Three-gene molecular diagnostic model for thyroid cancer

A systematic review of emerging RNA markers in thyroid fine needle aspiration cytology samples: advancements and challenges

BACKGROUND

Significant advances have been made in detecting RNA markers that may indicate malignancy in fine needle aspiration cytology (FNAC) samples.

OBJECTIVE

To review the roles of protein-coding and non-coding RNAs in differentiating between malignant and benign thyroid nodules.

METHODS

A comprehensive literature search using PubMed, Science Direct, Web of Science, and SCOPUS databases was performed. We searched up until September 2024 and complemented by manual citation search.

RESULTS

A total of 28 full-text articles were reviewed, encompassing 5770 FNAC samples, which included 3489 benign lesions and 2281 malignant lesions. The studies identified 43 messenger RNAs (mRNAs), 16 microRNAs (miRNAs), and 3 long non-coding RNAs (lncRNAs) that have the potential to distinguish malignant nodules. Among the mRNAs, PAPPA, TIMP1, and HMGA2, as well as the miRNAs, miR-146b, miR-375 and miR-222, appear to be the most promising molecules for diagnosis.

CONCLUSION

Numerous RNA markers have been shown to differentiate malignant from benign lesions. However, there is still a lack of patient-specific classification for thyroid cancer subtypes. Additionally, future studies should prioritize using a combination of molecular markers rather than relying on individual ones. Although current research mainly focuses on identifying cancer-specific molecules, it is important for future studies to shift towards a more patient-specific approach.

Identification of immune-related mitochondrial metabolic disorder genes in septic shock using bioinformatics and machine learning

PURPOSE

Mitochondria are involved in septic shock and inflammatory response syndrome, which severely affects the life security of patients. It is necessary to recognize and explore the immune-mitochondrial genes in septic shock.

METHODS

The GSE57065 dataset was acquired from the Gene Expression Omnibus (GEO) database and filtered by limma and the weighted correlation network analysis (WGCNA) to identify mitochondrial-related differentially expressed genes (MitoDEGs) in septic shock. The function of MitoDEGs was analyzed using the Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA), respectively. The Protein-Protein Interaction (PPI) network composed of MitoDEGs was established using Cytoscape. Support Vector Machine Recursive Feature Elimination (SVM-RFE), Random Forest (RF), and Least Absolute Shrinkage and Selection Operator (LASSO) were used to identify diagnostic MitoDEGs, which were validated using receiver operating characteristic (ROC) analysis and Quantitative Real-time Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Furthermore, the infiltration of immunocytes was analyzed using CIBERSORT, and the correlation between diagnostic MitoDEGs and immunocytes was explored using Spearman.

RESULTS

A total of 44 MitoDEGs were filtered, and functional enrichment analysis showed they were associated with mitochondrial function, and the PPI network had 457 nodes and 547 edges. Four diagnostic genes, MitoDEGs, PGS1, C6orf136, THEM4, and EPHX2, were identified by three machine learning algorithms, and qRT-PCR results obtained similar expression levels as bioinformatics analysis. Furthermore, the diagnostic model constructed by the diagnostic genes had fine diagnostic efficacy. Immunocyte infiltration analysis showed that activated immunocytes were abundant and correlated with hub genes, with neutrophils accounting for the largest proportion in septic shock.

CONCLUSIONS

In this study, we recognized four immune-mitochondrial key genes (PGS1, C6orf136, THEM4, and EPHX2) in septic shock and designed a novel gene diagnosis model that provided a new and meaningful way for the diagnosis of septic shock.

Increased gene expression of TIMP1 and CHI3L1 in fine-needle aspiration biopsy samples from papillary thyroid cancer as compared to benign nodules

BACKGROUND

Thyroid nodules are common ultrasound findings with malignancy rate 7%-15%. Our objective was to assess the relative expression of the tissue inhibitor of metalloproteinase-1 gene (TIMP1) and chitinase-3-like protein 1 gene (CHI3L1) in fine-needle aspiration biopsy (FNAB) washouts and the serum levels of their protein products (TIMP-1 and chitinase-3-like protein 1 known as YKL-40) in patients with papillary thyroid cancer (PTC) and patients with benign nodules. Furthermore, the correlation between gene expression and circulating protein product was evaluated.

METHODS

Eighty patients who underwent FNAB in one tertiary center were recruited in the study. Forty with Bethesda V and VI nodules were operated and PTC was confirmed. The other 40 patients were with Bethesda II nodules. TIMP-1 and YKL-40 serum levels were measured in all subjects. The TIMP1 and CHI3L1 expression was assessed in FNAB washouts from 20 PTC patients and 20 benign cases using quantitative PCR.

RESULTS

The relative expression of TIMP1 and CHI3L1 was significantly higher in the PTC group than in the benign group (p < .001 for TIMP1; p = .018 for CHI3L1). The PTC patients had higher serum TIMP-1 than the patients with benign nodules (p = .036). We did not find significant difference in the YKL-40 level between the two groups. TIMP1 and CHI3L1 expression did not correlate with the serum levels of their protein products.

CONCLUSION

FNAB washouts could be used for identification of diagnostic markers. The increased TIMP1 and CHI3L1 expression implies a role of these genes in the PTC carcinogenesis.

