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Zhang P, Guan L, Sun W, Zhang Y, Du Y, Yuan S, Cao X, Yu Z, Jia Q, Zheng X, Meng Z, Li X, Zhao L. Targeting miR-31 represses tumourigenesis and dedifferentiation of BRAF V600E-associated thyroid carcinoma. Clin Transl Med 2024; 14:e1694. [PMID: 38797942 PMCID: PMC11128713 DOI: 10.1002/ctm2.1694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND BRAFV600E is the most common genetic mutation in differentiated thyroid cancer (DTC) occurring in 60% of patients and drives malignant tumour cell phenotypes including proliferation, metastasis and immune-escape. BRAFV600E-mutated papillary thyroid cancer (PTC) also displays greatly reduced expression of thyroid differentiation markers, thus tendency to radioactive iodine (RAI) refractory and poor prognosis. Therefore, understanding the molecular mechanisms and main oncogenic events underlying BRAFV600E will guide future therapy development. METHODS Bioinformatics and clinical specimen analyses, genetic manipulation of BRAFV600E-induced PTC model, functional and mechanism exploration guided with transcriptomic screening, as well as systematic rescue experiments were applied to investigate miR-31 function within BRAFV600E-induced thyroid cancer development. Besides, nanoparticles carrying miR-31 antagomirs were testified to alleviate 131I iodide therapy on PTC models. RESULTS We identify miR-31 as a significantly increased onco-miR in BRAFV600E-associated PTC that promotes tumour progression, metastasis and RAI refractoriness via sustained Wnt/β-catenin signalling. Mechanistically, highly activated BRAF/MAPK pathway induces miR-31 expression via c-Jun-mediated transcriptional regulation across in vitro and transgenic mouse models. MiR-31 in turn facilitates β-catenin stabilisation via directly repressing tumour suppressors CEBPA and DACH1, which direct the expression of multiple essential Wnt/β-catenin pathway inhibitors. Genetic functional assays showed that thyroid-specific knockout of miR-31 inhibited BRAFV600E-induced PTC progression, and strikingly, enhanced expression of sodium-iodide symporter and other thyroid differentiation markers, thus promoted 131I uptake. Nanoparticle-mediated application of anti-miR-31 antagomirs markedly elevated radio-sensitivity of BRAFV600E-induced PTC tumours to 131I therapy, and efficiently suppressed tumour progression in the pre-clinical mouse model. CONCLUSIONS Our findings elucidate a novel BRAF/MAPK-miR-31-Wnt/β-catenin regulatory mechanism underlying clinically BRAFV600E-associated DTC tumourigenesis and dedifferentiation, also highlight a potential adjuvant therapeutic strategy for advanced DTC.
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Affiliation(s)
- Peitao Zhang
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Lizhao Guan
- Department of Thyroid and Neck Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Sun
- Laboratory of molecular genetics, School of Medicine, Nankai University, Tianjin, China
| | - Yu Zhang
- Department of Thyroid and Neck Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yaying Du
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Shukai Yuan
- Department of Thyroid and Neck Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaolong Cao
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiang Jia
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhaowei Meng
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Li Zhao
- Department of Thyroid and Neck Oncology, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for Cancer, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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Van Branteghem C, Augenlicht A, Demetter P, Craciun L, Maenhaut C. Unraveling the Roles of miR-204-5p and HMGA2 in Papillary Thyroid Cancer Tumorigenesis. Int J Mol Sci 2023; 24:10764. [PMID: 37445942 PMCID: PMC10341554 DOI: 10.3390/ijms241310764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/15/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
Thyroid cancer is the most common endocrine malignant tumor with an increasing incidence rate. Although differentiated types of thyroid cancer generally present good clinical outcomes, some dedifferentiate into aggressive and lethal forms. However, the molecular mechanisms governing aggressiveness and dedifferentiation are still poorly understood. Aberrant expression of miRNAs is often correlated to tumor development, and miR-204-5p has previously been identified in papillary thyroid carcinoma as downregulated and associated with aggressiveness. This study aimed to explore its role in thyroid tumorigenesis. To address this, gain-of-function experiments were performed by transiently transfecting miR-204-5p in thyroid cancer cell lines. Then, the clinical relevance of our data was evaluated in vivo. We prove that this miRNA inhibits cell invasion by regulating several targets associated with an epithelial-mesenchymal transition, such as SNAI2, TGFBR2, SOX4 and HMGA2. HMGA2 expression is regulated by the MAPK pathway but not by the PI3K, IGF1R or TGFβ pathways, and the inhibition of cell invasion by miR-204-5p involves direct binding and repression of HMGA2. Finally, we confirmed in vivo the relationship between miR-204-5p and HMGA2 in human PTC and a corresponding mouse model. Our data suggest that HMGA2 inhibition offers promising perspectives for thyroid cancer treatment.
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Affiliation(s)
- Cindy Van Branteghem
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université libre de Bruxelles, 1070 Brussels, Belgium; (C.V.B.); (A.A.)
| | - Alice Augenlicht
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université libre de Bruxelles, 1070 Brussels, Belgium; (C.V.B.); (A.A.)
| | - Pieter Demetter
- Anatomie Pathologique, Hôpital Universitaire de Bruxelles, Université libre de Bruxelles, 1070 Brussels, Belgium; (P.D.); (L.C.)
| | - Ligia Craciun
- Anatomie Pathologique, Hôpital Universitaire de Bruxelles, Université libre de Bruxelles, 1070 Brussels, Belgium; (P.D.); (L.C.)
| | - Carine Maenhaut
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université libre de Bruxelles, 1070 Brussels, Belgium; (C.V.B.); (A.A.)
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De Martino M, Esposito F, Capone M, Pallante P, Fusco A. Noncoding RNAs in Thyroid-Follicular-Cell-Derived Carcinomas. Cancers (Basel) 2022; 14:cancers14133079. [PMID: 35804851 PMCID: PMC9264824 DOI: 10.3390/cancers14133079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Thyroid tumors represent the most common neoplastic pathology of the endocrine system. Mutations occurring in oncogenes and tumor suppressor genes are responsible for thyroid carcinogenesis; however, the complete mutational landscape characterizing these neoplasias has not been completely unveiled. It has been established that only the 2% of the human genome codes for proteins, suggesting that the vast majority of the genome has regulatory capabilities, which, if altered, could account for the onset of cancer. Hence, many scientific efforts are currently focused on the characterization of the heterogeneous class of noncoding RNAs, which represent an abundant part of the transcribed noncoding genome. In this review, we mainly focus on the involvement of microRNAs, long noncoding RNAs, and pseudogenes in thyroid cancer. The determination of the diagnosis, prognosis, and treatment of thyroid cancers based on the evaluation of the noncoding RNA network could allow the implementation of a more personalized approach to fighting these pathologies. Abstract Among the thyroid neoplasias originating from follicular cells, we can include well-differentiated carcinomas, papillary (PTC) and follicular (FTC) thyroid carcinomas, and the undifferentiated anaplastic (ATC) carcinomas. Several mutations in oncogenes and tumor suppressor genes have already been observed in these malignancies; however, we are still far from the comprehension of their full regulation-altered landscape. Even if only 2% of the human genome has the ability to code for proteins, most of the noncoding genome is transcribed, constituting the heterogeneous class of noncoding RNAs (ncRNAs), whose alterations are associated with the development of several human diseases, including cancer. Hence, many scientific efforts are currently focused on the elucidation of their biological role. In this review, we analyze the scientific literature regarding the involvement of microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and pseudogenes in FTC, PTC, and ATC. Recent findings emphasized the role of lncRNAs in all steps of cancer progression. In particular, lncRNAs may control progression steps by regulating the expression of genes and miRNAs involved in cell proliferation, apoptosis, epithelial–mesenchymal transition, and metastatization. In conclusion, the determination of the diagnosis, prognosis, and treatment of cancer based on the evaluation of the ncRNA network could allow the implementation of a more personalized approach to fighting thyroid tumors.
