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Liang R, Xiang Y, Hu C, Tang X. Expression and clinical significance of RBBP4 gene in lower-grade glioma: An integrative analysis. Biochem Biophys Rep 2023; 35:101533. [PMID: 37664524 PMCID: PMC10469049 DOI: 10.1016/j.bbrep.2023.101533] [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: 06/19/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
This study investigated the expression pattern of retinoblastoma binding protein 4 (RBBP4) gene in glioma and explored its associations with clinicopathologic characteristics and prognosis of patients. Data retrieved from the GEPIA, CGGA, HPA and TIMER databases were processed to analyze RBBP4 expression in glioma and investigate its relationship with clinicopathologic characteristics, tumor immune infiltration and prognosis in glioma patients. Immunohistochemistry was applied to determine the expression of RBBP4 protein in glioma tissue. Additionally, the Coexpedia database was visited to identify co-expressed genes for RBBP4 gene, while the Cytoscape software was run to visualize the enriched GO entries and KEGG pathways of these co-expressed genes. The expression levels of RBBP4 in lower-grade glioma (LGG) and glioblastoma (GBM) tissues were markedly elevated when compared to normal tissues (both p < 0.05). The up-regulation of RBBP4 expression was associated with an increase in WHO grade (II-IV), wild-type IDH, and 1p/19q non-codeletion (all p < 0.05). Multi-variate Cox regression analysis showed that both increased abundance of infiltrating macrophages and up-regulated RBBP4 expression independently predicted poor survival outcomes in LGG patients (both p < 0.05). Furthermore, RBBP4 expression exhibited significant positive correlations with the abundance of infiltrating B cell, CD8+ T cell, CD4+ T cell, macrophage, neutrophil, and dendritic cell in LGG (all p < 0.05). Functional enrichment analyses indicated that the co-expressed genes associated with RBBP4 were highly involved in pathways such as the p53 signaling pathway, cell cycle, DNA replication, glutathione metabolism, as well as biological processes including cell cycle process, DNA replication, and DNA repair. High levels of RBBP4 are predictive for the poor survival outcome of LGG patients. RBBP4 gene, therefore, is expected to be a potential biomarker for prognosis of LGG and a target for immunotherapy.
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Affiliation(s)
- Ruofei Liang
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, China
| | - Yue Xiang
- Department of Pathology, Affiliated Hospital of North Sichuan Medical College, China
| | - Chao Hu
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, China
| | - Xiaoping Tang
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, China
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Yuile A, Satgunaseelan L, Wei JQ, Rodriguez M, Back M, Pavlakis N, Hudson A, Kastelan M, Wheeler HR, Lee A. CDKN2A/B Homozygous Deletions in Astrocytomas: A Literature Review. Curr Issues Mol Biol 2023; 45:5276-5292. [PMID: 37504251 PMCID: PMC10378679 DOI: 10.3390/cimb45070335] [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: 05/31/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023] Open
Abstract
Genomic alterations of CDKN2A and CDKN2B in astrocytomas have been an evolving area of study for decades. Most recently, there has been considerable interest in the effect of CDKN2A and/or CDKN2B (CDKN2A/B) homozygous deletions (HD) on the prognosis of isocitrate dehydrogenase (IDH)-mutant astrocytomas. This is highlighted by the adoption of CDKN2A/B HD as an essential criterion for astrocytoma and IDH-mutant central nervous system (CNS) WHO grade 4 in the fifth edition of the World Health Organisation (WHO) Classification of Central Nervous System Tumours (2021). The CDKN2A and CDKN2B genes are located on the short arm of chromosome 9. CDKN2A encodes for two proteins, p14 and p16, and CDKN2B encodes for p15. These proteins regulate cell growth and angiogenesis. Interpreting the impact of CDKN2A/B alterations on astrocytoma prognosis is complicated by recent changes in tumour classification and a lack of uniform standards for testing CDKN2A/B. While the prognostic impact of CDKN2A/B HD is established, the role of different CDKN2A/B alterations-heterozygous deletions (HeD), point mutations, and promoter methylation-is less clear. Consequently, how these alternations should be incorporated into patient management remains controversial. To this end, we reviewed the literature on different CDKN2A/B alterations in IDH-mutant astrocytomas and their impact on diagnosis and management. We also provided a historical review of the changing impact of CDKN2A/B alterations as glioma classification has evolved over time. Through this historical context, we demonstrate that CDKN2A/B HD is an important negative prognostic marker in IDH-mutant astrocytomas; however, the historical data is challenging to interpret given changes in tumour classification over time, variation in the quality of evidence, and variations in the techniques used to identify CDKN2A/B deletions. Therefore, future prospective studies using uniform classification and detection techniques are required to improve the clinical interpretation of this molecular marker.
