Predominant RET Germline Mutations in Exons 10, 11, and 16 in Iranian Patients with Hereditary Medullary Thyroid Carcinoma

The role of genetic and epigenetic modifications as potential biomarkers in the diagnosis and prognosis of thyroid cancer

Thyroid cancer (TC) is the most common endocrine cancer, which contributes to more than 43,600 deaths and 586,000 cases worldwide every year. Among the TC types, PTC and FTC comprise 90% of all TCs. Genetic modifications in genes are responsible for encoding proteins of mitogen-associated protein kinase cascade, which is closely related with numerous cellular mechanisms, including controlling programmed cell death, differentiation, proliferation, gene expression, as well as in genes encoding the PI3K (phosphatidylinositol 3-kinase)/protein kinase B (AKT) cascade, which has contribution in controlling cell motility, adhesion, survival, and glucose metabolism, have been associated with the TC pathogenesis. Various genetic modifications including BRAF mutations, RAS mutations, RET mutations, paired-box gene 8/peroxisome proliferator-activated receptor-gamma fusion oncogene, RET/PTC rearrangements, telomerase reverse transcriptase mutations, neurotrophic tyrosine receptor kinase fusion genes, TP53 mutations, and eukaryotic translation initiation factor 1A X-linked mutations can effectively serve as potential biomarkers in both diagnosis and prognosis of TC. On the other hand, epigenetic modifications can lead to aberrant functions or suppression of a range of signalling cascades, which can ultimately result in cancer. Various studies have observed the link between epigenetic modification and multiple cancers including TC. It has been reported that several epigenetic alterations including histone modifications, aberrant DNA methylation, and epigenetic modulations of non-coding RNAs can play significant roles as potential biomarkers in the diagnosis and prognosis of TC. Therefore, a good understanding regarding the genetic and epigenetic modifications is not only essential for the diagnosis and prognosis of TC, but also for the development of novel therapeutics. In this review, most of the major TC-related genetic and epigenetic modifications and their potential as biomarkers for TC diagnosis and prognosis have been extensively discussed.

RET T244I Germline Variant Mutation in a Patient with Pancreatic Paraganglioma and Primary Hyperparathyroidism

INTRODUCTION

Paragangliomas are rare neuroendocrine tumors that arise from chromaffin cells. Often termed extra-adrenal pheochromocytomas, these tumors vary with regards to their functionality, location, and malignant potential. Mutations in the RET proto-oncogene are associated with multiple endocrine neoplasia syndrome type 2 (MEN-2) and paragangliomas. The phenotypes of the individual mutations are documented to help determine prognosis.

CASE PRESENTATION

We report a case of a 64-year-old man with a history of parathyroid adenoma who developed a pancreatic retroperitoneal paraganglioma. Despite having laboratory evidence of excess circulating catecholamines, the patient's only presenting symptom was hip pain. The patient underwent resection, and histologic findings were consistent with paraganglioma with lymph node metastasis. Genetic testing revealed a variant of uncertain significance within the RET gene [c.731C>T (p.T244I)].

CONCLUSIONS

Paragangliomas are rare extra-adrenal neuroendocrine tumors that can be associated with germline mutations. Our patient was diagnosed with a pancreatic paraganglioma associated with a RET T244I mutation. Identifying patients with germline mutations is important for documenting phenotypic presentations of RET gene variants of uncertain significance, which will allow physicians to provide proper management and surveillance of paragangliomas and other associated tumors.

RET Proto-Oncogene Mutational Analysis in 45 Iranian Patients Affected with Medullary Thyroid Carcinoma: Report of a New Variant

Background

The aim of this study was to identify germline mutation of the RET (rearranged during transfection) gene in patients with medullary thyroid carcinoma (MTC) and their first-degree relatives to find presymptomatic carriers for possible prophylactic thyroidectomy. Methods/Patients. We examined all six hot spot exons (exons 10, 11, 13, and 14-16) of the RET gene by PCR and bidirectional Sanger sequencing in 45 Iranian patients with MTC (either sporadic or familial form) from 7 unrelated kindred and 38 apparently sporadic cases. First-degree relatives of RET positive cases were also genotyped for index mutation. Moreover, presymptomatic carriers were referred to the endocrinologist for further clinical management and prophylactic thyroidectomy if needed.

