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Yang Q, Gong Y. Construction of the Classification Model Using Key Genes Identified Between Benign and Malignant Thyroid Nodules From Comprehensive Transcriptomic Data. Front Genet 2022; 12:791349. [PMID: 35096008 PMCID: PMC8795894 DOI: 10.3389/fgene.2021.791349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 01/15/2023] Open
Abstract
Thyroid nodules are present in upto 50% of the population worldwide, and thyroid malignancy occurs in only 5–15% of nodules. Until now, fine-needle biopsy with cytologic evaluation remains the diagnostic choice to determine the risk of malignancy, yet it fails to discriminate as benign or malignant in one-third of cases. In order to improve the diagnostic accuracy and reliability, molecular testing based on transcriptomic data has developed rapidly. However, gene signatures of thyroid nodules identified in a plenty of transcriptomic studies are highly inconsistent and extremely difficult to be applied in clinical application. Therefore, it is highly necessary to identify consistent signatures to discriminate benign or malignant thyroid nodules. In this study, five independent transcriptomic studies were combined to discover the gene signature between benign and malignant thyroid nodules. This combined dataset comprises 150 malignant and 93 benign thyroid samples. Then, there were 279 differentially expressed genes (DEGs) discovered by the feature selection method (Student’s t test and fold change). And the weighted gene co-expression network analysis (WGCNA) was performed to identify the modules of highly co-expressed genes, and 454 genes in the gray module were discovered as the hub genes. The intersection between DEGs by the feature selection method and hub genes in the WGCNA model was identified as the key genes for thyroid nodules. Finally, four key genes (ST3GAL5, NRCAM, MT1F, and PROS1) participated in the pathogenesis of malignant thyroid nodules were validated using an independent dataset. Moreover, a high-performance classification model for discriminating thyroid nodules was constructed using these key genes. All in all, this study might provide a new insight into the key differentiation of benign and malignant thyroid nodules.
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Affiliation(s)
- Qingxia Yang
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yaguo Gong
- School of Pharmacy, Macau University of Science and Technology, Macau, China
- *Correspondence: Yaguo Gong,
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Novel expression of vascular endothelial growth factor isoforms in the pancreas and pancreatic cystic lesions. Biochimie 2020; 181:234-239. [PMID: 33387563 DOI: 10.1016/j.biochi.2020.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Vascular endothelial growth factor (VEGF)-A is known to play key biological roles in angiogenesis and vascular permeability. We previously identified VEGF-A as an accurate biomarker of benign pancreatic cystic lesions known as serous cystic neoplasms (SCN). In the present study, we seek to further characterize the expression of VEGF-A and its splice isoforms in different pancreatic cysts including SCN. Patients undergoing surgery were consented for the collection of pancreatic cystic lesion tissue (SCN, pseudocysts, mucinous cysts) and normal adjacent pancreas as well as pancreatic cyst fluid. Following RNA isolation from the tissues, relative VEGF-A gene expression was quantitatively analyzed using real-time PCR (qPCR), and VEGF-A isoform expression was evaluated by reverse transcriptase (RT)-PCR. Relative VEGF-A gene expression was significantly increased in SCN, demonstrating transcriptional upregulation in SCN compared to other pancreatic cyst tissues (P < 0.0001). VEGF-189, -165, -145, and -121 splice variants were detected in both normal adjacent pancreas and pancreatic cystic lesions; the novel VEGF-111 isoform was variably expressed in normal and cyst tissues. Finally, VEGF isoform levels in pancreatic cyst fluid were measured by isoform-specific ELISAs. VEGF-165, -145, and -121 proteins were present in pancreatic cyst fluids; VEGF-165 levels were significantly higher in SCN cyst fluid. Thus, multiple VEGF isoforms were expressed in normal pancreas and pancreatic cysts. Of particular interest are VEGF-145 and -111, which have not previously been described in human pancreas where they may exhibit unique biological activities in health and/or disease.
