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Song Y, Wang L, Ren Y, Zhou X, Tan J. Identification of LINC02454-related key pathways and genes in papillary thyroid cancer by weighted gene coexpression network analysis (WGCNA). Thyroid Res 2024; 17:17. [PMID: 39218967 PMCID: PMC11367880 DOI: 10.1186/s13044-024-00205-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 06/19/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Our previous study demonstrated that long intergenic noncoding RNA 02454 (LINC02454) may act as an oncogene to promote the proliferation and inhibit the apoptosis of papillary thyroid cancer (PTC) cells. This study was designed to investigate the mechanisms whereby LINC02454 is related to PTC tumorigenesis. METHODS Thyroid cancer RNA sequence data were obtained from The Cancer Genome Atlas (TCGA) database. Weighted gene coexpression network analysis (WGCNA) was applied to identify modules closely associated with PTC. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to identify the key pathways, and the maximal clique centrality (MCC) topological method was used to identify the hub genes. The Gene Expression Profiling Interactive Analysis (GEPIA) database was used to compare expression levels of key genes between PTC samples and normal samples and explore the prognostic value of key genes. The key genes were further validated with GEO dataset. RESULTS The top 5000 variable genes were investigated, followed by an analysis of 8 modules, and the turquoise module was the most positively correlated with the clinical stage of PTC. KEGG pathway analysis found the top two pathways of the ECM - receptor interaction and MAPK signaling pathway. In addition, five key genes (FN1, LAMB3, ITGA3, SDC4, and IL1RAP) were identified through the MCC algorithm and KEGG analysis. The expression levels of the five key genes were significantly upregulated in thyroid cancer in both TCGA and GEO datasets, and of these five genes, FN1 and ITGA3 were associated with poor disease-free prognosis. CONCLUSIONS Our study identified five key genes and two key pathways associated with LINC02454, which might shed light on the underlying mechanism of LINC02454 action in PTC.
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Affiliation(s)
- Yingjian Song
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, China
| | - Lin Wang
- Department of General Practice, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huaian, 223300, Jiangsu, China
| | - Yi Ren
- Department of Breast and Thyroid Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, China
| | - Xilei Zhou
- Department of Radiation Oncology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, China
| | - Juan Tan
- Department of General Practice, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huaian, 223300, Jiangsu, China.
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Yan T, Jiang Q, Ni G, Ma H, Meng Y, Kang G, Xu M, Peng F, Li H, Chen X, Wang M. WZ-3146 acts as a novel small molecule inhibitor of KIF4A to inhibit glioma progression by inducing apoptosis. Cancer Cell Int 2024; 24:221. [PMID: 38937742 PMCID: PMC11209999 DOI: 10.1186/s12935-024-03409-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Glioma is considered the most common primary malignant tumor of the central nervous system. Although traditional treatments have not achieved satisfactory outcomes, recently, targeted therapies for glioma have shown promising efficacy. However, due to the single-target nature of targeted therapy, traditional targeted therapies are ineffective; thus, novel therapeutic targets are urgently needed. METHODS The gene expression data for glioma patients were derived from the GEO (GSE4290, GSE50161), TCGA and CGGA databases. Next, the upregulated genes obtained from the above databases were cross-analyzed, finally, 10 overlapping genes (BIRC5, FOXM1, EZH2, CDK1, KIF11, KIF4A, NDC80, PBK, RRM2, and TOP2A) were ultimately screened and only KIF4A expression has the strongest correlation with clinical characteristics in glioma patients. Futher, the TCGA and CGGA database were utilized to explore the correlation of KIF4A expression with glioma prognosis. Then, qRT-PCR and Western blot was used to detect the KIF4A mRNA and protein expression level in glioma cells, respectively. And WZ-3146, the small molecule inhibitor targeting KIF4A, were screened by Cmap analysis. Subsequently, the effect of KIF4A knockdown or WZ-3146 treatment on glioma was measured by the MTT, EdU, Colony formation assay and Transwell assay. Ultimately, GSEA enrichment analysis was performed to find that the apoptotic pathway could be regulated by KIF4A in glioma, in addition, the effect of WZ-3146 on glioma apoptosis was detected by flow cytometry and Western blot. RESULTS In the present study, we confirmed that KIF4A is abnormally overexpressed in glioma. In addition, KIF4A overexpression is a key indicator of glioma prognosis; moreover, suppressing KIF4A expression can inhibit glioma progression. We also discovered that WZ-3146, a small molecule inhibitor of KIF4A, can induce apoptosis in glioma cells and exhibit antiglioma effects. CONCLUSION In conclusion, these observations demonstrated that targeting KIF4A can inhibit glioma progression. With further research, WZ-3146, a small molecule inhibitor of KIF4A, could be combined with other molecular targeted drugs to cooperatively inhibit glioma progression.
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Affiliation(s)
- Tao Yan
- Central Laboratory, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
- Linyi Key Laboratory of Neurophysiology, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
| | - Qing Jiang
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
- Key Laboratory of Neurosurgery of Colleges and Universities in Heilongjiang Province, Harbin, Heilongjiang Province, 150001, China
| | - Guangpu Ni
- Linyi Key Laboratory of Neurophysiology, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
- Department of Neurosurgery, Linyi People's Hospital, Shandong Second Medical University, Linyi, Shandong Province, 276000, China
| | - Haofeng Ma
- Linyi Key Laboratory of Neurophysiology, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
- Department of Neurosurgery, Linyi People's Hospital, Shandong Second Medical University, Linyi, Shandong Province, 276000, China
| | - Yun Meng
- Central Laboratory, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
- Linyi Key Laboratory of Neurophysiology, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
| | - Guiqiong Kang
- Central Laboratory, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
- Linyi Key Laboratory of Neurophysiology, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
| | - Meifang Xu
- Linyi Key Laboratory of Neurophysiology, Linyi People's Hospital, Linyi, Shandong Province, 276000, China
- Department of Neurology, Linyi People's Hospital, Shandong Second Medical University, Linyi, Shandong Province, 276000, China
| | - Fei Peng
- Department of Neurosurgery and Neurosurgical Disease Research Centre, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Huadong Li
- Department of Neurosurgery, Linyi People's Hospital, Shandong Second Medical University, Linyi, Shandong Province, 276000, China.
| | - Xin Chen
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China.
- Key Laboratory of Neurosurgery of Colleges and Universities in Heilongjiang Province, Harbin, Heilongjiang Province, 150001, China.
| | - Mingguang Wang
- Department of Neurosurgery, Linyi People's Hospital, Shandong Second Medical University, Linyi, Shandong Province, 276000, China.
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Liu Q, Jiang X, Tu W, Liu L, Huang Y, Xia Y, Xia X, Shi Y. Comparative efficiency of differential diagnostic methods for the identification of BRAF V600E gene mutation in papillary thyroid cancer (Review). Exp Ther Med 2024; 27:149. [PMID: 38476918 PMCID: PMC10928970 DOI: 10.3892/etm.2024.12437] [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: 07/13/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) encodes a serine-threonine kinase. The V600E point mutation in the BRAF gene is the most common mutation, predominantly occurring in melanoma, and colorectal, thyroid and non-small cell lung cancer. Particularly in the context of thyroid cancer research, it is routinely employed as a molecular biomarker to assist in diagnosing and predicting the prognosis of papillary thyroid cancer (PTC), and to formulate targeted therapeutic strategies. Currently, several methods are utilized in clinical settings to detect BRAF V600E mutations in patients with PTC. However, the sensitivity and specificity of various detection techniques vary significantly, resulting in diverse detection outcomes. The present review highlights the advantages and disadvantages of the methods currently employed in medical practice, with the aim of guiding clinicians and researchers in selecting the most suitable detection approach for its high sensitivity, reproducibility and potential to develop targeted therapeutic regimens for patients with BRAF gene mutation-associated PTC.
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Affiliation(s)
- Qian Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xue Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Lina Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Ying Huang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuxiao Xia
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xuliang Xia
- Department of General Surgery, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
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Amjad E, Asnaashari S, Jahanban-Esfahlan A, Sokouti B. The role of MAPK, notch and Wnt signaling pathways in papillary thyroid cancer: Evidence from a systematic review and meta-analyzing microarray datasets employing bioinformatics knowledge and literature. Biochem Biophys Rep 2024; 37:101606. [PMID: 38371530 PMCID: PMC10873880 DOI: 10.1016/j.bbrep.2023.101606] [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: 09/15/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 02/20/2024] Open
Abstract
Papillary thyroid cancer (PTC) is a prevalent kind of thyroid cancer (TC), with the risk of metastasis increasing faster than any other malignancy. So, understanding the role of PTC in pathogenesis requires studying the various gene expressions to find out which particular molecular biomarkers will be helpful. The authors conducted a comprehensive search on the PubMed microarray database and a meta-analysis approach on the remaining ones to determine the differentially expressed genes between PTC and normal tissues, along with the analyses of overall survival (OS) and recurrence-free survival (RFS) rates in patients with PTC. We considered the associated genes with MAPK, Wnt, and Notch signaling pathways. Two GEO datasets have been included in this research, considering inclusion and exclusion criteria. Nineteen genes were found to have higher differences through the meta-analysis procedure. Among them, ten genes were upregulated, and nine genes were downregulated. The expression of 19 genes was examined using the GEPIA2 database, and the Kaplan-Meier plot statistics were used to analyze RFS and the OS rates. We discovered seven significant genes with the validation: PRICKLE1, KIT, RPS6KA5, GADD45B, FGFR2, FGF7, and DTX4. To further explain these findings, it was discovered that the mRNA expression levels of these seven genes and the remaining 12 genes were shown to be substantially linked with the results of the experimental literature investigations on the PTC. Our research found nineteen panels of genes that could be involved in the PTC progression and metastasis and the immune system infiltration of these cancers.
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Ouyang J, Feng Y, Zhang Y, Liu Y, Li S, Wang J, Tan L, Zou L. Integration of metabolomics and transcriptomics reveals metformin suppresses thyroid cancer progression via inhibiting glycolysis and restraining DNA replication. Biomed Pharmacother 2023; 168:115659. [PMID: 37864896 DOI: 10.1016/j.biopha.2023.115659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023] Open
Abstract
The anti-tumoral effects of metformin have been widely studied in several types of cancer, including thyroid cancer; however, the underlying molecular mechanisms remain poorly understood. As an oral hypoglycemic drug, metformin facilitates glucose catabolism and disrupts metabolic homeostasis. Metabolic reprogramming, particularly cellular glucose metabolism, is an important characteristic of malignant tumors. This study aimed to explore the therapeutic effects of metformin in thyroid cancer and the underlying metabolic mechanism. In the present study, it was shown that metformin reduced cell viability, invasion, migration, and EMT, and induced apoptosis and cell cycle G1 phase arrest in thyroid cancer. Transcriptome analysis demonstrated that the differentially expressed genes induced by metformin were involved in several signaling pathways including apoptosis singling pathways, TGF-β signaling, and cell cycle regulation in human thyroid cancer cell lines. In addition, the helicase activity of the CDC45-MCM2-7-GINS complex and DNA replication related genes such as RPA2, RAD51, and PCNA were downregulated in metformin-treated thyroid cancer cells. Moreover, metabolomics analysis showed that metformin-induced significant alterations in metabolic pathways such as glutathione metabolism and polyamine synthesis. Integrative analysis of transcriptomes and metabolomics revealed that metformin suppressed glycolysis by downregulating the key glycolytic enzymes LDHA and PKM2 and upregulating IDH1 expression in thyroid cancer. Furthermore, the anti-tumor role of metformin in thyroid cancer in vivo was shown. Together these results show that metformin plays an anti-tumor role by inhibiting glycolysis and restraining DNA replication in thyroid cancer.
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Affiliation(s)
- Jielin Ouyang
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, PR China
| | - Yang Feng
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, PR China
| | - Yiyuan Zhang
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China
| | - Yarong Liu
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, PR China
| | - Shutong Li
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China; Key Laboratory of Molecular Epidemiology of Hunan Province, Hunan Normal University, Changsha, Hunan 410013, PR China
| | - Jingjing Wang
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China
| | - Lihong Tan
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China.
| | - Lianhong Zou
- The First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital), Changsha, Hunan 410005, PR China; Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, PR China.
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Bertol BC, Massaro JD, Debortoli G, Santos ALP, de Araújo JNG, Giorgenon TMV, Costa e Silva M, de Figueiredo-Feitosa NL, Collares CVA, de Freitas LCC, Soares EG, Neder L, Silbiger VN, Calado RT, Maciel LMZ, Donadi EA. BRAF, TERT and HLA-G Status in the Papillary Thyroid Carcinoma: A Clinicopathological Association Study. Int J Mol Sci 2023; 24:12459. [PMID: 37569841 PMCID: PMC10419559 DOI: 10.3390/ijms241512459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
As BRAF, TERT, HLA-G, and microRNAs have been individually associated with papillary thyroid carcinoma (PTC), we aimed to evaluate the individual and collaborative role of these markers in PTC in the same patient cohort. HLA-G and BRAF tumor expression was evaluated by immunohistochemistry. Using molecular methods, BRAFV600E and TERT promoter mutations were evaluated in thyroid fine needle aspirates. MicroRNA tumor profiling was investigated using massively parallel sequencing. We observed strong HLA-G (67.96%) while BRAF (62.43%) staining was observed in PTC specimens. BRAF overexpression was associated with poor response to therapy. The BRAFV600E (52.9%) and TERTC228T (13%) mutations were associated with extrathyroidal extension, advanced-age, and advanced-stage cancer. The TERT rs2853669 CC+TC genotypes (38%) were overrepresented in metastatic tumors. Nine modulated microRNAs targeting the BRAF, TERT, and/or HLA-G genes were observed in PTC and involved with cancer-related signaling pathways. The markers were individually associated with PTC features, emphasizing the synergistic effect of BRAFV600E and TERTC228T; however, their collaborative role on PTC outcome was not fully demonstrated. The differentially expressed miRNAs targeting the BRAF and/or HLA-G genes may explain their increased expression in the tumor milieu.