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Affiliation(s)
- Alexander Yuile
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
- The Brain Cancer Group, North Shore Private Hospital, Sydney, NSW 2065, Australia
| | - Laveniya Satgunaseelan
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Joe Q Wei
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
| | - Michael Rodriguez
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- The Brain Cancer Group, North Shore Private Hospital, Sydney, NSW 2065, Australia
- Department of Pathology, Prince of Wales Hospital, Sydney, NSW 2065, Australia
| | - Michael Back
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
- The Brain Cancer Group, North Shore Private Hospital, Sydney, NSW 2065, Australia
- Department of Radiation Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Nick Pavlakis
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
| | - Amanda Hudson
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
| | - Marina Kastelan
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- The Brain Cancer Group, North Shore Private Hospital, Sydney, NSW 2065, Australia
| | - Helen R Wheeler
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
- The Brain Cancer Group, North Shore Private Hospital, Sydney, NSW 2065, Australia
| | - Adrian Lee
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia
- The Brain Cancer Group, North Shore Private Hospital, Sydney, NSW 2065, Australia
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Phon BWS, Kamarudin MNA, Bhuvanendran S, Radhakrishnan AK. Transitioning pre-clinical glioblastoma models to clinical settings with biomarkers identified in 3D cell-based models: A systematic scoping review. Biomed Pharmacother 2021; 145:112396. [PMID: 34775238 DOI: 10.1016/j.biopha.2021.112396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 11/02/2022] Open
Abstract
Glioblastoma (GBM) remains incurable despite the overwhelming discovery of 2-dimensional (2D) cell-based potential therapeutics since the majority of them have met unsatisfactory results in animal and clinical settings. Incremental empirical evidence has laid the widespread need of transitioning 2D to 3-dimensional (3D) cultures that better mimic GBM's complex and heterogenic nature to allow better translation of pre-clinical results. This systematic scoping review analyses the transcriptomic data involving 3D models of GBM against 2D models from 22 studies identified from four databases (PubMed, ScienceDirect, Medline, and Embase). From a total of 499 genes reported in these studies, 313 (63%) genes were upregulated across 3D models cultured using different scaffolds. Our analysis showed that 4 of the replicable upregulated genes are associated with GBM stemness, epithelial to mesenchymal transition (EMT), hypoxia, and migration-related genes regardless of the type of scaffolds, displaying close resemblances to primitive undifferentiated tumour phenotypes that are associated with decreased overall survival and increased hazard ratio in GBM patients. The upregulation of drug response and drug efflux genes (e.g. cytochrome P450s and ABC transporters) mirrors the GBM genetic landscape that contributes to in vivo and clinical treatment resistance. These upregulated genes displayed strong protein-protein interactions when analysed using an online bioinformatics software (STRING). These findings reinforce the need for widespread transition to 3D GBM models as a relatively inexpensive humanised pre-clinical tool with suitable genetic biomarkers to bridge clinical gaps in potential therapeutic evaluations.
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Affiliation(s)
- Brandon Wee Siang Phon
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Muhamad N A Kamarudin
- Brain Research Institute Monash Sunway, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor, Malaysia.
| | - Saatheeyavaane Bhuvanendran
- Brain Research Institute Monash Sunway, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor, Malaysia
| | - Ammu K Radhakrishnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
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Jiang JS, Hua Y, Zhou XJ, Shen DD, Shi JL, Ge M, Geng QN, Jia ZZ. Quantitative Assessment of Tumor Cell Proliferation in Brain Gliomas with Dynamic Contrast-Enhanced MRI. Acad Radiol 2019; 26:1215-1221. [PMID: 30416002 DOI: 10.1016/j.acra.2018.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/12/2018] [Accepted: 10/13/2018] [Indexed: 02/06/2023]
Abstract
RATIONALE AND OBJECTIVES This study aimed to investigate whether volume transfer constant (Ktrans) and volume of extravascular extracellular space per unit volume of tissue (Ve) derived from dynamic contrast-enhanced magnetic resonance imaging (DCE MRI) could quantitatively assess the tumor proliferation index (Ki-67) of gliomas noninvasively. MATERIALS AND METHODS The preoperative DCE MRI data of 69 patients with pathologically confirmed glioma (28, 8, and 33 cases in grades Ⅱ, Ⅲ, and Ⅳ) were retrospectively reviewed. The maximal Ktrans and Ve were measured in the tumor body. The immunohistochemistry was used to detect the expression of Ki-67 proteins in glioma specimens. The Mann-Whitney U test was applied to analyze the differences in Ktrans, Ve, and Ki-67 index across histologically defined glioma grades. Spearman correlation was performed between Ktrans, Ve, and Ki-67 index. The receiver operating characteristic curve analysis was used to determine the cutoff values of Ktrans and Ve in distinguishing different Ki-67 index expression levels. RESULTS Ktrans, Ve, and Ki-67 index of grade Ⅱ (0.027 min-1, 0.065, 4.04%) were significantly lower than those of grade Ⅲ (0.093 min-1, 0.297, 25.13%) and Ⅳ (0.100 min-1, 0.299, 25.37%). Both Ktrans and Ve significantly correlated with the Ki-67 index in all tumors and high-grade gliomas (HGGs, grade Ⅲ and Ⅳ). The receiver operating characteristic curve analysis revealed that the cutoff values for Ktrans (0.079 min-1) and Ve (0.249) provided the best combination of sensitivity and specificity to distinguish the gliomas with high Ki-67 index from those with low Ki-67 index. CONCLUSION The DCE MRI-derived parameters were valuable in assessing the tumor cell proliferation in HGG noninvasively.