Results

Overall, the genetic status of all of the participants was determined by RET mutation screening, including 61 affected individuals, 22 presymptomatic carriers, and 29 genetically healthy subjects. In 37.5% (17 of 45) of the MTC referral index patients, 8 distinct RET germline mutations were found, including p.C634R (35.3%), p.M918T (17.6%), p.C634Y (11.8%), p.C634F (5.9%), p.C611Y (5.9%), p.C618R (5.9%), p.C630R (5.9%), p.L790F (5.9%), and one uncertain variant p.V648I (5.9%). Also, we found a novel variant p.H648R in one of our apparently sporadic patients.

Conclusion

RET mutation detection is a promising/golden screening test and provides an accurate presymptomatic diagnostic test for at-risk carriers (the siblings and offspring of the patients) to consider prophylactic thyroidectomy. Thus, according to the ATA recommendations, the screening of the RET proto-oncogene is indicated for patients with MTC.

The Prognostic Value of MicroRNAs in Thyroid Cancers-A Systematic Review and Meta-Analysis

Thyroid cancer (TC) includes various phenotypes, from indolent to highly aggressive cancer. The limitations of the current prognostication systems to predict the recurrence risk and the variability in expression of the genes involved in the thyroid carcinogenesis uncover the need for new prognostic biomarkers by taking into account potential epigenetic differences. We aimed to summarize the current knowledge regarding the prognostic impact of microRNAs (miRNAs) in TC. A literature search was conducted in PubMed, Embase, Scopus, and Web of Science databases. Both upregulated and downregulated miRNAs are significantly correlated with worse overall survival (hazard ratio (HR) = 5.94, 95% CI: 2.73-12.90, p < 0.001; HR = 0.51, 95% CI: 0.26-0.96, p = 0.048) disease/recurrence-free survival (HR = 1.58, 95% CI: 1.08-2.32, p = 0.003; HR = 0.37, 95%, CI: 0.24-0.60, p < 0.001). Sensitivity analysis revealed a significant association between the higher expression of miR-146b, miR-221, and miR-222 and the recurrence of papillary TC (OR = 9.11, 95% CI 3.00 to 27.52; p < 0.001; OR = 3.88, 95% CI 1.34 to 11.19, p < 0.001; OR = 6.56, 95% CI 2.75 to 15.64, p < 0.001). This research identified that miR-146b, miR-221, and miR-222 could serve as potential prognostic biomarkers in TC, particularly in PTC. Further studies are needed to strengthen these findings and sustain its clinical applicability.

Medullary thyroid cancer is associated with high serum vitamin D level and polymorphism of vitamin D receptors

Background

Thyroid cancer is the most common endocrine malignancy. Studies have observed an anti-cancer effect for vitamin D and found that polymorphisms of vitamin D receptors can influence the prevalence of various cancers. The present study investigated the serum level of vitamin D and FokI, BsmI and Tru9I polymorphisms of vitamin D receptors.

Methods

Forty patients with medullary thyroid cancer and 40 healthy controls were investigated. The genomic DNA of the subjects was extracted using saturated salt/proteinase K and investigated by PCR sequencing. Serum levels of vitamin D were evaluated by ELISA. The results were analyzed in SPSS and GraphPad Prism 5 software.