Retrospective analysis of cancer-specific gene expression panel for thyroid fine needle aspiration specimens

BACKGROUND

While molecular testing is a promising strategy for preoperative assessment of cytologically indeterminate thyroid nodules, thyroid fine needle aspiration biopsy (FNA) presents unique challenges for molecular assays, including contaminating peripheral blood mononuclear cells (PBMC) and variable numbers of evaluable epithelial thyroid cells. Moreover, the newly recognized entity, noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), has added an additional challenge to the currently available molecular diagnostic platforms. New diagnostic tools are still needed to correctly distinguish benign and malignant thyroid nodules preoperatively.

METHODS

Twenty-two transcript splice variants from 12 genes we previously identified as discriminating benign from malignant thyroid nodules were characterized in 80 frozen thyroid tumors from 8 histological subtypes. Isoforms detectable in PBMC were excluded, and the 5 most discriminating isoforms were further validated by real-time quantitative PCR (qPCR) on intraoperative FNA samples from 59 malignant tumors, 55 benign nodules, and 23 NIFTP samples. The qPCR threshold cycle values for each transcript were normalized to the thyrocyte-specific thyroid peroxidase isoform 1 (TPO1) and z-transformed. Receiver operating characteristic (ROC) analyses of the composite transcript scores were used to evaluate classification of thyroid FNAs by the 5-gene isoform expression panel.

RESULTS

A molecular signature was developed by combining expression levels of specific isoforms of CDH3, FNDC4, HMGA2, KLK7, and PLAG1. FNAs containing at least 12-36 thyrocytes were sufficient for this assay. The 5-gene composite score achieved an area under the ROC curve (AUC) of 0.86 for distinguishing malignant from benign nodules, with a specificity of 91%, sensitivity of 75%, negative predictive value of 91%, and positive predictive value of 74%.

CONCLUSION

Our newly developed 5-gene isoform expression panel distinguishes benign from malignant thyroid tumors and, may help distinguish benign from malignant thyroid nodules in the context of the new NIFTP subtype.

The role of miRNAs in MDMX-p53 interplay

MicroRNAs (miRNAs) are endogenous noncoding RNAs of 19-24 nucleotides in length and are tightly related to tumorigenesis and progression. Recent studies have demonstrated that the tumor suppressor p53 and its negative controller MDMX are regulated by miRNAs in different ways. Some miRNAs directly target p53 and regulate its expression and function, whereas some miRNAs target MDMX and regulate p53's activity indirectly. The overexpression of several miRNAs can restore the activity of p53 by negatively regulating MDMX in cancer cells. Therefore, a better understanding of the miRNAs-MDMX-p53 network will put forward potential research directions for developing anticancer therapeutics. In the present review, we mainly focus on the regulatory effects of miRNAs on the MDMX-p53 interplay as well as the role of the miRNAs-MDMX-p53 network in human cancer.

CCNA1 gene as a potential diagnostic marker in papillary thyroid cancer

The malignancy that most affects the endocrine system is thyroid neoplasm, with an increasing incidence over the years. The most prevalent histological type of the carcinomas that affect the thyroid gland is papillary carcinoma with a prevalence of 80 % worldwide. The current diagnostic methodology may present inconclusive results, emphasizing the need for new effective and sensitive techniques to aid the diagnosis. For this, it is necessary to understand molecular and protein mechanisms in the identification of diagnostic and predictive markers in the lesions. The Cyclin A1 protein, encoded by the CCNA1 gene, is an important cell cycle regulator, belonging to the MAPK/ERK signaling pathway directly involved with thyroid cancer. The aim of this study was to evaluate the CCNA1 gene and Cyclin A1 protein expression in papillary thyroid carcinoma, follicular thyroid carcinoma, and benign thyroid lesions, by real time quantitative PCR and immunohistochemistry analysis, respectively, to verify their roles as potential diagnostic and predictive markers to future applications in the clinical routine. Overexpression of CCNA1 gene was observed in the papillary carcinoma group compared to the normal group (P = 0.0023), benign lesions (P = 0.0011), colloid goiter (P = 0.0124), and follicular carcinoma (P = 0.0063). No differential expression was observed in the papillary primary tumor group from negative lymph nodes compared with the one from positive lymph nodes (P = 0.3818). Although an increased expression of Cyclin A1 was observed in the PTC group compared to the other one in the IHC analysis, no significant difference was observed (Fisher's exact Test). A Cyclin A1 overexpression was detected with weak to mid-moderate immunoreactivity in the benign group (k = 0.56), (score 1.5); mid-moderate to moderate in the goiter group (k = 0.58); weak in the FTC group (k = 0.33); and mid-moderate to moderate in the PTC group (k = 0.48). Due to the small sample size in the IHC analysis and to the fact that not all RNA is translated into protein, the diagnostic potential of Cyclin A1 could not be assessed. However, these findings highlight the potential of the CCNA1 gene as a diagnostic marker for papillary thyroid carcinoma.