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Li Y, Wang Z, Wang Y, Zhao Z, Zhang J, Lu J, Xu J, Li X. Identification and characterization of lncRNA mediated transcriptional dysregulation dictates lncRNA roles in glioblastoma. Oncotarget 2018; 7:45027-45041. [PMID: 26943771 PMCID: PMC5216703 DOI: 10.18632/oncotarget.7801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) modulate gene expression, and lncRNA misregulation is associated with cancer. However, precise functional roles in biological and disease processes have been described for only a few lncRNAs. Identification of genome-wide lncRNA-mediated transcriptional dysregulations may improve cancer treatments. In the present study, we used a computational framework that combined lncRNA and gene expression profiles with transcription factor (TF)-target relationships to comprehensively identify dysregulatory lncRNA-TF-gene triplets. In glioblastoma (GBM), we found that most lncRNAs affect multiple targets and primarily affect TF activity in trans. Six different classes of lncRNA-mediated transcriptional dysregulations were identified, with most lncRNAs either enhancing or attenuating target gene expression. Functional analysis of lncRNAs via their dysregulated targets implicated lncRNA modulators in some hallmarks of cancer, providing a new way to predict lncRNA function. Finally, we identified several lncRNA-TF-gene triplets (including HOTAIR-MXI1-CD58/PRKCE and HOTAIR-ATF5-NCAM1) that are associated with glioblastoma prognosis. The integration of lncRNA modulators into transcriptional regulatory networks will further enhance our understanding of lncRNA functions in cancer.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Zishan Wang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Yuan Wang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Zheng Zhao
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Jinwen Zhang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
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Hsu YM, Yin MC. EPA or DHA enhanced oxidative stress and aging protein expression in brain of d-galactose treated mice. Biomedicine (Taipei) 2016; 6:17. [PMID: 27514534 PMCID: PMC4980825 DOI: 10.7603/s40681-016-0017-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/20/2016] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Effects of eicosapentaenoic acid (EPA, 20:5) and docosahexaenoic acid (DHA, 22:6) upon fatty acid composition, oxidative and inflammatory factors and aging proteins in brain of d-galactose (DG) treated aging mice were examined. METHODS Each fatty acid at 7 mg/kg BW/week was supplied for 8 weeks. Brain aging was induced by DG treatment (100 mg/kg body weight) via daily subcutaneous injection for 8 weeks. RESULTS DG, EPA and DHA treatments changed brain fatty acid composition. DG down-regulated brain Bcl-2 expression and up-regulated Bax expression. Compared with DG groups, EPA and DHA further enhanced Bax expression. DG decreased glutathione content, increased reactive oxygen species (ROS) and oxidized glutathione (GSSG) production, the intake of EPA or DHA caused greater ROS and GSSG formation. DG treatments up-regulated the protein expression of p47(phox) and gp91(phox), and the intake of EPA or DHA led to greater p47(phox) and gp91(phox) expression. DG increased brain prostaglandin E2 (PGE2) levels, and cyclooxygenase (COX)-2 expression and activity, the intake of EPA or DHA reduced brain COX-2 activity and PGE2 formation. DG enhanced brain p53, p16 and p21 expression. EPA and DHA intake led to greater p21 expression, and EPA only caused greater p53 and p16 expression. CONCLUSION These findings suggest that these two PUFAs have toxic effects toward aging brain.