Results

The genotypic and allelic frequencies of FokI and BsmI polymorphisms showed no significant differences between test and control groups. For Tru9I polymorphism, Tt genotype and t allelic frequency in the test group were significantly different from those of the control group. Also, we found Tt genotype and t allelic frequency to be significantly associated with medullary thyroid cancer (MTC) type and the agressiveness of the disease. The average serum vitamin D level was 23.32 ng/mL and 18.95 ng/mL for patients and controls, respectively, and the difference between the two groups was statistically significant. Moreover, we found high serum vitamin D level to be associated with t allelic frequency.

Conclusions

Unexpectedly, the mean serum vitamin D level of the test group was significantly higher than that of the control group. Tru9I polymorphism was found to be significantly correlated with the prevalence of medullary thyroid carcinoma.

Altered Epigenetic Mechanisms in Thyroid Cancer Subtypes

Thyroid carcinoma (TC) is the most frequent malignant neoplasm of the endocrine system. Molecular methods for diagnosis of invasive thyroid disease can be effectively adopted. Epigenetic factors play an important role in the diversity patterns of gene expression and the phenotypic and biological characteristics of TC subtypes. We aimed to review epigenetic changes in the main subtypes of TC, along with a presentation of the methods that have examined these changes, and active clinical trials for the treatment of advanced TCs targeting epigenetic changes. A literature analysis was performed in MEDLINE using PubMed, Elsevier, and Google Scholar for studies published up to 2016, using the keywords: "Epigenetic alterations" OR "Epigenetic changes", "thyroid cancers", "papillary thyroid cancer", "medullary thyroid cancer", "follicular thyroid cancer", and "anaplastic thyroid cancer", which resulted in 310 articles in English. All related abstracts were reviewed and studies were included that were published in English, had available full text, and determined the details of the methods and materials associated with the epigenetic patterns of TC and its subtypes (100 articles). Analysis of epigenetic alterations in TC subtypes helps to identify pathogenesis and can play an important role in the classification and diagnosis of tumors. Epigenetic mechanisms, especially aberrant methylation of DNA and microRNAs (miRs), are likely to play an important role in thyroid tumorigenesis. Further studies are required to elucidate the role of histone modification mechanisms in TC development.

Evaluation of miRNAs expression in medullary thyroid carcinoma tissue samples: miR-34a and miR-144 as promising overexpressed markers in MTC

Medullary thyroid carcinoma (MTC) is a rare neoplasia derived from neural parafollicular C cells. MicroRNAs (miRNAs) are small regulatory RNAs with essential roles in the biology of cancers such as MTC and can be applied as diagnostic markers. According to previous studies, miR-144 and miR-34 and their two oncogenes target, mammalian target of rapamycin (mTOR) and AXL receptor tyrosine kinase (AXL), were selected for further investigations in our study. Thirty MTC samples as well as thirty adjacent normal thyroid tissues were applied in this study including 28 formalin-fixed, paraffin-embedded (FFPE) and 2 fresh-frozen MTC samples. RNA extraction and complementary DNA (cDNA) synthesis were performed for all samples. After primer pairs and probes were designed, real-time polymerase chain reaction (real-time PCR) method was used, and the results were analyzed using 2^-ΔΔCt method. Receiver operating characteristic (ROC) curve analysis was applied to assess the diagnostic value of the two miRNAs. AXL protein level was measured in all clinical samples using enzyme-linked immunosorbent assay (ELISA) method. Both miRNAs were up-regulated in all clinical samples compared to the normal tissues. AXL was up-regulated in most clinical samples while mTOR was down-regulated in most samples. Furthermore, the level of AXL protein increased. ROC curve analysis demonstrated that increased expression of miR-34a and miR-144 in MTC patients had significant predictive value. The results demonstrated that high expression of miR-144 and miR-34a can be considered as biomarkers of MTC. However, there was no statistically significant correlation between the expression of these miRNAs and target genes in MTC clinical samples.