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Affiliation(s)
- Marco De Martino
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
| | - Francesco Esposito
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
| | - Maria Capone
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli “Federico II”, Via S. Pansini 5, 80131 Napoli, Italy
| | - Pierlorenzo Pallante
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
- Correspondence: (P.P.); (A.F.)
| | - Alfredo Fusco
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale (IEOS) “G. Salvatore”, Consiglio Nazionale delle Ricerche (CNR), Via S. Pansini 5, 80131 Napoli, Italy; (M.D.M.); (F.E.); (M.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli “Federico II”, Via S. Pansini 5, 80131 Napoli, Italy
- Correspondence: (P.P.); (A.F.)
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Papaioannou M, Chorti AG, Chatzikyriakidou A, Giannoulis K, Bakkar S, Papavramidis TS. MicroRNAs in Papillary Thyroid Cancer: What Is New in Diagnosis and Treatment. Front Oncol 2022; 11:755097. [PMID: 35186709 PMCID: PMC8851242 DOI: 10.3389/fonc.2021.755097] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction Papillary thyroid cancer (PTC) accounts for up to 80% of thyroid malignancies. New diagnostic and therapeutic options are suggested including innovative molecular methods. MicroRNAs (miRNAs) are nonprotein coding single-stranded RNAs that regulate many cell processes. The aim of the present study is to review the deregulated miRNAs associated with PTCs. Methods A bibliographic research was conducted, resulting in 272 articles referred to miRNAs and PTC. Regarding our exclusion criteria, 183 articles were finally included in our review. Results A remarkably large number of miRNAs have been found to be deregulated during PTC manifestation in the literature. The deregulated miRNAs are detected in tissue samples, serum/plasma, and FNA samples of patients with PTC. These miRNAs are related to several molecular pathways, involving genes and proteins responsible for important biological processes. MiRNA deregulation is associated with tumor aggressiveness, including larger tumor size, multifocality, extrathyroidal extension, lymphovascular invasion, lymph node and distant metastasis, and advanced tumor node metastasis stage. Conclusion MiRNAs are proposed as new diagnostic and therapeutic tools regarding PTC. They could be essential biomarkers for PTC diagnosis applied in serum and FNA samples, while their contribution to prognosis is of great importance.
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Affiliation(s)
- Maria Papaioannou
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Angeliki G. Chorti
- 1st Propedeutic Department of Surgery, American Hellenic Educational Progressive Association (AHEPA) University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anthoula Chatzikyriakidou
- Laboratory of Medical Biology, School of Medicine, Faculty of Health Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kleanthis Giannoulis
- 1st Propedeutic Department of Surgery, American Hellenic Educational Progressive Association (AHEPA) University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sohail Bakkar
- Department of Surgery, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Theodosios S. Papavramidis
- 1st Propedeutic Department of Surgery, American Hellenic Educational Progressive Association (AHEPA) University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Theodosios S. Papavramidis,
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Xia Y, Jiang X, Huang Y, Liu Q, Huang Y, Zhang B, Mei Z, Xu D, Shi Y, Tu W. Construction of a Tumor Immune Microenvironment-Related Prognostic Model in BRAF-Mutated Papillary Thyroid Cancer. Front Endocrinol (Lausanne) 2022; 13:895428. [PMID: 35757399 PMCID: PMC9215106 DOI: 10.3389/fendo.2022.895428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/05/2022] [Indexed: 12/14/2022] Open
Abstract
BRAF mutation is a representative oncogenic mutation, with a frequency of 60% in papillary thyroid carcinoma (PTC), but the reasons for the poor prognosis and more aggressive course of BRAF-mutated PTC are controversial. Tumor immune microenvironment (TIME) is an essential factor permitting the development and progression of malignancy, but whether TIME participates in the prognosis of BRAF-mutated PTC has not yet been reported. The primary goal of the present study was to provide a comprehensive TIME-related prognostic model to increase the predictive accuracy of progression-free survival (PFS) in patients with BRAF-mutated PTC. In this study, we analyzed the mRNA-seq data and corresponding clinical data of PTC patients obtained from the TCGA database. By calculating the TIME scores (immune score, stromal score and ESTIMATE score), the BRAF mutation group (n=237) was dichotomized into the high- and low-score groups. By functional analysis of differentially expressed genes (DEGs) in different high/low score groups, we identified 2 key TIME-related genes, HTR3A and NIPAL4, which affected PFS in BRAF-mutated PTC. A risk scoring system was developed by multivariate Cox analysis based on the abovementioned 2 TIME-related genes. Then, the BRAF-mutated cohort was divided into the high- and low-risk groups using the median risk score as a cutoff. A high risk score correlated positively with a higher HTR3A/NIPAL4 expression level but negatively with PFS in BRAF-mutated PTC. Ultimately, a nomogram was constructed by combining risk score with clinical parameter (Tumor stage), and the areas under the ROC curve (AUCs) of the nomogram for predicting 1-, 3- and 5-year PFS were then calculated and found to be 0.694, 0.707 and 0.738, respectively, indicating the improved accuracy and clinical utility of the nomogram versus the risk score model in the BRAF-mutated PTC cohort. Moreover, we determined the associations between prognostic genes or risk score and immune cell infiltration by two-way ANOVA. In the high-risk score, high HTR3A expression, and high NIPAL4 expression groups, higher infiltration of immune cells was found. Collectively, these findings confirm that the nomogram is effective in predicting the outcome of BRAF-mutated PTC and will add a spatial dimension to the developing risk stratification system.
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Affiliation(s)
- Yuxiao Xia
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Xue Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuan Huang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Qian Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yin Huang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Bo Zhang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Zhanjun Mei
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Dongkun Xu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
- *Correspondence: Wenling Tu, ; Yuhong Shi,
| | - Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
- *Correspondence: Wenling Tu, ; Yuhong Shi,
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Li M, Zhang J, Zhang Z, Qian Y, Qu W, Jiang Z, Zhao B. Identification of Transcriptional Pattern Related to Immune Cell Infiltration With Gene Co-Expression Network in Papillary Thyroid Cancer. Front Endocrinol (Lausanne) 2022; 13:721569. [PMID: 35185791 PMCID: PMC8854657 DOI: 10.3389/fendo.2022.721569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/06/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A growing body of evidence suggests that immune cell infiltration in cancer is closely related to clinical outcomes. However, there is still a lack of research on papillary thyroid cancer (PTC). METHODS Based on single-sample gene set enrichment analysis (SSGSEA) algorithm and weighted gene co-expression network analysis (WGCNA) tool, the infiltration level of immune cell and key modules and genes associated with the level of immune cell infiltration were identified using PTC gene expression data from The Cancer Genome Atlas (TCGA) database. In addition, the co-expression network and protein-protein interactions network analysis were used to identify the hub genes. Moreover, the immunological and clinical characteristics of these hub genes were verified in TCGA and GSE35570 datasets and quantitative real-time polymerase chain reaction (PCR). Finally, receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value of hub genes. RESULTS Activated B cell, activated dendritic cell, CD56bright natural killer cell, CD56dim natural killer cell, Eosinophil, Gamma delta T cell, Immature dendritic cell, Macrophage, Mast cell, Monocyte, Natural killer cell, Neutrophil and Type 17 T helper cell were significantly changed between PTC and adjacent normal groups. WGCNA results showed that the black model had the highest correlation with the infiltration level of activated dendritic cells. We found 14 hub genes whose expression correlated to the infiltration level of activated dendritic cells in both TCGA and GSE35570 datasets. After validation in the TCGA dataset, the expression level of only 5 genes (C1QA, HCK, HLA-DRA, ITGB2 and TYROBP) in 14 hub genes were differentially expressed between PTC and adjacent normal groups. Meanwhile, the expression levels of these 5 hub genes were successfully validated in GSE35570 dataset. Quantitative real-time PCR results showed the expression of these 4 hub genes (except C1QA) was consistent with the results in TCGA and GSE35570 dataset. Finally, these 4 hub genes had diagnostic value to distinguish PTC and adjacent normal controls. CONCLUSIONS HCK, HLA-DRA, ITGB2 and TYROBP may be key diagnostic biomarkers and immunotherapy targets in PTC.
