Employing genetic markers to improve diagnosis of thyroid tumor fine needle biopsy

NIBAN1, Exploring its Roles in Cell Survival Under Stress Context

Cell survival must quickly activate specific mechanisms that enable to detect changes in the cellular microenvironment. The impact of these cell alteration has direct consequences on cellular homeostasis. Cellular stress, as well as its regulation and implication, has been studied in different pathologies. In this sense, the alteration in NIBAN1 expression seems to act in response to different cellular disturbances. Over the years, the knowledge of NIBAN1 functions has improved, demonstrating its important cell roles, favoring the cell survival under stress context. In response to the disturbances, NIBAN1 seems to be involved in the decision-making process between cell survival and death. The increase in NIBAN1 expression has been related to cellular mechanisms that seek to minimize the damage caused to cellular homeostasis. In this review, the main biological insights attributed to the NIBAN1 gene in different cellular contexts and its role as a mediator of cellular stress are discussed.

Utility of microdissected cytology smears for molecular analysis of thyroid malignancy

Background

Molecular testing of thyroid fine‐needle aspirates has demonstrated value in cases of indeterminate cytology (Bethesda categories III, IV, and V) enabling optimized individual patient management leading to better outcomes with health economic benefits. For most molecular testing modalities, including mutational panels and classifier analyses, part or all of a dedicated needle aspiration pass is required to obtain an adequate sample for testing. Our analysis, which is based on a combination approach (mutation detection and microRNA classifier status), has documented clinical validity and utility when performed on thyroid fine‐needle aspirates placed directly into RNA preservative fluid. Here we show that the combination approach can be extended to microdissected stained cytology slides provides the physician greater opportunity to resolve cytological indeterminacy.

Methods

Extracted nucleic acid from needle aspirate and corresponding cytology preparations of 47 thyroid nodules were analyzed using identical methodology and results were compared.

Results

Of 94 molecular analyses (47 mutational analyses, 47 microRNA classifier assessments based on a validated 10 marker panel) only 5 samples showed discordant results.

Conclusion

These findings, together with supplementary work using archival specimens shows that the combination approach can be effectively applied to both direct aspirated thyroid nodule aspirates or to nucleic acid extracted from macrodissected and microdissected cytology slide smears, with the expectation of equivalent results. The advantages of both specimen sources, direct aspirate, and cytology slide smears are discussed.

RAS Mutations, and RET/PTC and PAX8/PPAR-gamma Chromosomal Rearrangements Are Also Prevalent in Benign Thyroid Lesions: Implications Thereof and A Systematic Review

BACKGROUND

Molecular markers associated with thyroid malignancy are increasingly being used as differential diagnostic tools for thyroid nodules. However, little has been reported recently regarding the prevalence of these markers in benign lesions. The literature was systematically reviewed to examine studies that reported on the prevalence of these markers in benign thyroid lesions.

METHODS

Appropriate studies published between January 1, 2000, and April 30, 2015, and cataloged in PubMed, Embase, Cochrane, Scopus, and Web of Science databases were searched for by combining different keywords for "thyroid tumor" with both general and specific keywords for "molecular marker" by using "AND" as the Boolean operator. All studies meeting criteria that reported the prevalence of RAS mutations, and RET/PTC and PAX8/PPAR-gamma chromosomal rearrangements in benign thyroid lesions were included for study.

RESULTS

A total of 64 articles (including 8162 patients, of whom 42.5% had benign lesions) that met all the study criteria were systematically reviewed and abstracted. Among 35 studies examining RAS mutations, the reported prevalence of RAS mutation in benign lesions ranged from 0% to 48%. In 38 studies examining RET/PTC rearrangements, the prevalence in benign lesions ranged from 0% to 68%. PAX8/PPAR-gamma rearrangements were examined in 27 studies, with the prevalence in benign lesions ranging from 0% to 55%.

CONCLUSION

The presence of these biomarkers and the tremendous variation in reports of their prevalence in benign lesions suggests the need for caution when including these markers in diagnostic decisions. Further understanding of the importance of these markers, as well as newly discovered markers of thyroid malignancy, may be required in order to avoid overtreatment of patients with benign thyroid tumors.