High mobility group A protein-2 as a tumor cancer diagnostic and prognostic marker: a systematic review and meta-analysis

High mobility group A protein-2 (HMGA2) is an architectural transcription factor that binds to the A/T-rich DNA minor groove and is responsible for regulating transcriptional activity of multiple genes indirectly through chromatin change and assembling enhanceosome. HMGA2 is overexpressed in multiple tumor types, suggesting its involvement in cancer initiation and progression, thus, making it an ideal candidate for cancer diagnostic and prognostic. We performed a systematic review to examine the role of HMGA2 as a universal tumor cancer diagnostic and prognostic marker. We used Reporting Recommendations for Tumor Marker Prognostic Studies to systematically search OvidMedline, PubMed, and the Cochrane Library for English language studies, published between 1995 and June 2019. Meta-analysis provided pooled risk estimates and their 95% confidence intervals (CIs) for an association between overall survival and recurrence of cancers for studies with available estimates. We identified 42 eligible studies with a total of 5123 tumor samples in 15 types of cancer. The pooled percentage of HMGA2 gene expression in tumor samples was 65.14%. Meta-analysis showed that cancer patients with HMGA2 positive have significantly reduced survival, compared to patients without HMGA2 gene [pooled-hazard ratio (HR) = 1.85, 95% CI 1.48-2.22]. There was a positive association between cancer patients with HMGA2 overexpression and cancer recurrence though this association did not reach significance (pooled-HR = 1.44, 95% CI 0.80-2.07). Overexpression of HMGA2 was found in 15 types of cancer. There was an association between HMGA2 overexpression with reduced survival of cancer patients. HMGA2 is thus considered a promising universal tumor marker for prognostics.

miR-98-5p promotes apoptosis and inhibits migration and cell growth in papillary thyroid carcinoma through Bax/Caspase-3 by HMGA2

Background

The aims of this study were to investigate the function and mechanism of miRNA‐98‐5p in papillary thyroid carcinoma.

Methods

Quantitative real‐time polymerase chain reaction (qRT‐PCR) was used to measure the expression of miRNA‐98‐5p in papillary thyroid carcinoma. Western blotting and caspase‐3/9 activity levels, flow cytometric analysis, cell migration assays, DAPI assay, cell proliferation assay, and LDH activity levels were used in this study.

Results

In patient with papillary thyroid carcinoma, miRNA‐98‐5p was reduced, and HMGA2 was increased. Downregulation of miRNA‐98‐5p promoted the cell growth, inhibited apoptosis, and induced HMGA2 protein expression in papillary thyroid carcinoma cell via activation of HMGA2. Overexpression of miRNA‐98‐5p inhibited the cell growth, induced apoptosis, and suppressed HMGA2 protein expression in papillary thyroid carcinoma cell through the suppression of HMGA2. Si‐HMGA2 inhibited the effects of anti‐miRNA‐98‐5p on cell growth of papillary thyroid carcinoma.

Conclusion

Therefore, these results suggested the regulation of HMGA2 suppresses proliferation of papillary thyroid carcinoma through miRNA‐98‐5p.

miRNA-766 induces apoptosis of human colon cancer cells through the p53/Bax signaling pathway by MDM4

miRNAs are closely associated with tumor genesis and development. The present study investigated the role of the expression of miRNA-766 in the survival of patients with colon cancer and the underlying molecular mechanisms. Reverse transcription-quantitative polymerase chain reaction analysis and microarray analysis were used to analyze the expression of miRNA-766. The results revealed that the expression of miRNA-766 was decreased in patients with colon cancer. The overall survival and disease-free survival rates of patients with colon cancer with a high expression of miRNA-766 were prolonged, compared with those with a low expression of miRNA-766. The overexpression of miRNA-766 reduced cell growth and induced apoptosis in colon cancer cells through suppression of the MDM4/p53 pathway. By contrast, the downregulation of miRNA-766 promoted cell growth and reduced apoptosis in colon cancer cells through activation of the MDM4/p53 pathway. The promotion of MDM4 attenuated the anticancer effect of miRNA-766 in colon cancer cells. These results demonstrated that miRNA-766 induced cell apoptosis in human colon cancer through MDM4/p53.

Diagnostic performance of HMGA2 gene expression for differentiation of malignant thyroid nodules: A systematic review and meta-analysis

OBJECTIVE

The purpose of the current study was to investigate the diagnostic performance of high mobility group A2 (HMGA2) gene expression for differentiation of malignant thyroid nodules through a systematic review and meta-analysis.

DESIGN

The MEDLINE/PubMed and EMBASE database, from the earliest available date of indexing through 10 April 2018, were searched for studies evaluating the diagnostic performance of HMGA2 expression for differentiation of thyroid nodules.

METHODS

We determined the sensitivities and specificities across studies, calculated positive and negative likelihood ratios (LR+ and LR-), and constructed summary receiver operating characteristic (ROC) curves.

RESULTS

Across 7 studies, the pooled sensitivity for HMGA2 expression was 0.78 (95% CI; 0.67-0.86) with heterogeneity (I²  = 86.6) and a pooled specificity of 0.94 (95% CI: 0.85-0.98) with heterogeneity (I²  = 94.7). Likelihood ratio (LR) syntheses gave an overall positive likelihood ratio (LR+) of 12.6 (95% CI: 5.1-31.3) and negative likelihood ratio (LR-) of 0.24 (95% CI: 0.15-0.36). The pooled diagnostic odds ratio (DOR) was 53 (95% CI: 18-159). Hierarchical summary ROC curve indicates that the areas under the curve were 0.92 (95% CI: 0.89-0.94). In meta-regression analysis, no definite variable was the source of the study heterogeneity.

CONCLUSION

The current meta-analysis showed the moderate sensitivity and high specificity of HMGA2 expression for differentiation of malignant thyroid nodules. The likelihood ratio scatter-gram suggested that HMGA2 expression analysis could be useful for confirmation of the presence of malignant thyroid nodules. Considering the heterogeneity of included studies, further large prospective studies are necessary to confirm these results.

