extent of necrosis in xenografted human carcinomas during natural tumor evolution, using contrast-enhanced high-frequency ultrasonography with (HFCDUS) or without (HFUS) color Doppler. We showed that quantification of intra-tumor microvessels between HFCDUS and immunohistochemistry is correlated using an anti-CD31 antibody. Furthermore, quantification of tumor necrosis with HFUS was confirmed by histological examination of hematoxylin-eosin-saffranin-stained sections over the observation period. Subsequently, for the assessment of novel angiogenic inhibitors, HFCDUS and HFUS were used to elucidate the underlying dynamics linking vessel inhibition and tumor eradication. We describe a novel application for HFCDUS/HFUS that constitutes an effective, convenient, and non-invasive method for clinical assessment of angiogenic inhibitors. In conclusion, we showed that tumor cells abruptly became necrotic following an antivascular therapy, whereas untreated tumors were protected from degeneration by a significant blood supply.
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MESH Headings
- Adenoviridae/genetics
- Angiogenesis Inhibitors/genetics
- Angiogenesis Inhibitors/therapeutic use
- Animals
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized
- Bevacizumab
- Breast Neoplasms/blood supply
- Breast Neoplasms/diagnostic imaging
- Breast Neoplasms/drug therapy
- Cell Line, Tumor
- Genetic Therapy/methods
- Genetic Vectors/administration & dosage
- Genetic Vectors/genetics
- Humans
- Mice
- Mice, Nude
- Necrosis
- Neovascularization, Pathologic
- Random Allocation
- Transduction, Genetic/methods
- Ultrasonography, Doppler, Color
- Ultrasonography, Interventional
- Xenograft Model Antitumor Assays
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Affiliation(s)
- C Magnon
- UMR 8121 Vectorologie et transfert de gènes, Institut Gustave Roussy, Villejuif cedex, France.
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Alcázar JL, Mercé LT, García Manero M. Three-dimensional power Doppler vascular sampling: a new method for predicting ovarian cancer in vascularized complex adnexal masses. J Ultrasound Med 2005; 24:689-696. [PMID: 15840800 DOI: 10.7863/jum.2005.24.5.689] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
OBJECTIVE The purpose of this study was to explore the role of a new concept ("vascular sampling") as a third step to discriminate benign and malignant lesions in B-mode and color Doppler sonographically suggestive adnexal masses. METHODS Forty-five women (mean age, 52.3 years; range, 17-82 years) with the diagnosis of complex adnexal masses on B-mode sonography were evaluated using 3-dimensional power Doppler sonography. Four women had bilateral masses. After a morphologic reevaluation was done, color pulsed Doppler sonography was used to obtain flow velocity waveforms, and velocimetric indices were calculated (resistive index, pulsatility index, and peak systolic velocity). Thereafter, 3-dimensional power Doppler sonography was used to assess vascularization of highly suggestive areas (gross papillary projections, solid areas, and thick septations), meaning a focused assessment ("sampling") of a suggestive area of the tumor. With a virtual organ computer-aided analysis program, vascular indices (vascularization index, flow index, and vascular flow index) were automatically calculated. A definitive histologic diagnosis was obtained in each case. RESULTS Forty masses (82%) were malignant and 9 (18%) were benign. Morphologic evaluation revealed 10 (20%) unilocular solid masses, 20 (41%) multilocular solid masses, and 19 (39%) mostly solid masses. Blood flow was found in all cases. Median vascularization index (15.5% versus 8.2%; P = .002), flow index (33.6 versus 20.8; P = .007), and vascular flow index (5.2 versus 2.3; P = .001) were significantly higher in malignant tumors. No differences were found in resistive index (0.43 versus 0.45; P = .770), pulsatility index (0.62 versus 0.65; P = .694), and peak systolic velocity (15.6 versus 12 cm/s; P = .162). CONCLUSIONS Three-dimensional power Doppler vascular sampling seems to be a promising tool for predicting ovarian cancer in vascularized complex adnexal masses. It could be better than conventional color pulsed Doppler imaging.
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Affiliation(s)
- Juan Luis Alcázar
- Department of Obstetrics and Gynecology, Clínica Universitaria de Navarra, Avenida Pio XII 36, 31008 Pamplona, Spain.
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Chen CA, Cheng WF, Lee CN, Su YN, Hsieh CY, Hsieh FJ. Power Doppler vascularity index for predicting the response of neoadjuvant chemotherapy in cervical carcinoma. Acta Obstet Gynecol Scand 2004; 83:591-7. [PMID: 15144343 DOI: 10.1111/j.0001-6349.2004.00522.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND To evaluate whether the power Doppler vascularity index (PDVI) can predict the response to neoadjuvant chemotherapy (NACT) in cervical carcinoma. METHODS Twenty-five women with bulky early stage cervical carcinoma treated by NACT followed by surgery were enrolled. Their response to NACT was evaluated. Clinical characteristics and pathologic data were recorded. Transvaginal power Doppler was performed before, during and after NACT. PDVI was detected using power Doppler and a quantitative image processing system. Factors that can potentially correlate with the response to NACT were analyzed. RESULTS Twelve (48%) patients showed a response (responders) to NACT and 13 (52%) were unchanged or had progressive disease (nonresponders) after NACT. Higher PDVI values were noted in tumors with lymphovascular emboli and pelvic lymph node metastasis both before and after NACT. The mean values of the PDVI of the nonresponders before (19.27 +/- 6.01 vs. 12.28 +/- 7.06, p = 0.014), during (20.2 +/- 1.5 vs. 12.9 +/- 2.1, p = 0.009) and after NACT (18.1 +/- 6.0 vs. 9.3 +/- 5.4, p = 0.001) were significantly higher than those of the responders. When the cutoff point for predicting nonresponders to NACT was set at a PDVI value of 15%, the sensitivity was 92.3% and the specificity 66.7%. CONCLUSIONS The power Doppler vascularity index can predict the response to neoadjuvant chemotherapy in cervical cancer, and might be useful for the evaluation of response to chemotherapy in cancer patients in the future.
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Affiliation(s)
- Chi-An Chen
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
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