Follicular Thyroid Adenoma and Follicular Thyroid Carcinoma-A Common or Distinct Background? Loss of Heterozygosity in Comprehensive Microarray Study.

Pre- and postsurgical differentiation between follicular thyroid adenoma (FTA) and follicular thyroid cancer (FTC) represents a significant diagnostic challenge. Furthermore, it remains unclear whether they share a common or distinct background and what the mechanisms underlying follicular thyroid lesions malignancy are. The study aimed to compare FTA and FTC by the comprehensive microarray and to identify recurrent regions of loss of heterozygosity (LOH). We analyzed formalin-fixed paraffin-embedded (FFPE) samples acquired from 32 Caucasian patients diagnosed with FTA (16) and FTC (16). We used the OncoScan™ microarray assay (Affymetrix, USA), using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP). The total number of LOH was higher in FTC compared with FTA (18 vs. 15). The most common LOH present in 21 cases, in both FTA (10 cases) and FTC (11 cases), was 16p12.1, which encompasses many cancer-related genes, such as TP53, and was followed by 3p21.31. The only LOH present exclusively in FTA patients (56% vs. 0%) was 11p11.2-p11.12. The alteration which tended to be detected more often in FTC (6 vs. 1 in FTA) was 12q24.11-q24.13 overlapping FOXN4, MYL2, PTPN11 genes. FTA and FTC may share a common genetic background, even though differentiating rearrangements may also be detected.

High incidence of FLT3 mutations in follicular thyroid cancer: potential therapeutic target in patients with advanced disease stage.

BACKGROUND: Conventional treatments for follicular thyroid cancer (FTC) can be ineffective, leading to poor prognosis. The aim of this study was to identify mutations associated with FTC that would serve as novel molecular markers of the disease and its outcome and could potentially identify new therapeutic targets. METHODS: FLT3 mutations were first detected in a 29-year-old White female diagnosed with metastasized, treatment-refractory FTC. Analyses of FLT3 mutational status through next-generation sequencing of formalin-fixed, paraffin-embedded FTC specimens were subsequently performed in 35 randomly selected patients diagnosed with FTC. RESULTS: FLT3 mutations were found in 69% of patients. FLT3 mutation-positive patients were significantly older than those that were FLT3 mutation-negative [median age at diagnosis 54 (36-82) versus 45 (27-58) (p = 0.023)]. Patients over 60 years were 23 times more likely to be FLT3 mutation-positive (p = 0.006). However, the number of FLT3 mutations did not correlate with age (r-Pearson: -0.244, p-value: 0.25). A total of 26 mutations were identified in the FLT3 gene with 2-16 FLT3 mutations in each FLT3 mutation-positive patient (mean: 5.6 mutations/patient). Tyrosine kinase domain (TKD) mutations in the FLT3 gene were detected in 58% of FLT3 mutation-positive patients. All FLT3 mutation-positive patients with a disease stage of pT2N1 or worse harbored at least one mutation in the TKD of FLT3. CONCLUSIONS: There is a wide spectrum and high frequency of FLT3 mutations in FTC. The precise role of FLT3 mutations in the genesis of FTC, as well as its potential role as a therapeutic target, requires further investigation.

Genetic heterogeneity of indeterminate thyroid nodules assessed preoperatively with next-generation sequencing reflects the diversity of the final histopathologic diagnosis.

INTRODUCTION: Inconclusive cytologic results of thyroid fine­needle aspiration biopsy (FNAB) include atypia or follicular lesion of undetermined significance (FLUS) and follicular neoplasm or suspicious for follicular neoplasm (SFN). OBJECTIVES: We aimed to assess the genetic background of indeterminate thyroid nodules and to identify new genetic pathways potentially involved in the development of follicular thyroid cancer. PATIENTS AND METHODS: Genomic DNA was isolated from FNAB samples from 25 white patients (2 men; 23 women) diagnosed preoperatively with FLUS (n = 16) and SFN (n = 9). Next­generation sequencing (NGS) was performed. The results were compared with clinical data, including final postsurgical diagnoses. RESULTS: The malignancy rate was 28%. KDR, RET, and TP53 gene mutations were most frequent in FLUS and SFN samples finally diagnosed as cancers, whereas alterations in RET, TP53, FLT3, APC, and PDGFRA predominated in benign tumors. KDR tended to be more common in malignant samples (75% vs 20%, P = 0.1). A total number of mutated genes was higher in patients with benign tumors (17 vs 11, P = 0.02), but there was no difference between groups in the mean number of mutations per patient (4.9 [range, 1-9]). CONCLUSIONS: We showed that the heterogeneity in the genetic background of indeterminate thyroid nodules corresponds to their histopathologic diversity. The role of KDR as a possible malignancy marker needs to be confirmed. Glass slides with FNAB samples may constitute a reliable source of genetic material for NGS studies, providing a better insight into the molecular profile of thyroid nodules.