Evaluation and management of thyroid nodules in children

PURPOSE OF REVIEW

The review is focused on new information about the presentation and management of thyroid nodules in children and adolescents.

RECENT FINDINGS

Palpable thyroid nodules are uncommon in children but many children have nodules detected by radiologic imaging. How to evaluate them, when to suspect thyroid cancer, and how best to follow apparently benign nodules has become an area of great interest. The American Thyroid Association recently published treatment guidelines for children with thyroid nodules and cancers but much has been learned since that publication.

SUMMARY

Personal and family history, ultrasound features, and fine needle aspiration cytology are used to determine the risk of cancer in thyroid nodules, which are then managed according to cancer risk.

Cytopathologic diagnosis of fine needle aspiration biopsies of thyroid nodules

Fine-needle aspiration (FNA) cytology is an important diagnostic tool in patients with thyroid lesions. Several systems have been proposed for the cyropathologic diagnosis of the thyroid nodules. However cases with indeterminate cytological findings still remain a matter of debate. In this review we analyze all literature regarding Thyroid Cytopathology Reporting systems trying to identify the most suitable methodology to use in clinical practice for the preoperative diagnosis of thyroid nodules. A review of the English literature was conducted, and data were analyzed and summarized and integrated from the authors’ perspective. The main purpose of thyroid FNA is to identify patients with higher risk for malignancy, and to prevent unnecessary surgeries for benign conditions. The Bethesda System for Reporting Thyroid Cytopathology is the most widely used system for the diagnosis of thyroid FNA specimens. This system also contains guidelines for the diagnosis and treatment of indeterminate or suspicious for malignancy cases. In conclusion, patients who require repeated FNAs for indeterminate diagnoses will be resolved by repeat FNA in a percentage of 72%-80%.

The combination of four molecular markers improves thyroid cancer cytologic diagnosis and patient management

Background

Papillary thyroid cancer is the most common endocrine malignancy. The most sensitive and specific diagnostic tool for thyroid nodule diagnosis is fine-needle aspiration (FNA) biopsy with cytological evaluation. Nevertheless, FNA biopsy is not always decisive leading to “indeterminate” or “suspicious” diagnoses in 10 %–30 % of cases. BRAF V600E detection is currently used as molecular test to improve the diagnosis of thyroid nodules, yet it lacks sensitivity. The aim of the present study was to identify novel molecular markers/computational models to improve the discrimination between benign and malignant thyroid lesions.

Methods

We collected 118 pre-operative thyroid FNA samples. All 118 FNA samples were characterized for the presence of the BRAF V600E mutation (exon15) by pyrosequencing and further assessed for mRNA expression of four genes (KIT, TC1, miR-222, miR-146b) by quantitative polymerase chain reaction. Computational models (Bayesian Neural Network Classifier, discriminant analysis) were built, and their ability to discriminate benign and malignant tumors were tested. Receiver operating characteristic (ROC) analysis was performed and principal component analysis was used for visualization purposes.

Results

In total, 36/70 malignant samples carried the V600E mutation, while all 48 benign samples were wild type for BRAF exon15. The Bayesian neural network (BNN) and discriminant analysis, including the mRNA expression of the four genes (KIT, TC1, miR-222, miR-146b) showed a very strong predictive value (94.12 % and 92.16 %, respectively) in discriminating malignant from benign patients. The discriminant analysis showed a correct classification of 100 % of the samples in the malignant group, and 95 % by BNN. KIT and miR-146b showed the highest diagnostic accuracy of the ROC curve, with area under the curve values of 0.973 for KIT and 0.931 for miR-146b.

Conclusions

The four genes model proposed in this study proved to be highly discriminative of the malignant status compared with BRAF assessment alone. Its implementation in clinical practice can help in identifying malignant/benign nodules that would otherwise remain suspicious.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-015-1917-2) contains supplementary material, which is available to authorized users.

