scholarly journals Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Valentina D. Yakushina ◽  
Vladimir V. Strelnikov ◽  
Alexander S. Tanas ◽  
Alexander V. Lavrov
Keyword(s):  
Thyroid Carcinoma ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Follicular Adenoma ◽  
Enrichment Analysis ◽  
Thyroid Neoplasms ◽  
Anaplastic Thyroid Carcinoma ◽  
Progression Rate ◽  
Histological Subtypes ◽  
Histological Variants

AbstractThe main types of thyroid neoplasms, follicular adenoma (FA), follicular thyroid carcinoma (FTC), classical and follicular variants of papillary carcinoma (clPTC and fvPTC), and anaplastic thyroid carcinoma (ATC), differ in prognosis, progression rate and metastatic behaviour. Specific patterns of lncRNAs involved in the development of clinical and morphological features can be presumed. LncRNA landscapes within distinct benign and malignant histological variants of thyroid neoplasms were not investigated. The aim of the study was to discover long noncoding RNA landscapes common and specific to major benign and malignant histological subtypes of thyroid neoplasms. LncRNA expression in FA, FTC, fvPTC, clPTC and ATC was analysed with comprehensive microarray and RNA-Seq datasets. Putative biological functions were evaluated via enrichment analysis of coexpressed coding genes. In the results, lncRNAs common and specific to FTC, clPTC, fvPTC, and ATC were identified. The discovered lncRNAs are putatively involved in L1CAM interactions, namely, pre-mRNA processing (lncRNAs specific to FTC); PCP/CE and WNT pathways (lncRNAs specific to fvPTC); extracellular matrix organization (lncRNAs specific to clPTC); and the cell cycle (lncRNAs specific to ATC). Known oncogenic and suppressor lncRNAs (RMST, CRNDE, SLC26A4-AS1, NR2F1-AS1, and LINC00511) were aberrantly expressed in thyroid carcinomas. These findings enhance the understanding of lncRNAs in the development of subtype-specific features in thyroid cancer.

scholarly journals Long non-coding RNA landscapes in benign and malignant thyroid neoplasms of distinct histological subtypes

2019 ◽  
Author(s):  
Valentina Yakushina ◽  
Alexander Lavrov
Keyword(s):  
Thyroid Carcinoma ◽  
Cancer Progression ◽  
Follicular Adenoma ◽  
Enrichment Analysis ◽  
Thyroid Neoplasms ◽  
Anaplastic Thyroid Carcinoma ◽  
Malignant Neoplasms ◽  
Beta Catenin ◽  
Non Coding Rna ◽  
Metastatic Behavior

Abstract Background: The main types of thyroid neoplasms, follicular adenoma (FA), follicular thyroid carcinoma (FTC), classical and follicular variants of papillary carcinoma (clPTC and fvPTC), anaplastic thyroid carcinoma (ATC), are differ in the prognosis, rate of progression and metastatic behavior. It can be supposed that there are specific patterns of lncRNAs involved in the development of clinical and morphological features. The lncRNA landscapes within distinct benign and malignant histological variants of thyroid neoplasm are unknown. Methods: Comprehensive set of Microarray and RNA-Seq datasets was analyzed for the expression of lncRNAs in FA, FTC, fvPTC, clPTC and ATC. The potential biological functions were evaluated via coexpression and enrichment analysis. Results and conclusion: Abberant expression of lncRNA in FA, FTC, fvPTC, clPTC and ATC was established. The lncRNAs common for benign and malignant neoplasms, specific for papillary carcinomas, specific for clPTC, fvPTC and ATC are determined. The determined common and specific lncRNAs are found to be putatively involved into L1CAM interactions; processing of capped intron-containing pre-mRNA; Tryptophan metabolism; PCP/CE pathway and Beta-catenin independent WNT signaling; extracellular matrix organization and cell cycle and mitotic. The patterns of lncRNA expression in FA and FTC are appeared to be similar with no genes significantly differentially expressed within these subtypes. Previously known oncogenic and supressor lncRNAs (NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, LINC01116, RMST) are found aberrantly expressed in thyroid carcinomas. The findings enhance the understanding of lncRNA landscape in thyroid neoplasms and its role in thyroid cancer progression.

scholarly journals An epithelial–mesenchymal transition-related long noncoding RNA signature correlates with the prognosis and progression in patients with bladder cancer

2021 ◽  
Vol 41 (1) ◽  
Author(s):  
Hang Tong ◽  
Tinghao Li ◽  
Shun Gao ◽  
Hubin Yin ◽  
Honghao Cao ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Epithelial Mesenchymal Transition ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Risk Groups ◽  
Functional Enrichment ◽  
Diagnostic Efficacy ◽  
Mesenchymal Transition