Differences in Mutational Profile between Follicular Thyroid Carcinoma and Follicular Thyroid Adenoma Identified Using Next Generation Sequencing.

We aimed to identify differences in mutational status between follicular thyroid adenoma (FTA) and follicular thyroid cancer (FTC). The study included 35 patients with FTA and 35 with FTC. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) samples from thyroidectomy. Next-generation sequencing (NGS) was performed with the 50-gene Ion AmpliSeq Cancer Hotspot Panel v2. Potentially pathogenic mutations were found in 14 (40%) FTA and 24 (69%) FTC patients (OR (95%CI) = 3.27 (1.22-8.75)). The number of mutations was higher in patients with FTC than FTA (p-value = 0.03). SMAD4 and STK11 mutations were present only in patients with FTA, while defects in FBXW7, JAK3, KIT, NRAS, PIK3CA, SMARCB1, and TP53 were detected exclusively in FTC patients. TP53 mutations increased the risk of FTC; OR (95%CI) = 29.24 (1.64-522.00); p-value = 0.001. FLT3-positivity was higher in FTC than in the FTA group (51.4% vs. 28.6%; p-value = 0.051). The presence of FLT3 and TP53 with no RET mutations increased FTC detectability by 17.1%, whereas the absence of FLT3 and TP53 with a presence of RET mutations increased FTA detectability by 5.7%. TP53 and FLT3 are candidate markers for detecting malignancy in follicular lesions. The best model to predict FTA and FTC may consist of FLT3, TP53, and RET mutations considered together.

Correction to: Evaluation of 167 Gene Expression Classifier (GEC) and ThyroSeq v2 Diagnostic Accuracy in the Preoperative Assessment of Indeterminate Thyroid Nodules: Bivariate/HROC Meta-analysis.

The original version of the article unfortunately contained an error.

Evaluation of 167 Gene Expression Classifier (GEC) and ThyroSeq v2 Diagnostic Accuracy in the Preoperative Assessment of Indeterminate Thyroid Nodules: Bivariate/HROC Meta-analysis.

The objective of this meta-analysis was to evaluate the performance of the Gene Expression Classifier (GEC) and ThyroSeq v2 (ThyroSeq) in the preoperative diagnosis of thyroid nodules with indeterminate fine-needle aspiration biopsy results. We searched literature databases from January 2001 to April 2018. The bivariate model analysis was performed to estimate pooled sensitivity, specificity, positive likelihood ratio (LR+), negative likelihood ratio (LR-), positive predictive value (PPV), and negative predictive value (NPV). Pooled data from 1086 nodules with histopathologic confirmation from 16 GEC studies enabled calculation of diagnostic parameters (95% confidence interval): sensitivity 98% (96-99%), specificity 12% (8-20%), PPV 45% (37-53%), and NPV 91% (85-96%). Pooled data from five ThyroSeq studies assessing 459 nodules showed sensitivity of 84% (74-91%), specificity 78% (50-92%), PPV 58% (31-81%), and NPV 93% (89-97%). When both tools were compared, GEC had a significantly higher sensitivity (p = 0.003), while ThyroSeq had a significantly higher specificity (p < 0.001) and accuracy (p = 0.015). Pooled LR+ was higher for ThyroSeq: 3.79 (1.40-10.27) vs. 1.12 (1.05-1.20). Pooled LR- was higher for GEC, 0.20 (0.10-0.39) vs. 0.13 (0.05-0.31). The bivariate summary estimates of sensitivity and specificity for GEC and ThyroSeq and their pooled accuracy showed a superiority of the ThyroSeq test. The GEC with a high sensitivity and NPV may be helpful in ruling out malignancy in cases of indeterminate thyroid nodule cytology. ThyroSeq has a significantly higher specificity and accuracy with an acceptable sensitivity so that it has the potential for use as an all-round test of malignancy of thyroid nodules.

Genomic markers of ovarian adenocarcinoma and its relevancy to the effectiveness of chemotherapy.