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Affiliation(s)
- Meiye Li
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Jimei Zhang
- School of Pharmacy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Zongjing Zhang
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Ying Qian
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Wei Qu
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
| | - Zhaoshun Jiang
- Department of Endocrinology, No. 960 Hospital of PLA Joint Logistics Support Force, Jinan, China
- *Correspondence: Baochang Zhao, ; Zhaoshun Jiang,
| | - Baochang Zhao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
- *Correspondence: Baochang Zhao, ; Zhaoshun Jiang,
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Yang X, Fang L, Zhang C. CNV Analysis of the Correlation between Preoperative Lymph Node Metastasis and Prognosis of Early Tongue Cancer. J Cancer 2021; 12:6135-6144. [PMID: 34539886 PMCID: PMC8425219 DOI: 10.7150/jca.60447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/07/2021] [Indexed: 11/17/2022] Open
Abstract
Objective: To investigate the relationship between preoperative concealed lymph node metastasis (LNM) and prognosis in patients with early tongue cancer. Methods: According to preoperative lymph node dissection, 41 patients with tongue cancer were divided into the LNM group (n=19) and the non-LNM group (n=22). Analysis of single nucleotide variation (SNV), tumor mutation burden (TMB), mutant allele tumor heterogeneity (MATH), aneuploidy and copy number variation (CNV) was performed to identify differentially expressed genes (DEGs) related to LNM. While KEGG analysis was conducted to reveal the CNV differentially expressed genes and main enriched pathways, the correlation between pathways and genes was analyzed by hierarchical clustering. The clinical information of LNM and data on overall survival (OS) rate were obtained from The Cancer Genome Atlas (TCGA), and survival analysis was performed based on combined LNM information. Results: We observed significant correlations for the mTOR signaling pathway, Hippo signaling pathway and Wnt signaling pathway with the LNM group, while leukocyte transendothelial migration and cytokine-cytokine receptor interaction were markedly correlated with the non-LNM group. Moreover, TNFRSF10C was identified as the main DEG in the leukocyte transendothelial migration pathway. TCGA-based validation revealed that the disease-free survival (DFS) of the non-LNM group was significantly higher than that of the LNM group (P<0.005) when TNFRSF10C CNV was set to a log2 ratio>-0.163. Conclusion: The differential expression of TNFRSF10C in leukocyte transendothelial migration, an immune-related pathway, is associated with LNM and DFS. The TNFRSF10C CNV log2 ratio could potentially serve as an indicator of good prognosis for tongue cancer patients with non-LNM after neck dissection.
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Affiliation(s)
- Xi Yang
- Department of Oral & MaxillofacialeHead & Neck Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China
| | - Lu Fang
- Genecast Biotechnology Co., Ltd, Wuxi 214104, China
| | - Chenping Zhang
- Department of Oral & MaxillofacialeHead & Neck Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China
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Next-Generation Biomarkers in Multiple Myeloma: Understanding the Molecular Basis for Potential Use in Diagnosis and Prognosis. Int J Mol Sci 2021; 22:ijms22147470. [PMID: 34299097 PMCID: PMC8305153 DOI: 10.3390/ijms22147470] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022] Open
Abstract
Multiple myeloma (MM) is considered to be the second most common blood malignancy and it is characterized by abnormal proliferation and an accumulation of malignant plasma cells in the bone marrow. Although the currently utilized markers in the diagnosis and assessment of MM are showing promising results, the incidence and mortality rate of the disease are still high. Therefore, exploring and developing better diagnostic or prognostic biomarkers have drawn global interest. In the present review, we highlight some of the recently reported and investigated novel biomarkers that have great potentials as diagnostic and/or prognostic tools in MM. These biomarkers include angiogenic markers, miRNAs as well as proteomic and immunological biomarkers. Moreover, we present some of the advanced methodologies that could be utilized in the early and competent diagnosis of MM. The present review also focuses on understanding the molecular concepts and pathways involved in these biomarkers in order to validate and efficiently utilize them. The present review may also help in identifying areas of improvement for better diagnosis and superior outcomes of MM.
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Yu W, Ma B, Zhao W, Liu J, Yu H, Tian Z, Fan Z, Han H. The combination of circRNA-UMAD1 and Galectin-3 in peripheral circulation is a co-biomarker for predicting lymph node metastasis of thyroid carcinoma. Am J Transl Res 2020; 12:5399-5415. [PMID: 33042427 PMCID: PMC7540136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The diagnosis of lymph node metastasis (LNM) by liquid biopsy is a novel concept prompted by the necessity to develop a more convenient and accurate method to guide the clinical management of early LNM in papillary thyroid carcinoma (PTC). However, the sensitivity and specificity of many biomarkers are not high enough. We aimed to detect circRNAs from peripheral circulation that may be better associated with the prognosis of LNM in PTC. First, Galectin-3 (Gal3) in blood was determined to be highly expressed in LNM patients. Second, based on a bioinformatics analysis and miRNA sequencing analysis from 2 paired primary and LNM tumors, miR-873 was identified to directly target Gal3, which was significantly associated with clinical parameters including LNM. Third, from additional circRNA sequencing, circRNA-UMAD1 was selected as a specific sponge for miR-873 and was correlated with Gal3 levels in peripheral circulation. Fourth, circRNA-UMAD1 and Gal3 were identified to have stronger co-biomarker potential with relatively high expression in the serum of LNM patients compared with primary tumor patients, as demonstrated by the RNA expression levels in the serum of 50 PTC patients with or without LNM by quantitative real-time PCR. Overall, the combination of circRNA-UMAD1 and Gal3 is a useful and effective co-biomarker for the prognosis of LNM in PTC patients. This new molecular typing method for LNM in PTC is more precise.