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

Gene expression profiling (GEP) of normal thyroid tissue from 43 patients with thyroid carcinoma, 6 with thyroid adenoma, 42 with multinodular goiter, and 6 with Graves-Basedow disease was carried out with the aim of achieving a better understanding of the genetic mechanisms underlying the role of normal cells surrounding the tumor in the thyroid cancer progression. Unsupervised and supervised analyses were performed to compare samples from neoplastic and non-neoplastic diseases. GEP and subsequent RT-PCR analysis identified 28 differentially expressed genes. Functional assessment revealed that they are involved in tumorigenesis and cancer progression. The distinct GEP is likely to reflect the onset and/or progression of thyroid cancer, its molecular classification, and the identification of new potential prognostic factors, thus allowing to pinpoint selective gene targets with the aim of realizing more precise preoperative diagnostic procedures and novel therapeutic approaches.

Low expression of long non-coding RNA GAS5 is associated with poor prognosis of patients with thyroid cancer

The study aims to investigate the role of long non-coding RNA (lncRNA) GAS5 in the diagnosis and prognosis of patients suffering from thyroid cancer (TC). A total of 212 patients with TC and 61 patients with benign thyroid tumor were enrolled in the study. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to detect the lncRNA GAS5 expression in TC and benign tumor tissues. All TC patients were categorized into high-risk and low-risk groups according to the MACIS, AGES and AMES prognostic scoring system. A 5-year follow-up was conducted in order to determine the disease free survival (DFS) rates and overall survival (OS) rates. The associations between lncRNA GAS5 expression and prognosis of TC patients were analyzed by The Kaplan-Meier survival curves and the Cox regression models. There was a decrease in the lncRNA GAS5 expression in TC tissues in comparison to benign tumor tissues. Expression of lncRNA GAS5 showed significant association with tumor node metastasis (TNM) staging, lymph node metastasis and the multiple cancer foci of TC. AMES high-risk patients showed a decreased expression of lncRNA GAS5 expression than the AMES low-risk patients. The AGES and MACIS high-risk patients showed lower lncRNA GAS5 expression than low-risk patients. The survival rate of TC patients with high lncRNA GAS5 expression was higher than that of TC patients with low lncRNA GAS5 expression during the DFS and OS periods. Cox regression analysis indicated that lncRNA GAS5 expression, TNM staging, lymph node metastasis and multiple cancer foci were independent risk factors for poor prognosis in TC patients. LncRNA GAS5 may be closely related to the diagnosis and prognosis of TC.

Distribution of RET Mutations in Multiple Endocrine Neoplasia 2 in Denmark 1994-2014: A Nationwide Study

BACKGROUND

Germline mutations of the REarranged during Transfection (RET) proto-oncogene cause multiple endocrine neoplasia 2 (MEN2). It is unclear whether the distribution of RET mutations varies among populations. The first nationwide study of the distribution of RET mutations was conducted, and the results were compared to those of other populations.

METHODS

This retrospective cohort study included 1583 patients who underwent RET gene testing in one of three centers covering all of Denmark between September 1994 and December 2014. Primary testing method was Sanger sequencing, which included exons 8-11 and 13-16. Mutations were defined according to the ARUP database July 1, 2016.

RESULTS

RET mutations were identified in 163 patients from 36 apparently unrelated families. Among the 36 families 13 (36.1%) carried mutations in codon 611, four (11.1%) in codon 618, three (8.3%) in codon 620, one (2.8%) in codon 631, six (16.7%) in codon 634, one (2.8%) in codon 790, one (2.8%) in codon 804, one (2.8%) in codon 852, one (2.8%) in codon 883, and five (13.9%) in codon 918. Among the 13 families with codon 611 mutations, 12 had the p.C611Y mutation.

CONCLUSIONS

The distribution of RET mutations in Denmark appears to differ from that of other populations. Mutations in codon 611 were the most prevalent, followed by more frequently reported mutations. This might be due to a possible founder effect for the p.C611Y mutation. However, further studies are needed to find possible explanations for the skewed mutational spectrum in Denmark.