Ovarian cancer is the eighth most common cancer and the seventh highest cause of cancer-associated mortality in women worldwide. It is the second highest cause of mortality among female reproductive malignancies. The current standard first-line treatment for advanced ovarian cancer includes a combination of surgical debulking and standard systemic platinum-based chemotherapy with carboplatin and paclitaxel. Although a deeper understanding of this disease has been attained, relapse occurs in 70% of patients 18 months subsequent to the first-line treatment. Therefore, it is crucial to develop a novel drug that effectively affects ovarian cancer, particularly tumors that are resistant to current chemotherapy. The aim of the present study was to identify genes whose expression may be used to predict survival time or prognosis in ovarian cancer patients treated with chemotherapy. Gene or protein expression is an important issue in chemoresistance and survival prediction in ovarian cancer. In the present study, the research group consisted of patients treated at the Surgical Clinic of the Gynecology and Obstetrics Gynecological Clinical Hospital, Poznan University of Medical Sciences (Poznan, Poland) between May 2006 and November 2014. Additional eligibility criteria were a similar severity (International Federation of Gynecolgy and Obstetrics stage III) at the time of diagnosis, treatment undertaken in accordance with the same schedule, and an extremely good response to treatment or a lack of response to treatment. The performance of the OncoScan® assay was evaluated by running the assay on samples obtained from the four patients and by following the recommended protocol outlined in the OncoScan assay manual. The genomic screening using Affymetrix OncoScan Arrays resulted in the identification of large genomic rearrangements across all cancer tissues. In general, chromosome number changes were detected in all examined tissues. The OncoScan arrays enabled the identification of ~100 common somatic mutations. Chemotherapy response in ovarian cancer is extremely complex and challenging to study. The present study identified specific genetic alterations associated with ovarian cancer, but not with response for treatment.

PAX6 3' deletion in a family with aniridia.

BACKGROUND: Aniridia is a congenital panocular malformation defined as iris aplasia or hypoplasia. It can be either isolated or be a part of multiple ocular anomalies such as cataracts, glaucoma, corneal pannus, optic nerve hypoplasia, absence of macular reflex or ectopia lentis. In the majority of cases the disease is caused by mutation in the PAX6 gene. MATERIAL AND METHODS: A Polish family with aniridia was screened for the presence of genomic rearrangements in PAX6, WT1 and the flanking genes by means of multiplex ligation probe amplification (MLPA). MLPA reaction was performed using the P219-B1 PAX6 commercial kit from MRC-Holland. Additionally, the coding sequence of PAX6 gene was sequenced in the proband. Array comparative genomic hybridization analysis was performed using the NimbleGen CGX-12 format. RESULTS: MLPA examination revealed a heterozygous deletion of approximately 0.6 Mb, downstream of PAX6 gene on chromosome 11. Four genes lie in the deleted region. Bi-directional sequencing of 14 exons of the PAX6 gene did not reveal any causative alteration. Microarray analysis confirmed the deletion and determined its size which ranged from 598.87-651.76 kb. CONCLUSIONS: A small subset of aniridia cases is caused by rearrangements of PAX6 neighboring regions, and the so-called "position effect" is considered to be the underlying pathogenic mechanism. Molecular testing of aniridia patients should include sequencing of the PAX6 gene, followed by screening for larger structural abnormalities located on chromosome 11p13. MLPA can be a useful method in molecular testing of aniridia patients.

Apicidin decreases phospholipase C gamma-1 transcript and protein in Hut-78 T lymphoma cells.

Phospholipase C gamma-1 (PLCgamma1) phosphorylation is a key step in intracellular signal transduction in T cells. We used Hut-78 T lymphoma cells to demonstrate the effect of apicidin on cellular levels of the PLCgamma1 molecule. Using reverse-transcription, real-time quantitative PCR and Western blot analysis, we observed that apicidin reduced the PLCgamma1 transcript and protein contents in Hut-78 T lymphoma cells. Our results indicate that protein synthesis appears to be crucial in the apicidin decrease of PLCgamma1 mRNA steadiness. Moreover, we determined that apicidin reduces the half-life of PLCgamma1 mRNAs from approximately 2 to 4h. Since PLCgamma1 is considered a key molecule in signal transduction in T cells, apicidin may be useful in the treatment of some autoimmune diseases in which autoreactive T cells occur.

Occurrence rate and genotype distribution of the JC virus (JCV) in a sample from the Polish population.

The JC virus (JCV) is a common human virus persisting in renal tissue. In immunocompromised individuals it may reactivate and cause progressive multifocal leukoencephalopathy (PML). JCV has also been implicated in cancerogenesis, leading to various brain tumors and cancers of gastrointestinal tract. In this study the JCV excretion in urine of 113 healthy Polish donors was analyzed. A 215-bp region of the viral gene coding for a major capsid protein VP1 was PCR-amplified and detected in 52 individuals (46.0%). The occurrence rate increased with age and was highest in the group of over 60-year-old donors (63.6%). Sequence analysis of the VP1 gene fragment revealed the following distribution of JCV genotypes in the investigated group: 1A, 31 (59.6%); 1B, 13 (25.0%); 2A, 2 (3.8%); and 2C, 6 samples (11.5%). The frequency and distribution of the JCV genotypes in the Polish population resembles that in other European countries, with the most abundant genotype 1 (84.6%). However, while in those countries the second most frequent genotype was usually 4, in the investigated group genotype 4 was not detected.