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Affiliation(s)
- Wenbin Yu
- Department of Hand and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
| | - Bo Ma
- Department of Lymphoma, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
| | - Wei Zhao
- Department of Cell Biology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
| | - Jingtao Liu
- Department of Pharmacy, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
| | - Hao Yu
- Department of Hand and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
| | - Zhihua Tian
- Department of Central Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
| | - Zhiqin Fan
- Day Surgery Department, Affiliated Tumor Hospital of Xinjiang Medical UniversityUrumqi 830011, P. R. China
| | - Haibo Han
- Department of Clinical Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and InstituteBeijing 100142, P. R. China
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10
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Liu D, Li P, Wang X, Wang W. hsa-miR-195-5p inhibits cell proliferation of human thyroid carcinoma cells via modulation of p21/cyclin D1 axis. Transl Cancer Res 2020; 9:5190-5199. [PMID: 35117886 PMCID: PMC8799136 DOI: 10.21037/tcr-20-1083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022]
Abstract
Background Based on existing evidence, microRNAs (miRs) are gene regulators that undertake key functions in the oncogenesis and tumor progression of every single human malignant disease, such as thyroid carcinoma (TC). Previous clinical findings showed that expression of miR-195 is down-regulated in TC, which implies that miR-195 may be practically involved in TC pathogenesis. Nevertheless, the function of hsa-miR-195-5p in TC is still largely unclear. Herein, we detected the conceivable involvement of hsa-miR-195-5p in TC cell proliferation. Methods Real time PCR examination was performed to assess the expression level of hsa-miR-195-5p in TC cell lines TPC-1 and B-CPAP. TPC-1 cells were transfected with either hsa-miR-195-5p mimics or hsa-miR-195-5p inhibitor. After confirmation of transfection efficiency, the effect of hsa-miR-195-5p on proliferation and cell cycle of TPC-1 cells was assessed. The expression of cyclin D1 and p21 was simultaneously detected by western blotting. Moreover, targetScan 6.2 was used to predict hsa-miR-195-5p target genes. Subsequently, luciferase reporter was performed to examine whether there is a possible binding of hsa-miR-195-5p to 3’-UTR of cyclin D1 mRNA. Furthermore, cyclin D1 mRNA and protein levels were measured to check whether hsa-miR-195-5p exerts its function at the post-transcriptional level. In addition, to explore the function of cyclin D1 in TPC-1 cells overexpressing hsa-miR-195-5p, cyclin D1 siRNA was used to silence the expression of cyclin D1 in TPC-1 cells overexpressing hsa-miR-195-5p. Results We quantified the expression of hsa-miR-195-5p in TC cells and normal thyroid cells and found a remarkable decrease in hsa-miR-195-5p expression in TC cells. Over-expression of hsa-miR-195-5p obviously resulted in downgraded proliferation of TC cells. Moreover, hsa-miR-195-5p caused cell arrest at the GO/G1 phase. Further in silico analyses and the dual-luciferase reporter assay confirmed that 3’-UTR of cyclin D1 is a direct target of hsa-miR-195-5p. Western blot analysis uncovered that hsa-miR-195-5p over-expression led to decreased levels of cyclin D1 and p21. In mechanistic analyses, we found that silencing of cyclin D1 reversed the inhibitory effect of hsa-miR-195-5p on the proliferation of TC cells, which indicates that hsa-miR-195-5p suppresses TC cell proliferation by adversely regulating cyclin D1. Conclusions We concluded that hsa-miR-195-5p is a candidate tumor-suppressor miRNA in TC and that the hsa-miR-195-5p/p21/cyclin D1 pathway could be a potential therapeutic target for TC.
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Affiliation(s)
- Dexin Liu
- Department of Radiology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Ping Li
- Department of Radiology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xiaodong Wang
- Department of Radiology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Wei Wang
- Department of Radiology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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11
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Differential MicroRNA-Signatures in Thyroid Cancer Subtypes. JOURNAL OF ONCOLOGY 2020; 2020:2052396. [PMID: 32565797 PMCID: PMC7290866 DOI: 10.1155/2020/2052396] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/05/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022]
Abstract
Thyroid cancer is one of the most common endocrine cancers, with an increasing trend in the last few decades. Although papillary thyroid cancer is the most frequent subtype compared with follicular or anaplastic thyroid cancer, it can dedifferentiate to a more aggressive phenotype, and the recurrence rate is high. The cells of follicular adenomas and follicular carcinomas appear identical in cytology, making the preoperative diagnosis difficult. On the other hand, anaplastic thyroid cancer poses a significant clinical challenge due to its aggressive nature with no effective therapeutic options. In the past several years, the roles of genetic alterations of thyroid tumors have been documented, with a remarkable correlation between genotype and phenotype, indicating that distinct molecular changes are associated with a multistep tumorigenic process. Besides mRNA expression profiles, small noncoding microRNA (miRNA) expression also showed critical functions for cell differentiation, proliferation, angiogenesis, and resistance to apoptosis and finally activating invasion and metastasis in cancer. Several high-throughput sequencing studies demonstrate that miRNA expression signatures contribute clinically relevant information including types of thyroid cancer, tumor grade, and prognosis. This review summarizes recent findings on miRNA signatures in thyroid cancer subtypes.
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12
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13
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Yusof AM, Jamal R, Saidin S, Muhammad R, Suhaimi SNA, Rose IM, Nazarie WFW, Fu FTY, Mutalib NSA. Deep Small RNA Sequencing of BRAF V600E Mutated Papillary Thyroid Carcinoma With Lymph Node Metastasis. Front Genet 2019; 10:941. [PMID: 31649724 PMCID: PMC6791926 DOI: 10.3389/fgene.2019.00941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023] Open
Affiliation(s)
- Azliana Mohamad Yusof
- Cytogenetics and Molecular Diagnostics Laboratory, Pantai Premier Pathology Sdn Bhd, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Sazuita Saidin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rohaizak Muhammad
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Isa Mohamed Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Wan Fahmi Wan Nazarie
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Francis Tieng Yew Fu
- Institute of Bioscience (IBS), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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14
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Li J, Luo M, Ou H, Liu X, Kang X, Yin W. Integrin β4 promotes invasion and anoikis resistance of papillary thyroid carcinoma and is consistently overexpressed in lymphovascular tumor thrombus. J Cancer 2019; 10:6635-6648. [PMID: 31777592 PMCID: PMC6856897 DOI: 10.7150/jca.36125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Although the majority of papillary thyroid cancers (PTC) are indolent, a subset of PTCs behaves aggressively due to extensive invasion and distant metastasis. Integrin β4, a member of the integrin family, has been shown to enhance the progression in some malignancies; however, its role in PTC remains unclear. Here, we demonstrated that β4 overexpression was associated with extrathyroid extension, lymph node metastasis, high TNM stage, and poor overall survival based on The Cancer Genome Atlas cohort. Immunohistochemistry showed that β4 expression was significantly upregulated in the tumors with infiltrating growth pattern, as well as those with positive lymphovascular invasion. Moreover, β4 was invariably overexpressed in the lymphovascular tumor thrombi, which has not been reported before. After shRNA-induced knockdown of β4 in vitro, the migration, invasion and scratch repair ability of the tumor cells were significantly reduced. Furthermore, β4 reduction decreased anchorage-independent growth and increased anoikis. The bioinformatics analysis revealed that approximately 70 pathways were significantly dysregulated in the high β4 expression group. The MAPK pathway and propanoate metabolism were located in the network center of those pathways. Taken together, our results suggest that β4 could promote the tumor's aggressiveness by enhancing invasion and antagonizing anoikis. The upregulated expression of β4 in the tumor thrombi is intrinsically linked to its role in strengthening the anoikis resistance.
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Affiliation(s)
- Jian Li
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, 518036, China.,State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong Province, 518055, China
| | - Minghua Luo
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, 518036, China
| | - Huiting Ou
- Department of Endocrinology, Shenzhen Second People's Hospital, Guangdong Province, 518035, China
| | - Xiaoling Liu
- Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, 518036, China
| | - Xueling Kang
- Department of Oncology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, 518036, China
| | - Weihua Yin
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, 518036, China
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15
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Qi L, Zhang T, Yao Y, Zhuang J, Liu C, Liu R, Sun C. Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network. PeerJ 2019; 7:e7727. [PMID: 31576252 PMCID: PMC6753923 DOI: 10.7717/peerj.7727] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/22/2019] [Indexed: 12/24/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) play a role in the formation, development, and prognosis of various cancers. Our study aimed to identify prognostic-related lncRNAs in lung squamous cell carcinoma (LUSC), which may provide new perspectives for individualized treatment of patients. Materials and Methods The RNA sequencing (lncRNA, microRNA (miRNA), mRNA) data and clinical information related to LUSC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA sequences were used to construct the competitive endogenous RNA (ceRNA) network. In present study, we mainly used two prognostic verification methods, Cox analysis and survival analysis, to identify the prognostic relevance of specific lncRNAs and construct prognostic model of lncRNA. Results Datasets on 551 samples of lncRNA and mRNA and 523 miRNA samples were retrieved from the TCGA database. Analysis of the normal and LUSC samples identified 170 DElncRNAs, 331 DEmiRNAs, and 417 DEmRNAs differentially expressed RNAs. The ceRNA network contained 27 lncRNAs, 43 miRNAs, and 11 mRNAs. Furthermore, we identified seven specific lncRNAs (ERVH48-1, HCG9, SEC62-AS1, AC022148.1, LINC00460, C5orf17, LINC00261) as potential prognostic factors after correlation analysis, and five of the seven lncRNAs (AC022148.1, HCG9, LINC00460, C5orf17, LINC00261) constructed a prognostic model of LUSC. Conclusion In present study, we identified seven lncRNAs in the ceRNA network that are associated with potential prognosis in LUSC patients, and constructed a prognostic model of LUSC which can be used to assess the prognosis risk of clinical patients. Further biological experiments are needed to elucidate the specific molecular mechanisms underlying them.