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Haytaoglu G, Kuzu F, Arpaci D, Altas A, Can M, Barut F, Kokturk F, Ilikhan SU, Bayraktaroglu T. Correlation of vascular endothelial growth factor and vascular endothelial growth factor receptor-1 levels in serum and thyroid nodules with histopathological and radiological variables. J Lab Physicians 2020; 11:51-57. [PMID: 30983803 PMCID: PMC6437829 DOI: 10.4103/jlp.jlp_41_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND/AIM: Vascular endothelial growth factor (VEGF) is a major cytokine in angiogenesis and has a role on aggressivity of various tumors. The expression of VEGF has been shown to increase in differential thyroid cancer. The aim of the study was to evaluate serum and intranodular VEGF (nVEGF) and VEGF receptor-1 (VEGFR-1) levels in patients with thyroid nodules and their relevance to ultrasonographic and pathological results. MATERIALS AND METHODS: A total of eighty patients were included in the study. Thyroid fine-needle aspiration biopsies were performed, and the levels of serum and nVEGF and VEGFR-1 were measured. Any possible correlations between serum and nVEGF, VEGFR-1, and biochemical/radiological variables were investigated. RESULTS: There were no significant differences between serum VEGF (sVEGF), nVEGF, sVEGFR-1, nVEGFR-1 levels, number of nodules, size of nodules, and benign and malignant ultrasonographic features. sVEGF and nVEGF were higher in malignant or suspicious nodules than that in benign nodules, but did not reach statistical significance (P > 0.05). sVEGFR-1 and nVEGFR-1 levels were higher in hyperthyroid patients than that in euthyroid patients (P < 0.05 and P = 0.003, respectively). nVEGFR-1 level was higher in hypothyroid patients than that in euthyroid patients (P = 0.016). sVEGF level was found to be higher in hyperactive nodules than that in others. Both sVEGFR-1 (P = 0.008) and nVEGF levels (P = 0.01) significantly increased with increasing age. nVEGFR-1 decreased with increasing body mass index (BMI) (P = 0.004). CONCLUSIONS: Our study showed the relationships of sVEGF, nVEGF, sVEGFR-1, and nVEGFR-1 levels with age, gender, BMI, and hyperthyroidism. To determine the role of VEGF/VEGFR-1 in thyroid nodules, further studies are required with a large number of patients.
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Affiliation(s)
- Gurkan Haytaoglu
- Department of Internal Medicine, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Fatih Kuzu
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Evliya Çelebi Training and Research Hospital, Dumlupinar University, Kütahya, Turkey
| | - Dilek Arpaci
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Ayfer Altas
- Department of Internal Medicine, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Murat Can
- Department of Biochemistry, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Figen Barut
- Department of Pathology, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Furuzan Kokturk
- Department of Biostatistics, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Sevil Uygun Ilikhan
- Department of Internal Medicine, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
| | - Taner Bayraktaroglu
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Faculty of Medicine, Bulent Ecevit University, Zonguldak, Turkey
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Gupta B, Chandra S, Singh A, Sah K, Raj V, Gupta V. The role of vascular endothelial growth factor in proliferation of odontogenic cysts and tumors: An immunohistochemical study. Dent Res J (Isfahan) 2016; 13:256-63. [PMID: 27274347 PMCID: PMC4878211 DOI: 10.4103/1735-3327.182187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: Vascular endothelial growth factor (VEGF) is capable of initiating angiogenesis in blood vessels and may act as mitogenic agent for epithelium of odontogenic cysts and tumors. This study was conducted to evaluate the role of epithelial VEGF expression in odontogenic cysts and ameloblastoma and its correlation with argyrophilic nucleolar organizer region counts to assess its role in their biological behavior. Materials and Methods: In this retrospective cross-sectional study, 45 histologically confirmed cases, 15 cases of each of keratocystic odontogenic tumors (KCOTs), dentigerous cysts, and ameloblastomas were examined for immunohistochemical expression for epithelial VEGF, and argyrophilic nucleolar organizer regions (AgNORs) (used as secondary marker in this study) staining was done for comparing the proliferative capacity with VEGF. Results: KCOT shows mild expression within the basal layers and strong expression in the suprabasal layer whereas, in dentigerous cysts, a majority showed no VEGF expression whereas ameloblastomas showed strong expression in all cases by stellate reticulum-like cells at the center of the follicles and suprabasal layers of epithelium. The results of AgNOR counts were higher in KCOTs as compared to ameloblastoma and least in dentigerous cysts. Conclusion: VEGF expression by the epithelium of odontogenic cysts and tumors may play a role in epithelial proliferation via autocrine mechanism as reflected by increased AgNOR counts. The angiogenic activity via paracrine pathway may be responsible for the difference in growth rate and neoplastic behavior of the lesions.