Long non-coding RNAs in thyroid cancer: Biological functions and clinical significance

Thyroid cancer is the most common endocrine malignant tumor with rapidly increasing incidence in recent decades. Although the majority of thyroid cancers are relatively indolent, some cases still have a risk of developing into more aggressive and lethal forms of thyroid cancers. Similar to other malignancies, thyroid tumorigenesis is a multistep process involving the accumulation of a large number of genetic and epigenetic alterations. Thus, determination of the mechanisms of tumorigenesis is an urgent need for thyroid cancer treatment. Long noncoding RNAs (LncRNAs) have recently been demonstrated to participate in cancer progression. However, their role and molecular mechanism in thyroid cancer remain largely unclear. In this review, we focus on the dysregulation of lncRNAs in thyroid cancer, summarize the latest findings regarding the functions and mechanism of lncRNAs in thyroid cancer, and discuss their potential clinical significance in diagnosis and prognosis of thyroid cancer.

Thyroid follicular adenomas and carcinomas: molecular profiling provides evidence for a continuous evolution

Non-autonomous thyroid nodules are common in the general population with a proportion found to be cancerous. A current challenge in the field is to be able to distinguish benign adenoma (FA) from preoperatively malignant thyroid follicular carcinoma (FTC), which are very similar both histologically and genetically. One controversial issue, which is currently not understood, is whether both tumor types represent different molecular entities or rather a biological continuum. To gain a better insight into FA and FTC tumorigenesis, we defined their molecular profiles by mRNA and miRNA microarray. Expression data were analyzed, validated by qRT-PCR and compared with previously published data sets. The majority of deregulated mRNAs were common between FA and FTC and were downregulated, however FTC showed additional deregulated mRNA. Both types of tumors share deregulated pathways, molecular functions and biological processes. The additional deregulations in FTC include the lipid transport process that may be involved in tumor progression. The strongest candidate genes which may be able to discriminate follicular adenomas and carcinomas, CRABP1, FABP4 and HMGA2, were validated in independent samples by qRT-PCR and immunohistochemistry. However, they were not able to adequately classify FA or FTC, supporting the notion of continuous evolving tumors, whereby FA and FTC appear to show quantitative rather than qualitative changes. Conversely, miRNA expression profiles showed few dysregulations in FTC, and even fewer in FA, suggesting that miRNA play a minor, if any, role in tumor progression.

HMGA2 Gene Expression in Fine-needle Aspiration Samples of Thyroid Nodules as a Marker for Preoperative Diagnosis of Thyroid Cancer

There is a great interest in molecular markers that would help in the preoperative diagnosis of malignant thyroid nodules in cases of indeterminate fine-needle aspiration cytology. The aim of this study was to determine the diagnostic accuracy of HMGA2 gene expression in discriminating benign from malignant thyroid nodules. In this study, 237 preoperative thyroid fine-needle aspiration samples were analyzed prospectively for the expression of the HMGA2 gene by real-time reverse transcription polymerase chain reaction. The results were evaluated against the postoperative histopathologic diagnosis or definitive cytologic diagnosis in cases of nodular goiter and Hashimoto thyroiditis. Among 237 samples from patients with thyroid nodules that were analyzed, 231 were adequate for real-time reverse transcription polymerase chain reaction analysis. With a cutoff value of 8.71 for relative gene expression, HMGA2 was positive in 19 (16.4%) of 116 nodular goiter, 1 (2.6%) of 39 Hashimoto thyroiditis, 9 (28.1%) of 32 follicular adenoma, 0 (0%) of 5 Hurthle cell adenoma, 32 (88.9%) of 36 papillary carcinoma, and 3 (100%) of 3 follicular carcinoma samples. In discriminating between malignant and benign thyroid nodules, HMGA2 has shown specificity of 84.5%, sensitivity of 91.9%, positive predictive value of 53.1%, and negative predictive value of 98.2%. High sensitivity and negative predictive value of HMGA2 for preoperative detection of malignant thyroid nodules shown in this study indicate that it may have a role as an ancillary marker in cytology in the management of patients with thyroid nodules.

The Correlation-Base-Selection Algorithm for Diagnostic Schizophrenia Based on Blood-Based Gene Expression Signatures

Microarray analysis of gene expression is often used to diagnose different types of disease. Many studies report remarkable achievements in nervous system disease. Clinical diagnosis of schizophrenia (SCZ) still depends on doctors' experience, which is unreliable and needs to be more objective and quantified. To solve this problem, we collected whole blood gene expression data from four studies, including 152 individuals with schizophrenia (SCZ) and 138 normal controls in different regions. The correlation-based feature selection (CFS, one of the machine learning methods) algorithm was applied in this study, and 103 significantly differentially expressed genes between patients and controls, called “feature genes,” were selected; then, a model for SCZ diagnosis was built. The samples were subdivided into 10 groups, and cross-validation showed that the model we constructed achieved nearly 100% classification accuracy. Mathematical evaluation of the datasets before and after data processing proved the effectiveness of our algorithm. Feature genes were enriched in Parkinson's disease, oxidative phosphorylation, and TGF-beta signaling pathways, which were previously reported to be associated with SCZ. These results suggest that the analysis of gene expression in whole blood by our model could be a useful tool for diagnosing SCZ.