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Affiliation(s)
- Yuan-Man Hsu
- Department of Biological Science and Technology, China Medical University, 404, Taichung, Taiwan
| | - Mei-Chin Yin
- Department of Nutrition, China Medical University, 91, Hsueh-shih Rd., 404, Taichung, Taiwan.
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Elevated E2F7 expression predicts poor prognosis in human patients with gliomas. J Clin Neurosci 2016; 33:187-193. [PMID: 27460513 DOI: 10.1016/j.jocn.2016.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/16/2022]
Abstract
E2F transcription factors have been studied extensively in a broad range of organisms as major regulators of cell cycle, apoptosis, and differentiation. The E2F family includes the atypical member E2F7, which has been rarely studied in gliomas. The aim of this study is to determine the expression status of E2F7 in gliomas, its relationship to clinicopathological features, and patients' outcome. The mRNA levels of E2F7 in the human brain and different grades of gliomas were analysed using datasets from the publically available Oncomine database. One of the most significant co-expression factors, CDK1, together with E2F7, was further validated by immunohistochemistry in 90 different grades of gliomas. Furthermore, univariate and multivariate analyses were performed to identify prognostic variables relative to patient and tumour characteristics and treatment modalities. E2F7 mRNA expression was found to be elevated in gliomas by Oncomine-database analysis. Immunohistochemistry showed an increase in E2F7 labelling index in high- versus low-grade gliomas (62.1±11.8% vs. 18.9±10.2%, p<0.0001). There was a positive correlation between E2F7 and CDK1 immunoreactivity (Spearman r=0.446, p=0.037). Clinicopathological evaluation suggested that E2F7 expression was associated with tumour grade (p<0.0001) and recurrence (p=0.025). In Cox multivariate analysis, pathological classification and recurrence were independent prognostic factors of gliomas, and E2F7 was significantly related to progression-free survival (p=0.011), but not overall survival (p=0.062). Our findings suggested that E2F7 might act as an independent prognostic factor of gliomas and might constitute a potential therapeutic target for this disease.
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Expression Analysis of Genes Involved in the RB/E2F Pathway in Astrocytic Tumors. PLoS One 2015; 10:e0137259. [PMID: 26317630 PMCID: PMC4552853 DOI: 10.1371/journal.pone.0137259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/13/2015] [Indexed: 02/08/2023] Open
Abstract
Astrocytic gliomas, which are derived from glial cells, are considered the most common primary neoplasias of the central nervous system (CNS) and are histologically classified as low grade (I and II) or high grade (III and IV). Recent studies have shown that astrocytoma formation is the result of the deregulation of several pathways, including the RB/E2F pathway, which is commonly deregulated in various human cancers via genetic or epigenetic mechanisms. On the basis of the assumption that the study of the mechanisms controlling the INK4/ARF locus can help elucidate the molecular pathogenesis of astrocytic tumors, identify diagnostic and prognostic markers, and help select appropriate clinical treatments, the present study aimed to evaluate and compare methylation patterns using bisulfite sequencing PCR and evaluate the gene expression profile using real-time PCR in the genes CDKN2A, CDKN2B, CDC6, Bmi-1, CCND1, and RB1 in astrocytic tumors. Our results indicate that all the evaluated genes are not methylated independent of the tumor grade. However, the real-time PCR results indicate that these genes undergo progressive deregulation as a function of the tumor grade. In addition, the genes CDKN2A, CDKN2B, and RB1 were underexpressed, whereas CDC6, Bmi-1, and CCND1 were overexpressed; the increase in gene expression was significantly associated with decreased patient survival. Therefore, we propose that the evaluation of the expression levels of the genes involved in the RB/E2F pathway can be used in the monitoring of patients with astrocytomas in clinical practice and for the prognostic indication of disease progression.
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Sibin MK, Bhat DI, Narasingarao KVL, Lavanya C, Chetan GK. CDKN2A (p16) mRNA decreased expression is a marker of poor prognosis in malignant high-grade glioma. Tumour Biol 2015; 36:7607-14. [DOI: 10.1007/s13277-015-3480-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/20/2015] [Indexed: 12/30/2022] Open
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Adaptive localization of focus point regions via random patch probabilistic density from whole-slide, Ki-67-stained brain tumor tissue. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:673658. [PMID: 25793010 PMCID: PMC4352493 DOI: 10.1155/2015/673658] [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: 07/19/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022]
Abstract
Analysis of whole-slide tissue for digital pathology images has been clinically approved to provide a second opinion to pathologists. Localization of focus points from Ki-67-stained histopathology whole-slide tissue microscopic images is considered the first step in the process of proliferation rate estimation. Pathologists use eye pooling or eagle-view techniques to localize the highly stained cell-concentrated regions from the whole slide under microscope, which is called focus-point regions. This procedure leads to a high variety of interpersonal observations and time consuming, tedious work and causes inaccurate findings. The localization of focus-point regions can be addressed as a clustering problem. This paper aims to automate the localization of focus-point regions from whole-slide images using the random patch probabilistic density method. Unlike other clustering methods, random patch probabilistic density method can adaptively localize focus-point regions without predetermining the number of clusters. The proposed method was compared with the k-means and fuzzy c-means clustering methods. Our proposed method achieves a good performance, when the results were evaluated by three expert pathologists. The proposed method achieves an average false-positive rate of 0.84% for the focus-point region localization error. Moreover, regarding RPPD used to localize tissue from whole-slide images, 228 whole-slide images have been tested; 97.3% localization accuracy was achieved.