Management Guidelines for Children with Thyroid Nodules and Differentiated Thyroid Cancer

BACKGROUND

Previous guidelines for the management of thyroid nodules and cancers were geared toward adults. Compared with thyroid neoplasms in adults, however, those in the pediatric population exhibit differences in pathophysiology, clinical presentation, and long-term outcomes. Furthermore, therapy that may be recommended for an adult may not be appropriate for a child who is at low risk for death but at higher risk for long-term harm from overly aggressive treatment. For these reasons, unique guidelines for children and adolescents with thyroid tumors are needed.

METHODS

A task force commissioned by the American Thyroid Association (ATA) developed a series of clinically relevant questions pertaining to the management of children with thyroid nodules and differentiated thyroid cancer (DTC). Using an extensive literature search, primarily focused on studies that included subjects ≤18 years of age, the task force identified and reviewed relevant articles through April 2014. Recommendations were made based upon scientific evidence and expert opinion and were graded using a modified schema from the United States Preventive Services Task Force.

RESULTS

These inaugural guidelines provide recommendations for the evaluation and management of thyroid nodules in children and adolescents, including the role and interpretation of ultrasound, fine-needle aspiration cytology, and the management of benign nodules. Recommendations for the evaluation, treatment, and follow-up of children and adolescents with DTC are outlined and include preoperative staging, surgical management, postoperative staging, the role of radioactive iodine therapy, and goals for thyrotropin suppression. Management algorithms are proposed and separate recommendations for papillary and follicular thyroid cancers are provided.

CONCLUSIONS

In response to our charge as an independent task force appointed by the ATA, we developed recommendations based on scientific evidence and expert opinion for the management of thyroid nodules and DTC in children and adolescents. In our opinion, these represent the current optimal care for children and adolescents with these conditions.

Clinical Implication of Highly Sensitive Detection of the BRAFV600E Mutation in Fine-Needle Aspirations According to the Thyroid Bethesda System in Patients With Conventional Papillary Thyroid Carcinoma

BACKGROUND

We investigated the additional diagnostic yield of the mutation test and evaluated the frequency of the BRAF mutation in conventional PTC (cPTC) according to ultrasound (US) features and the Bethesda System for Reporting Thyroid Cytopathology (BSRTC) based on the BRAFV600E mutation status.

MATERIALS AND METHODS

During the study period, 279 patients who underwent FNA with an additional BRAFV600E mutation test were diagnosed as cPTC after surgery. We analyzed the association between the mutation and several clinical factors.

RESULTS

Of the 279 cPTCs, 250 (89.6%) had the BRAFV600E mutation. The BRAF mutation test was helpful in diagnosing an additional 19% (53/279) of cPTCs. The frequency of the BRAF mutation in cPTCs with suspicious US features was higher than that of cPTCs with negative US features regardless of the BSRTC.

CONCLUSIONS

Suspicious US features may be helpful in deciding whether an additional BRAFV600E mutation test should be done in thyroid nodules with indeterminate cytology.

Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: promises and challenges for routine clinical diagnostics

Increasing use of fine needle aspiration for oncological diagnosis, while minimally invasive, poses a challenge for molecular testing by traditional sequencing platforms due to high sample requirements. The advent of affordable benchtop next-generation sequencing platforms such as the semiconductor-based Ion Personal Genome Machine (PGM) Sequencer has facilitated multi-gene mutational profiling using only nanograms of DNA. We describe successful next-generation sequencing-based testing of fine needle aspiration cytological specimens in a clinical laboratory setting. We selected 61 tumor specimens, obtained by fine needle aspiration, with known mutational status for clinically relevant genes; of these, 31 specimens yielded sufficient DNA for next-generation sequencing testing. Ten nanograms of DNA from each sample was tested for mutations in the hotspot regions of 46 cancer-related genes using a 318-chip on Ion PGM Sequencer. All tested samples underwent successful targeted sequencing of 46 genes. We showed 100% concordance of results between next-generation sequencing and conventional test platforms for all previously known point mutations that included BRAF, EGFR, KRAS, MET, NRAS, PIK3CA, RET and TP53, deletions of EGFR and wild-type calls. Furthermore, next-generation sequencing detected variants in 19 of the 31 (61%) patient samples that were not detected by traditional platforms, thus increasing the utility of mutation analysis; these variants involved the APC, ATM, CDKN2A, CTNNB1, FGFR2, FLT3, KDR, KIT, KRAS, MLH1, NRAS, PIK3CA, SMAD4, STK11 and TP53 genes. The results of this study show that next-generation sequencing-based mutational profiling can be performed on fine needle aspiration cytological smears and cell blocks. Next-generation sequencing can be performed with only nanograms of DNA and has better sensitivity than traditional sequencing platforms. Use of next-generation sequencing also enhances the power of fine needle aspiration by providing gene mutation results that can direct personalized cancer therapy.

