Gene expression profiling of normal thyroid tissue from patients with thyroid carcinoma

Surgical Outcomes of Thyroid Nodules Positive for Gene Expression Alterations Using ThyroSeq V3 Genomic Classifier

ThyroSeq V3 (TsV3) tests for various genetic alterations, including gene expression alterations (GEAs), to improve diagnostic accuracy and clinical decision-making for indeterminate thyroid nodules. This study aimed to clarify the clinico-pathological features and outcomes of GEA-positive thyroid nodules, which have not yet been well-described in the literature. A retrospective chart review was performed whereby patients were included if they underwent thyroid surgery between January 2018 and May 2022 at two McGill University teaching hospitals and their surgery was preceded by pre-operative molecular TsV3 testing. In total, 75 of the 328 patients with thyroid nodules (22.9%) who underwent molecular testing and surgery were GEA-positive. On surgical pathology, GEA-positive nodules showed a significantly higher malignancy rate compared to their GEA-negative counterparts (90.7% vs. 77.7%, respectively, p = 0.011). Among those that were malignant, 48.5% had at least one aggressive pathological feature, including histological subtype, extra-thyroidal extension, or lymph node metastasis. BRAF V600E mutation had a significantly greater association with aggressive malignant GEA-positive nodules compared to non-aggressive ones (p < 0.001). This study demonstrates that GEA may be an effective diagnostic and prognostic tool for thyroid nodule management. However, further investigation is needed to characterize the clinico-pathological features of GEA in isolation and in association with other gene alterations.

Differential gene expression profile of multinodular goiter

Introduction

The goiter, a neglected heterogeneous molecular disease, remains a major indication for thyroidectomies in its endemic regions.

Objectives

This study analyzed differential gene expression in surgical specimens diagnosed with multi nodular and compared the data to that of thyroid tissue without multinodular goiter from patients undergoing thyroidectomy in Manaus-AM, Brazil using RNA-seq technology.

Methodology

The transcriptome information of the surgical specimen fragments with and without multinodular goiter was accessed by Illumina HiSeq 2000 New Generation Sequencing (NGS) using the RNA-seq NEBNext^® Ultra^™ RNA Library Prep Kit for Illumina^®—#E7530L protocol and differential gene expression analysis.

Results

Differences were found between the gene expression profiles of the diseased tissues and those of the healthy control tissues; at least 70 genes were differentially expressed. The HOTS gene was expressed only in multinodular goiter tissues (p < 0.05).

Conclusion

These results demonstrate that the gene expression profile of multinodular goiter is pro-tumoral and that HOTS can play a central role in multinodular goiter development.

Ago-RIP Sequencing Identifies New MicroRNA-449a-5p Target Genes Increasing Sorafenib Efficacy in Hepatocellular Carcinoma

BACKGROUND: Patients with hepatocellular carcinoma (HCC) have very limited treatment options. For the last fourteen years, the multi-tyrosine kinase inhibitor sorafenib has been used as standard-of-care therapeutic agent in advanced HCC. Unfortunately, drug resistance develops in many cases. Therefore, we aimed to find a way to mitigate drug resistance and to improve the sorafenib efficacy in HCC cells. MicroRNAs play a significant role in targeting genes involved in tumor control suggesting microRNA/sorafenib combination therapy as a promising treatment option in advanced HCC. METHODS: MiR-449a-5p target genes were identified by Ago-RIP sequencing and validated by luciferase reporter assays and expression analyses. Target gene expression and survival data were analyzed in public HCC datasets. Tumor-relevant functional effects of miR-449a-5p and its target genes as well as their impact on the effects of sorafenib were analyzed using in vitro assays. An indirect transwell co-culture system was used to survey anti-angiogenic effects of miR-449a-5p. RESULTS: PEA15, PPP1CA and TUFT1 were identified as direct target genes of miR-449a-5p. Overexpression of these genes correlated with a poor outcome of HCC patients. Transfection with miR-449a-5p and repression of miR-449a-5p target genes inhibited cell proliferation and angiogenesis, induced apoptosis and reduced AKT and ERK signaling in HLE and Huh7 cells. Importantly, miR-449a-5p potentiated the efficacy of sorafenib in HCC cells via downregulation of PEA15, PPP1CA and TUFT1. CONCLUSIONS: This study provides detailed insights into the targetome and regulatory network of miR-449a-5p. Our results demonstrate for the first time that targeting PEA15, PPP1CA and TUFT1 via miR-449a overexpression could have significant implications in counteracting sorafenib resistance suggesting miR-449a-5p as a promising candidate for a microRNA/sorafenib combination therapy.

Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. The molecular characteristics of histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed total RNA sequencing with fresh frozen thyroid tissues from a cohort of three categories of samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex or the presence of lymphocytic thyroiditis. Among the differentially expressed genes (DEGs) of NAT vs N, 256 coding genes and 5 noncoding genes have been reported as cancer genes involved in cell proliferation, apoptosis, and/or tumorigenesis. Bioinformatics analysis with Ingenuity Pathway Analysis software revealed that “Cancer, Organismal Injury and Abnormalities, Cellular Response to Therapeutics, and Cellular Movement” were major dysregulated pathways in the NAT tissues. This study provides improved insight into the complexity of gene expression changes in the thyroid glands of patients with PTC.

Prognostic and Therapeutic Role of Angiogenic Microenvironment in Thyroid Cancer

Simple Summary

Angiogenesis is an essential event for the progression of solid tumors and is promoted by angiogenic cytokines released in the tumor microenvironment by neoplastic and stromal cells. Over the last 20 years, the role of the microenvironment and the implication of several angiogenic factors in tumorigenesis of solid and hematological neoplasms have been widely studied. The tumor microenvironment has also been well-defined for thyroid cancer, clarifying the importance of angiogenesis in cancer progression, spread, and metastasis. Furthermore, recent studies have evaluated the association of circulating angiogenic factors with the clinical outcomes of differentiated thyroid cancer, potentially providing noninvasive, low-cost, and safe tests that can be used in screening, diagnosis, and follow-up. In this review, we highlight the mechanisms of action of these proangiogenic factors and their different molecular pathways, as well as their applications in the treatment and prognosis of thyroid cancer.

Abstract

Thyroid cancer is the most common endocrine malignancy, with a typically favorable prognosis following standard treatments, such as surgical resection and radioiodine therapy. A subset of thyroid cancers progress to refractory/metastatic disease. Understanding how the tumor microenvironment is transformed into an angiogenic microenvironment has a role of primary importance in the aggressive behavior of these neoplasms. During tumor growth and progression, angiogenesis represents a deregulated biological process, and the angiogenic switch, characterized by the formation of new vessels, induces tumor cell proliferation, local invasion, and hematogenous metastases. This evidence has propelled the scientific community’s effort to study a number of molecular pathways (proliferation, cell cycle control, and angiogenic processes), identifying mediators that may represent viable targets for new anticancer treatments. Herein, we sought to review angiogenesis in thyroid cancer and the potential role of proangiogenic cytokines for risk stratification of patients. We also present the current status of treatment of advanced differentiated, medullary, and poorly differentiated thyroid cancers with multiple tyrosine kinase inhibitors, based on the rationale of angiogenesis as a potential therapeutic target.

Network-Based Genetic Profiling Reveals Cellular Pathway Differences Between Follicular Thyroid Carcinoma and Follicular Thyroid Adenoma

Molecular mechanisms underlying the pathogenesis and progression of malignant thyroid cancers, such as follicular thyroid carcinomas (FTCs), and how these differ from benign thyroid lesions, are poorly understood. In this study, we employed network-based integrative analyses of FTC and benign follicular thyroid adenoma (FTA) lesion transcriptomes to identify key genes and pathways that differ between them. We first analysed a microarray gene expression dataset (Gene Expression Omnibus GSE82208, n = 52) obtained from FTC and FTA tissues to identify differentially expressed genes (DEGs). Pathway analyses of these DEGs were then performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) resources to identify potentially important pathways, and protein-protein interactions (PPIs) were examined to identify pathway hub genes. Our data analysis identified 598 DEGs, 133 genes with higher and 465 genes with lower expression in FTCs. We identified four significant pathways (one carbon pool by folate, p53 signalling, progesterone-mediated oocyte maturation signalling, and cell cycle pathways) connected to DEGs with high FTC expression; eight pathways were connected to DEGs with lower relative FTC expression. Ten GO groups were significantly connected with FTC-high expression DEGs and 80 with low-FTC expression DEGs. PPI analysis then identified 12 potential hub genes based on degree and betweenness centrality; namely, TOP2A, JUN, EGFR, CDK1, FOS, CDKN3, EZH2, TYMS, PBK, CDH1, UBE2C, and CCNB2. Moreover, transcription factors (TFs) were identified that may underlie gene expression differences observed between FTC and FTA, including FOXC1, GATA2, YY1, FOXL1, E2F1, NFIC, SRF, TFAP2A, HINFP, and CREB1. We also identified microRNA (miRNAs) that may also affect transcript levels of DEGs; these included hsa-mir-335-5p, -26b-5p, -124-3p, -16-5p, -192-5p, -1-3p, -17-5p, -92a-3p, -215-5p, and -20a-5p. Thus, our study identified DEGs, molecular pathways, TFs, and miRNAs that reflect molecular mechanisms that differ between FTC and benign FTA. Given the general similarities of these lesions and common tissue origin, some of these differences may reflect malignant progression potential, and include useful candidate biomarkers for FTC and identifying factors important for FTC pathogenesis.