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Expressions of p16 and p27 in urothelial carcinoma and their prognostic value. Kaohsiung J Med Sci 2014; 30:453-8. [DOI: 10.1016/j.kjms.2014.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 03/16/2014] [Accepted: 01/22/2014] [Indexed: 01/01/2023] Open
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Jensen RL, Mumert ML, Gillespie DL, Kinney AY, Schabel MC, Salzman KL. Preoperative dynamic contrast-enhanced MRI correlates with molecular markers of hypoxia and vascularity in specific areas of intratumoral microenvironment and is predictive of patient outcome. Neuro Oncol 2013; 16:280-91. [PMID: 24305704 DOI: 10.1093/neuonc/not148] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Measures of tumor vascularity and hypoxia have been correlated with glioma grade and outcome. Dynamic contrast-enhanced (DCE) MRI can noninvasively map tumor blood flow, vascularity, and permeability. In this prospective observational cohort pilot study, preoperative imaging was correlated with molecular markers of hypoxia, vascularity, proliferation, and progression-free and overall patient survival. METHODS Pharmacokinetic modeling methods were used to generate maps of tumor blood flow, extraction fraction, permeability-surface area product, transfer constant, washout rate, interstitial volume, blood volume, capillary transit time, and capillary heterogeneity from preoperative DCE-MRI data in human glioma patients. Tissue was obtained from areas of peritumoral edema, active tumor, hypoxic penumbra, and necrotic core and evaluated for vascularity, proliferation, and expression of hypoxia-regulated molecules. DCE-MRI parameter values were correlated with hypoxia-regulated protein expression at tissue sample sites. RESULTS Patient survival correlated with DCE parameters in 2 cases: capillary heterogeneity in active tumor and interstitial volume in areas of peritumoral edema. Statistically significant correlations were observed between several DCE parameters and tissue markers. In addition, MIB-1 index was predictive of overall survival (P = .044) and correlated with vascular endothelial growth factor expression in hypoxic penumbra (r = 0.7933, P = .0071) and peritumoral edema (r = 0.4546). Increased microvessel density correlated with worse patient outcome (P = .026). CONCLUSIONS Our findings suggest that DCE-MRI may facilitate noninvasive preoperative predictions of areas of tumor with increased hypoxia and proliferation. Both imaging and hypoxia biomarkers are predictive of patient outcome. This has the potential to allow unprecedented prognostic decisions and to guide therapies to specific tumor areas.
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Affiliation(s)
- Randy L Jensen
- Corresponding author: Randy L. Jensen, MD, PhD, Huntsman Cancer Institute and Departments of Neurosurgery, Radiation Oncology, Oncological Sciences, Clinical Neuroscience Center, University of Utah, 175 North Medical Drive, Salt Lake City, Utah 84132.
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Zolota V, Sirinian C, Kefalopoulou Z, Panagiotopoulos V, Spinos P, Argyriou AA, Kalofonos HP. Mitogen-activated protein kinases in gliomas and correlation with patients' prognosis. Acta Neurol Scand 2013. [DOI: 10.1111/ane.12175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- V. Zolota
- Department of Pathology; Medical School; University Hospital of Patras; Patras Greece
| | - C. Sirinian
- Department of Pathology; Medical School; University Hospital of Patras; Patras Greece
| | - Z. Kefalopoulou
- Department of Pathology; Medical School; University Hospital of Patras; Patras Greece
| | - V. Panagiotopoulos
- Department of Neurosurgery; Medical School; University Hospital of Patras; Patras Greece
| | - P. Spinos
- Department of Neurosurgery; Medical School; University Hospital of Patras; Patras Greece
| | - A. A. Argyriou
- Division of Oncology/Clinical Oncology Laboratory-Department of Medicine of the University Hospital of Patras; Medical School; University Hospital of Patras; Patras Greece
| | - H. P. Kalofonos
- Division of Oncology/Clinical Oncology Laboratory-Department of Medicine of the University Hospital of Patras; Medical School; University Hospital of Patras; Patras Greece
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Chen J, Zhu HH, Xu YJ, Gu X, Zhu P. Expression of vascular endothelial growth factor and its receptor KDR in verrucose gastritis and gastric cancer. Shijie Huaren Xiaohua Zazhi 2013; 21:2031-2037. [DOI: 10.11569/wcjd.v21.i21.2031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the relationship between verrucose gastritis and gastric cancer.