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Affiliation(s)
- Bhavana Gupta
- Department of Oral Pathology, RAMA Dental College, Kanpur, India
| | - Shaleen Chandra
- Department of Oral Pathology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anil Singh
- Department of Oral Pathology, Saraswati Dental College and Hospital, Lucknow, Uttar Pradesh, India
| | - Kunal Sah
- Department of Oral Pathology, Saraswati Dental College and Hospital, Lucknow, Uttar Pradesh, India
| | - Vineet Raj
- Department of Oral Pathology, Chandra Dental College, Lucknow, Uttar Pradesh, India
| | - Vivek Gupta
- Department of Periodontology, RAMA Dental College, Kanpur, India
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Gupta B, Chandra S, Raj V, Gupta V. Immunohistochemical expression of vascular endothelial growth factor in orofacial lesions - A review. J Oral Biol Craniofac Res 2016; 6:231-236. [PMID: 27761389 DOI: 10.1016/j.jobcr.2016.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/30/2016] [Indexed: 01/13/2023] Open
Abstract
Angiogenesis is considered to be an important biological process in disease progression and tumorigenesis. Among the various factors associated with angiogenesis, vascular endothelial growth factor (VEGF) is a leading candidate. VEGF induces the proliferation, differentiation, and migration of vascular endothelial cells, increases capillary permeability, and enhances endothelial cell survival by preventing apoptosis. This article reviews and highlights the role of VEGF in health, and various oral diseases.
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Affiliation(s)
- Bhavana Gupta
- Senior Lecturer, Department of Oral Pathology, Rama Dental College, Kanpur, U.P., India
| | - Shaleen Chandra
- Professor and Head, Department of Oral Pathology, King George's Medical University, Lucknow, India
| | - Vineet Raj
- Associate Professor, Department of Oral Pathology, Chandra Dental College, Lucknow, U.P., India
| | - Vivek Gupta
- Professor, Department of Periodontology, Rama Dental College and Hospital, Kanpur, India
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Bilgici B, Ecemis GC, Tuncel OK, Bayrak IK, Kan EK, Atmaca A. VEGF and GM-CSF levels in nodular thyroid diseases. Endocrine 2014; 45:61-6. [PMID: 23625193 DOI: 10.1007/s12020-013-9945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 03/26/2013] [Indexed: 10/26/2022]
Abstract
VEGF is a specific mitogen for endothelial cells. GM-CSF is a key player in the regulation of steady-state functions. The aim of this study was to evaluate VEGF and GM-CSF levels in thyroid nodules >1 cm, which are negative for malignancy with fine needle aspiration biopsy. Age, serum VEGF, GM-CSF, TSH, fT3, fT4, anti-TG, anti-TPO, thyroid size, and thyroid volume were compared between 41 female patients and 20 healthy female volunteers. This study was performed with 41 female patients who were euthyroid and whose nodules were benign. Twenty healthy female volunteers were enrolled as the control group. VEGF and GM-CSF were assayed by ELISA; TSH, fT3, and fT4 were detected by electrochemiluminescence method and anti-TPO and anti-TG were detected by competitive immunoassay method. Only thyroid volume and anti-TG levels were significantly different between the two groups (p < 0.007 and p < 0.026, respectively). Other parameters including VEGF and GM-CSF were not significantly different. VEGF has a weak positive correlation only with anti-TPO levels in the patient group (r = 0.325, p = 0.036). There was a weak positive correlation between anti-TPO and anti-TG (r = 0.388, p = 0.007). There was a positive correlation between nodule size and thyroid volume (r = 0.464, p = 0.015). GM-CSF was not correlated with any parameters. VEGF and GM-CSF were not found to be increased in euthyroid patients with benign nodules and they do not seem to play a role in development of simple nodular goiter.