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Affiliation(s)
- Lingyu Qi
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tingting Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Tuersong T, Li L, Abulaiti Z, Feng S. Comprehensive analysis of the aberrantly expressed lncRNA‑associated ceRNA network in breast cancer. Mol Med Rep 2019; 19:4697-4710. [PMID: 31059025 PMCID: PMC6522813 DOI: 10.3892/mmr.2019.10165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/01/2019] [Indexed: 12/11/2022] Open
Abstract
Previous studies have suggested that long non-coding RNAs (lncRNAs) are closely associated with human diseases, particularly cancer, including cancer of the lung, breast and stomach. A variety of lncRNAs are abnormally expressed in cancer and participate in several pathways including cell proliferation and apoptosis; these elements are closely associated with the development of cancer. The Cancer Genome Atlas (TCGA) is an important cancer database. It consists of clinical data, genomic variation, mRNA, microRNA (miRNA) and lncRNAs expression, methylation and other data for various types of human cancer. In the present study, differential expression of RNA was identified using the edgeR package. A total 1,222 RNA sequencing profiles from patients with breast cancer were downloaded from TCGA. A competing endogenous RNA (ceRNA) network was constructed for breast cancer based on miRcode and miRTarBase. The top 10 lncRNAs were selected using Cox regression analysis. Survival analysis was performed using Kaplan-Meier analysis. A total of 1,028 breast cancer-associated lncRNAs and 89 miRNAs (fold change >2; P<0.05) were identified; among these, 93 lncRNAs and 19 miRNAs were included in the ceRNA network. Subsequently, 10 basic lncRNAs were selected and their associations with overall survival were identified. In addition, 5 lncRNAs (ADAM metallopeptidase with thrombospondin type 1 motif 9-antisense RNA 1, AL513123.1, chromosome 10 open reading frame 126, long intergenic non-protein coding RNA 536 and Wilms tumor 1 antisense RNA) were identified to be significantly associated with overall survival (P<0.05, log rank test). These results suggested that mRNAs, lncRNAs and miRNAs were involved in pathological mechanisms of breast cancer. The newly-identified ceRNA network included 93 breast cancer-specific lncRNAs, 19 miRNAs and 27 mRNAs. The results of the present study highlight the potential of lncRNAs in understanding the development and pathogenesis of breast cancer, and suggest novel concepts and an experimental basis for the identification of prognostic biomarkers and therapeutic targets for breast cancer.
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Affiliation(s)
- Tayier Tuersong
- Department of Pharmacology, Pharmacy College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
| | - Linlin Li
- Department of Pharmacology, Pharmacy College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
| | - Zumureti Abulaiti
- Department of Internal Medicine, Traditional Medical College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
| | - Shumei Feng
- Department of Histology and Embryology, Basic Medical Sciences College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
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Lin P, Guo YN, Shi L, Li XJ, Yang H, He Y, Li Q, Dang YW, Wei KL, Chen G. Development of a prognostic index based on an immunogenomic landscape analysis of papillary thyroid cancer. Aging (Albany NY) 2019; 11:480-500. [PMID: 30661062 PMCID: PMC6366981 DOI: 10.18632/aging.101754] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/29/2018] [Indexed: 04/24/2023]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common subtype of thyroid cancer, and inflammation relates significantly to its initiation and prognosis. Systematic exploration of the immunogenomic landscape therein to assist in PTC prognosis is therefore urgent. The Cancer Genome Atlas (TCGA) project provides a large number of genetic PTC samples that enable a comprehensive and reliable immunogenomic study. METHODS We integrated the expression profiles of immune-related genes (IRGs) and progression-free intervals (PFIs) in survival in 493 PTC patients based on the TCGA dataset. Differentially-expressed and survival-associated IRGs in PTC patients were estimated a computational difference algorithm and COX regression analysis. The potential molecular mechanisms and properties of these PTC-specific IRGs were also explored with the help of computational biology. A new prognostic index based on immune-related genes was developed by using multivariable COX analysis. RESULTS A total of 46 differentially expressed immune-related genes were significantly correlated with clinical outcome of PTC patients. Functional enrichment analysis revealed that these genes were actively involved in a cytokine-cytokine receptor interaction KEGG pathway. A prognostic signature based on RGs (AGTR1, CTGF, FAM3B, IL11, IL17C, PTH2R and SPAG11A) performed moderately in prognostic predictions and correlated with age, tumor stage, metastasis, number of lesions, and tumor burden. Intriguingly, the prognostic index based on IRGs reflected infiltration by several types of immune cells. CONCLUSIONS Together, our results screened several IRGs of clinical significance, revealed drivers of the immune repertoire, and demonstrated the importance of a personalized, IRG-based immune signature in the recognition, surveillance, and prognosis of PTC.
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Affiliation(s)
- Peng Lin
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yi-nan Guo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Lin Shi
- Department of Pathology, Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Xiao-jiao Li
- Department of PET/CT, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Hong Yang
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yun He
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Qing Li
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yi-wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Kang-lai Wei
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
- Department of Pathology, Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
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18
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Yang XH, Yang K, An YL, Wang LB, Luo G, Hu XH. MicroRNA-705 regulates the differentiation of mouse mandible bone marrow mesenchymal stem cells. PeerJ 2019; 7:e6279. [PMID: 30648022 PMCID: PMC6330203 DOI: 10.7717/peerj.6279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
The craniofacial skeleton is the foundation of most stomatological treatments, including prosthodontics and maxillofacial surgery. Although histologically similar to the appendicular skeleton, the craniofacial skeleton manifests many unique properties in response to external stimuli and signals. However, the mandibular or maxillary bone marrow mesenchyme, which is the intrinsic foundation of the functions of craniofacial skeleton, has not been well studied, and its homeostasis mechanism remains elusive. Osteoporosis is a systemic disease that affects all skeletons and is characterized by bone mass loss. Osteoporotic bone marrow mesenchymal stem cells (BMMSCs) exhibit disturbed homeostasis and distorted lineage commitment. Many reports have shown that microRNAs (miRNAs) play important roles in regulating MSCs homeostasis. Here, to obtain a better understanding of mandibular bone marrow MSCs homeostasis, we isolated and cultured mandible marrow MSCs from mouse mandibles. Using miR-705 mimics and an inhibitor, we demonstrated that miR-705 played a vital role in shifting the mandibular MSCs lineage commitment in vitro. Utilizing an osteoporosis mouse model, we demonstrated that MSCs from ovariectomized (OVX) mouse mandibular bone marrow exhibited impaired osteogenic and excessive adipogenic differentiation. miR-705 was found overexpressed in OVX mandibular MSCs. The knock down of miR-705 in vitro partially attenuated the differentiation disorder of the OVX mandibular MSCs by upregulating the expression of osteogenic marker genes but suppressing adipogenic genes. Taken together, our findings provide a better understanding of the homeostasis mechanism of mandibular BMMSCs and a novel potential therapeutic target for treating mandibular osteoporosis.