METHODS: The expression of vascular endothelial growth factor (VEGF) and kinase insert domain-containing receptor (KDR) in chronic superficial gastritis, verrucose gastritis and gastric cancer was detected by immunohistochemistry. Helicobacter pylori (H. pylori) infection was detected by the 13C breath test.
RESULTS: The rates of H. pylori infection in patients with verrucose gastritis and gastric cancer were both higher than that in patients with chronic superficial gastritis (χ2 = 26.4, 29.697, both P < 0.01), but there was no significant difference in the rate of H. pylori infection between patients with verrucose gastritis and those with gastric cancer (χ2 = 2.229, P > 0.05). The positive rates of VEGF and KDR expression in verrucose gastritis and gastric cancer were significantly higher than those in chronic superficial gastritis (χ2 = 20.008, 29.697; 15.428, 24.300, all P < 0.01), but there were no significant differences in the positive rates of VEGF and KDR expression between verrucose gastritis and gastric cancer (χ2 = 3.461, 3.793, both P > 0.05). The positive rates of VEGF and KDR expression in mature verrucose gastritis were significantly higher than those in non-mature verrucose gastritis (χ2 = 6.084, 10.026, both P < 0.05), but there were no significant differences between matured verrucose gastritis and gastric cancer (χ2 = 0.728, 0.080, both P > 0.05). The positive rates of VEGF and KDR expression were significantly higher in verrucose gastritis patients with H. pylori infection than in those without H. pylori infection (χ2 = 5.637, 5.398, both P < 0.05), but there were no significant differences between verrucose gastritis patients with H. pylori infection and patients with gastric cancer (χ2 = 0.839, 1.006, both P > 0.05).
CONCLUSION: H. pylori infection is involved in the formation of verrucous gastritis. Expression of VEGF and KDR in verrucose gastritis is similar to that in gastric cancer, suggesting that both VEGF and KDR may be involved in the evolution of verrucose gastritis to gastric cancer. The observation that expression of VEGF and KDR in mature verrucose gastritis and patients with H. pylori infection was higher may imply that mature verrucose gastritis and H. pylori infection increase the risk of malignant transformation of verrucose gastritis.
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15
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Lopez XM, Debeir O, Maris C, Rorive S, Roland I, Saerens M, Salmon I, Decaestecker C. Clustering methods applied in the detection of Ki67 hot-spots in whole tumor slide images: an efficient way to characterize heterogeneous tissue-based biomarkers. Cytometry A 2012; 81:765-75. [PMID: 22730412 DOI: 10.1002/cyto.a.22085] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 04/23/2012] [Accepted: 05/23/2012] [Indexed: 12/15/2022]
Abstract
Whole-slide scanners allow the digitization of an entire histological slide at very high resolution. This new acquisition technique opens a wide range of possibilities for addressing challenging image analysis problems, including the identification of tissue-based biomarkers. In this study, we use whole-slide scanner technology for imaging the proliferating activity patterns in tumor slides based on Ki67 immunohistochemistry. Faced with large images, pathologists require tools that can help them identify tumor regions that exhibit high proliferating activity, called "hot-spots" (HSs). Pathologists need tools that can quantitatively characterize these HS patterns. To respond to this clinical need, the present study investigates various clustering methods with the aim of identifying Ki67 HSs in whole tumor slide images. This task requires a method capable of identifying an unknown number of clusters, which may be highly variable in terms of shape, size, and density. We developed a hybrid clustering method, referred to as Seedlink. Compared to manual HS selections by three pathologists, we show that Seedlink provides an efficient way of detecting Ki67 HSs and improves the agreement among pathologists when identifying HSs.