Classification of thyroid nodules using a resonance-frequency-based electrical impedance spectroscopy: a preliminary assessment

BACKGROUND

Ultrasound and ultrasound-guided fine-needle aspiration biopsy are considered the most effective approaches for both identifying and classifying thyroid nodules. However, despite continuing improvements in scanner technology and refinements in ultrasound/cytological classification guidelines, indeterminate findings still lead to diagnostic lobectomy under general anesthesia. This study aims to investigate the feasibility of applying a modified noninvasive electrical impedance spectroscopy (EIS) approach to classifying thyroid nodules.

METHOD

To increase nodule classification sensitivity, we developed a new EIS-based model that introduces an optimized inductance component, which increases the measured signal-to-noise ratio of capacitance variation in and about thyroid nodules. Our model then measures the change of resonance frequency when the positive reactance of the system inductor cancels out the negative reactance of the nodule capacitance in a multi-frequency electrical signal scan. The system is termed "resonance-frequency-based electrical impedance spectroscopy" (REIS). A portable REIS system with multiple probes was assembled and preliminarily tested in our clinical facility. From an ongoing prospective study, an initial data set of 160 REIS examinations including 27 verified cancer cases was used. From the data set, a number of EIS signal features was extracted and analyzed. A multi-feature-based Bayesian Belief Network was built to classify the detected thyroid nodules. A receiver operating characteristic data analysis method was applied to evaluate classification performance.

RESULTS

The results showed that (i) the median resonance frequency measured by the probe nearest to malignant nodules was in general lower than that measured in benign cases, and (ii) the median descending slope of EIS signal sweep curves computed from cancer cases was larger than that computed from benign cases. The Bayesian Belief Network yielded a classification performance as measured by the area under the receiver operating characteristic curve of 0.794 [with a 95% confidence interval of 0.709-0.863].

CONCLUSIONS

The study demonstrates that noninvasive measurement of REIS signal features may potentially provide useful supplementary information to assist in classifying between malignant and benign thyroid nodules. Such an approach may ultimately lead to a reduction in the number of unnecessary thyroid surgeries.

Proteomic analysis of differentially expressed proteins in normal human thyroid cells transfected with PPFP

The fusion gene encoding the thyroid-specific transcription factor PAX8 and peroxisome proliferator-activated receptor γ (PPARγ (PPARG)) (designated as the PPFP gene) is oncogenic and implicated in the development of follicular thyroid carcinoma (FTC). The effects of PPFP transfection on the biological characteristics of Nthy-ori 3-1 cells were studied by MTT assay, colony formation, soft-agar colony formation, and scratch wound-healing assays as well as by flow cytometry. Furthermore, the differentially expressed proteins were analyzed on 2-DE maps and identified by MALDI-TOF-MS. Validation of five identified proteins (prohibitin, galectin-1, cytokeratin 8 (CK8), CK19, and HSP27) was determined by western blot analysis. PPFP not only significantly increased the viability, proliferation, and mobility of the Nthy-ori 3-1 cells but also markedly inhibited cellular apoptosis. Twenty-eight differentially expressed proteins were identified, among which 19 proteins were upregulated and nine proteins were downregulated in Nthy-ori 3-1(PPFP) (Nthy-ori 3-1 cells transfected with PPFP). The western blot results, which were consistent with the proteome analysis results, showed that prohibitin was downregulated, whereas galectin-1, CK8, CK19, and HSP27 were upregulated in Nthy-ori 3-1(PPFP). Our results suggest that PPFP plays an important role in malignant thyroid transformation. Proteomic analysis of the differentially expressed proteins in PPFP-transfected cells provides important information for further study of the carcinogenic mechanism of PPFP in FTCs.