MiR-376c-3p targets heparin-binding EGF-like growth factor (HBEGF) to inhibit proliferation and invasion in medullary thyroid carcinoma cells

INTRODUCTION

Aggressive medullary thyroid carcinomas (MTC) have a high mortality rate and the treatment for patients diagnosed with advanced MTC is comparatively ineffective. We hence aimed to test the effects of miR-376c-3p on MTC and to explore the relevant mechanism.

MATERIAL AND METHODS

Cell Counting Kit-8 (CCK-8) and soft agar colony formation assay were applied to evaluate the proliferation of transfected MZ-CRC-1 cells. Wound healing and transwell assay were employed to evaluate MTC cell migration and invasion, respectively. Luciferase assay was performed to validate the downstream target of miR-376c-3p in MZ-CRC-1 cells. Quantitative polymerase chain reaction was used to detect mRNA abundance of key genes. Western blot technique was used to analyze protein levels of HBEGF, E-cadherin, ZO-1, N-cadherin and vimentin.

RESULTS

MiR-376c-3p inhibited the viability, migration and invasion of MZ-CRC-1 cells. Moreover, miR-376c-3p mimic downregulated expression of N-cadherin and vimentin but upregulated that of E-cadherin and ZO-1 in MZ-CRC-1 cells. Results for the luciferase reporter assay showed that miR-376c-3p was able to bind the 3' untranslated region of heparin-binding EGF-like growth factor (HBEGF), of which overexpression nearly nullified the miR-376c-3p mimic-induced inhibitory effects in the MTC cells.

CONCLUSIONS

MiR-376c-3p showed suppressive effects on MZ-CRC-1 cells via targeting and downregulating HBEGF, suggesting that miR-376c-3p could potentially be targeted for the treatment of MTC.

A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map

BACKGROUND

The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal growth and skeletal maturation. To date a quantitative, validated transcriptional atlas of the whole normal human thyroid does not exist and the availability of a detailed expression map might be an excellent occasion to investigate the many features of the thyroid transcriptome.

RESULTS

We present a view at the molecular level of the normal human thyroid histology and physiology obtained by a systematic meta-analysis of all the available gene expression profiles for the whole organ. A quantitative transcriptome reference map was generated by using the TRAM (Transcriptome Mapper) software able to combine, normalize and integrate a total of 35 suitable datasets from different sources thus providing a typical reference expression value for each of the 27,275 known, mapped transcripts obtained. The experimental in vitro validation of data was performed by "Real-Time" reverse transcription polymerase chain reaction showing an excellent correlation coefficient (r = 0.93) with data obtained in silico.

CONCLUSIONS

Our study provides a quantitative global reference portrait of gene expression in the normal human thyroid and highlights differential expression between normal human thyroid and a pool of non-thyroid tissues useful for modeling correlations between thyroidal gene expression and specific thyroid functions and diseases. The experimental in vitro validation supports the possible usefulness of the human thyroid transcriptome map as a reference for molecular studies of the physiology and pathology of this organ.

Diagnostic Value of Semiquantitative Analysis of 99mTechnetium-Methoxyisobutylisonitrile (99mTc-MIBI) Imaging in Predicting Early-Stage Cervical Lymph Node Metastasis of Thyroid Carcinoma

Background

The aim of this study was to evaluate the value of semiquantitative analysis (SQA) of ^99mTc-MIBI imaging in predicting early-stage cervical lymph node metastasis (CLNM) in thyroid carcinoma (TC).

Material/Methods

TC patients (n=106) undergoing surgical resection and histopathological examination were enrolled. All patients received ^99mTc-MIBI imaging prior to surgery. P-glycoprotein (P-gp) expression was detected by PT-PCR and immunohistochemistry. With pathological results as the criterion standard, the diagnostic efficiency of ^99mTc-MIBI imaging in predicting early-stage CLNM was evaluated. The correlation of P-gp with ^99mTc-MIBI imaging was investigated. Logistic regression analysis was applied for analyzing the factors affecting early-stage CLNM.

Results

The detection rate and misdiagnosis rate of ^99mTc-MIBI imaging for early-stage CLNM diagnosis were 87.3% and 12.7%, respectively. Receiver operating characteristic (ROC) curve analysis showed an accuracy of ^99mTc-MIBI imaging of 85.85%. Preoperative ^99mTc-MIBI scan showed statistical differences between metastasis and non-metastasis groups in early and delayed T/NT and washout rate (all P<0.05). The percentage of P-gp-expressing cells and the expression rate of P-gp gene both exhibited statistical differences between metastasis and no-metastasis groups (both P<0.05). Tumor diameter, lesion distribution, the percentage of P-gp-expressing cells, and the expression rate of P-gp gene were risk factors for CLNM (all P<0.05).

Conclusions

^99mTc-MIBI imaging has value in qualitative diagnosis of early-stage CLNM in TC. Tumor diameter, lesion distribution, the percentage of P-gp-expressing cells, and the expression rate of P-gp gene were risk factors for CLNM.