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Affiliation(s)
- Xiao Hong Yang
- Department of Prosthetics, the Affiliated Stomatology Hospital of Zunyi Medical University, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kun Yang
- Department of Periodontology, the Affiliated Stomatology Hospital of Zunyi Medical University, Zunyi Medical university, Zunyi, Guizhou, China
| | - Yu Lin An
- Department of Stomatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Li Bo Wang
- Department of Prosthetics, the Affiliated Stomatology Hospital of Zunyi Medical University, Zunyi Medical University, Zunyi, Guizhou, China.,Department of Stomatology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guo Luo
- Department of Stomatology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xiao Hua Hu
- Department of Oral and Maxillofacial Surgery, the Affiliated Stomatology Hospital of Zunyi Medical University, Zunyi, Guizhou, China
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Gao C, Li H, Zhuang J, Zhang H, Wang K, Yang J, Liu C, Liu L, Zhou C, Sun C. The construction and analysis of ceRNA networks in invasive breast cancer: a study based on The Cancer Genome Atlas. Cancer Manag Res 2018; 11:1-11. [PMID: 30588106 PMCID: PMC6301306 DOI: 10.2147/cmar.s182521] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Studies have shown that long noncoding RNAs (lncRNAs) make up the major proportion of the ceRNA network and can regulate gene expression by competitively binding to miRNAs. This reveals the existence of an RNA-miRNA regulatory pathway and is of great biological significance. CeRNAs, as competitive endogenous RNAs, have revealed a new mechanism of interaction between RNAs. Until now, the role of lncRNA-mediated ceRNAs in breast cancer and their regulatory mechanisms have been elucidated to some extent. Purpose In this study, comprehensive analysis of large-scale invasive breast cancer samples in TCGA were conducted to further explore the developmental mechanism of invasive breast cancer and the potential predictive markers for invasive breast cancer prognosis in the ceRNA network. Methods Abnormal expression profiles of invasive breast cancer associated mRNAs, lncRNAs and miRNAs were obtained from the TCGA database. Through further alignment and prediction of target genes, an abnormal lncRNA-miRNA-mRNA ceRNA network was constructed for invasive breast cancer. Through the overall survival analysis, Identification prognostic bio-markers for invasive breast cancer patients. In addition, we used Cytoscape plug-in BinGo for the different mRNA performance functional cluster analysis. Results Differential analysis revealed that 1059 lncRNAs, 86 miRNAs, and 2138 mRNAs were significantly different in invasive breast cancer samples versus normal samples. Then we construct an abnormal lncRNA-miRNA-mRNA ceRNA network for invasive breast cancer, consisting of 90 DElncRNAs, 18 DEmiRNAs and 26 DEmRNAs.Further, 4 out of 90 lncRNAs, 3 out of 26 mRNAs, and 2 out of 18 miRNAs were useful as prognostic biomarkers for invasive breast cancer patients (P value < 0.05). It is worth noting that based on the ceRNA network, we found that the LINC00466-Hsa-mir-204- NTRK2 LINC00466-hsa-mir-204-NTRK2 axis was present in 9 RNAs associated with the prognosis of invasive breast cancer. Conclusion This study provides an effective bioinformatics basis for further understanding of the molecular mechanism of invasive breast cancerand for predicting outcomes, which can guide the use of invasive breast cancerdrugs and subsequent related research.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People's Republic of China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People's Republic of China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
| | - HongXiu Zhang
- Institute of Virology, Jinan Center for Disease Control and Prevention, Jinan 250021, People's Republic of China
| | - Kejia Wang
- College of Basic Medicine, Qingdao University, Qingdao 266071, People's Republic of China
| | - Jing Yang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China,
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People's Republic of China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
| | - Chao Zhou
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
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Luo D, Zhan S, Xia W, Huang L, Ge W, Wang T. Proteomics study of serum exosomes from papillary thyroid cancer patients. Endocr Relat Cancer 2018; 25:879-891. [PMID: 29895528 DOI: 10.1530/erc-17-0547] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 01/11/2023]
Abstract
Lymph node metastasis (LNM) in papillary thyroid cancer (PTC) is related to increased risk of recurrence and poor prognosis. Tumour exosomes have been shown to be associated with metastasis of cancer cells. Therefore, we aim to identify the characteristics and biological functions of serum exosomes in lymph node metastases of PTC. We compared proteome profiles of serum-purified exosomes (SPEs) from PTC patients with LNM, PTC patients without LNM, and healthy donors, using a combination of liquid chromatography-tandem mass spectroscopy analyses and tandem mass tag label quantitation analysis. We identified 1569 proteins by two or more unique peptides. Compared with the SPEs of PTC patients without LNM, we found 697 differentially expressed proteins in the SPEs of PTC patients with LNM. Our results revealed overexpression of specific proteins with well-established links to cancer cell metastasis, such as SRC, TLN1, ITGB2 and CAPNS1. Consistent with mass spectrum results, we performed Western blot to detect the expression of these proteins in individual sample. Biological pathway analyses showed that integrin signalling was aberrantly activated in the SPEs of PTC patients with LNM compared to those without LNM. Our study reveals that SPEs of PTC patients with lymph node metastases promote BHT101 thyroid cancer cell invasiveness, but have no apparent influence on cell migration. In the serum exosomes of PTC patients with LNM, integrin-associated proteins are obviously upregulated. These proteomic findings will contribute to elucidation of the pathophysiological functions of tumour-derived exosomes.
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Affiliation(s)
- Dan Luo
- National Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Shaohua Zhan
- National Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenchao Xia
- National Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Liang Huang
- Department of Blood TransfusionTongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Ge
- National Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianxiao Wang
- Department of Head and Neck SurgeryKey Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing, China
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Wang X, Huang S, Li X, Jiang D, Yu H, Wu Q, Gao C, Wu Z. A potential biomarker hsa-miR-200a-5p distinguishing between benign thyroid tumors with papillary hyperplasia and papillary thyroid carcinoma. PLoS One 2018; 13:e0200290. [PMID: 30005075 PMCID: PMC6044525 DOI: 10.1371/journal.pone.0200290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/22/2018] [Indexed: 12/16/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common endocrine cancer with a significantly increase of the incidence recently. Several cytokines, such as thyroid peroxidase (TPO), cluster of differentiation 56 (CD56), Galectin-3, mesothelial cell (MC), cytokeratin 19 (CK19) and BRAF (B-raf) were recommended to be tested by immunohistochemistry (IHC) for a definitive diagnosis, but were still limited in clinical use because of their relative lower sensitivity and specificity. MicroRNA (miRNA), as a new molecular biomarkers, however, has not been reported yet so far. To address this, hsa-miR-200a-5p, a miRNA, was selected and detected in PTC patients by in situ hybrization with benign thyroid tumor with papillary hyperplasia as a control, and the differential expression of hsa-miR-200a-5p between fresh PTC tissues and control was detected by qRT-PCR. Expressive levels of cytokines of TPO, CD56, Galectin-3, MC, CK19 and B-raf were also detected by immunohistochemistry. The correlation was analyzed by SPSS software using Spearman methods. As expected, the hsa-miR-200a-5p expressive level was significantly increased in PTC patients, compared to that of control, and was consistent with that of TPO, CD56, Galectin-3, MC, CK19 and B-raf. In addition, expression of hsa-miR-200a-5p showed negative correlation to that of TPO (rs = - 0.734; **: P < 0.01) and CD56 (rs = - 0.570; **: P < 0.01), but positive correlation to that of Galectin-3 (rs = 0.601; **: P < 0.01), MC (rs = 0.508; **: P < 0.01), CK19 (rs = 0.712; **: P < 0.01) and B-raf (rs = 0.378; **: P < 0.01). PTC and papillary benign thyroid papillary hyperplasia are difficult to distinguish in morphology, so requiring immunohistochemistry to further differentiate the diagnosis, however, for the existing clinical common diagnostic marker for immunohistochemistry, the sensitivity and accuracy are low, it is easy to miss diagnosis. Therefore, there is an urgent need for a rapid and sensitive molecular marker. So miR-200a-5p can be used to assist in the diagnosis of PTC at the molecular level, and as a biomarker, can be effectively used to distinguish between PTC and benign thyroid tumor with papillary hyperplasia.