Long noncoding RNA HIT000218960 promotes papillary thyroid cancer oncogenesis and tumor progression by upregulating the expression of high mobility group AT-hook 2 (HMGA2) gene

Accumulating evidence suggests that long noncoding RNAs (lncRNAs) play an important role in oncogenesis and tumor progression. However, our knowledge of lncRNAs in thyroid cancer is still limited. To explore the crucial lncRNAs involved in oncogenesis of papillary thyroid cancer (PTC), we acquired data of differentially expressed lncRNAs between PTC tissues and paired adjacent noncancerous thyroid tissues through lncRNA microarray. In the microarray data, we observed that a newly identified lncRNA, HIT000218960, was significantly upregulated in PTC tissues and associated with a well-known oncogene, high mobility group AT-hook 2 (HMGA2) gene. Both in normal thyroid tissues and PTC tissues, the expression of HIT000218960 was significantly positively correlated with that of HMGA2 mRNA. Knockdown of HIT000218960 in PTC cells resulted in downregulation of HMGA2. In addition, functional assays indicated that inhibition of HIT000218960 in PTC cells suppressed cell proliferation, colony formation, migration and invasion in vitro. Increased HIT000218960 expression in PTC tissues was obviously correlated with lymph node metastasis and multifocality, as well as TNM stage. Those findings suggest that HIT000218960 might acts as a tumor promoter through regulating the expression of HMGA2.

Value of Molecular Tests in Cytologically Indeterminate Lesions of Thyroid

CONTEXT

Fine-needle aspiration has been the initial step in the workup of thyroid nodular lesions and has successfully reduced the number of unnecessary surgeries and improved preoperative malignancy detection. However, up to one-third of cases fall in the diagnostically "indeterminate group," which poses a patient-management challenge. objective: To review the characteristics of molecular tests useful for stratifying the malignancy risk of indeterminate thyroid lesions, including their advantages and limitations.

DATA SOURCES

PubMed.

CONCLUSIONS

Molecular tests are useful for triage of indeterminate thyroid nodules initially diagnosed by using fine-needle aspiration. Immunocytochemistry is readily available with the shortest turnaround time among the molecular tests but suffers from poor reproducibility and low interpretation concordance. Gene mutation analysis is superior in detecting malignancies as a rule-in test, despite low specificity. Next-generation sequencing seems promising but needs more validations before widespread use. Gene expression profiling is more suitable for detecting benign lesions as a rule-out test to avoid unnecessary surgeries but is not reliable in excluding malignancies. MicroRNA profiling has great potential for both risk stratification and predicting prognosis but is limited by significant variations in sensitivity and specificity. Although many questions still need to be answered, taken together, molecular tests are a promising option for classifying cytologically indeterminate thyroid nodular lesions.

A robust biomarker of differential correlations improves the diagnosis of cytologically indeterminate thyroid cancers

The fine-needle aspiration of thyroid nodules and subsequent cytological analysis is unable to determine the diagnosis in 15 to 30% of thyroid cancer cases; patients with indeterminate cytological results undergo diagnostic surgery which is potentially unnecessary. Current gene expression biomarkers based on well-determined cytology are complex and their accuracy is inconsistent across public datasets. In the present study, we identified a robust biomarker using the differences in gene expression values specifically from cytologically indeterminate thyroid tumors and a powerful multivariate search tool coupled with a nearest centroid classifier. The biomarker is based on differences in the expression of the following genes: CCND1, CLDN16, CPE, LRP1B, MAGI3, MAPK6, MATN2, MPPED2, PFKFB2, PTPRE, PYGL, SEMA3D, SERGEF, SLC4A4 and TIMP1. This 15-gene biomarker exhibited superior accuracy independently of the cytology in six datasets, including The Cancer Genome Atlas (TCGA) thyroid dataset. In addition, this biomarker exhibited differences in the correlation coefficients between benign and malignant samples that indicate its discriminatory power, and these 15 genes have been previously related to cancer in the literature. Thus, this 15-gene biomarker provides advantages in clinical practice for the effective diagnosis of thyroid cancer.

Consensus reference gene(s) for gene expression studies in human cancers: end of the tunnel visible?

BACKGROUND

Gene expression studies are increasingly used to provide valuable information on the diagnosis and prognosis of human cancers. Also, for in vitro and in vivo experimental cancer models gene expression studies are widely used. The complex algorithms of differential gene expression analyses require normalization of data against a reference or normalizer gene, or a set of such genes. For this purpose, mostly invariant housekeeping genes are used. Unfortunately, however, there are no consensus (housekeeping) genes that serve as reference or normalizer for different human cancers. In fact, scientists have employed a wide range of reference genes across different types of cancer for normalization of gene expression data. As a consequence, comparisons of these data and/or data harmonizations are difficult to perform and challenging. In addition, an inadequate choice for a reference gene may obscure genuine changes and/or result in erroneous gene expression data comparisons.

METHODS

In our effort to highlight the importance of selecting the most appropriate reference gene(s), we have screened the literature for gene expression studies published since the turn of the century on thirteen of the most prevalent human cancers worldwide.

CONCLUSIONS

Based on the analysis of the data at hand, we firstly recommend that in each study the suitability of candidate reference gene(s) should carefully be evaluated in order to yield reliable differential gene expression data. Secondly, we recommend that a combination of PPIA and either GAPDH, ACTB, HPRT and TBP, or appropriate combinations of two or three of these genes, should be employed in future studies, to ensure that results from different studies on different human cancers can be harmonized. This approach will ultimately increase the depth of our understanding of gene expression signatures across human cancers.