Whole genome sequence analysis of the TALLYHO/Jng mouse

Background

The TALLYHO/Jng (TH) mouse is a polygenic model for obesity and type 2 diabetes first described in the literature in 2001. The origin of the TH strain is an outbred colony of the Theiler Original strain and mice derived from this source were selectively bred for male hyperglycemia establishing an inbred strain at The Jackson Laboratory. TH mice manifest many of the disease phenotypes observed in human obesity and type 2 diabetes.

Results

We sequenced the whole genome of TH mice maintained at Marshall University to a depth of approximately 64.8X coverage using data from three next generation sequencing runs. Genome-wide, we found approximately 4.31 million homozygous single nucleotide polymorphisms (SNPs) and 1.10 million homozygous small insertions and deletions (indels) of which 98,899 SNPs and 163,720 indels were unique to the TH strain compared to 28 previously sequenced inbred mouse strains. In order to identify potentially clinically-relevant genes, we intersected our list of SNP and indel variants with human orthologous genes in which variants were associated in GWAS studies with obesity, diabetes, and metabolic syndrome, and with genes previously shown to confer a monogenic obesity phenotype in humans, and found several candidate variants that could be functionally tested using TH mice. Further, we filtered our list of variants to those occurring in an obesity quantitative trait locus, tabw2, identified in TH mice and found a missense polymorphism in the Cidec gene and characterized this variant’s effect on protein function.

Conclusions

We generated a complete catalog of variants in TH mice using the data from whole genome sequencing. Our findings will facilitate the identification of causal variants that underlie metabolic diseases in TH mice and will enable identification of candidate susceptibility genes for complex human obesity and type 2 diabetes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3245-6) contains supplementary material, which is available to authorized users.

Signaling pathways in medullary thyroid carcinoma: therapeutic implications

Medullary thyroid cancer (MTC) is the third most frequent thyroid cancer arising from thyroid parafollicular cells. Surgery is the first-line strategy in treatment of MTC but disease relapse and patient's death have been observed in approximately two out of three of MTC cases. Identification of molecular mechanisms and different signaling pathways has offered new insights for disease treatment. The development of tyrosine kinase inhibitors targeting these pathways has provided a promising landscape for prevention of progression in patients with advanced metastatic MTC. In this review article different altered molecular pathways implicated in the development of MTC and the therapeutic strategies based on targeting the identified signaling pathways have been summarized.

PI3K/AKT Pathway and Its Mediators in Thyroid Carcinomas

Thyroid malignancies are the most common endocrine system carcinomas, with four histopathological forms. The phosphoinositide 3-kinase-protein kinase B/AKT (PI3K-PKB/AKT) pathway is one of the most critical molecular signaling pathways implicated in key cellular processes. Its continuous activation by several aberrant receptor tyrosine kinases (RTKs) and genetic mutations in its downstream effectors result in high cell proliferation in a broad number of cancers, including thyroid carcinomas. In this review article, the role of different signaling pathways of PI3K/AKT in thyroid cancers, with the emphasis on the PI3K/AKT/mammalian target of rapamycin (mTOR), PI3K/AKT/forkhead box O (FOXO) and PI3K/AKT/phosphatase and tensin homolog deleted on chromosome ten (PTEN) pathways, and various therapeutic strategies targeting these pathways have been summarized. In most of the in vitro studies, agents inhibiting mTOR in monotherapy or in combination with chemotherapy for thyroid malignancies have been introduced as promising anticancer therapies. FOXOs and PTEN are two outstanding downstream targets of the PI3K/AKT pathway. At the present time, no study has been undertaken to consider thyroid cancer treatment via FOXOs and PTEN targeting. According to the critical role of these proteins in cell cycle arrest, it seems that a treatment strategy based on the combination of FOXOs or PTEN activity induction with PI3K/AKT downstream mediators (e.g., mTOR) inhibition will be beneficial and promising in thyroid cancer treatment.