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Affiliation(s)
- Xian Wang
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shan Huang
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaocan Li
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dongrui Jiang
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hongzhen Yu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiang Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Chaobing Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhengsheng Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
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Liu Z, Zhang J, Gao J, Li Y. MicroRNA-4728 mediated regulation of MAPK oncogenic signaling in papillary thyroid carcinoma. Saudi J Biol Sci 2018; 25:986-990. [PMID: 30108452 PMCID: PMC6088101 DOI: 10.1016/j.sjbs.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 12/24/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer that accounts for 85% of thyroid cancers. MicroRNAs (miRNAs) have been reported to play important roles in the biological processes in cancer. In this study, we analyzed the biological role of miR-4728 in human PTC process in human PTC cell lines in vitro. MiRNA-4728 was observed to down-regulated in human PTC tissues and PTC cell lines. Additionally, miR-4728 inhibited PTC cell proliferation. Further study demonstrated SOS1 was repressed by miR-4728 and overexpression of miR-4728 down-regulated both the mRNA and protein levels of SOS1. Moreover, miR-4728 overexpression also decreased the MAPK signaling activity. These observations suggested that miR-4728 could inhibit the process of human PTC through regulating MAPK signaling pathway. And, appropriate regulation of miR-4728 might be vital to improve human PTC treatment.
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Affiliation(s)
- Zhibao Liu
- Hebei Cangzhou Central Hospital, Cangzhou 061001, PR China
| | - Jinghua Zhang
- Hebei Cangzhou Central Hospital, Cangzhou 061001, PR China
| | - Jinghua Gao
- Hebei Cangzhou Central Hospital, Cangzhou 061001, PR China
| | - Yunnan Li
- Massey University, Private Bag 11, 222 Palmerston North, 4442, New Zealand
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Ho SY, Chang BH, Chung CH, Lin YL, Chuang CH, Hsieh PJ, Huang WC, Tsai NM, Huang SC, Liu YK, Lo YC, Liao KW. Development of a computational promoter with highly efficient expression in tumors. BMC Cancer 2018; 18:480. [PMID: 29703163 PMCID: PMC5924487 DOI: 10.1186/s12885-018-4421-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/22/2018] [Indexed: 11/25/2022] Open
Abstract
Background Gene therapy is a potent method to increase the therapeutic efficacy against cancer. However, a gene that is specifically expressed in the tumor area has not been identified. In addition, nonspecific expression of therapeutic genes in normal tissues may cause side effects that can harm the patients’ health. Certain promoters have been reported to drive therapeutic gene expression specifically in cancer cells; however, low expression levels of the target gene are a problem for providing good therapeutic efficacy. Therefore, a specific and highly expressive promoter is needed for cancer gene therapy. Methods Bioinformatics approaches were utilized to analyze transcription factors (TFs) from high-throughput data. Reverse transcription polymerase chain reaction, western blotting and cell transfection were applied for the measurement of mRNA, protein expression and activity. C57BL/6JNarl mice were injected with pD5-hrGFP to evaluate the expression of TFs. Results We analyzed bioinformatics data and identified three TFs, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), cyclic AMP response element binding protein (CREB), and hypoxia-inducible factor-1α (HIF-1α), that are highly active in tumor cells. Here, we constructed a novel mini-promoter, D5, that is composed of the binding sites of the three TFs. The results show that the D5 promoter specifically drives therapeutic gene expression in tumor tissues and that the strength of the D5 promoter is directly proportional to tumor size. Conclusions Our results show that bioinformatics may be a good tool for the selection of appropriate TFs and for the design of specific mini-promoters to improve cancer gene therapy. Electronic supplementary material The online version of this article (10.1186/s12885-018-4421-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shu-Yi Ho
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Bo-Hau Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chen-Han Chung
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30050, Taiwan, Republic of China
| | - Yu-Ling Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China.,Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Cheng-Hsun Chuang
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30050, Taiwan, Republic of China
| | - Pei-Jung Hsieh
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan, Republic of China
| | - Nu-Man Tsai
- School of Medical and Laboratory Biotechnology, Chung Shan Medical University, Taichung, Taiwan, Republic of China.,Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Sheng-Chieh Huang
- Department of Surgery, National Yang Ming University, Taipei, Taiwan, Republic of China.,Division of Colon and Rectal surgery, Department of surgery, Taipei Veteran General Hospital, Taipei, Taiwan, Republic of China
| | - Yen-Ku Liu
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30050, Taiwan, Republic of China
| | - Yu-Chih Lo
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China. .,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30050, Taiwan, Republic of China. .,College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China. .,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China.
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24
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Liao X, Zhu G, Huang R, Yang C, Wang X, Huang K, Yu T, Han C, Su H, Peng T. Identification of potential prognostic microRNA biomarkers for predicting survival in patients with hepatocellular carcinoma. Cancer Manag Res 2018; 10:787-803. [PMID: 29713196 PMCID: PMC5912208 DOI: 10.2147/cmar.s161334] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The aim of the present study was to identify potential prognostic microRNA (miRNA) biomarkers for hepatocellular carcinoma (HCC) prognosis prediction based on a dataset from The Cancer Genome Atlas (TCGA). Materials and methods A miRNA sequencing dataset and corresponding clinical parameters of HCC were obtained from TCGA. Genome-wide univariate Cox regression analysis was used to screen prognostic differentially expressed miRNAs (DEMs), and multivariable Cox regression analysis was used for prognostic signature construction. Comprehensive survival analysis was performed to evaluate the prognostic value of the prognostic signature. Results Five miRNAs were regarded as prognostic DEMs and used for prognostic signature construction. The five-DEM prognostic signature performed well in prognosis prediction (adjusted P < 0.0001, adjusted hazard ratio = 2.249, 95% confidence interval =1.491-3.394), and time-dependent receiver-operating characteristic (ROC) analysis showed an area under the curve (AUC) of 0.765, 0.745, 0.725, and 0.687 for 1-, 2-, 3-, and 5-year HCC overall survival (OS) prediction, respectively. Comprehensive survival analysis of the prognostic signature suggests that the risk score model could serve as an independent factor of HCC and perform better in prognosis prediction than other traditional clinical indicators. Functional assessment of the target genes of hsa-mir-139 and hsa-mir-5003 indicates that they were significantly enriched in multiple biological processes and pathways, including cell proliferation and cell migration regulation, pathways in cancer, and the cyclic adenosine monophosphate (cAMP) signaling pathway. Conclusion Our study indicates that the novel miRNA expression signature may be a potential prognostic biomarker for HCC patients.
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Affiliation(s)
- Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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25
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Matsui D, Zaidi AH, Martin SA, Omstead AN, Kosovec JE, Huleihel L, Saldin LT, DiCarlo C, Silverman JF, Hoppo T, Finley GG, Badylak SF, Kelly RJ, Jobe BA. Primary tumor microRNA signature predicts recurrence and survival in patients with locally advanced esophageal adenocarcinoma. Oncotarget 2018; 7:81281-81291. [PMID: 27793030 PMCID: PMC5348392 DOI: 10.18632/oncotarget.12832] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/26/2016] [Indexed: 12/11/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is an aggressive cancer necessitating the development of improved risk stratification tools for personalized care. Previously, microRNAs have been shown to correlate with the progression and prognosis of various cancer types; however, the value in EAC remains largely unexplored. We performed global microRNA profiling on 32 formalin-fixed, paraffin-embedded EAC specimens to identify microRNAs associated with progression. Literature search and pathway analysis further refined output to five significantly deregulated candidate biomarkers. Four of the five microRNAs (miR-652-5p, miR-7-2-3p, miR-3925-3p, and miR-219-3p) were validated by qRT-PCR. Survival outcomes were evaluated in testing set of 26 stage II/III EAC patients to determine the prognostic relevance of the selected microRNAs. In the testing set, miR-652-5p and miR-7-2-3p expressions were significantly associated with progression-free survival (p-value = .00771 and p-value = .00293). The highest area under receiver operating characteristic (ROC) curve was 0.8212 for the combination of miR-652-5p and miR-7-2-3p. Collectively, our findings demonstrated that the miR-652-5p/miR-7-2-3p signature may serve as a promising prognostic marker in patients with locally advanced EAC.