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Affiliation(s)
- Bruna C. Bertol
- Postgraduate Program of Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Juliana D. Massaro
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada;
| | - André L. P. Santos
- Department of Medical Imaging, Hematology, and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (A.L.P.S.); (R.T.C.)
| | - Jéssica N. G. de Araújo
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal 59012-570, Brazil; (J.N.G.d.A.); (V.N.S.)
| | - Tatiana M. V. Giorgenon
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (T.M.V.G.); (N.L.d.F.-F.); (L.M.Z.M.)
| | - Matheus Costa e Silva
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
| | - Nathalie L. de Figueiredo-Feitosa
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (T.M.V.G.); (N.L.d.F.-F.); (L.M.Z.M.)
| | - Cristhianna V. A. Collares
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
| | - Luiz Carlos C. de Freitas
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Edson G. Soares
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (E.G.S.); (L.N.)
| | - Luciano Neder
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (E.G.S.); (L.N.)
| | - Vivian N. Silbiger
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal 59012-570, Brazil; (J.N.G.d.A.); (V.N.S.)
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (A.L.P.S.); (R.T.C.)
| | - Léa M. Z. Maciel
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (T.M.V.G.); (N.L.d.F.-F.); (L.M.Z.M.)
| | - Eduardo A. Donadi
- Postgraduate Program of Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
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Identifying the Carcinogenic Mechanism of Malignant Struma Ovarii Using Whole-Exome Sequencing and DNA Methylation Analysis. Curr Issues Mol Biol 2023; 45:1843-1851. [PMID: 36975488 PMCID: PMC10047136 DOI: 10.3390/cimb45030118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Background: Since malignant struma ovarii is a very rare disease, its carcinogenic mechanism has not been elucidated. Here, we sought to identify the genetic lesions that may have led to the carcinogenesis of a rare case of malignant struma ovarii (follicular carcinoma) with peritoneal dissemination. Methods: DNA was extracted from the paraffin-embedded sections of normal uterine tissues and malignant struma ovarii for genetic analysis. Whole-exome sequencing and DNA methylation analysis were then performed. Results: Germline variants of RECQL4, CNTNAP2, and PRDM2, which are tumor-suppressor genes, were detected by whole-exome sequencing. Somatic uniparental disomy (UPD) was also observed in these three genes. Additionally, the methylation of FRMD6-AS2, SESN3, CYTL1, MIR4429, HIF3A, and ATP1B2, which are associated with tumor growth suppression, was detected by DNA methylation analysis. Conclusions: Somatic UPD and DNA methylation in tumor suppressor genes may be associated with the pathogenesis of malignant struma ovarii. To our knowledge, this is the first report of whole-exome sequencing and DNA methylation analysis in malignant struma ovarii. Genetic and DNA methylation analysis may help elucidate the mechanism of carcinogenesis in rare diseases and guide treatment decisions.
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Wang B, Shen W, Yan L, Li X, Zhang L, Zhao S, Jin X. Reveal the potential molecular mechanism of circRNA regulating immune-related mRNA through sponge miRNA in the occurrence and immune regulation of papillary thyroid cancer. Ann Med 2023; 55:2244515. [PMID: 37603701 PMCID: PMC10443982 DOI: 10.1080/07853890.2023.2244515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common endocrine malignant tumour. The purpose of this study was to explore the potential molecular mechanism of circRNA regulating immune-related mRNA through sponge miRNA in the occurrence and immune regulation of PTC. METHODS All data were downloaded from public databases, such as GEO, Immport and TCGA. Differentially expressed (DE) mRNAs (DEmRNAs), DEmiRNAs and DEcircRNAs were identified using metaMA and limma packages. Subsequently, immune-related DEmRNAs were screened, and circRNA-miRNA-mRNA (ceRNA) regulatory network was constructed. In addition, functional annotation, protein-protein interaction (PPI) network construction, immune cell infiltration analysis and Pearson correlation analysis were performed. Finally, qRT-PCR validation and cell experiments were also performed. RESULTS In total, 2962 DEmRNAs, 78 DEmiRNAs and 51 DEcircRNAs were obtained. Subsequently, 195 immune-related DEmRNAs were obtained based on Immport database. Cytokine-cytokine receptor interaction was the only signalling pathway obtained in KEGG analysis. Then, 8 hub immune-related DEmRNAs were identified based on PPI network and CytoHubba plug-in. Subsequently, ceRNA sub-network containing hub immune-related DEmRNAs was extracted from ceRNA regulatory network. In ceRNA sub-network, hsa_circ_0082182-hsa-miR-18b-5p-FGF1/PDGFC, hsa_circ_0016404-hsa-miR-1275-FGF1/CTSB/IL13RA1, hsa_circ_0070100-hsa-miR-27a-3p/hsa-miR-27b-3p-TGFBR3, hsa_circ_0060055/hsa_circ_0038718-hsa-miR-150-3p-CXCL14, hsa_circ_0030427/hsa_circ_0002917-hsa-miR-22-3p-BMP7 and hsa_circ_0030427/hsa_circ_0002917-hsa-miR-125a-5p-LIFR axes were identified. Moreover, FGF1, PDGFC, CTSB, IL13RA1, TGFBR3, CXCL14, BMP7, LIFR, hsa-miR-125a-5p, hsa-miR-1275, hsa-miR-150-3p, hsa-miR-18b-5p and hsa-miR-27b-3p were also found to have good diagnostic accuracy and may be potential novel diagnostic markers for PTC. XCell analysis showed that the levels of immune cell infiltration (including Tregs, HSC, DC and Monocytes) were significantly different between the PTC and the control groups. Knockdown of the expression of hsa_circ_0082182 significantly inhibits the activity, proliferation, migration and invasion of TPC-1 cells. CONCLUSION Several circRNA-miRNA-mRNA axes identified in this study may be related to the occurrence, progression and survival of PTC. This lays a theoretical foundation for further understanding the molecular mechanism of PTC, and also contributes to clinical management and research.
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Affiliation(s)
- Bo Wang
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
| | - Wei Shen
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
| | - Li Yan
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
| | - Xiaoyu Li
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
| | - Linlei Zhang
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
| | - Suyuan Zhao
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
| | - Xiao Jin
- Surgical Department of Thyroid and Breast, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, P.R. China
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9
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Yang T, Ma X, Wang R, Liu H, Wei S, Jing M, Li H, Zhao Y. Berberine inhibits IFN-γ signaling pathway in DSS-induced ulcerative colitis. Saudi Pharm J 2022; 30:764-778. [PMID: 35812150 PMCID: PMC9257906 DOI: 10.1016/j.jsps.2022.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
Aims The potential signaling pathways and core genes in ulcerative colitis (UC) were investigated in this study. Furthermore, potential mechanisms of BBR in treating UC were also explored. Methods Expression profiling by array of UC patients were obtained from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were determined with the differential analysis. The biological functions of DEGs were analyzed through the Database for Annotation, Visualization and Integrated Discovery (DAVID). The Gene Set Enrichment Analysis (GSEA) was applied to analyze the expression differences between two different phenotype sample sets. Dextran sulfate sodium (DSS) was applied to establish UC model of mice and lipopolysaccharide (LPS) was utilized to induce inflammatory damage of NCM460 cells. Therapeutic effects of berberine (BBR) on disease performance, pathologic changes and serum supernatant indices were analyzed in vivo. To further investigate the potential mechanisms of BBR in treating UC, the expression of genes and proteins in vivo and in vitro were examined by RT-qPCR, immunohistochemical staining and western blotting. Results Immune-inflammatory genes were identified and up-regulated significantly in UC patients. In addition, IFN-γ signaling pathway and its core genes were significantly up-regulated in the phenotype of UC. All disease performance and the pathologic changes of UC in mice were evidently ameliorated by BBR treatment. The pro-inflammatory cytokines of serum, including CXCL9, CXCL1, IL-17 and TNF-α, in UC mice were significantly reduced by treatment of BBR. In terms of mechanisms of BBR in treating UC, the pro-inflammatory and immune-related genes, encoding IFN-γ, IRF8, NF-κB and TNF-α decreased significantly in UC mice followed by BBR treatment. Meanwhile, the expression of IFN-γ and its initiated targets, including IRF8, Ifit1, Ifit3, IRF1, were suppressed significantly by BBR treatment in vivo. The blocking of IFN-γ in vitro led to the silence of IFN-γ signaling pathway after exposure to BBR. Furthermore, the blocking of IFN-γ in vitro led to the silence of IFN-γ signaling pathway after exposure to BBR. Conclusion BBR holds anti-inflammatory activity and can treat UC effectively. The anti-inflammatory property of BBR is tightly related to the suppression of IFN-γ signaling pathway, which is crucial in immune-inflammatory responses of the colon mucosa.
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Affiliation(s)
- Tao Yang
- Colorectal and Anal Surgery, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No 71 Baoshan North Road, Guiyang 550001, China
| | - Xiao Ma
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611100, China
| | - Ruilin Wang
- Integrative Medical Center, Chinese PLA General Hospital, Beijing 100039, China
| | - Honghong Liu
- Department of Policlinic, Chinese PLA General Hospital, Beijing 100039, China
| | - Shizhang Wei
- Department of Pharmacy, Chinese PLA General Hospital, Beijing 100039, China
| | - Manyi Jing
- Department of Pharmacy, Chinese PLA General Hospital, Beijing 100039, China
| | - Haotian Li
- Department of Pharmacy, Chinese PLA General Hospital, Beijing 100039, China
| | - Yanling Zhao
- Department of Pharmacy, Chinese PLA General Hospital, Beijing 100039, China
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10
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Li CC, Ullah MHE, Lin X, Shan SK, Guo B, Zheng MH, Wang Y, Li F, Yuan LQ. Identifying key genes of classic papillary thyroid cancer in women aged more than 55 years old using bioinformatics analysis. Front Endocrinol (Lausanne) 2022; 13:948285. [PMID: 36120433 PMCID: PMC9478488 DOI: 10.3389/fendo.2022.948285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The incidence rate of thyroid carcinoma (THCA) markedly increased in the recent few decades and has been likely over-diagnosed, especially papillary thyroid cancer (PTC) in women. However, the incidence of advanced-stage papillary thyroid cancer is also rising. According to earlier studies, tumors with identical pathology might have different clinical outcomes, which implies some variances in papillary thyroid cancer. Although the mortality of thyroid cancer has remained stable or declined, there is still an important problem in estimating whether it is benign or needs surgery for patients with papillary thyroid cancer. METHODS After obtaining data from The Cancer Genome Atlas (TCGA) Project-THCA database by R package TCGA bio links, 18 samples (11 at stage IV as high-risk group and 7 at stage I as low-risk group) were obtained using survival package and edgeR to ensure differential expression; ClusterProfiler package was used to carry on gene set enrichment analysis and searched the possible pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. STRING and Cytoscape were used to construct and modify the protein-protein interaction (PPI) network to get hub genes of differentially expressed genes. Next, the pROC package was used to get the receiver operating characteristic (ROC) curves of hub genes' disease-free survival (DFS). Then, transcription factors (TFs) and miRNAs of key genes were predicted by ENCORI and AnimalTFDB. In the end, TF-target genes-miRNA regulatory network was also constructed by Cytoscape. RESULTS Our research obtained the top 9 candidate genes from the whole network (IFNA1, MRC1, LGALS3, LOX, POSTN, TIMP1, CD276, SDC4, and TLR2). According to the ROC results, TIMP1, LOX, CD276, IFNA1, TLR2, and POSTN were considered to play a more critical role in malignant papillary thyroid cancer or immature cancer of papillary thyroid cancer. Our analysis concludes that TIMP1, LOX, CD276, IFNA1, TLR2, and POSTN are identified as thyroid cancer biomarkers, which lead to the different clinical courses of a woman older than 55 years old with papillary thyroid cancer. Especially CD276, POSTN, and IFNA1 may be considered as new biomarkers associated with the prognosis of thyroid cancer. CONCLUSIONS TIMP1, LOX, CD276, IFNA1, TLR2, and POSTN have different expressions in PTCs, which lead to the various clinical courses of a woman older than 55 years old with papillary thyroid cancer. Especially CD276, POSTN, and IFNA1 may be considered as new potential biomarkers associated with the prognosis of thyroid cancer. In addition, TF-miRNA-target gene regulatory network may help further reach for PTC.