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Affiliation(s)
- Birsen Bilgici
- Department of Biochemistry, Faculty of Medicine, School of Medicine, Ondokuz Mayis University, Samsun, Turkey,
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Heparanase expression in periapical granulomas and radicular cysts. Odontology 2011; 101:96-102. [PMID: 22020734 DOI: 10.1007/s10266-011-0045-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Accepted: 09/16/2011] [Indexed: 10/16/2022]
Abstract
Heparanase is an endo-β-D-glucuronidase enzyme which degrades heparan sulfate glycosaminoglycan side chains of proteoglycans in the extracellular matrix and in basement membranes. The aim of this study was to evaluate the expression of heparanase in periapical granulomas (PGs) and radicular cysts (RCs). Immunohistochemistry was used to assess heparanase expression in PGs and RCs. Parameters including stain intensity, location and cell type were used to characterize heparanase expression in the periapical lesions. Ordered categories (from weak to strong) were used to compare the level of heparanase staining in the PG and RC groups. Both epithelial cells and inflammatory cells were positive for heparanase. The relative staining of the epithelial cells was strong, whereas the relative staining of the inflammatory cells was weak. Significant differences in immunohistochemical staining of epithelial cells were observed between RCs and PGs (p = 0.002). The relative expression of heparanase in epithelial cells in RCs was strong. In PGs, lesions with few or no epithelial cells, heparanase was predominantly expressed weakly by inflammatory cells. PGs and RCs have the same infectious origin. Therefore, the different cellular sources of heparanase in these periapical lesions may imply that this enzyme has specific pathogenetic functions in RCs and PGs.
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Malkomes P, Oppermann E, Bechstein WO, Holzer K. Significantly high expression of platelet-derived growth factor (PDGF) in benign nodules of the thyroid: relevance in the development of goitre recurrence? Langenbecks Arch Surg 2011; 396:1165-72. [PMID: 21553231 DOI: 10.1007/s00423-011-0799-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 04/12/2011] [Indexed: 12/19/2022]
Abstract
PURPOSE Platelet-derived growth factor (PDGF) is a critical regulator of cell proliferation and influences the development of tumors. The role of PDGF in benign thyroid diseases is presently not well-determined. The purpose is to evaluate PDGF isoforms and receptors in primary culture of thyrocytes isolated from human thyroid tissue. METHODS Forty patients with uninodular (n = 11), multinodular (n = 15) and recurrent goitre (n = 14) were investigated. Nodular and corresponding paranodular thyroid tissues were characterized. RNA and protein were extracted from primary thyrocyte monoculture. RT-PCR, western blot and ELISA were performed to evaluate PDGF isoforms AA, BB, CC, DD and PDGF receptors α and β. RESULTS Significantly higher mRNA expression of PDGF-AA, -BB, -CC and PDGFR molecules α and β was measured by RT-PCR in thyrocytes from uninodular and recurrent nodular tissue compared with corresponding paranodular tissue. Elevated PDGF protein and PDGFR-α and -β were confirmed by western blot. Likewise, higher secretion of PDGF-AA and -BB was detected in the supernatant of thyrocyte culture from all nodular tissue compared with paranodular tissue. Interestingly, comparison of nodular and corresponding paranodular tissues in multinodular goitre did not show significant difference of expression levels of PDGF isoforms or receptors. CONCLUSION These findings suggest that the overexpression of PDGF isoforms and receptors may play a crucial role in the development of thyroid nodules and recurrent goitre.