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Affiliation(s)
- Xavier Moles Lopez
- Laboratory of Image Analysis and Synthesis, LIST department, Ecole polytechnique de Bruxelles (EPB), Université Libre de Bruxelles (ULB), Brussels, Belgium
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16
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Ha SY, Lee CH, Chang HK, Chang S, Kwon KY, Lee EH, Roh MS, Seo B. Differential expression of forkhead box M1 and its downstream cyclin-dependent kinase inhibitors p27(kip1) and p21(waf1/cip1) in the diagnosis of pulmonary neuroendocrine tumours. Histopathology 2012; 60:731-9. [PMID: 22296117 DOI: 10.1111/j.1365-2559.2011.04137.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AIMS Pulmonary neuroendocrine (NE) tumours represent a spectrum of phenotypically distinct entities with different biological behaviours. Difficulties in classifying these tumours are frequently encountered in clinical practice. Forkhead box M1 (FoxM1) is essential for the development of various cancers and is a proliferation-specific transcription factor that regulates transcription of cell cycle genes, including cyclin-dependent kinase inhibitors p27(kip1) and p21(waf1/cip1) . This study was performed to determine the utility of FoxM1, p27(kip1) and p21(waf1/cip1) as immunomarkers for subtyping pulmonary NE tumours. METHODS AND RESULTS FoxM1, p27(kip1) and p21(waf1/cip1) expression was evaluated by immunohistochemistry in 60 pulmonary NE tumours [19 typical carcinoids (TCs), six atypical carcinoids (ACs), 17 large cell neuroendocrine carcinomas (LCNECs) and 18 small cell lung cancers (SCLCs)]. The frequencies of FoxM1 and p21(waf1/cip1) expression were significantly different between TCs and ACs (each P = 0.009), and those of FoxM1 and p27(kip1) expression were significantly different between LCNECs and SCLCs (P = 0.012 and P = 0.002, respectively). The combined FoxM1((-)) /p21(waf1/cip1(-)) and FoxM1((+)) /p27(kip1(high)) phenotypes had the best diagnostic accuracy for distinguishing TCs from ACs, and SCLCs from LCNECs, respectively. CONCLUSIONS FoxM1, p27(kip1) and p21(waf1/cip1) showed distinct immunoreactivity according to histological subtype, which may be of value as an ancillary test in the differential diagnosis of pulmonary NE tumours.
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Affiliation(s)
- Seung Yeon Ha
- Department of Pathology, Gachon University of Medicine and Science, Incheon, South Korea
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17
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Abstract
In recent years, advances in the understanding of low-grade glioma (LGG) biology have driven new paradigms in molecular markers, diagnostic imaging, operative techniques and technologies, and adjuvant therapies. Taken together, these developments are collectively pushing the envelope toward improved quality of life and survival. In this article, the authors evaluate the recent literature to synthesize a comprehensive review of LGGs in the modern neurosurgical era.
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Affiliation(s)
- Nader Sanai
- Barrow Brain Tumor Research Center, Department of Neurological Surgery, Barrow Neurological Institute, Phoenix, Arizona, USA
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18
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Abstract
In recent years, advances in the understanding of low-grade glioma (LGG) biology have driven new paradigms in molecular markers, diagnostic imaging, operative techniques and technologies, and adjuvant therapies. Taken together, these developments are collectively pushing the envelope toward improved quality of life and survival. In this article, the authors evaluate the recent literature to synthesize a comprehensive review of LGGs in the modern neurosurgical era.
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Affiliation(s)
- Nader Sanai
- 1Barrow Brain Tumor Research Center, Department of Neurological Surgery, Barrow Neurological Institute, Phoenix, Arizona; and
| | - Susan Chang
- 2Brain Tumor Research Center, Department of Neurological Surgery, University of California at San Francisco, California
| | - Mitchel S. Berger
- 2Brain Tumor Research Center, Department of Neurological Surgery, University of California at San Francisco, California
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19
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Abstract
Clinicians and pathologists have been inundated by published reports of new and potentially interesting diagnostic, prognostic, and putative predictive "markers" whose expression (or loss) holds great promise for more enlightened diagnoses and ultimately better patient care. Although an understanding of therapeutically (and possibly diagnostically) relevant pathways of glioblastoma may be at hand, significant challenges remain. Many immunohistochemical and genetic tests have proven to be useful in the stratification of clinical trials, whereas the utility of many others for the day-to-day practice of pathology awaits further study and validation. The importance of critical literature review and careful consideration of practical issues such as test standardization, compliance, cost-effectiveness, and availability must all be considered before implementing any new diagnostic test. This review will focus on the role of immunohistochemistry in the routine diagnosis of astrocytic and oligodendrocytic tumors and in assisting with the diagnosis of some less common gliomas that have ependymal-like features. It will conclude with a summary of molecular and genetic studies, which not only hold great promise for improved diagnosis, but also reveal prognostic information on disease outcome and predict response to treatment or provide biologic targets for novel therapies.