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Affiliation(s)
- Chang-Chun Li
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Muhammad Hasnain Ehsan Ullah
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Lin
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Su-Kang Shan
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Bei Guo
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Hui Zheng
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yi Wang
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fuxingzi Li
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ling-Qing Yuan
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Ling-Qing Yuan,
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11
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Pan J, Ye F, Yu C, Zhu Q, Li J, Zhang Y, Tian H, Yao Y, Zhu M, Shen Y, Zhu F, Wang Y, Zhou X, Guo G, Wu Y. Papillary Thyroid Carcinoma Landscape and Its Immunological Link With Hashimoto Thyroiditis at Single-Cell Resolution. Front Cell Dev Biol 2021; 9:758339. [PMID: 34805166 PMCID: PMC8602800 DOI: 10.3389/fcell.2021.758339] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
The tumor microenvironment heterogeneity of papillary thyroid cancer (PTC) is poorly characterized. The relationship between PTC and Hashimoto thyroiditis (HT) is also in doubt. Here, we used single-cell RNA sequencing to map the transcriptome landscape of PTC from eight PTC patients, of which three were concurrent with HT. Predicted copy number variation in epithelial cells and mesenchymal cells revealed the distinct molecular signatures of carcinoma cells. Carcinoma cells demonstrated intertumoral heterogeneity based on BRAF V600E mutation or lymph node metastasis, and some altered genes were identified to be correlated with disease-free survival in The Cancer Genome Atlas datasets. In addition, transcription factor regulons of follicular epithelial cells unveil the different transcription activation state in PTC patients with or without concurrent HT. The immune cells in tumors exhibited distinct transcriptional states, and the presence of tumor-infiltrating B lymphocytes was predominantly linked to concurrent HT origin. Trajectory analysis of B cells and plasma cells suggested their migration potential from HT adjacent tissues to tumor tissues. Furthermore, we revealed diverse ligand–receptor pairs between non-immune cells, infiltrating myeloid cells, and lymphocytes. Our results provided a single-cell landscape of human PTC. These data would deepen the understanding of PTC, as well as the immunological link between PTC and HT.
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Affiliation(s)
- Jun Pan
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinsheng Zhu
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaohui Zhang
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hedi Tian
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunjin Yao
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minjie Zhu
- Surgical Department, Hangzhou Third Hospital, Hangzhou, China
| | - Yibin Shen
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingying Wang
- Kidney Disease Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinhui Zhou
- Department of Gynecology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University, Hangzhou, China.,Stem Cell Institute, Zhejiang University, Hangzhou, China
| | - Yijun Wu
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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12
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Kim JH, Kim H, Dan K, Kim SI, Park SH, Han D, Kim YH. In-depth proteomic profiling captures subtype-specific features of craniopharyngiomas. Sci Rep 2021; 11:21206. [PMID: 34707096 PMCID: PMC8551227 DOI: 10.1038/s41598-021-00483-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Craniopharyngiomas are rare epithelial tumors derived from pituitary gland embryonic tissue. This epithelial tumor can be categorized as an adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) subtype with histopathological and genetic differences. Genomic and transcriptomic profiles of craniopharyngiomas have been investigated; however, the proteomic profile has yet to be elucidated and added to these profiles. Recent improvements in high-throughput quantitative proteomic approaches have introduced new opportunities for a better understanding of these diseases and the efficient discovery of biomarkers. We aimed to confirm subtype-associated proteomic changes between ACP and PCP specimens. We performed a system-level proteomic study using an integrated approach that combines mass spectrometry-based quantitative proteomic, statistical, and bioinformatics analyses. The bioinformatics analysis showed that differentially expressed proteins between ACP and PCP were significantly involved in mitochondrial organization, fatty acid metabolic processes, exocytosis, the inflammatory response, the cell cycle, RNA splicing, cell migration, and neuron development. Furthermore, using network analysis, we identified hub proteins that were positively correlated with ACP and PCP phenotypes. Our findings improve our understanding of the pathogenesis of craniopharyngiomas and provide novel insights that may ultimately translate to the development of craniopharyngioma subtype-specific therapeutics.
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Affiliation(s)
- Jung Hee Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Pituitary Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Yong Hwy Kim
- Pituitary Center, Seoul National University Hospital, Seoul, Republic of Korea. .,Department of Neurosurgery, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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13
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Hazini A, Fisher K, Seymour L. Deregulation of HLA-I in cancer and its central importance for immunotherapy. J Immunother Cancer 2021; 9:e002899. [PMID: 34353849 PMCID: PMC8344275 DOI: 10.1136/jitc-2021-002899] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/28/2022] Open
Abstract
It is now well accepted that many tumors undergo a process of clonal selection which means that tumor antigens arising at various stages of tumor progression are likely to be represented in just a subset of tumor cells. This process is thought to be driven by constant immunosurveillance which applies selective pressure by eliminating tumor cells expressing antigens that are recognized by T cells. It is becoming increasingly clear that the same selective pressure may also select for tumor cells that evade immune detection by acquiring deficiencies in their human leucocyte antigen (HLA) presentation pathways, allowing important tumor antigens to persist within cells undetected by the immune system. Deficiencies in antigen presentation pathway can arise by a variety of mechanisms, including genetic and epigenetic changes, and functional antigen presentation is a hard phenomenon to assess using our standard analytical techniques. Nevertheless, it is likely to have profound clinical significance and could well define whether an individual patient will respond to a particular type of therapy or not. In this review we consider the mechanisms by which HLA function may be lost in clinical disease, we assess the implications for current immunotherapy approaches using checkpoint inhibitors and examine the prognostic impact of HLA loss demonstrated in clinical trials so far. Finally, we propose strategies that might be explored for possible patient stratification.
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Affiliation(s)
- Ahmet Hazini
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Kerry Fisher
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Len Seymour
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
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14
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Lv Q, Xia Q, Li A, Wang Z. The Potential Role of IL1RAP on Tumor Microenvironment-Related Inflammatory Factors in Stomach Adenocarcinoma. Technol Cancer Res Treat 2021; 20:1533033821995282. [PMID: 33602046 PMCID: PMC7897808 DOI: 10.1177/1533033821995282] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This study was performed to investigate the role of interleukin-1 receptor accessory protein (IL1RAP) in stomach carcinoma in vitro and in vivo, determine whether IL1RAP knockdown could regulate the development of stomach carcinoma, and elucidate the relationship between IL1RAP knockdown and inflammation by tumor microenvironment-related inflammatory factors in stomach carcinoma. We first used TCGA and GEPIA systems to predict the potential function of IL1RAP. Second, western blot and RT-PCR were used to analyze the expression, or mRNA level, of IL1RAP at different tissue or cell lines. Third, the occurrence and development of stomach carcinoma in vitro and in vivo were observed by using IL1RAP knockdown lentivirus. Finally, the inflammation of stomach carcinoma in vitro and in vivo was observed. Results show that in GEPIA and TCGA systems, IL1RAP expression in STAD tumor tissue was higher than normal, and high expression of IL1RAP in STAD patients had a worse prognostic outcome. Besides, GSEA shown IL1RAP was negative correlation of apopopsis, TLR4 and NF-κB signaling pathway. We also predicted that IL1RAP may related to IL-1 s, IL-33, and IL-36 s in STAD. The IL1RAP expression and mRNA level in tumor, or MGC803, cells were increased. Furthermore, IL1RAP knockdown by lentivirus could inhibit stomach carcinoma development in vitro and in vivo through weakening tumor cell proliferation, migration, invasion, therefore reducing tumor volume, weight, and biomarker levels, and increasing apoptotic level. Finally, we found IL1RAP knockdown could increase inflammation of tumor microenvironment-related inflammatory factors of stomach carcinoma, in vitro and in vivo. Our study demonstrates that IL1RAP is possibly able to regulate inflammation and apoptosis in stomach carcinoma. Furthermore, TLR4, NF-κB, IL-1 s, IL-33, and IL-36 s maybe the downstream target factor of IL1RAP in inflammation. These results may provide a new strategy for stomach carcinoma development by regulating inflammation.
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Affiliation(s)
- Qing Lv
- Department of Gastrointestinal Surgery, Wuhan Union Hospital, Wuhan, Hubei, China
| | - Qinghua Xia
- Department of Gastrointestinal Surgery, Wuhan Union Hospital, Wuhan, Hubei, China
| | - Anshu Li
- Department of Gastrointestinal Surgery, Wuhan Union Hospital, Wuhan, Hubei, China
| | - Zhiyong Wang
- Department of Gastrointestinal Surgery, Wuhan Union Hospital, Wuhan, Hubei, China
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15
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Qi T, Rong X, Feng Q, Sun H, Cao H, Yang Y, Feng H, Zhu L, Wang L, Du Q. Somatic Mutation Profiling of Papillary Thyroid Carcinomas by Whole-exome Sequencing and Its Relationship with Clinical Characteristics. Int J Med Sci 2021; 18:2532-2544. [PMID: 34104084 PMCID: PMC8176168 DOI: 10.7150/ijms.50916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/16/2021] [Indexed: 01/18/2023] Open
Abstract
The incidence of papillary thyroid carcinomas (PTCs) has increased rapidly during the past several decades. Until now, the mechanisms underlying the tumorigenesis of PTCs have remained largely unknown. Next-generation-sequencing (NGS) provides new ways to investigate the molecular pathogenesis of PTCs. To characterize the somatic alterations associated with PTCs, we performed whole-exome sequencing (WES) of PTCs from 23 Chinese patients. This study revealed somatic mutations in genes with relevant functions for tumorigenesis, such as BRAF, BCR, CREB3L2, DNMT1, IRS2, MSH6, and TP53. We also identified novel somatic gene alterations which may be potentially involved in PTC progression. Gene set enrichment analysis revealed that the cellular response to hormone stimulus, epigenetic modifications, such as protein/histone methylation and protein alkylation, as well as MAPK, PI3K-AKT, and FoxO/mTOR signaling pathways, were significantly altered in the PTCs studied here. Moreover, Protein-Protein Interaction (PPI) network analysis of our mutated gene selection highlighted EP300, KRAS, PTEN, and TP53 as major core genes. The correlation between gene mutations and clinicopathologic features of the PTCs defined by conventional ultrasonography (US) and contrast-enhanced ultrasonography (CEUS) were assessed. These analyses established significant associations between subgroups of mutations and respectively taller-than-wide, calcified, and peak time iso- or hypo-enhanced and metastatic PTCs. In conclusion, our study supplements the genomic landscape of PTCs and identifies new actionable target candidates and clinicopathology-associated mutations. Extension of this study to larger cohorts will help define comprehensive genomic aberrations in PTCs and validate target candidates. These new targets may open methods of individualized treatments adapted to the clinicopathologic specifics of the patients.
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Affiliation(s)
- Tingyue Qi
- Department of Ultrasound, Medical Imaging Center, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China.,Department of Critical Care Medicine, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Xin Rong
- Department of Ultrasound, Medical Imaging Center, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Qingling Feng
- Department of Critical Care Medicine, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Hongguang Sun
- Department of Ultrasound, Medical Imaging Center, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Haiyan Cao
- Department of Ultrasound, Medical Imaging Center, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Yan Yang
- Department of Ultrasound, Medical Imaging Center, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Hao Feng
- Department of Ultrasound, Medical Imaging Center, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Linhai Zhu
- Department of Thyroid and Breast Surgery, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Lei Wang
- Department of Pathology, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China
| | - Qiu Du
- Department of Neurosurgery, the Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225012, China.,Central Laboratory, the Affiliated Hospital of Yangzhou University, Yangzhou 225012, Yangzhou University, China
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16
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Poli R, Scatolini M, Grosso E, Maletta F, Gallo M, Liscia D, Nelva A, Cesario F, Forte G, Metovic J, Volante M, Arvat E, Papotti M. Malignant struma ovarii: next-generation sequencing of six cases revealed Nras, Braf, and Jak3 mutations. Endocrine 2021; 71:216-224. [PMID: 32743766 DOI: 10.1007/s12020-020-02438-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/25/2020] [Indexed: 11/30/2022]
Abstract
PURPOSE Struma ovarii (SO) is a highly specialized ovarian teratoma, consisting of thyroid tissue. Rarely, carcinomas histologically identical to their thyroid counterparts may occur, and are comprehensively defined as malignant struma ovarii (MSO). Their optimal management is controversial, and the molecular profile of the malignant counterpart in the ovary is incompletely known. In this study, the clinicopathological and molecular features of six MSO from different Italian Institutions were analysed, to explore genetic profiles of potential therapeutic interest. METHODS The histopathological features and immunoprofile (according to the known markers Galectin-3, HBME1, cytokeratin 19 and CD56) were reviewed. In addition, all cases underwent genetic analysis with a next-generation sequencing (NGS) hot spot cancer panel detecting mutations in 50 genes involved in cancerogenesis. RET/PTC rearrangements and TERT promoter alterations were also evaluated. RESULTS Papillary carcinoma in all similar to its thyroid counterpart was found in five of six cases, including classical (two tumors) and follicular variant (three tumors) types. The last case was a poorly differentiated carcinoma. An activating gene mutation, was detected in five of six cases, including two NRAS, two BRAF, and one JAK3 oncogene mutations. No alterations were found in the other panel genes, nor in TERT promoter, or in RET chromosomal regions. CONCLUSIONS MSO is a rare condition. Papillary carcinoma is the predominant malignant type, sharing both histomorphological and molecular features of its thyroid counterpart. Interestingly, the single case of poorly differentiated carcinoma displayed a JAK3 mutation. The presence of such driving mutation could be of potential interest in guiding postoperative treatment.