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Affiliation(s)
- Patrizia Malkomes
- Department of General Surgery, Johann-Wolfgang Goethe University, Universitätsklinikum Frankfurt am Main, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
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Suzuki K, Kimura H, Wu H, Kudo N, Kim WB, Suzuki S, Yoshida A, Caturegli P, Kohn LD. Excess iodide decreases transcription of NIS and VEGF genes in rat FRTL-5 thyroid cells. Biochem Biophys Res Commun 2010; 393:286-90. [PMID: 20132794 DOI: 10.1016/j.bbrc.2010.01.123] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Accepted: 01/29/2010] [Indexed: 12/20/2022]
Abstract
Although it is well known that an excess of iodide suppresses thyroid function and blood flow in vivo, the underlying molecular mechanisms are not fully known. The functional effect of iodide occurs at multiple steps, which include inhibition of sodium/iodide symporter (NIS) expression, transient block of organification, and inhibition of hormonal release. The vascular effect likely involves suppression of the vascular endothelial growth factor (VEGF) gene. In this report, we show that excess iodide coordinately suppresses the expression of the NIS and VEGF genes in FRTL-5 thyroid cells. We also demonstrate that the mechanism of iodide suppression of NIS gene expression is transcriptional, which is synergized by the addition of thyroglobulin. Based on the findings of reporter gene assays and electrophoretic gel mobility shift analysis, we also report two novel DNA binding proteins that responded specifically to iodide and modulated NIS promoter activity. The results suggest that excess iodide affects thyroid vascular function in addition to iodide uptake. This study provides additional insights into the mechanism of action of excess iodide on thyroid function.
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Affiliation(s)
- Koichi Suzuki
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
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Jebreel A, England J, Bedford K, Murphy J, Karsai L, Atkin S. Vascular endothelial growth factor (VEGF), VEGF receptors expression and microvascular density in benign and malignant thyroid diseases. Int J Exp Pathol 2007; 88:271-7. [PMID: 17696908 PMCID: PMC2517322 DOI: 10.1111/j.1365-2613.2007.00533.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Angiogenesis is critical for the growth and metastatic spread of tumours. Vascular endothelial growth factor (VEGF) is the most potent inducer of neovasculature, and its increased expression has been related to a worse clinical outcome in many diseases. The purpose of this study was to evaluate the relation between VEGF, its receptors (VEGFR-1 and VEGFR-2) and microvessel density (MVD) in thyroid diseases. Immunostaining for VEGF and VEGF receptors was performed in 66 specimens of thyroid tissue, comprising 17 multinodular goitre (MNG), 14 Graves' disease, 10 follicular adenoma, 8 Hashimoto's thyroiditis, 7 papillary carcinoma and 10 normal thyroid specimens. Thyrocyte positivity for VEGF and VEGF receptors was scored 0-3. Immunohistochemistry for CD31, and CD34 on the same sections was performed to evaluate MVD. Immunohistochemical staining of VEGF in thyrocytes was positive in 92% of all the thyroid tissues studied. Using an immunostaining intensity cut off of 2, increased thyrocyte staining was seen in follicular adenoma specimens, MNG and normal thyroids compared with Hashimoto's thyroiditis and Graves' disease (P < 0.05). Similarly, VEGF thyrocyte expression in Graves' disease was less than other pathologies (P < 0.05). VEGFR-1 expression and the average MVD score did not differ between the different thyroid pathologies. VEGF expression was lower in autoimmune pathologies compared to autonomous growth processes. Conversely, both VEGFR-1 and VEGFR-2 were widely expressed in benign and neoplastic thyroid disease, suggesting that the up-regulation of VEGF and not its receptors occurs as tissue becomes autonomous. There was no clear relationship between MVD measurement and thyroid pathology.
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