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Affiliation(s)
- Daisuke Matsui
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Ali H Zaidi
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Samantha A Martin
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Ashten N Omstead
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Juliann E Kosovec
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Luai Huleihel
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lindsey T Saldin
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christina DiCarlo
- Department of Pathology and Laboratory Medicine, Allegheny Health Network, Pittsburgh, PA, USA
| | - Jan F Silverman
- Department of Pathology and Laboratory Medicine, Allegheny Health Network, Pittsburgh, PA, USA
| | - Toshitaka Hoppo
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Gene G Finley
- Department of Medicine, Division of Hematology and Oncology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Stephen F Badylak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ronan J Kelly
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Blair A Jobe
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, USA
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26
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Mohamad Yusof A, Jamal R, Muhammad R, Abdullah Suhaimi SN, Mohamed Rose I, Saidin S, Ab Mutalib NS. Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma. Front Endocrinol (Lausanne) 2018; 9:158. [PMID: 29713312 PMCID: PMC5911478 DOI: 10.3389/fendo.2018.00158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/26/2018] [Indexed: 01/08/2023] Open
Abstract
The incidence rate of papillary thyroid carcinoma (PTC) has rapidly increased in the recent decades, and the microRNA (miRNA) is one of the potential biomarkers in this cancer. Despite good prognosis, certain features such as lymph node metastasis (LNM) and BRAF V600E mutation are associated with a poor outcome. More than 50% of PTC patients present with LNM and BRAF V600E is the most common mutation identified in this cancer. The molecular mechanisms underlying these features are yet to be elucidated. This study aims to elucidate miRNA-genes interaction networks in PTC with or without LNM and to determine the association of BRAF V600E mutation with miRNAs and genes expression profiles. Next generation sequencing was performed to characterize miRNA and gene expression profiles in 20 fresh frozen tumor and the normal adjacent tissues of PTC with LNM positive (PTC LNM-P) and PTC without LNM (PTC LNN). BRAF V600E was genotyped using Sanger sequencing. Bioinformatics integration and pathway analysis were performed to determine the regulatory networks involved. Based on network analysis, we then investigated the association between miRNA and gene biomarkers, and pathway enrichment analysis was performed to study the role of candidate biomarkers. We identified 138 and 43 significantly deregulated miRNAs (adjusted p value < 0.05; log2 fold change ≤ -1.0 or ≥1.0) in PTC LNM-P and PTC LNN compared to adjacent normal tissues, respectively. Ninety-six miRNAs had significant expression ratios of 3p-to-5p in PTC LNM-P as compared to PTC LNN. In addition, ribosomal RNA-reduced RNA sequencing analysis revealed 699 significantly deregulated genes in PTC LNM-P versus normal adjacent tissues, 1,362 genes in PTC LNN versus normal adjacent tissue, and 1,576 genes in PTC LNM-P versus PTC LNN. We provide the evidence of miRNA and gene interactions, which are involved in LNM of papillary thyroid cancer. These findings may lead to better understanding of carcinogenesis and metastasis processes. This study also complements the existing knowledge about deregulated miRNAs in papillary thyroid carcinoma development.
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Affiliation(s)
- Azliana Mohamad Yusof
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rohaizak Muhammad
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Isa Mohamed Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Sazuita Saidin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- *Correspondence: Nurul-Syakima Ab Mutalib,
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27
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Lima CR, Gomes CC, Santos MF. Role of microRNAs in endocrine cancer metastasis. Mol Cell Endocrinol 2017; 456:62-75. [PMID: 28322989 DOI: 10.1016/j.mce.2017.03.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022]
Abstract
The deregulation of transcription and processing of microRNAs (miRNAs), as well as their function, has been involved in the pathogenesis of several human diseases, including cancer. Despite advances in therapeutic approaches, cancer still represents one of the major health problems worldwide. Cancer metastasis is an aggravating factor in tumor progression, related to increased treatment complexity and a worse prognosis. After more than one decade of extensive studies of miRNAs, the fundamental role of these molecules in cancer progression and metastasis is beginning to be elucidated. Recent evidences have demonstrated a significant role of miRNAs on the metastatic cascade, acting either as pro-metastatic or anti-metastatic. They are involved in distinct steps of metastasis including epithelial-to-mesenchymal transition, migration/invasion, anoikis survival, and distant organ colonization. Studies on the roles of miRNAs in cancer have focused mainly on two fronts: the establishment of a miRNA signature for different tumors, which may aid in early diagnosis using these miRNAs as markers, and functional studies of specific miRNAs, determining their targets, function and regulation. Functional miRNA studies on endocrine cancers are still scarce and represent an important area of research, since some tumors, although not frequent, present a high mortality rate. Among the endocrine tumors, thyroid cancer is the most common and best studied. Several miRNAs show lowered expression in endocrine cancers (i.e. miR-200s, miR-126, miR-7, miR-29a, miR-30a, miR-137, miR-206, miR-101, miR-613, miR-539, miR-205, miR-9, miR-195), while others are commonly overexpressed (i.e. miR-21, miR-183, miR-31, miR-let7b, miR-584, miR-146b, miR-221, miR-222, miR-25, miR-595). Additionally, some miRNAs were found in serum exosomes (miR-151, miR-145, miR-31), potentially serving as diagnostic tools. In this review, we summarize studies concerning the discovery and functions of miRNAs and their regulatory roles in endocrine cancer metastasis, which may contribute for the finding of novel therapeutic targets. The review focus on miRNAs with at least some identified targets, with established functions and, if possible, upstream regulation.
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Affiliation(s)
- Cilene Rebouças Lima
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Prédio I, CEP 05508-000, São Paulo, SP, Brazil.
| | - Cibele Crastequini Gomes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Prédio I, CEP 05508-000, São Paulo, SP, Brazil.
| | - Marinilce Fagundes Santos
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Prédio I, CEP 05508-000, São Paulo, SP, Brazil.
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Zhang M, Wu W, Gao M, Fei Z. MicroRNA-451 as a prognostic marker for diagnosis and lymph node metastasis of papillary thyroid carcinoma. Cancer Biomark 2017; 19:437-445. [DOI: 10.3233/cbm-170059] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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Brooks J, Watson A, Korcsmaros T. Omics Approaches to Identify Potential Biomarkers of Inflammatory Diseases in the Focal Adhesion Complex. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:101-109. [PMID: 28373027 PMCID: PMC5414711 DOI: 10.1016/j.gpb.2016.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 12/12/2022]
Abstract
Inflammatory diseases such as inflammatory bowel disease (IBD) require recurrent invasive tests, including blood tests, radiology, and endoscopic evaluation both to diagnose and assess disease activity, and to determine optimal therapeutic strategies. Simple ‘bedside’ biomarkers could be used in all phases of patient management to avoid unnecessary investigation and guide further management. The focal adhesion complex (FAC) has been implicated in the pathogenesis of multiple inflammatory diseases, including IBD, rheumatoid arthritis, and multiple sclerosis. Utilizing omics technologies has proven to be an efficient approach to identify biomarkers from within the FAC in the field of cancer medicine. Predictive biomarkers are paving the way for the success of precision medicine for cancer patients, but inflammatory diseases have lagged behind in this respect. This review explores the current status of biomarker prediction for inflammatory diseases from within the FAC using omics technologies and highlights the benefits of future potential biomarker identification approaches.
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Affiliation(s)
- Johanne Brooks
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Gastroenterology Department, Norfolk and Norwich University Hospital, Norwich NR4 7UY, United Kingdom
| | - Alastair Watson
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Gastroenterology Department, Norfolk and Norwich University Hospital, Norwich NR4 7UY, United Kingdom
| | - Tamas Korcsmaros
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom.
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