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20
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Gli1 inhibition induces cell-cycle arrest and enhanced apoptosis in brain glioma cell lines. J Neurooncol 2009; 98:319-27. [DOI: 10.1007/s11060-009-0082-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Accepted: 11/30/2009] [Indexed: 12/22/2022]
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21
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Frequent aberrant expression of p53 protein in gliomas but not in capillary hemangioblastomas and pheochromocytomas. Acta Med Litu 2009. [DOI: 10.2478/v10140-009-0019-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Zolota VG, Tzelepi VN, Leotsinidis M, Zili PE, Panagopoulos ND, Dougenis D, Tsamandas AC, Scopa CD. Histologic-type specific role of cell cycle regulators in non-small cell lung carcinoma. J Surg Res 2009; 164:256-65. [PMID: 19691991 DOI: 10.1016/j.jss.2009.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/16/2009] [Accepted: 03/18/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND Lung cancer is the most lethal type of cancer in humans. Cell cycle alterations have commonly been encountered in lung cancer and may have prognostic value. MATERIALS AND METHODS This study investigates the immunohistochemical expression of the important cell cycle regulators phosphatase and tensin homolog deleted on chromosome 10 (PTEN), p27, Cks1, and Skp2 in 128 non-small cell lung carcinomas (64 adenocarcinomas, 46 squamous cell carcinomas, and 18 large cell undifferentiated carcinomas) and adjacent non-neoplastic lung tissue. RESULTS PTEN and p27 were always highly expressed in non-neoplastic lung whereas Cks1 and Skp2 were not expressed in normal tissue. Decreased PTEN expression was noted in 19/64 adenocarcinomas, 15/46 squamous cell carcinomas, and 7/18 undifferentiated large cell carcinomas. Reduced expression of p27 was noted in 28/64, 19/46, and 6/18 of the tumors, respectively. Increased expression of Cks1 was seen in 38/64, 26/46, and 11/18 and increased expression of Skp2 in 29/64, 30/46, and 14/18 of the tumors, respectively. An inverse relationship between p27 and Skp2 levels was found in adenocarcinomas and between p27 and Cks1 levels in squamous cell carcinomas. Decreased PTEN and p27 expression were associated with advanced tumor stage in squamous cell carcinomas. Univariate analysis showed that high p27 and PTEN and low Cks1 expression correlated with increased survival in patients with squamous cell carcinoma independently of tumor stage. CONCLUSIONS Aberrant expression of PTEN, p27, Cks1, and Skp2 is a common feature of all three major types of non-small cell lung cancer NSCLC, but seems to be involved in the progression of squamous cell carcinoma alone.
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Affiliation(s)
- Vassiliki G Zolota
- Department of Pathology, Medical School, University of Patras, Patras, Greece.
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23
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Swamy MV, Citineni B, Patlolla JMR, Mohammed A, Zhang Y, Rao CV. Prevention and treatment of pancreatic cancer by curcumin in combination with omega-3 fatty acids. Nutr Cancer 2009; 60 Suppl 1:81-9. [PMID: 19003584 DOI: 10.1080/01635580802416703] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Pancreatic cancer BxPC-3 cells were exposed to curcumin, docosahexaenoic acid (DHA), or combinations of both and analyzed for proliferation and apoptosis. Pancreatic tumor xenografts were established by injecting BxPC-3 cells into each flank of nude mice. After the tumors reached a size of approximately 190-200 mm(3), animals were fed diets with or without 2,000 ppm curcumin in 18% corn oil or 15% fish oil + 3% corn oil for 6 more wk before assessing the tumor volume and expression of inducible nitric oxide synthase (iNOS), cyclooxygeanse-2 (COX-2), 5-lipoxinase (5-LOX), and p21. A synergistic effect was observed on induction of apoptosis (approximately sixfold) and inhibition of cell proliferation (approximately 70%) when cells were treated with curcumin (5 microM) together with the DHA (25 microM). Mice fed fish oil and curcumin showed a significantly reduced tumor volume, 25% (P < 0.04) and 43% (P < 0.005), respectively, and importantly, a combination of curcumin and fish oil diet showed > 72% (P < 0.0001) tumor volume reduction. Expression and activity of iNOS, COX-2, and 5-LOX are downregulated, and p21 is upregulated in tumor xenograft fed curcumin combined with fish oil diet when compared to individual diets. The preceding results evidence for the first time that curcumin combined with omega-3 fatty acids provide synergistic pancreatic tumor inhibitory properties.
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Affiliation(s)
- Malisetty V Swamy
- Department of Medicine, Hem-Onc Section, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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