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Affiliation(s)
- Roberta Poli
- Division of Internal Medicine, Ospedale degli Infermi, via dei Ponderanesi 2 Ponderano, 13875, Biella, Italy.
| | - Maria Scatolini
- Molecular Oncology Laboratory, Fondazione "Edo ed Elvo Tempia Valenta", via dei Ponderanesi 2, Ponderano, 13875, Biella, Italy
| | - Enrico Grosso
- Molecular Oncology Laboratory, Fondazione "Edo ed Elvo Tempia Valenta", via dei Ponderanesi 2, Ponderano, 13875, Biella, Italy
| | - Francesca Maletta
- Pathology Unit, AOU Città della Salute e della Scienza Hospital, via Santena 7, 10126, Turin, Italy
| | - Marco Gallo
- Oncological Endocrinology, AOU Città della Salute e della Scienza di Torino Hospital, via Genova 3, 10126, Turin, Italy
| | - Daniele Liscia
- Pathology Unit, Ospedale degli Infermi, via dei Ponderanesi 2 Ponderano, 13875, Biella, Italy
| | - Anna Nelva
- Endocrinology and Diabetology Unit, Ospedale degli Infermi, via dei Ponderanesi 2 Ponderano, 13875, Biella, Italy
| | - Flora Cesario
- Division of Endocrinology, Diabetes and Metabolism, Santa Croce e Carle Hospital, Cuneo, Italy
| | - Giuseppe Forte
- Pathology Unit, Santa Croce e Carle Hospital, via M Coppino 26, 12100, Cuneo, Italy
| | - Jasna Metovic
- Pathology Unit, Department of Oncology, University of Turin, via Santena 7, 10126, Turin, Italy
| | - Marco Volante
- Pathology Unit, Department of Oncology, University of Turin, via Santena 7, 10126, Turin, Italy
| | - Emanuela Arvat
- Oncological Endocrinology, Department of Medical Sciences, University of Turin, via Genova 3, 10126, Turin, Italy
| | - Mauro Papotti
- Pathology Unit, Department of Oncology, University of Turin, via Santena 7, 10126, Turin, Italy
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17
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Liu C, Pan Y, Li Q, Zhang Y. Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer. Int J Med Sci 2021; 18:3478-3487. [PMID: 34522174 PMCID: PMC8436097 DOI: 10.7150/ijms.63402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Although the etiology of Hashimoto's thyroiditis (HT), a common autoimmune endocrine disease, is unknown, studies suggest a potential association with genetic factors and environmental conditions inducing excessive iodine intake. Additionally, HT patients have a high risk of papillary thyroid cancer (PTC), which is probably related to the chronic inflammation and autoimmune pathologic process occurring in HT, as it is thought to be associated with neoplastic transformation. Methods: Bioinformatics approaches can identify differentially expressed genes (DEGs) and analyze DEG functions in diseases. R software was used in this study to identify DEGs in HT and PTC using data in Gene Expression Omnibus (GEO). The online tools DAVID, Reactome, and AmiGO were employed for annotation, visualization, and integration of DEGs related to HT and PTC, and the STRING database and Cytoscape software were applied to predict and visualize protein-protein networks (PPIs) for DEG-encoded proteins. Coexpressed DEGs in HT and PTC were validated by reverse transcription PCR (RT-PCR). Results: In total, 326, 231, and 210 DEGs in HT specimens and samples of central PTC and PTC invasive areas, respectively, were detected. According to the PPI network, PTPN6, HLA-A, C3AR1, LCK and ITGB2 are hub genes among HT-DEGs, whereas FN1, CDH2, SERPINA1, and CYR61 are PTC-DEG hub genes. The shared DEGs LTF and CCL21 were validated by RT-PCR. Both bioinformatics and RT-PCR analyses showed LTF and CCL21 to be upregulated in HT tissues and downregulated in PTC tissues. Conclusions: We identified that expression of LTF and CCL21 are significantly different in HT and PTC, suggesting an underlying association between HT and PTC.
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Affiliation(s)
- Chang Liu
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Pan
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qinyu Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yifan Zhang
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Śmiech M, Leszczyński P, Kono H, Wardell C, Taniguchi H. Emerging BRAF Mutations in Cancer Progression and Their Possible Effects on Transcriptional Networks. Genes (Basel) 2020; 11:genes11111342. [PMID: 33198372 PMCID: PMC7697059 DOI: 10.3390/genes11111342] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Gene mutations can induce cellular alteration and malignant transformation. Development of many types of cancer is associated with mutations in the B-raf proto-oncogene (BRAF) gene. The encoded protein is a component of the mitogen-activated protein kinases/extracellular signal-regulated kinases (MAPK/ERK) signaling pathway, transmitting information from the outside to the cell nucleus. The main function of the MAPK/ERK pathway is to regulate cell growth, migration, and proliferation. The most common mutations in the BRAF gene encode the V600E mutant (class I), which causes continuous activation and signal transduction, regardless of external stimulus. Consequently, cell proliferation and invasion are enhanced in cancer patients with such mutations. The V600E mutation has been linked to melanoma, colorectal cancer, multiple myeloma, and other types of cancers. Importantly, emerging evidence has recently indicated that new types of mutations (classes II and III) also play a paramount role in the development of cancer. In this minireview, we discuss the influence of various BRAF mutations in cancer, including aberrant transcriptional gene regulation in the affected tissues.
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Affiliation(s)
- Magdalena Śmiech
- Institute of Genetics and Animal Biotechnology, Laboratory for Genome Editing and Transcriptional, Regulation, Polish Academy of Sciences, 05-552 Jastrzębiec, Poland; (M.Ś.); (P.L.)
| | - Paweł Leszczyński
- Institute of Genetics and Animal Biotechnology, Laboratory for Genome Editing and Transcriptional, Regulation, Polish Academy of Sciences, 05-552 Jastrzębiec, Poland; (M.Ś.); (P.L.)
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan;
| | - Christopher Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA;
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Biotechnology, Laboratory for Genome Editing and Transcriptional, Regulation, Polish Academy of Sciences, 05-552 Jastrzębiec, Poland; (M.Ś.); (P.L.)
- Correspondence: ; Tel.: +48-22-736-70-95
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Xie Z, Li X, He Y, Wu S, Wang S, Sun J, He Y, Lun Y, Zhang J. Immune Cell Confrontation in the Papillary Thyroid Carcinoma Microenvironment. Front Endocrinol (Lausanne) 2020; 11:570604. [PMID: 33193087 PMCID: PMC7642595 DOI: 10.3389/fendo.2020.570604] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
Background Papillary thyroid cancer has been associated with chronic inflammation. A systematic understanding of immune cell infiltration in PTC is essential for subsequent immune research and new diagnostic and therapeutic strategies. Methods Three different algorithms, single-sample gene set enrichment analysis (ssGSEA), immune cell marker and CIBERSORT, were used to evaluate immune cell infiltration levels (abundance and proportion) in 10 data sets (The Cancer Genome Atlas [TCGA], GSE3467, GSE3678, GSE5364, GSE27155, GSE33630, GSE50901, GSE53157, GSE58545, and GSE60542; a total of 799 PTC and 194 normal thyroid samples). Consensus unsupervised clustering divided PTC patients into low-immunity and high-immunity groups. Weighted gene coexpression network analysis (WGCNA) and gene set enrichment analysis (GSEA) were used to analyze the potential mechanisms causing differences in the immune response. Results Compared with normal tissues, PTC tissues had a higher overall immune level and higher abundance levels and proportions of M2 macrophages, Tregs, monocytes, neutrophils, dendritic cells (DCs), mast cells (MCs), and M0 macrophages. Compared with early PTC, advanced PTC showed higher immune infiltration and higher abundance levels and proportions of M2 macrophages, Tregs, monocytes, neutrophils, DCs, MCs, and M0 macrophages. Compared to the low-immunity group, the high-immunity group exhibited more advanced stages, larger tumor sizes, greater lymph node metastases, higher tall-cell PTCs, lower follicular PTC proportions, more BRAF mutations, and fewer RAS mutations. Epstein-Barr virus (EBV) infection was the most significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for key module genes. Conclusions In human PTC, M2 macrophages, Tregs, monocytes, neutrophils, DCs, MCs, and M0 macrophages appear to play a tumor-promoting role, while M1 macrophages, CD8+ T cells, B cells, NK cells, and T follicular helper (TFH) cells (including eosinophils, γδ T cells, and Th17 cells with weak supporting evidence) appear to play an antitumor role. During the occurrence and development of PTC, the overall immune level was increased, and the abundance and proportion of tumor-promoting immune cells were significantly increased, indicating that immune escape had been aggravated. Finally, we speculate that EBV may play an important role in changing the immune microenvironment of PTC tumors.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Zhang
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
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20
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Macerola E, Poma AM, Basolo F. NanoString in the screening of genetic abnormalities associated with thyroid cancer. Semin Cancer Biol 2020; 79:132-140. [PMID: 33091600 DOI: 10.1016/j.semcancer.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 10/12/2020] [Indexed: 11/24/2022]
Abstract
In the setting of cancer pathology, molecular characterization of tumors providing diagnostic and predictive information is acquiring more and more relevance. Moreover, the advent of innovative technologies continuously improves the knowledge of the molecular landscape of tumors and strengthens the links between clinics, tumor pathology and molecular features. In the clinical management of patients with thyroid nodules and thyroid tumors, the aid of molecular testing is encouraged but still not strongly recommended by current guidelines. Also for this reason this field of study is attracting much interest. The nCounter system is a relatively new technology based on a direct hybridization of fluorescent probes to specific nucleic acid targets, followed by digital measurement of signals; the reaction is highly multiplexable and results are robust and reproducible. This review reports and discusses the available data related to the application of this specific technique to thyroid nodules and thyroid tumors samples. The available data indicate that nCounter system represents a solid approach for the research of relevant diagnostic and prognostic biomarkers in thyroid pathology.
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Affiliation(s)
- Elisabetta Macerola
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi, 10, 56126, Pisa, Italy.
| | - Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi, 10, 56126, Pisa, Italy.
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi, 10, 56126, Pisa, Italy.
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21
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Szpak-Ulczok S, Pfeifer A, Rusinek D, Oczko-Wojciechowska M, Kowalska M, Tyszkiewicz T, Cieslicka M, Handkiewicz-Junak D, Fujarewicz K, Lange D, Chmielik E, Zembala-Nozynska E, Student S, Kotecka-Blicharz A, Kluczewska-Galka A, Jarzab B, Czarniecka A, Jarzab M, Krajewska J. Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma-Do They Exist? Int J Mol Sci 2020; 21:E4629. [PMID: 32610693 PMCID: PMC7369779 DOI: 10.3390/ijms21134629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
Molecular mechanisms of distant metastases (M1) in papillary thyroid cancer (PTC) are poorly understood. We attempted to analyze the gene expression profile in PTC primary tumors to seek the genes associated with M1 status and characterize their molecular function. One hundred and twenty-three patients, including 36 M1 cases, were subjected to transcriptome oligonucleotide microarray analyses: (set A-U133, set B-HG 1.0 ST) at transcript and gene group level (limma, gene set enrichment analysis (GSEA)). An additional independent set of 63 PTCs, including 9 M1 cases, was used to validate results by qPCR. The analysis on dataset A detected eleven transcripts showing significant differences in expression between metastatic and non-metastatic PTC. These genes were validated on microarray dataset B. The differential expression was positively confirmed for only two genes: IGFBP3, (most significant) and ECM1. However, when analyzed on an independent dataset by qPCR, the IGFBP3 gene showed no differences in expression. Gene group analysis showed differences mainly among immune-related transcripts, indicating the potential influence of tumor immune infiltration or signal within the primary tumor. The differences in gene expression profile between metastatic and non-metastatic PTC, if they exist, are subtle and potentially detectable only in large datasets.
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Affiliation(s)
- Sylwia Szpak-Ulczok
- Nuclear Medicine and Endocrine Oncology Department; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (S.S.-U.); (D.H.-J.); (A.K.-B.); (A.K.-G.); (B.J.)
| | - Aleksandra Pfeifer
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (A.P.); (D.R.); (M.O.-W.); (M.K.); (T.T.); (M.C.)
| | - Dagmara Rusinek
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (A.P.); (D.R.); (M.O.-W.); (M.K.); (T.T.); (M.C.)
| | - Malgorzata Oczko-Wojciechowska
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (A.P.); (D.R.); (M.O.-W.); (M.K.); (T.T.); (M.C.)
| | - Malgorzata Kowalska
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (A.P.); (D.R.); (M.O.-W.); (M.K.); (T.T.); (M.C.)
| | - Tomasz Tyszkiewicz
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (A.P.); (D.R.); (M.O.-W.); (M.K.); (T.T.); (M.C.)
| | - Marta Cieslicka
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (A.P.); (D.R.); (M.O.-W.); (M.K.); (T.T.); (M.C.)
| | - Daria Handkiewicz-Junak
- Nuclear Medicine and Endocrine Oncology Department; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (S.S.-U.); (D.H.-J.); (A.K.-B.); (A.K.-G.); (B.J.)
| | - Krzysztof Fujarewicz
- Institute of Automatic Control, Silesian University of Technology, 44-100 Gliwice, Poland; (K.F.); (S.S.)
| | - Dariusz Lange
- Tumor Pathology Department; Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (D.L.); (E.C.); (E.Z.-N.)
| | - Ewa Chmielik
- Tumor Pathology Department; Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (D.L.); (E.C.); (E.Z.-N.)
| | - Ewa Zembala-Nozynska
- Tumor Pathology Department; Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (D.L.); (E.C.); (E.Z.-N.)
| | - Sebastian Student
- Institute of Automatic Control, Silesian University of Technology, 44-100 Gliwice, Poland; (K.F.); (S.S.)
| | - Agnieszka Kotecka-Blicharz
- Nuclear Medicine and Endocrine Oncology Department; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (S.S.-U.); (D.H.-J.); (A.K.-B.); (A.K.-G.); (B.J.)
| | - Aneta Kluczewska-Galka
- Nuclear Medicine and Endocrine Oncology Department; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (S.S.-U.); (D.H.-J.); (A.K.-B.); (A.K.-G.); (B.J.)
| | - Barbara Jarzab
- Nuclear Medicine and Endocrine Oncology Department; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (S.S.-U.); (D.H.-J.); (A.K.-B.); (A.K.-G.); (B.J.)
| | - Agnieszka Czarniecka
- The Oncologic and Reconstructive Surgery Clinic; Maria Sklodowska, Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland;
| | - Michal Jarzab
- Breast Unit; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland;
| | - Jolanta Krajewska
- Nuclear Medicine and Endocrine Oncology Department; Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-101 Gliwice, Poland; (S.S.-U.); (D.H.-J.); (A.K.-B.); (A.K.-G.); (B.J.)