Abstract Bladder cancer is a common malignant tumour worldwide. Epithelial–mesenchymal transition (EMT)-related biomarkers can be used for early diagnosis and prognosis of cancer patients. To explore, accurate prediction models are essential to the diagnosis and treatment for bladder cancer. In the present study, an EMT-related long noncoding RNA (lncRNA) model was developed to predict the prognosis of patients with bladder cancer. Firstly, the EMT-related lncRNAs were identified by Pearson correlation analysis, and a prognostic EMT-related lncRNA signature was constructed through univariate and multivariate Cox regression analyses. Then, the diagnostic efficacy and the clinically predictive capacity of the signature were assessed. Finally, Gene set enrichment analysis (GSEA) and functional enrichment analysis were carried out with bioinformatics. An EMT-related lncRNA signature consisting of TTC28-AS1, LINC02446, AL662844.4, AC105942.1, AL049840.3, SNHG26, USP30-AS1, PSMB8-AS1, AL031775.1, AC073534.1, U62317.2, C5orf56, AJ271736.1, and AL139385.1 was constructed. The diagnostic efficacy of the signature was evaluated by the time-dependent receiver-operating characteristic (ROC) curves, in which all the values of the area under the ROC (AUC) were more than 0.73. A nomogram established by integrating clinical variables and the risk score confirmed that the signature had a good clinically predict capacity. GSEA analysis revealed that some cancer-related and EMT-related pathways were enriched in high-risk groups, while immune-related pathways were enriched in low-risk groups. Functional enrichment analysis showed that EMT was associated with abundant GO terms or signaling pathways. In short, our research showed that the 14 EMT-related lncRNA signature may predict the prognosis and progression of patients with bladder cancer.

scholarly journals An angiogenesis-related long noncoding RNA signature correlates with prognosis in patients with hepatocellular carcinoma

2021 ◽  
Vol 41 (4) ◽  
Author(s):  
Dengliang Lei ◽  
Yue Chen ◽  
Yang Zhou ◽  
Gangli Hu ◽  
Fang Luo
Keyword(s):  
Hepatocellular Carcinoma ◽  
Liver Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Enrichment Analysis ◽  
Clinical Information ◽  
Roc Curves ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Highly Correlated

Abstract Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal cancers worldwide. Neovascularization is closely related to the malignancy of tumors. We constructed a signature of angiogenesis-related long noncoding RNA (lncRNA) to predict the prognosis of patients with HCC. The lncRNA expression matrix of 424 HCC patients was downloaded from The Cancer Genome Atlas (TCGA). First, gene set enrichment analysis (GSEA) was used to distinguish the differentially expressed genes of the angiogenesis genes in liver cancer and adjacent tissues. Next, a signature of angiogenesis-related lncRNAs was constructed using univariate and multivariate analyses, and receiver operating characteristic (ROC) curves were used to assess the accuracy. The signature and relevant clinical information were used to construct the nomogram. A 5-lncRNA signature was highly correlated with overall survival (OS) in HCC patients and performed well in evaluations using the C-index, areas under the curve, and calibration curves. In summary, the 5-lncRNA model can serve as an accurate signature to predict the prognosis of patients with liver cancer, but its mechanism of action must be further elucidated by experiments.

scholarly journals Functional enrichment analysis based on long noncoding RNA associations

2018 ◽  
Vol 12 (S4) ◽  
Author(s):  
Kuo-Sheng Hung ◽  
Chung-Chi Hsiao ◽  
Tun-Wen Pai ◽  
Chin-Hwa Hu ◽  
Wen-Shyong Tzou ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment

scholarly journals Pathogenesis, diagnosis and management of thyroid nodules in children

2006 ◽  
Vol 13 (2) ◽  
pp. 427-453 ◽  
Author(s):  
M Niedziela
Keyword(s):  
Thyroid Carcinoma ◽  
Medullary Thyroid Carcinoma ◽  
Preoperative Diagnosis ◽  
Thyroid Nodules ◽  
Follicular Adenoma ◽  
Critical Factor ◽  
Anaplastic Thyroid Carcinoma ◽  
Duct Cyst ◽  
Medullary Thyroid ◽  
Molecular Studies

According to the literature thyroid nodules are quite rare in the first two decades of life. However, there are some exceptions, relating to areas with an iodine deficiency or affected by radioactive fallout, where the risk of nodules and carcinomas is increased. Therefore, it is a great challenge for the physician to distinguish between benign and malignant lesions preoperatively, and not only in these areas of greater risk. A careful work-up, comprising the patient’s history, clinical examination, laboratory tests, thyroid ultrasound, scintigraphy, fine-needle aspiration biopsy (FNAB) and molecular studies, is mandatory to improve the preoperative diagnosis. The differential diagnosis should also include benign thyroid conditions such as: (i) congenital hypothyroidism due to dyshormonogenesis or ectopy, (ii) thyroid hemiagenesis, (iii) thyroglossal duct cyst, (iv) simple goiter, (v) cystic lesion, (vi) nodular hyperplasia, (vii) follicular adenoma, (viii) Graves’ disease and (ix) Hashimoto thyroiditis, all of which can predispose to the development of thyroid nodules. The majority of thyroid carcinomas derive from the follicular cell (papillary, follicular, insular and undifferentiated (or anaplastic) thyroid carcinoma), whereas medullary thyroid carcinoma derives from calcitonin-producing cells. Inherited forms of thyroid cancer may occur, especially in relation to medullary thyroid carcinoma. FNAB is a critical factor in establishing the preoperative diagnosis. However, we should keep in mind the fact that a conventional cytological evaluation can miss the neoplastic nature of a lesion and the employment of immunocytochemical and molecular studies of aspirates from FNAB can give us a more precise diagnosis of neoplasia in thyroid nodules once they are detected.

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