The diagnostic utility of combination of HMGA2 and IMP3 qRT-PCR testing in thyroid neoplasms

The diagnosis of malignant thyroid tumors in some cytologic and histologic specimens remains challenging. High-mobility group A2 (HMGA2) expression and insulin-like growth factor II mRNA-binding protein-3 (IMP3) expression were evaluated by relative quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The aim of this study was to evaluate whether the combination of HMGA2 and IMP3 qRT-PCR was diagnostically useful in differentiating benign from malignant thyroid neoplasms. Fine-needle aspiration (FNA) specimens from 120 patients including 56 benign lesions and 64 carcinomas were used. The available 80 corresponding formalin-fixed paraffin-embedded (FFPE) thyroid tissues from 66 patients were also included in this study. HMGA2 and IMP3 expression levels were detected by qRT-PCR and reported as relative fold change after normalizing with a calibrator. The diagnostic utilities of HMGA2 and IMP3 qRT-PCR tests were evaluated individually and in combination. In FNA specimens, HMGA2 and IMP3 expression was consistently higher in thyroid malignancies compared with benign lesions in all subgroups except in Hürthle cell tumors. After exclusion of Hürthle cell tumors, the sensitivity was 90.2% for HMGA2, 88.2% for IMP3, and 98% for HMGA2+IMP3; the specificity was 97.1% for HMGA2, 79.4% for IMP3, and 79.4% for HMGA+IMP3. qRT-PCR data showed similar results in FFPE tissues: the sensitivity was 84.2% for HMGA2, 85.7% for IMP3, and 94.7% for HMGA2+IMP3; the specificity was 96.9% for HMGA2, 91.2% for IMP3, and 90.6% for HMGA2+IMP3. qRT-PCR data were concordant between FNA and FFPE samples for HMGA2 (97.4%) and IMP3 (96.9%). The results indicate that HMGA2 qRT-PCR with high specificity may be a useful ancillary technique to assist in the classification of difficult thyroid specimens, excluding Hürthle cell tumors. The HMGA2 and IMP3 qRT-PCR combination model with increased sensitivity and negative predictive value (96.4%) may be useful in screening thyroid cytology specimens.

Molecular Assays in Cytopathology for Thyroid Cancer

Background

Despite lack of adequate, validated, independently performed clinical studies, several molecular tests are commercially available on the market and are being used on indeterminate thyroid nodules to guide patient-care decisions.

Methods

We summarize the current evidence on the role and limitations of molecular tests used in combination with thyroid cytopathology to refine the presurgical diagnosis of thyroid nodules.

Results

The clinical performance of molecular tests depends on the pretest risk of malignancy within the specific cytological group being assessed. This risk is variable and should be assessed at each institution to optimize the selection of the molecular test and the interpretation of its results. Next-generation sequencing has increased the sensitivity of oncogene panels while maintaining high specificity. Tests assessing the gene expression pattern have shown promising results, with high sensitivity but low specificity. The impacts of molecular markers on clinical practice remains in flux and their effect on health care costs remains poorly understood.

Conclusions

Further large, independent, confirmatory, clinical validation studies and real-world, cost-effectiveness studies are necessary before the widespread adoption of these tests can be endorsed as standard of care.

The Diagnostic Usefulness of HMGA2, Survivin, CEACAM6, and SFN/14-3-3 δ in Follicular Thyroid Carcinoma

Background:

Follicular thyroid carcinoma (FTC) is the second most common thyroid malignancy and its differential diagnosis includes follicular adenoma (FA) and adenomatous goiter (AG). Several ancillary markers have been suggested to aid in the diagnosis of FTC, but the successful use of these methods still needs to be validated.

Methods:

In the present study, we verified the immunoexpression of HMGA2, CEACAM6, survivin, and SFN/14-3-3 δ in lesions including 41 AGs, 72 FAs, and 79 FTCs. We evaluated their diagnostic usefulness, combined with galectin 3, Hector Battifora mesothelial 1 (HBME1), cytokeratin 19, and cyclin D1, in diagnosing FTC.

Results:

The expressions of HBME1 (65.8%) and HMGA2 (55.7%) were significantly higher in FTCs than in FAs and AGs (p<.001 and p=.005, respectively). HBME1 was the only marker that was more frequently expressed in FTCs than in FAs (p=.021) and it was more frequently expressed in follicular neoplasms than in AGs (p<.001). Among the novel markers, the combination of HMGA2 and HBME1 showed the highest sensitivity (72.2%) and specificity (76.1%) for diagnosing FTC. CEACAM6, survivin, and SFN/14-3-3 δ were barely expressed in most cases.

Conclusions:

Our present results show that only HMGA2 can be beneficial in differentiating FTC using the novel markers.

A three-gene panel that distinguishes benign from malignant thyroid nodules

Reliable preoperative diagnosis of malignant thyroid tumors remains challenging because of the inconclusive cytological examination of fine-needle aspiration biopsies. Although numerous studies have successfully demonstrated the use of high-throughput molecular diagnostics in cancer prediction, the application of microarrays in routine clinical use remains limited. Our aim was, therefore, to identify a small subset of genes to develop a practical and inexpensive diagnostic tool for clinical use. We developed a two-step feature selection method composed of a linear models for microarray data (LIMMA) linear model and an iterative Bayesian model averaging model to identify a suitable gene set signature. Using one public dataset for training, we discovered a three-gene signature dipeptidyl-peptidase 4 (DPP4), secretogranin V (SCG5) and carbonic anhydrase XII (CA12). We then evaluated the robustness of our gene set using three other independent public datasets. The gene signature accuracy was 85.7, 78.8 and 85.7%, respectively. For experimental validation, we collected 70 thyroid samples from surgery and our three-gene signature method achieved an accuracy of 94.3% by quantitative polymerase chain reaction (QPCR) experiment. Furthermore, immunohistochemistry in 29 samples showed proteins expressed by these three genes are also differentially expressed in thyroid samples. Our protocol discovered a robust three-gene signature that can distinguish benign from malignant thyroid tumors, which will have daily clinical application.