Epigenetic modifications in human thyroid cancer

Thyroid carcinoma is the most common endocrine malignancy of the endocrine organs, and its incidence rate has steadily increased over the last decade. Over 95% of thyroid carcinoma is derived from follicular cells that have a spectrum of differentiation to the most invasive malignancy. The molecular pathogenesis of thyroid cancer remains to be clarified, although activating the RET, RAS and BRAF oncogenes have been well characterized. Increasing evidence from previous studies demonstrates that acquired epigenetic abnormalities participating with genetic alteration results in altered patterns of gene expression/function. Aberrant DNA methylation has been established in the CpG regions and microRNAs (miRNAs) expression profile recognized in cancer development. In the present review, a literature review was performed using MEDLINE and PubMed with the terms 'epigenetic patterns in thyroid cancer [or papillary thyroid carcinoma (PTC), follicular thyroid carcinoma (FTC), medullary thyroid cancer (MTC), anaplastic thyroid cancer (ATC)]', 'DNA methylation in thyroid cancer (or PTC, FTC, MTC, ATC)', 'miRNA expression in thyroid cancer (or PTC, FTC, MTC, ATC)', 'epigenetic patterns in cancer' and the current understanding of epigenetic patterns in thyroid cancer was discussed.

Haplotype Frequency of G691S/S904S in the RET Proto-Onco-gene in Patients with Medullary Thyroid Carcinoma

BACKGROUND

Medullary thyroid carcinoma (MTC) occurs in both sporadic (75%) and hereditary (25%) forms. The missense mutations of the REarranged during Transfection (RET) proto-oncogene in MTC development have been well demonstrated. The aim of this study was to investigate frequency of G691S/S904S haplotype in MTC patients and their relatives.

METHODS

In this research 293 participants were studied, including 181 patients (102 female, 79 male) and 112 their relatives (58 female, 54 male). Genomic DNA was extracted from peripheral blood leucocytes using the standard Salting Out/Proteinase K method. Nucleotide change detection was performed using PCR and direct DNA sequencing methods.

RESULTS

According to DNA sequencing results, 159 individuals (104 patients, 55 relatives) had both G691S (rs1799939) missense mutation in exon11 and S904S (rs1800863) synonymous mutation in exon 15 of RET proto-oncogene. The allele frequency of G691S/S904S haplotype was 21.15% in patients and 10.75% in their relatives.

CONCLUSION

The obtained data showed the frequency of G691S/S904S RET gene haplotype among Iranian MTC patients and their relatives. The G691S and S904S nucleotide changes were in complete linkage disequilibrium, so the results were grouped together and referred to as G691S/S904S haplotype. Further analysis is need to demonstrate the association between this haplotype and MTC development.

Detection of heterozygous c.1708C>T and c.1978C>G thyroid peroxidase (TPO) mutations in Iraqi patients with toxic and nontoxic goiter

Sixty-three Arabic patients (16 males and 47 females) with thyroid toxic and nontoxic goiter who attended the endocrinologist in Nuclear Medicine Hospital and Al Yarmok Nuclear Medicine Department in Baghdad, Iraq were examined for thyroid peroxidase (TPO) gene mutations. A total of ten heterozygous mutations have been identified in the human TPO gene associated with thyroid toxic and nontoxic goiter. These mutations involved transition or transversion of cysteine either by thymine or guanine at the position 1708 of the exon 10 (c.1708C>T) and the position 1978 of the exon 11 (c.1978C>G). From a total of ten detected mutations, two c.1978C>G mutations were detected in nontoxic goiter patients and eight (two c.1708C>T and six c.1978C>G mutations) were detected in toxic goiter. In conclusion, this study identified ten TPO mutations associated with toxic and nontoxic goiter that have not been yet reported in Iraq, and most of them are detected among females (90 %) and adults age between 30 and 50 years old (80 %).