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Bhalla S, Kaur H, Kaur R, Sharma S, Raghava GPS. Expression based biomarkers and models to classify early and late-stage samples of Papillary Thyroid Carcinoma. PLoS One 2020; 15:e0231629. [PMID: 32324757 PMCID: PMC7179925 DOI: 10.1371/journal.pone.0231629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Recently, the rise in the incidences of thyroid cancer worldwide renders it to be the sixth most common cancer among women. Commonly, Fine Needle Aspiration biopsy predominantly facilitates the diagnosis of the nature of thyroid nodules. However, it is inconsiderable in determining the tumor's state, i.e., benign or malignant. This study aims to identify the key RNA transcripts that can segregate the early and late-stage samples of Thyroid Carcinoma (THCA) using RNA expression profiles. MATERIALS AND METHODS In this study, we used the THCA RNA-Seq dataset of The Cancer Genome Atlas, consisting of 500 cancer and 58 normal (adjacent non-tumorous) samples obtained from the Genomics Data Commons (GDC) data portal. This dataset was dissected to identify key RNA expression features using various feature selection techniques. Subsequently, samples were classified based on selected features employing different machine learning algorithms. RESULTS Single gene ranking based on the Area Under the Receiver Operating Characteristics (AUROC) curve identified the DCN transcript that can classify the early-stage samples from late-stage samples with 0.66 AUROC. To further improve the performance, we identified a panel of 36 RNA transcripts that achieved F1 score of 0.75 with 0.73 AUROC (95% CI: 0.62-0.84) on the validation dataset. Moreover, prediction models based on 18-features from this panel correctly predicted 75% of the samples of the external validation dataset. In addition, the multiclass model classified normal, early, and late-stage samples with AUROC of 0.95 (95% CI: 0.84-1), 0.76 (95% CI: 0.66-0.85) and 0.72 (95% CI: 0.61-0.83) on the validation dataset. Besides, a five protein-coding transcripts panel was also recognized, which segregated cancer and normal samples in the validation dataset with F1 score of 0.97 and 0.99 AUROC (95% CI: 0.91-1). CONCLUSION We identified 36 important RNA transcripts whose expression segregated early and late-stage samples with reasonable accuracy. The models and dataset used in this study are available from the webserver CancerTSP (http://webs.iiitd.edu.in/raghava/cancertsp/).
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Affiliation(s)
- Sherry Bhalla
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Harpreet Kaur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rishemjit Kaur
- CSIR-Central Scientific Instruments Organization, Chandigarh, India
| | - Suresh Sharma
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Gajendra P. S. Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- * E-mail:
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Croce L, Coperchini F, Magri F, Chiovato L, Rotondi M. The multifaceted anti-cancer effects of BRAF-inhibitors. Oncotarget 2019; 10:6623-6640. [PMID: 31762942 PMCID: PMC6859927 DOI: 10.18632/oncotarget.27304] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
The BRAF gene is commonly involved in normal processes of cell growth and differentiation. The BRAF (V600E) mutation is found in several human cancer, causing an increase of cell proliferation due to a modification of the ERK/MAPK-signal cascade. In particular, BRAFV600E mutation is found in those melanoma or thyroid cancer refractory to the common therapy and with a more aggressive phenotype. BRAF V600E was found to influence the composition of the so-called tumour microenvironment modulating both solid (immune-cell infiltration) and soluble (chemokines) mediators, which balance characterize the ultimate behaviour of the tumour, making it more or less aggressive. In particular, the presence of BRAFV600E mutation would be associated with a change of this balance to a more aggressive phenotype of the tumour and a worse prognosis. The investigation of the possible modulation of those components of tumour microenvironment is nowadays object of several studies as a new potential target therapy in those more complicated cases. At present several clinical trials both in melanoma and thyroid cancer are using BRAF-inhibitors with encouraging results, which are derived also from numerous in vitro pre-clinical studies aimed at evaluate the possible modulation of immune-cell density and of specific pro-tumorigenic chemokine secretion (CXCL8 and CCL2) by several BRAF-inhibitors in the context of melanoma and thyroid cancer. This review will encompass in vitro and in vivo studies which investigated the modulation of the tumour microenvironment by BRAF-inhibitors, highlighting also the most recent clinical trials with a specific focus on melanoma and thyroid cancer.
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Affiliation(s)
- Laura Croce
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, University of Pavia, Pavia, Italy
- PHD course in Experimental Medicine, University of Pavia, Pavia, Italy
| | - Francesca Coperchini
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, University of Pavia, Pavia, Italy
| | - Flavia Magri
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, University of Pavia, Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Luca Chiovato
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, University of Pavia, Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Mario Rotondi
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, University of Pavia, Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
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Li H, Duan N, Zhang Q, Shao Y. IL1A & IL1B genetic polymorphisms are risk factors for thyroid cancer in a Chinese Han population. Int Immunopharmacol 2019; 76:105869. [DOI: 10.1016/j.intimp.2019.105869] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/11/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
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Valvo V, Nucera C. Coding Molecular Determinants of Thyroid Cancer Development and Progression. Endocrinol Metab Clin North Am 2019; 48:37-59. [PMID: 30717910 PMCID: PMC6366338 DOI: 10.1016/j.ecl.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Thyroid cancer is the most common endocrine malignancy. Its incidence and mortality rates have increased for patients with advanced-stage papillary thyroid cancer. The characterization of the molecular pathways essential in thyroid cancer initiation and progression has made huge progress, underlining the role of intracellular signaling to promote clonal evolution, dedifferentiation, metastasis, and drug resistance. The discovery of genetic alterations that include mutations (BRAF, hTERT), translocations, deletions (eg, 9p), and copy-number gain (eg, 1q) has provided new biological insights with clinical applications. Understanding how molecular pathways interplay is one of the key strategies to develop new therapeutic treatments and improve prognosis.
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Affiliation(s)
- Veronica Valvo
- Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Experimental Pathology, Department of Pathology, Cancer Research Institute (CRI), Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA; Department of Pathology, Center for Vascular Biology Research (CVBR), Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA
| | - Carmelo Nucera
- Laboratory of Human Thyroid Cancers Preclinical and Translational Research, Division of Experimental Pathology, Department of Pathology, Cancer Research Institute (CRI), Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA; Department of Pathology, Center for Vascular Biology Research (CVBR), Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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Pfeifer A, Rusinek D, Żebracka-Gala J, Czarniecka A, Chmielik E, Zembala-Nożyńska E, Wojtaś B, Gielniewski B, Szpak-Ulczok S, Oczko-Wojciechowska M, Krajewska J, Polańska J, Jarząb B. Novel TG-FGFR1 and TRIM33-NTRK1 transcript fusions in papillary thyroid carcinoma. Genes Chromosomes Cancer 2019; 58:558-566. [PMID: 30664823 PMCID: PMC6594006 DOI: 10.1002/gcc.22737] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is most common among all thyroid cancers. Multiple genomic alterations occur in PTC, and gene rearrangements are one of them. Here we screened 14 tumors for novel fusion transcripts by RNA‐Seq. Two samples harboring RET/PTC1 and RET/PTC3 rearrangements were positive controls whereas the remaining ones were negative regarding the common PTC alterations. We used Sanger sequencing to validate potential fusions. We detected 2 novel potentially oncogenic transcript fusions: TG‐FGFR1 and TRIM33‐NTRK1. We detected 4 novel fusion transcripts of unknown significance accompanying the TRIM33‐NTRK1 fusion: ZSWIM5‐TP53BP2, TAF4B‐WDR1, ABI2‐MTA3, and ARID1B‐PSMA1. Apart from confirming the presence of RET/PTC1 and RET/PTC3 in positive control samples, we also detected known oncogenic fusion transcripts in remaining samples: TFG‐NTRK1, ETV6‐NTRK3, MKRN1‐BRAF, EML4‐ALK, and novel isoform of CCDC6‐RET.
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Affiliation(s)
- Aleksandra Pfeifer
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Dagmara Rusinek
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Jadwiga Żebracka-Gala
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Agnieszka Czarniecka
- Department of Oncological and Reconstructive Surgery, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Ewa Chmielik
- Tumor Pathology Department, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Ewa Zembala-Nożyńska
- Tumor Pathology Department, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Bartosz Wojtaś
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartłomiej Gielniewski
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sylwia Szpak-Ulczok
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Małgorzata Oczko-Wojciechowska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Jolanta Krajewska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
| | - Joanna Polańska
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Barbara Jarząb
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute - Oncology Center Gliwice Branch, Gliwice, Poland
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Landa I, Pozdeyev N, Korch C, Marlow LA, Smallridge RC, Copland JA, Henderson YC, Lai SY, Clayman GL, Onoda N, Tan AC, Garcia-Rendueles MER, Knauf JA, Haugen BR, Fagin JA, Schweppe RE. Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies. Clin Cancer Res 2019; 25:3141-3151. [PMID: 30737244 DOI: 10.1158/1078-0432.ccr-18-2953] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/26/2018] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE Thyroid cancer cell lines are valuable models but have been neglected in pancancer genomic studies. Moreover, their misidentification has been a significant problem. We aim to provide a validated dataset for thyroid cancer researchers. EXPERIMENTAL DESIGN We performed next-generation sequencing (NGS) and analyzed the transcriptome of 60 authenticated thyroid cell lines and compared our findings with the known genomic defects in human thyroid cancers. RESULTS Unsupervised transcriptomic analysis showed that 94% of thyroid cell lines clustered distinctly from other lineages. Thyroid cancer cell line mutations recapitulate those found in primary tumors (e.g., BRAF, RAS, or gene fusions). Mutations in the TERT promoter (83%) and TP53 (71%) were highly prevalent. There were frequent alterations in PTEN, PIK3CA, and of members of the SWI/SNF chromatin remodeling complex, mismatch repair, cell-cycle checkpoint, and histone methyl- and acetyltransferase functional groups. Copy number alterations (CNA) were more prevalent in cell lines derived from advanced versus differentiated cancers, as reported in primary tumors, although the precise CNAs were only partially recapitulated. Transcriptomic analysis showed that all cell lines were profoundly dedifferentiated, regardless of their derivation, making them good models for advanced disease. However, they maintained the BRAFV600E versus RAS-dependent consequences on MAPK transcriptional output, which correlated with differential sensitivity to MEK inhibitors. Paired primary tumor-cell line samples showed high concordance of mutations. Complete loss of p53 function in TP53 heterozygous tumors was the most prominent event selected during in vitro immortalization. CONCLUSIONS This cell line resource will help inform future preclinical studies exploring tumor-specific dependencies.
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Affiliation(s)
- Iñigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikita Pozdeyev
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Laura A Marlow
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Robert C Smallridge
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida.,Division of Endocrinology, Internal Medicine Department, Mayo Clinic, Jacksonville, Florida
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Ying C Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Naoyoshi Onoda
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Aik Choon Tan
- University of Colorado Cancer Center, Aurora, Colorado
| | | | - Jeffrey A Knauf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bryan R Haugen
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rebecca E Schweppe
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado. .,Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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28
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Detection of BRAF V600E mutation in fine-needle aspiration fluid of papillary thyroid carcinoma by droplet digital PCR. Clin Chim Acta 2019; 491:91-96. [PMID: 30682328 DOI: 10.1016/j.cca.2019.01.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/06/2019] [Accepted: 01/17/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Papillary thyroid carcinoma (PTC) accounts for 85% of thyroid carcinoma, which is the most common endocrine tumor. For the diagnosis of PTC, ultrasound-guided fine needle aspiration (FNA) with pathological evaluation is the standard test and BRAF V600E mutation is the most common molecular marker associated with the occurrence, progression and poor clinicopathological characteristics of PTC. However, because of the small amount of the tumor cells obtained by FNA for pathological evaluation or BRAF V600E mutation detection, more sensitive and accurate methods are required. Our study aimed to investigate the performance of droplet digital PCR (ddPCR) in detecting BRAF V600E mutation in FNA samples from PTC patients. METHODS One hundred and sixty suspected thyroid cancer patients were enrolled, including 146 PTC patients, 2 follicular thyroid carcinoma (FTC) and 12 benign patients, identified by FNA biopsy according to the NCCN clinical practice guidelines of Thyroid Carcinoma. ddPCR and amplification-refractory mutation system (ARMS, AmoyDx) were used to detect BRAFV600E mutation and the results were compared. RESULTS ddPCR had high reproducibility (CV0.1% = 22.82% and CV10% = 4.85%) and the detection sensitivity can reach 1–2 copies/μl (0.01%). Among the 160 patients, 128 BRAF V600E mutations were detected, including 4 ARMS negative patients and 3 benign cases [corrected]. CONCLUSIONS Our results demonstrated that ddPCR could be used in detecting BRAF V600E mutation from FNA fluid samples with higher sensitivity and accuracy than ARMS.