Molecular diagnostic testing and the indeterminate thyroid nodule

PURPOSE OF REVIEW

To summarize the latest developments in the use of molecular diagnostic testing in cytologically indeterminate thyroid nodules.

RECENT FINDINGS

The majority of nodules with fine needle aspiration biopsy (FNAB) results that are classified as indeterminate (i.e., atypia of undetermined significance/lesion of undetermined significance, follicular neoplasm, and suspicious for malignancy) are histologically benign. Improvements in diagnostic discrimination can potentially be achieved with immunocytochemical analysis for candidate protein markers such as galectin-3, or analysis of differential microRNA expression patterns although larger prospective validation studies are still needed. After large-scale gene expression analysis, a marker panel was selected with the goal of optimizing the negative predictive value, and in indeterminate nodules, the panel may be helpful in lowering but not eliminating the risk of cancer. Another panel composed of gene mutations and rearrangements associated with thyroid cancer can improve the specificity and positive predictive value of preoperative FNAB, and better identify cytologically indeterminate nodules with a high risk of cancer.

SUMMARY

Molecular diagnostic testing improves preoperative risk stratification for nodules that have indeterminate FNAB results. Although currently available tests do not yet have the sensitivity to reliably exclude malignancy altogether, improvements in specificity can be used to guide the extent of initial surgery and clinical management.

Differential expression of degradome components in cutaneous squamous cell carcinomas

Although the cure rate for cutaneous squamous cell carcinoma is high, the diverse spectrum of squamous cell carcinoma has made it difficult for early diagnosis, particularly the aggressive tumors that are highly associated with mortality. Therefore, molecular markers are needed as an adjunct to current staging methods for diagnosing high-risk lesions, and stratifying those patients with aggressive tumors. To identify such biomarkers, we have examined a comprehensive set of 200 histologically defined squamous cell carcinoma and normal skin samples by using a combination of microarray, QRT-PCR and immunohistochemistry analyses. A characteristic and distinguishable profile including matrix metalloproteinase (MMP) as well as other degradome components was differentially expressed in squamous cell carcinoma compared with normal skin samples. The expression levels of some of these genes including matrix metallopeptidase 1 (MMP1), matrix metallopeptidase 10 (MMP10), parathyroid hormone-like hormone (PTHLH), cyclin-dependent kinase inhibitor 2A (CDKN2A), A disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1), FBJ osteosarcoma oncogene (FOS), interleukin 6 (IL6) and reversion-inducing-cysteine-rich protein with kazal motifs (RECK) were significantly differentially expressed (P≤0.02) in squamous cell carcinoma compared with normal skin. Furthermore, based on receiver operating characteristic analyses, the mRNA and protein levels of MMP1 are significantly higher in aggressive tumors compared with non-aggressive tumors. Given that MMPs represent the most prominent family of proteinases associated with tumorigenesis, we believe that they may have an important role in modulating the tumor microenvironment of squamous cell carcinoma.

Correlated expression of HMGA2 and PLAG1 in thyroid tumors, uterine leiomyomas and experimental models

In pleomorphic adenomas of the salivary glands (PASG) recurrent chromosomal rearrangements affecting either 8q12 or 12q14∼15 lead to an overexpression of the genes of the genuine transcription factor PLAG1 or the architectural transcription factor HMGA2, respectively. Both genes are also affected by recurrent chromosomal rearrangements in benign adipocytic tumors as e. g. lipomas and lipoblastomas. Herein, we observed a strong correlation between the expression of HMGA2 and PLAG1 in 14 benign and 23 malignant thyroid tumors. To address the question if PLAG1 can be activated by HMGA2, the expression of both genes was quantified in 32 uterine leiomyomas 17 of which exhibited an overexpression of HMGA2. All leiomyomas with HMGA2 overexpression also revealed an activation of PLAG1 in the absence of detectable chromosome 8 abnormalities affecting the PLAG1 locus. To further investigate if the overexpression of PLAG1 is inducible by HMGA2 alone, HMGA2 was transiently overexpressed in MCF-7 cells. An increased PLAG1 expression was observed 24 and 48 h after transfection. Likewise, stimulation of HMGA2 by FGF1 in adipose tissue-derived stem cells led to a simultaneous increase of PLAG1 mRNA. Altogether, these data suggest that HMGA2 is an upstream activator of PLAG1. Accordingly, this may explain the formation of tumors as similar as lipomas and lipoblastomas resulting from an activation of either of both genes by chromosomal rearrangements.

A model to discriminate malignant from benign thyroid nodules using artificial neural network

Objective

This study aimed to construct a model for using in differentiating benign and malignant nodules with the artificial neural network and to increase the objective diagnostic accuracy of US.

Materials and methods

618 consecutive patients (528 women, 161 men) with 689 thyroid nodules (425 malignant and 264 benign nodules) were enrolled in the present study. The presence and absence of each sonographic feature was assessed for each nodule - shape, margin, echogenicity, internal composition, presence of calcifications, peripheral halo and vascularity on color Doppler. The variables meet the following criteria: important sonographic features and statistically significant difference were selected as the input layer to build the ANN for predicting the malignancy of nodules.

Results

Six sonographic features including shape (Taller than wide, p<0.001), margin (Not Well-circumscribed, p<0.001), echogenicity (Hypoechogenicity, p<0.001), internal composition (Solid, p<0.001), presence of calcifications (Microcalcification, p<0.001) and peripheral halo (Absent, p<0.001) were significantly associated with malignant nodules. A three-layer 6-8-1 feed-forward ANN model was built. In the training cohort, the accuracy of the ANN in predicting malignancy of thyroid nodules was 82.3% (AUROC = 0.818), the sensitivity and specificity was 84.5% and 79.1%, respectively. In the validation cohort, the accuracy, sensitivity and specificity was 83.1%, 83.8% and 81.8%, respectively. The AUROC was 0.828.

Conclusion

ANN constructed by sonographic features can discriminate benign and malignant thyroid nodules with high diagnostic accuracy.

Classification of follicular cell-derived thyroid cancer by global RNA profiling

The incidence of thyroid cancer is increasing worldwide and thyroid nodules are a frequent clinical finding. Diagnosing follicular cell-derived cancers is, however, challenging both histopathologically and especially cytopathologically. The advent of high-throughput molecular technologies has prompted many researchers to explore the transcriptome and, in recent years, also the miRNome in order to generate new molecular classifiers capable of classifying thyroid tumours more accurately than by conventional cytopathological and histopathological methods. This has led to a number of molecular classifiers that may differentiate malignant from benign thyroid nodules. Molecular classification models based on global RNA profiles from fine-needle aspirations are currently being evaluated; results are preliminary and lack validation in prospective clinical trials. There is no doubt that molecular classification will not only contribute to our biological insight but also improve clinical and pathological examinations, thus advancing thyroid tumour diagnosis and ultimately preventing superfluous surgery. This review evaluates the status of classification and biological insights gained from molecular profiling of follicular cell-derived thyroid cancers.

What are the keys to successful thyroid FNA interpretation?

There is much concern expressed in the literature regarding the lack of predictive power of the thyroid fine needle aspiration/biopsy (TFNAB) approach to defining the nature of clinically detected thyroid nodules. This has been exacerbated in the past decade or more by the routine use of ultrasonography (US) in examining the thyroid as well as the introduction of molecular testing in the realm of thyroid pathology. Some have even gone so far as to suggest replacing the TFNAB with molecular signature testing to reduce the degree of uncertainty for a specific cytological diagnosis. This review addresses those concerns with a re-emphasis on understanding the basic keys to successfully evaluating a patient with a thyroid nodule by routine TFNAB examination. These keys include bringing to bear an experienced group of physicians in an integrated team approach, a sharpened focus on the TFNAB cytological categories and a grounded understanding of the predictive ability of molecular testing in a given patient when the cytological interpretation creates too much uncertainty in the minds of the patients and clinicians in attempting to reach a decision on how to manage a thyroid nodule. With this practical approach in mind, the false-negative and false-positive rates of "negative (benign)" and "positive (malignant)" thyroid aspirates should be no more than 1%; and the prevalence of an "indeterminate" aspirate - the area in TFNAB attracting the most attention for improvement with novel biomarkers - should be 10% or less. Thus, physicians should be capable of managing at least 90% of patients undergoing TFNAB in a confident manner without further testing beyond the routine, future re-examination of the patient's nodule to re-assess for any change in its nature or its impact on the patient's quality of life. The other 10% can then be considered for molecular testing in a manner tailored to those individuals truly in need of a more sophisticated - and expensive - approach to the characterization of their thyroid nodules. As the era of US has matured - just as with the era of serum PSA testing for prostate cancer in men - we have experienced a paradigm shift: Given the incidence of thyroid nodules in the U.S. adult population in comparison with the risk of dying of thyroid malignancy, the main role of TFNAB is to reduce the need for surgical intervention.

Differentiating benign from malignant thyroid nodules using micro ribonucleic acid amplification in residual cells obtained by fine needle aspiration biopsy

BACKGROUND

Fine needle aspiration biopsy (FNAB) is the most commonly used diagnostic tool to differentiate benign from malignant thyroid nodules. Nevertheless, some FNAB cytology results are not definite. In such cases diagnostic thyroid lobectomy is performed with malignancy rate on final histopathology ranging at 15%-75%. The aim of this study was to improve on the accuracy of FNAB-based cytology by amplification of microRNAs (micro ribonucleic acids [miRs]) from the residual cells left in the FNAB needle after submission for cytology.

METHODS

Residual cells were collected from the needle cup after FNAB cytology of 77 consecutive patients with thyroid nodules. miR-enriched RNA was extracted for all patients with cytology showing either follicular lesion or suspicion for malignancy (n=11). The expression of miR-21, -31, -146b, -187, -221, and -222 was determined using real-time polymerase chain reaction. Results were compared with final surgical histopathology.

RESULTS

RNA was successfully extracted from all FNAB specimens. Five patients had FNAB cytology suspicious for malignancy. The miR panel was positive in all five (100%). Six patients had follicular lesions on FNAB. The miR panel was positive in three of four patients (75%) with confirmed malignancy and was negative in two of two (0%) patients with benign pathology results. This corresponded to a specificity of 100%, sensitivity of 88%, and accuracy of 90%.

CONCLUSIONS

RNA extraction from FNAB residual cells is feasible, and a miR panel amplified from the extracted RNA seems like a promising diagnostic tool in this limited number of patients.