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29
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Shang J, Ding Q, Yuan S, Liu JX, Li F, Zhang H. Network Analyses of Integrated Differentially Expressed Genes in Papillary Thyroid Carcinoma to Identify Characteristic Genes. Genes (Basel) 2019; 10:E45. [PMID: 30646607 PMCID: PMC6356810 DOI: 10.3390/genes10010045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/26/2018] [Accepted: 01/09/2019] [Indexed: 12/18/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Identifying characteristic genes of PTC are of great importance to reveal its potential genetic mechanisms. In this paper, we proposed a framework, as well as a measure named Normalized Centrality Measure (NCM), to identify characteristic genes of PTC. The framework consisted of four steps. First, both up-regulated genes and down-regulated genes, collectively called differentially expressed genes (DEGs), were screened and integrated together from four datasets, that is, GSE3467, GSE3678, GSE33630, and GSE58545; second, an interaction network of DEGs was constructed, where each node represented a gene and each edge represented an interaction between linking nodes; third, both traditional measures and the NCM measure were used to analyze the topological properties of each node in the network. Compared with traditional measures, more genes related to PTC were identified by the NCM measure; fourth, by mining the high-density subgraphs of this network and performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, several meaningful results were captured, most of which were demonstrated to be associated with PTC. The experimental results proved that this network framework and the NCM measure are useful for identifying more characteristic genes of PTC.
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Affiliation(s)
- Junliang Shang
- School of Statistics, Qufu Normal University, Qufu 273165, China.
- School of Information Science and Engineering, Qufu Normal University, Rizhao 276800, China.
| | - Qian Ding
- School of Information Science and Engineering, Qufu Normal University, Rizhao 276800, China.
| | - Shasha Yuan
- School of Information Science and Engineering, Qufu Normal University, Rizhao 276800, China.
| | - Jin-Xing Liu
- School of Information Science and Engineering, Qufu Normal University, Rizhao 276800, China.
| | - Feng Li
- School of Computer Science and Technology, Xidian University, Xi'an 710071, China.
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China.
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30
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Immune Gene Signature Delineates a Subclass of Papillary Thyroid Cancer with Unfavorable Clinical Outcomes. Cancers (Basel) 2018; 10:cancers10120494. [PMID: 30563160 PMCID: PMC6316581 DOI: 10.3390/cancers10120494] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/02/2018] [Accepted: 12/03/2018] [Indexed: 12/16/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) represents a heterogeneous disease with diverse clinical outcomes highlighting a need to identify robust biomarkers with clinical relevance. We applied non-negative matrix factorization-based deconvolution to publicly available gene expression profiles of thyroid cancers in the Cancer Genome Atlas (TCGA) consortium. Among three metagene signatures identified, two signatures were enriched in canonical BRAF-like and RAS-like thyroid cancers with up-regulation of genes involved in oxidative phosphorylation and cell adhesions, respectively. The third metagene signature representing up-regulation of immune-related genes further segregated BRAF-like and RAS-like PTCs into their respective subgroups of immunoreactive (IR) and immunodeficient (ID), respectively. BRAF-IR PTCs showed enrichment of tumor infiltrating immune cells, tall cell variant PTC, and shorter recurrence-free survival compared to BRAF-ID PTCs. RAS-IR and RAS-ID PTC subtypes included majority of normal thyroid tissues and follicular variant PTC, respectively. Immunopathological features of PTC subtypes such as immune cell fraction, repertoire of T cell receptors, cytolytic activity, and expression level of immune checkpoints such as and PD-L1 and CTLA-4 were consistently observed in two different cohorts. Taken together, an immune-related metagene signature can classify PTCs into four molecular subtypes, featuring the distinct histologic type, genetic and transcriptional alterations, and potential clinical significance.
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31
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The Transcription Factor ETV5 Mediates BRAFV600E-Induced Proliferation and TWIST1 Expression in Papillary Thyroid Cancer Cells. Neoplasia 2018; 20:1121-1134. [PMID: 30265861 PMCID: PMC6161370 DOI: 10.1016/j.neo.2018.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/08/2018] [Accepted: 09/08/2018] [Indexed: 12/17/2022] Open
Abstract
The ETS family of transcription factors is involved in several normal remodeling events and pathological processes including tumor progression. ETS transcription factors are divided into subfamilies based on the sequence and location of the ETS domain. ETV5 (Ets variant gene 5; also known as ERM) is a member of the PEA3 subfamily. Our meta-analysis of normal, benign, and malignant thyroid samples demonstrated that ETV5 expression is upregulated in papillary thyroid cancer and was predominantly associated with BRAF V600E or RAS mutations. However, the precise role of ETV5 in these lesions is unknown. In this study, we used the KTC1 cell line as a model for human advanced papillary thyroid cancer (PTC) because the cells harbor the heterozygous BRAF (V600E) mutation together with the C250T TERT promoter mutation. The role of ETV5 in PTC proliferation was tested using RNAi followed by high-throughput screening. Signaling pathways driving ETV5 expression were identified using specific pharmacological inhibitors. To determine if ETV5 influences the expression of epithelial-to-mesenchymal (EMT) markers in these cells, an EMT PCR array was used, and data were confirmed by qPCR and ChIP-qPCR. We found that ETV5 is critical for PTC cell growth, is expressed downstream of the MAPK pathway, and directly upregulates the transcription factor TWIST1, a known marker of intravasation and metastasis. Increased ETV5 expression could therefore be considered as a marker for advanced PTCs and a possible future therapeutic target.
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32
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Ellis SE, Collado-Torres L, Jaffe A, Leek JT. Improving the value of public RNA-seq expression data by phenotype prediction. Nucleic Acids Res 2018; 46:e54. [PMID: 29514223 PMCID: PMC5961118 DOI: 10.1093/nar/gky102] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 02/01/2018] [Accepted: 02/15/2018] [Indexed: 12/26/2022] Open
Abstract
Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are often not well labeled or annotated. The lack of phenotype information for public genomic data severely limits their utility for addressing targeted biological questions. We develop an in silico phenotyping approach for predicting critical missing annotation directly from genomic measurements using well-annotated genomic and phenotypic data produced by consortia like TCGA and GTEx as training data. We apply in silico phenotyping to a set of 70 000 RNA-seq samples we recently processed on a common pipeline as part of the recount2 project. We use gene expression data to build and evaluate predictors for both biological phenotypes (sex, tissue, sample source) and experimental conditions (sequencing strategy). We demonstrate how these predictions can be used to study cross-sample properties of public genomic data, select genomic projects with specific characteristics, and perform downstream analyses using predicted phenotypes. The methods to perform phenotype prediction are available in the phenopredict R package and the predictions for recount2 are available from the recount R package. With data and phenotype information available for 70,000 human samples, expression data is available for use on a scale that was not previously feasible.
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Affiliation(s)
- Shannon E Ellis
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, USA
- Center for Computational Biology, Johns Hopkins University, USA
| | - Leonardo Collado-Torres
- Center for Computational Biology, Johns Hopkins University, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, USA
| | - Andrew Jaffe
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, USA
- Center for Computational Biology, Johns Hopkins University, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, USA
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, USA
- Center for Computational Biology, Johns Hopkins University, USA
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33
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Buj R, Mallona I, Díez-Villanueva A, Zafon C, Mate JL, Roca M, Puig-Domingo M, Reverter JL, Mauricio D, Peinado MA, Jordà M. Kallikreins Stepwise Scoring Reveals Three Subtypes of Papillary Thyroid Cancer with Prognostic Implications. Thyroid 2018; 28:601-612. [PMID: 29635968 DOI: 10.1089/thy.2017.0501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common type of thyroid cancer. Unlike most cancers, its incidence has dramatically increased in the last decades mainly due to increased diagnosis of indolent PTCs. Adequate risk stratification is crucial to avoid the over-treatment of low-risk patients, as well as the under-treatment of high-risk patients, but the currently available markers are still insufficient. Kallikreins (KLKs) are emergent biomarkers in cancer, but their involvement in PTC is unknown. METHODS This study analyzed DNA methylation (HumanMethylation arrays) and gene expression (RNA-Seq) of KLKs, BRAF and RAS mutations, and clinical data from four published thyroid cancer data sets including normal and tumor tissues (n = 73, n = 475, n = 20, and n = 82) as discovery, training, and validation series. The C4.5 classification algorithm was used to generate a decision tree. Disease-free survival was estimated using Kaplan-Meier and Cox approaches. Specific analyses were performed using real-time polymerase chain reaction and immunohistochemistry. RESULTS The entire KLK family was deregulated in PTC, displaying a specific epigenetic and transcriptional profile strongly associated with BRAFV600E or RAS mutations. Thus, a decision-tree algorithm was developed based on three KLKs with >80% sensitivity and >95% specificity, identifying BRAF- and RAS-mutated tumors. Notably, tumors lacking these mutations were classified as BRAF- or RAS-like. Most importantly, the KLK algorithm uncovered a novel PTC subtype showing favorable prognostic features. CONCLUSIONS The KLK algorithm could lead to a new clinically applicable strategy with important implications for the risk stratification of PTC and the management of patients.
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Affiliation(s)
- Raquel Buj
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
| | - Izaskun Mallona
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
| | - Anna Díez-Villanueva
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
| | - Carles Zafon
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 3 Diabetes and Metabolism Research Unit (VHIR) and Department of Endocrinology, University Hospital Vall d'Hebron and Autonomous University of Barcelona , Barcelona, Spain
- 4 Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases (CIBERDEM), Institute of Health Carlos III (ISCIII) , Madrid, Spain
| | - José L Mate
- 5 Department of Pathology, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
| | - Mireia Roca
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
| | - Manel Puig-Domingo
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 4 Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases (CIBERDEM), Institute of Health Carlos III (ISCIII) , Madrid, Spain
- 6 Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
- 7 Biomedical Research Networking Center in Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII) , Madrid, Spain
| | - Jordi L Reverter
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 6 Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
| | - Dídac Mauricio
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 4 Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases (CIBERDEM), Institute of Health Carlos III (ISCIII) , Madrid, Spain
- 6 Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital , Badalona, Spain
| | - Miguel A Peinado
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
| | - Mireia Jordà
- 1 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona, Spain
- 2 Consortium for the Study of Thyroid Cancer (CECaT) , Catalonia, Spain
- 7 Biomedical Research Networking Center in Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII) , Madrid, Spain
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Kim HK, Lee I, Lee J, Chang HS, Soh EY, Park IS, Kim JH, Rho YS, Lee DJ. BRAF wild papillary thyroid carcinoma has two distinct mRNA expression patterns with different clinical behaviors. Head Neck 2018; 40:1707-1718. [PMID: 29573027 DOI: 10.1002/hed.25151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Using a large set of genomic data from The Cancer Genome Atlas (TCGA), we classified BRAFwild papillary thyroid carcinomas (PTCs) into 2 subtypes with distinct molecular patterns and different clinical behaviors. We also suggested gene signatures (RAS-score) to predict molecular subtypes and clinical behaviors of BRAFwild PTC. METHOD Integrated genomic analysis was done using all genomic data of PTC in TCGA data portal (https://tcga-data.nci.nih.gov) and cancer browser (https://genome-cancer.ucsc.edu). Using Gene Ontology and a logistic regression test, we selected gene signatures (RAS-score) and applied this prediction model to the validation cohort (GSE60542). RESULT When we performed multiplatform genomic analysis, BRAFwild PTCs were divided into 2 molecular subtypes. Each subtype showed distinct molecular patterns and clinical behaviors. Gene signatures successfully predicted molecular subtype in another validation cohort. CONCLUSION We found that BRAFwild PTCs were divided into 2 molecular subtypes and each subtype showed distinct molecular patterns, different activated pathways, and different clinical behaviors.
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Affiliation(s)
- Hyeung Kyoo Kim
- Department of Surgery, Ajou University School of Medicine, Suwon, South Korea.,Department of Surgery, Graduate School, Yonsei University College of Medicine, Seoul, South Korea
| | - Inhwa Lee
- Department of Surgery, Ajou University School of Medicine, Suwon, South Korea
| | - Jeonghun Lee
- Department of Surgery, Ajou University School of Medicine, Suwon, South Korea
| | - Hang-Seok Chang
- Department of Surgery, Graduate School, Yonsei University College of Medicine, Seoul, South Korea
| | - Euy Young Soh
- Department of Surgery, Ajou University School of Medicine, Suwon, South Korea
| | - Il Seok Park
- Department of Otolaryngology - Head and Neck Surgery, Kangnam Sacret Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Jin Hwan Kim
- Department of Otolaryngology - Head and Neck Surgery, Kangnam Sacret Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Young Soo Rho
- Department of Otolaryngology - Head and Neck Surgery, Kangnam Sacret Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Dong Jin Lee
- Department of Otolaryngology - Head and Neck Surgery, Kangnam Sacret Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
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35
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Celestino R, Nome T, Pestana A, Hoff AM, Gonçalves AP, Pereira L, Cavadas B, Eloy C, Bjøro T, Sobrinho-Simões M, Skotheim RI, Soares P. CRABP1, C1QL1 and LCN2 are biomarkers of differentiated thyroid carcinoma, and predict extrathyroidal extension. BMC Cancer 2018; 18:68. [PMID: 29321030 PMCID: PMC5763897 DOI: 10.1186/s12885-017-3948-3] [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: 01/01/2017] [Accepted: 12/20/2017] [Indexed: 01/21/2023] Open
Abstract
Background The prognostic variability of thyroid carcinomas has led to the search for accurate biomarkers at the molecular level. Follicular thyroid carcinoma (FTC) is a typical example of differentiated thyroid carcinomas (DTC) in which challenges are faced in the differential diagnosis. Methods We used high-throughput paired-end RNA sequencing technology to study four cases of FTC with different degree of capsular invasion: two minimally invasive (mFTC) and two widely invasive FTC (wFTC). We searched by genes differentially expressed between mFTC and wFTC, in an attempt to find biomarkers of thyroid cancer diagnosis and/or progression. Selected biomarkers were validated by real-time quantitative PCR in 137 frozen thyroid samples and in an independent dataset (TCGA), evaluating the diagnostic and the prognostic performance of the candidate biomarkers. Results We identified 17 genes significantly differentially expressed between mFTC and wFTC. C1QL1, LCN2, CRABP1 and CILP were differentially expressed in DTC in comparison with normal thyroid tissues. LCN2 and CRABP1 were also differentially expressed in DTC when compared with follicular thyroid adenoma. Additionally, overexpression of LCN2 and C1QL1 were found to be independent predictors of extrathyroidal extension in DTC. Conclusions We conclude that the underexpression of CRABP1 and the overexpression of LCN2 may be useful diagnostic biomarkers in thyroid tumours with questionable malignity, and the overexpression of LCN2 and C1QL1 may be useful for prognostic purposes. Electronic supplementary material The online version of this article (10.1186/s12885-017-3948-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ricardo Celestino
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway.,School of Allied Health Technologies, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072, Porto, Portugal
| | - Torfinn Nome
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0424, Oslo, Norway
| | - Ana Pestana
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,ICBAS - Abel Salazar Biomedical Sciences Institute of the University of Porto, 4050-313, Porto, Portugal
| | - Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0424, Oslo, Norway
| | - A Pedro Gonçalves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,ICBAS - Abel Salazar Biomedical Sciences Institute of the University of Porto, 4050-313, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Luísa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Bruno Cavadas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Catarina Eloy
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Trine Bjøro
- Department of Medical Biochemistry, Norwegian Radium Hospital, Oslo University Hospital, 0424, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway
| | - Manuel Sobrinho-Simões
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Department of Pathology, Medical Faculty, University of Porto, 4200-319, Porto, Portugal.,Department of Pathology, Centro Hospitalar de São João, 4200-319, Porto, Portugal
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, P.O.Box 4953 Nydalen, 0424, Oslo, Norway. .,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0424, Oslo, Norway.
| | - Paula Soares
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Department of Pathology, Medical Faculty, University of Porto, 4200-319, Porto, Portugal.
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Bastos AU, de Jesus AC, Cerutti JM. ETV6-NTRK3 and STRN-ALK kinase fusions are recurrent events in papillary thyroid cancer of adult population. Eur J Endocrinol 2018; 178:83-91. [PMID: 29046324 DOI: 10.1530/eje-17-0499] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/08/2017] [Accepted: 10/16/2017] [Indexed: 12/27/2022]
Abstract
OBJECTIVE PTC-specific analysis identified novel fusions involving RET, BRAF, NTRK1, NTRK3, AGK and ALK genes in adults and pediatric PTCs. Although many novel fusions are PTC-specific events and, therefore, are ideal for diagnosis purposes, validation across additional and larger patient cohorts is essential for introducing these potential diagnostic or prognostic biomarkers into the clinical practice. As most of the BRAF, NTRK3 and ALK fusions were initially found in pediatric PTC or in more aggressive thyroid carcinomas, and there is a great disparity across population, in this study, we screened a large set of adult-sporadic PTC cases for the most prevalent kinase fusion lately described in the TCGA. DESIGN AND METHODS The prevalence of the fusions was determined by RT-PCR in 71 classical PTC, 45 follicular variants of PTC (FVPTC), 19 follicular thyroid adenomas (FTAs) and 22 follicular thyroid carcinomas (FTCs). RESULTS ETV6-NTRK3 was exclusively found in FVPTC, in both encapsulated and infiltrative variants, but was not found in FTAs and FTCs. STRN-ALK was found in both classical PTC and FVPTC. No AGK-BRAF fusion was identified in this series, endorsing that AGK-BRAF is a genetic event mainly associated with pediatric PTCs. CONCLUSIONS The identification of kinase fusions in thyroid carcinomas helps to expand our knowledge about the landscape of oncogenic alterations in PTC. As ETV6-NTRK3 and STRN-ALK are recurrent and not identified in benign lesions, they can certainly help with diagnosis of thyroid nodules. Further analysis is needed to define if they can also be useful for prognosis and guiding therapy.
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Affiliation(s)
- André Uchimura Bastos
- Departamento de Morfologia e Genética, Genetic Bases of Thyroid Tumors Laboratory, Disciplina de Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Carolina de Jesus
- Departamento de Morfologia e Genética, Genetic Bases of Thyroid Tumors Laboratory, Disciplina de Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Janete Maria Cerutti
- Departamento de Morfologia e Genética, Genetic Bases of Thyroid Tumors Laboratory, Disciplina de Genética, Universidade Federal de São Paulo, São Paulo, Brazil
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Characteristics of lymphocyte-infiltrating papillary thyroid cancer. JOURNAL OF CANCER RESEARCH AND PRACTICE 2017. [DOI: 10.1016/j.jcrpr.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Qiu J, Zhang W, Xia Q, Liu F, Zhao S, Zhang K, Chen M, Zang C, Ge R, Liang D, Sun Y. Investigating the mechanisms of papillary thyroid carcinoma using transcriptome analysis. Mol Med Rep 2017; 16:5954-5964. [PMID: 28849102 PMCID: PMC5865774 DOI: 10.3892/mmr.2017.7346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 06/12/2017] [Indexed: 01/29/2023] Open
Abstract
As the predominant thyroid cancer, papillary thyroid cancer (PTC) accounts for 75–85% of thyroid cancer cases. This research aimed to investigate transcriptomic changes and key genes in PTC. Using RNA-sequencing technology, the transcriptional profiles of 5 thyroid tumor tissues and 5 adjacent normal tissues were obtained. The single nucleotide polymorphisms (SNPs) were identified by SAMtools software and then annotated by ANNOVAR software. After differentially expressed genes (DEGs) were selected by edgR software, they were further investigated by enrichment analysis, protein domain analysis, and protein-protein interaction (PPI) network analysis. Additionally, the potential gene fusion events were predicted using FusionMap software. A total of 70,172 SNPs and 2,686 DEGs in the tumor tissues, as well as 83,869 SNPs in the normal tissues were identified. In the PPI network, fibronectin 1 (FN1; degree=31) and transforming growth factor β receptor 1 (TGFβR1; degree=22) had higher degrees. A total of 7 PPI pairs containing the non-synonymous risk SNP loci in the interaction domains were identified. Particularly, the interaction domains involved in the interactions of FN1 and 5 other proteins (such as FN1-tenascin C, TNC) had non-synonymous risk SNP loci. Furthermore, 11 and 4 gene fusion events were identified in all of the tumor tissues and normal tissues, respectively. Additionally, the NK2 homeobox 1-surfactant associated 3 (NKX2-1-SFTA3) gene fusion was identified in both tumor and normal tissues. These results indicated that TGFβR1 and the NKX2-1-SFTA3 gene fusion may be involved in PTC. Furthermore, FN1 and TNC containing the non-synonymous risk SNP loci might serve a role in PTC by interacting with each other.
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Affiliation(s)
- Jie Qiu
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Wenwei Zhang
- Radiology Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Qingsheng Xia
- Otolaryngology Head and Neck Surgery, Qingdao Municipal Hospital, Qingdao, Shandong 266071, P.R. China
| | - Fuxue Liu
- Otolaryngology Head and Neck Surgery, Shaoxing Municipal Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Shuwei Zhao
- Otolaryngology Head and Neck Surgery, Shanghai Chang Zheng Hospital, Shanghai 200003, P.R. China
| | - Kailing Zhang
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Min Chen
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Chuanshan Zang
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Ruifeng Ge
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Dapeng Liang
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yan Sun
- Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
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Overexpression of teneurin transmembrane protein 1 is a potential marker of disease progression in papillary thyroid carcinoma. Clin Exp Med 2016; 17:555-564. [PMID: 28004221 DOI: 10.1007/s10238-016-0445-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023]
Abstract
Although papillary thyroid cancer is a relatively indolent malignancy, its progression may be associated with dedifferentiation and resistance to radioactive iodine treatment. In this study, patterns of differentially expressed genes in association with disease progression were systemically evaluated. We firstly performed transcriptome analyses for four matched cancerous and noncancerous tissue pairs of the classical subtype of papillary thyroid cancer. Among the upregulated and downregulated genes, the expression of 164 and 183 genes increased and decreased, respectively, from stage I to stage IV. Functional enrichment and pathway analysis showed that angiogenesis pathway was upregulated, whereas oxidation-reduction and metabolism of reactive oxygen species were downregulated. Teneurin transmembrane protein 1 (TENM1) expression was highly upregulated in cancerous tissues and negative in benign thyroid tissues. By immunohistochemistry, TENM1 expression in papillary thyroid cancer was associated with the classical subtype (p = 0.018), extrathyroidal invasion (p = 0.001), BRAF V600E mutation (p < 0.001), and an advanced stage (p = 0.019). Taken together, our results indicate that distinct pathways are involved in papillary thyroid cancer progression, and TENM1 is a potential marker of cancer progression.
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40
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Wang Q, Yang H, Wu L, Yao J, Meng X, Jiang H, Xiao C, Wu F. Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer. Thyroid 2016; 26:1719-1732. [PMID: 27758138 DOI: 10.1089/thy.2016.0024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown. METHODS RNA sequencing and quantitative reverse transcription polymerase chain reaction were used to detect and verify changes to the transcriptome profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathologic characteristics was analyzed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs. Furthermore, the specific subgroup patterns of the PTC transcriptome remodeled by BRAF mutations were also analyzed. RESULTS A total of 188 lncRNAs and 505 mRNAs were differentially expressed in 50% or more of the PTC tissues (fold change >2; p < 0.05) as assessed by RNA-sequencing compared with paired normal adjacent tissues. Forty-seven lncRNAs and 39 mRNAs were verified in 31 pairs of PTC specimens using quantitative reverse transcription polymerase chain reaction, and the results were consistent with the RNA sequencing data. The lncRNAs NONHSAT076747 and NONHSAT122730 were associated with lymph node metastasis, and NONHSAG051968 expression was negatively correlated with tumor size. A co-expression network between differentially expressed lncRNAs and protein-coding RNAs was constructed and analyzed, and functional analysis suggested that the differentially expressed genes mainly participate in ECM-receptor interactions and the focal adhesion pathway. Furthermore, a specific PTC transcriptome subtype pattern stratified by BRAF mutation was also uncovered. The p53 signaling pathway was the most highly enriched pathway among the BRAF mutation-related genes. CONCLUSIONS This study reveals specific changes to the lncRNA profile associated with PTC, and provides new insight into its pathogenesis. The PTC-associated lncRNAs NONHSAG051968, NONHSAT076747, and NONHSAT122730 might be potential diagnostic and therapeutic targets for PTC patients, and lncRNAs with subtype-specific expression stratified by BRAF mutation might be significant in individual molecular subtypes.
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Affiliation(s)
- Qiangfeng Wang
- 1 Department of Surgical Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Huanxia Yang
- 1 Department of Surgical Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Lingjiao Wu
- 2 State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Jian Yao
- 2 State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Xiaohua Meng
- 2 State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Han Jiang
- 3 Department of Oncology, Shaoxing Second Hospital , Shaoxing, Zhejiang, China
| | - Cheng Xiao
- 4 Department of Medical Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
| | - Fusheng Wu
- 1 Department of Surgical Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University , Hangzhou, China
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Abstract
Next-generation sequencing (NGS) in thyroid cancer allows for simultaneous high-throughput sequencing analysis of variable genetic alterations and provides a comprehensive understanding of tumor biology. In thyroid cancer, NGS offers diagnostic improvements for fine needle aspiration (FNA) cytology of thyroid with indeterminate features. It also contributes to patient management, providing risk stratification of patients based on the risk of malignancy. Furthermore, NGS has been adopted in cancer research. It is used in molecular tumor classification, and molecular prediction of recurrence and metastasis in papillary thyroid carcinoma. This review covers previous NGS analyses in variable types of thyroid cancer, where samples including FNA cytology, fresh frozen tissue, and formalin-fixed, paraffin-embedded tissues were used. This review also focuses on the clinical and research implications of using NGS to study and treat thyroid cancer.
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Affiliation(s)
- Yoon Jin Cha
- Department of Pathology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 South Korea
| | - Ja Seung Koo
- Department of Pathology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 South Korea
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Awad MM, Jones RE, Liu H, Lizotte PH, Ivanova EV, Kulkarni M, Herter-Sprie GS, Liao X, Santos AA, Bittinger MA, Keogh L, Koyama S, Almonte C, English JM, Barlow J, Richards WG, Barbie DA, Bass AJ, Rodig SJ, Hodi FS, Wucherpfennig KW, Jänne PA, Sholl LM, Hammerman PS, Wong KK, Bueno R. Cytotoxic T Cells in PD-L1–Positive Malignant Pleural Mesotheliomas Are Counterbalanced by Distinct Immunosuppressive Factors. Cancer Immunol Res 2016; 4:1038-1048. [DOI: 10.1158/2326-6066.cir-16-0171] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/22/2016] [Accepted: 10/19/2016] [Indexed: 11/16/2022]
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Escalante DA, Wang H, Fundakowski CE. Fusion proteins in head and neck neoplasms: Clinical implications, genetics, and future directions for targeting. Cancer Biol Ther 2016; 17:995-1002. [PMID: 27636353 DOI: 10.1080/15384047.2016.1219823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Fusion proteins resulting from chromosomal rearrangements are known to drive the pathogenesis of a variety of hematological and solid neoplasms such as chronic myeloid leukemia and non-small-cell lung cancer. Efforts to elucidate the role they play in these malignancies have led to important diagnostic and therapeutic triumphs, including the famous development of the tyrosine kinase inhibitor dasatinib targeting the BCR-ABL fusion. Until recently, there has been a paucity of research investigating fusion proteins harbored by head and neck neoplasms. The discovery and characterization of novel fusion proteins in neoplasms originating from the thyroid, nasopharynx, salivary glands, and midline head and neck structures offer substantial contributions to our understanding of the pathogenesis and biological behavior of these neoplasms, while raising new therapeutic and diagnostic opportunities. Further characterization of these fusion proteins promises to facilitate advances on par with those already achieved with regard to hematologic malignancies in the precise, molecularly guided diagnosis and treatment of head and neck neoplasms. The following is a subsite specific review of the clinical implications of fusion proteins in head and neck neoplasms and the future potential for diagnostic targeting.
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Affiliation(s)
- Derek A Escalante
- a Temple University Katz School of Medicine , Philadelphia , PA , USA
| | - He Wang
- a Temple University Katz School of Medicine , Philadelphia , PA , USA.,b Department of Pathology and Lab Medicine , Temple University , Philadelphia , PA , USA
| | - Christopher E Fundakowski
- a Temple University Katz School of Medicine , Philadelphia , PA , USA.,c Department of Otolaryngology - Head & Neck Surgery , Temple University , Philadelphia , PA , USA.,d Department of Surgical Oncology, Fox Chase Cancer Center , Philadelphia , PA , USA
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44
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Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep 2016; 6:25521. [PMID: 27160768 PMCID: PMC4861919 DOI: 10.1038/srep25521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 04/15/2016] [Indexed: 12/26/2022] Open
Abstract
The estrogen receptor alpha (ERα) is highly expressed in both endometrial and breast cancers, and represents the most prevalent therapeutic target in breast cancer. However, anti-estrogen therapy has not been shown to be effective in endometrial cancer. Recently it has been shown that hormone-binding domain alterations of ERα in breast cancer contribute to acquired resistance to anti-estrogen therapy. In analyses of genomic data from The Cancer Genome Atlas (TCGA), we observe that endometrial carcinomas manifest recurrent ESR1 gene amplifications that truncate the hormone-binding domain encoding region of ESR1 and are associated with reduced mRNA expression of exons encoding the hormone-binding domain. These findings support a role for hormone-binding alterations of ERα in primary endometrial cancer, with potentially important therapeutic implications.
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Costa V, Esposito R, Pallante P, Ciccodicola A, Fusco A. The "next-generation" knowledge of papillary thyroid carcinoma. Cell Cycle 2016; 14:2018-21. [PMID: 26030480 DOI: 10.1080/15384101.2015.1049786] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The application of Next-Generation Sequencing for studying the genetics of papillary thyroid carcinomas (PTC) has recently revealed new somatic mutations and gene fusions as potential new tumor-initiating events in patients without any known driver lesion. Gene and miRNA expression analyses defined clinically relevant subclasses correlated to tumor progression. In addition, it has been shown that tumor driver mutations in BRAF, and RET rearrangements - altogether termed "BRAF-like" carcinomas - have a very similar expression pattern and constitute a distinct category. Conversely, "RAS-like" carcinomas have a different genomic, epigenomic, and proteomic profile. These findings justify the need to reconsider PTC classification schemes.
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Affiliation(s)
- Valerio Costa
- a Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," CNR ; Naples , Italy
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46
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Kekeeva T, Tanas A, Kanygina A, Alexeev D, Shikeeva A, Zavalishina L, Andreeva Y, Frank GA, Zaletaev D. Novel fusion transcripts in bladder cancer identified by RNA-seq. Cancer Lett 2016; 374:224-8. [PMID: 26898937 DOI: 10.1016/j.canlet.2016.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 10/25/2022]
Abstract
Urothelial carcinoma (UC) is the most common type of bladder cancer and is the second most frequently diagnosed genitourinary tumor. The identification of fusion genes in bladder cancer might provide new perspectives for its classification and significance. In this study, we present a thorough search on three UC samples for novel fusion transcripts in bladder cancer using high-throughput RNA sequencing. We used stringent requirements for 819 fusion candidates and nominated 10 candidate fusion transcripts. Among them four novel fusion genes SEPT9/CYHR, IGF1R/TTC23, SYT8/TNNI2 and CASZ1/DFFA were validated and characterized in 48 formalin-fixed paraffin-embedded (FFPE) specimens of bladder cancer. Chromosomal rearrangements of regions 17q25, 15q26.3 and 1p36.22 resulting in the fusion transcripts SEPT9/CYHR, IGF1R/TTC23 and CASZ1/DFFA, appeared to be rare or unique events because they were not detected in the 48 UC samples. In contrast, the SYT8/TNNI2 fusion transcript resulting from transcription-induced chimerism by read-through mechanisms was a rather common and tumor-specific event occurring in 37.5% (18/48) of the UC specimens. Further investigation of functional and clinical relevance of novel fusion genes remains to be elucidated to reveal their role in bladder carcinogenesis.
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Affiliation(s)
- T Kekeeva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation.
| | - A Tanas
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation
| | - A Kanygina
- Department of Molecular Biophysics, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny, 141700, Russian Federation
| | - D Alexeev
- Medical and Rehabilitation Center of Ministry of Healthcare of Russian Federation, Ivankovskoye, 3, Moscow, 125367, Russian Federation; Department of Molecular Biophysics, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny, 141700, Russian Federation
| | - A Shikeeva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - L Zavalishina
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - Y Andreeva
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - G A Frank
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - D Zaletaev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Laboratory of Human Molecular Genetics, I. M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, Moscow 119991, Russian Federation
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RNA sequencing identifies crucial genes in papillary thyroid carcinoma (PTC) progression. Exp Mol Pathol 2015; 100:151-9. [PMID: 26708423 DOI: 10.1016/j.yexmp.2015.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/15/2015] [Accepted: 12/15/2015] [Indexed: 11/21/2022]
Abstract
PURPOSE The study aims to uncover molecular mechanisms of PTC (papillary thyroid carcinoma) progression and provide therapeutic biomarkers. METHODS The paired tumor and control tissues were obtained from 5 PTC patients. RNA was extracted and cDNA libraries were constructed. RNA-sequencing (RNA-seq) was performed on the Illumina HiSeq2000 platform using paired-end method. After preprocessing of the RNA-seq data, gene expression value was calculated by RPKM. Then the differentially expressed genes (DEGs) were identified with edgeR. Functional enrichment and protein-protein interaction (PPI) network analyses were conducted for the DEGs. Module analysis of the PPI network was also performed. Transcription factors (TFs) of DEGs were predicted. RESULTS A cohort of 496 up-regulated DEGs mainly correlating with the ECM degradation pathways, and 440 down-regulated DEGs predominantly enriching in transmembrane transport process were identified. Hub nodes in the PPI network were RRM2 and a set of collagens (COL1A1, COL3A1 and COL5A1), which were also remarkable in module 3 and module 5, respectively. Genes in module 3 were associated with cell cycle pathways, while in module 5 were related to ECM degradation pathways. PLAU, PSG1 and EGR2 were the crucial TFs with higher transcriptional activity in PTC than in control. CONCLUSION Several genes including COL1A1, COL3A1, RRM2, PLAU, and EGR2 might be used as biomarkers of PTC therapy. Among them, COL1A1 and COL3A1 might exert their functions via involving in ECM degradation pathway, while RRM2 through cell cycle pathway. PLAU might be an active TF, whereas EGR2 might be a tumor suppressor.
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48
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Deconstructing innate immune signaling in myelodysplastic syndromes. Exp Hematol 2015; 43:587-598. [PMID: 26143580 DOI: 10.1016/j.exphem.2015.05.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 05/23/2015] [Indexed: 02/06/2023]
Abstract
Overexpression of immune-related genes is widely reported in myelodysplastic syndromes (MDSs), and chronic immune stimulation increases the risk for developing MDS. Aberrant innate immune activation, such as that caused by increased toll-like receptor (TLR) signaling, in MDS can contribute to systemic effects on hematopoiesis, in addition to cell-intrinsic defects on hematopoietic stem/progenitor cell (HSPC) function. This review will deconstruct aberrant function of TLR signaling mediators within MDS HSPCs that may contribute to cell-intrinsic consequences on hematopoiesis and disease pathogenesis. We will discuss the contribution of chronic TLR signaling to the pathogenesis of MDS based on evidence from patients and mouse genetic models.
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49
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Le Pennec S, Konopka T, Gacquer D, Fimereli D, Tarabichi M, Tomás G, Savagner F, Decaussin-Petrucci M, Trésallet C, Andry G, Larsimont D, Detours V, Maenhaut C. Intratumor heterogeneity and clonal evolution in an aggressive papillary thyroid cancer and matched metastases. Endocr Relat Cancer 2015; 22:205-16. [PMID: 25691441 DOI: 10.1530/erc-14-0351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The contribution of intratumor heterogeneity to thyroid metastatic cancers is still unknown. The clonal relationships between the primary thyroid tumors and lymph nodes (LN) or distant metastases are also poorly understood. The objective of this study was to determine the phylogenetic relationships between matched primary thyroid tumors and metastases. We searched for non-synonymous single-nucleotide variants (nsSNVs), gene fusions, alternative transcripts, and loss of heterozygosity (LOH) by paired-end massively parallel sequencing of cDNA (RNA-Seq) in a patient diagnosed with an aggressive papillary thyroid cancer (PTC). Seven tumor samples from a stage IVc PTC patient were analyzed by RNA-Seq: two areas from the primary tumor, four areas from two LN metastases, and one area from a pleural metastasis (PLM). A large panel of other thyroid tumors was used for Sanger sequencing screening. We identified seven new nsSNVs. Some of these were early events clonally present in both the primary PTC and the three matched metastases. Other nsSNVs were private to the primary tumor, the LN metastases and/or the PLM. Three new gene fusions were identified. A novel cancer-specific KAZN alternative transcript was detected in this aggressive PTC and in dozens of additional thyroid tumors. The PLM harbored an exclusive whole-chromosome 19 LOH. We have presented the first, to our knowledge, deep sequencing study comparing the mutational spectra in a PTC and both LN and distant metastases. This study has yielded novel findings concerning intra-tumor heterogeneity, clonal evolution and metastases dissemination in thyroid cancer.
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Affiliation(s)
- Soazig Le Pennec
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Tomasz Konopka
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - David Gacquer
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Danai Fimereli
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Maxime Tarabichi
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Gil Tomás
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Frédérique Savagner
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Myriam Decaussin-Petrucci
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Christophe Trésallet
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Guy Andry
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Denis Larsimont
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Vincent Detours
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Carine Maenhaut
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
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Angell TE, Lechner MG, Jang JK, LoPresti JS, Epstein AL. MHC class I loss is a frequent mechanism of immune escape in papillary thyroid cancer that is reversed by interferon and selumetinib treatment in vitro. Clin Cancer Res 2014; 20:6034-44. [PMID: 25294906 DOI: 10.1158/1078-0432.ccr-14-0879] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
PURPOSE To evaluate MHC class I expression on papillary thyroid cancer (PTC) and analyze changes in MHC expression and associated immune activation with current and experimental treatments for thyroid cancer using in vitro PTC cell lines. EXPERIMENTAL DESIGN MHC class I expression and assessment of tumor-infiltrating leukocyte populations were evaluated by immunohistochemistry. PTC cell lines were analyzed for HLA-ABC expression by flow cytometry following tyrosine kinase inhibitor, IFNα or IFNγ, or radiation treatment. Functional changes in antigenicity were assessed by coculture of allogeneic donor peripheral blood leukocytes (PBL) with pretreated or untreated PTC cell lines and measurement of T-cell activation and cytokine production. RESULTS Both MHC class I and β2-microglobulin expression was reduced or absent in 76% of PTC specimens and was associated with reduced tumor-infiltrating immune cells, including effector (CD3(+), CD8(+), CD16(+)) and suppressor (FoxP3(+)) populations. Treatment of PTC cell lines with the MEK1/2 inhibitor selumetinib or IFN increased HLA-ABC expression. This phenotypic change was associated with increased T-cell activation (%CD25(+) of CD3(+)) and IL2 production by PBL cocultured with treated PTC cell lines. Additive effects were seen with combination selumetinib and IFN treatment. CONCLUSIONS MHC class I expression loss is frequent in human PTC specimens and represents a significant mechanism of immune escape. Increased antigenicity following selumetinib and IFN treatment warrants further study for immunotherapy of progressive PTC.
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Affiliation(s)
- Trevor E Angell
- Division of Endocrinology and Diabetes, Keck Medical Center, University of Southern California, Los Angeles, California. Department of Pathology, Keck Medical Center, University of Southern California, Los Angeles, California. Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Melissa G Lechner
- Department of Pathology, Keck Medical Center, University of Southern California, Los Angeles, California. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Julie K Jang
- Department of Pathology, Keck Medical Center, University of Southern California, Los Angeles, California
| | - Jonathan S LoPresti
- Division of Endocrinology and Diabetes, Keck Medical Center, University of Southern California, Los Angeles, California
| | - Alan L Epstein
- Department of Pathology, Keck Medical Center, University of Southern California, Los Angeles, California.
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