Bartlomiej Budny

FOXE1 Polyalanine Tract Length Polymorphism in Patients with Thyroid Hemiagenesis and Subjects with Normal Thyroid

Background/Aims: Recent studies have pointed to the correlation between FOXE1 polyalanine tract (FOXE1-polyAla) length polymorphism and genetic susceptibility to thyroid dysgenesis causing congenital hypothyroidism. The objective of this study was a first assessment of the role of FOXE1-polyAla expansion in the genetic background of thyroid hemiagenesis (TH). Methods: The group studied consisted of 40 patients with TH, including 6 familial cases and a control group of 89 subjects with a normal thyroid. The polyAla tract and flanking sequence of FOXE1 was amplified using conventional PCR. Subsequently, capillary electrophoresis was performed to estimate the length of products. Results: A short variant of FOXE1-polyAla, containing 12 alanines, was present in 5 control subjects (5.6%), but was not found in TH. The incidence of longer variants (≧16 codons) of FOXE1-polyAla was significantly higher in patients with the familial form of TH in comparison to those with sporadic TH (p = 0.003) and controls (p = 0.005). Conclusions: There is high polymorphic variability of FOXE1-polyAla in both groups. Shorter variants of FOXE1-polyAla are underrepresented in subjects with familial TH. Therefore, FOXE1-polyAla tract expansion may contribute to the molecular background of familial but not sporadic forms of TH. Further studies are still required to confirm such findings.

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.

Mutations in proteasome-related genes are associated with thyroid hemiagenesis

PurposeHuman thyroid development is a complex and still unexplained process. Thyroid hemiagenesis is a congenital anomaly, where one of the thyroid lobes fails to develop. In the majority of patients with thyroid hemiagenesis, the genetic background remains unknown. The aim of the study was to search for novel genetic contributors to the etiology of thyroid hemiagenesis.MethodsA cohort of 34 sporadic patients diagnosed with thyroid hemiagenesis and one three-generation family were subjected to comprehensive genomic examination. Initially, targeted screening of associated transcription factors, known to be linked to thyroid development, was performed. As a next step, genomic examinations were applied using high-resolution microarrays, whereas for the thyroid hemiagenesis family, additionally the whole exome sequencing was performed.ResultsScreening of transcription factors revealed no causative mutations in the studied cohort. Genomic examinations revealed the presence of four recurrent defects (three deletions and one duplication) affecting highly conservative proteasome genes PSMA1, PSMA3, and PSMD3. In a thyroid hemiagenesis family a splice site mutation in a proteasome gene PSMD2 (c.612T > C cDNA.1170T > C, g.3271T > C) was found in both affected mother and daughter.ConclusionsOur results shed a new light on etiology of thyroid hemiagenesis, so far suspected to be linked only to mutations in the genes directly involved in the thyroid development. We demonstrated, for the first time, that genomic alterations in proteasome-associated genes co-occur in patients presenting this developmental anomaly.

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.

Genomic mapping of pathways in endometrial adenocarcinoma and a gastrointestinal stromal tumor located in Meckel's diverticulum

The present study reports the case of a 71-year-old female patient diagnosed with endometrial adenocarcinoma, which was confirmed by histopathology. In the course of performing an elective hysterectomy with adnexa removal, a solid tumor located in Meckels diverticulum (MD) was identified and excised. Due to the unique nature of the lesion, the tumor tissue underwent broad mapping of any genomic alterations once the histopathological examination was completed. The genetic testing was conducted using a high-resolution microarray and resulted in the identification of 45 genomic abnormalities, including 4 chromosomal aneuploidies. Within those regions, alterations of 87 known cancer genes were assigned. The involvement of v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog gene alteration was noted to be a key player for triggering gastrointestinal stromal tumor transformation for this unusual case. A total of 12 genes, showing mutual interaction in different cancer types or involved in diverse cellular processes, were identified. These reported data may shed light on the carcinogenesis of a rare MD tumor.

Modifying impact of RET gene haplotypes on medullary thyroid carcinoma clinical course

The clinical course of medullary thyroid carcinoma (MTC) associated with the MEN2A syndrome as well as of sporadic MTC shows considerable heterogeneity. The disease picture varies not only between the same RET proto-oncogene mutation carriers but also among sporadic MTC patients with no RET germinal mutations, which suggests the involvement of additional modulators of the disease. However, genetic factors responsible for this heterogeneity of the MTC clinical course still remain unknown. The aim of this study was to determine if polymorphic variants or specific haplotypes of the RET gene may modify the MTC clinical course. We genotyped the following loci: c.73+9277T>C, c.135G>A, c.1296A>G, c.2071G>A, c.2307T>C, c.2508C>T and c.2712C>G in 142 MTC patients and controls. We demonstrated considerable differences in the genotypes distribution within c.73+9277T>C, c.135G>A and c.2307T>C loci Our results show that the c.73+9277T variant associated with a decreased activity of the MCS+9.7 RET enhancer is rare in hereditary MTC patients with primary hyperparathyroidism, and thus, may influence the MTC clinical picture. The decreased activity of the RET promoter enhancer reduces RET expression level and may counterbalance the activating mutation in this gene. Frequent co-occurrence of the c.73+9277T allele with p.E768D, p.Y791F, p.V804M or p.R844Q RET mutations may be associated with their attenuation and milder clinical picture of the disease. Haplotypes analysis showed that C-G-A-G-T-(C)-C (c.73+9277T>C - c.135G>A - c.1296A>G - c.2071G>A - c.2307T>G - (c.2508C>T) - c.2712C>G) alleles combination predisposes to pheochromocytomas and primary hyperparathyroidism. We consider that RET haplotypes defining may become an auxiliary diagnostic tool in MTC patients.

VEGF-C Is a Thyroid Marker of Malignancy Superior to VEGF-A in the Differential Diagnostics of Thyroid Lesions

Introduction Thyroid nodular goiter is one of the most common medical conditions affecting even over a half of adult population. The risk of malignancy is rather small but noticeable–estimated by numerous studies to be about 3–10%. The definite differentiation between benign and malignant ones is a vital issue in endocrine practice. The aim of the current study was to assess the expression of vascular endothelial growth factor A (VEGF-A) and VEGF-C on the mRNA level in FNAB washouts in case of benign and malignant thyroid nodules and to evaluate the diagnostic value of these markers of malignancy. Materials and Methods Patients undergoing fine-needle aspiration biopsy (FNAB) in our department between January 2013 and May 2014 were included. In case of all patients who gave the written consent, after ultrasonography (US) and fine-needle aspiration biopsy (FNAB) performed as routine medical procedure the needle was flushed with RNA Later solution, the washouts were frozen in -80 Celsius degrees. Expression of VEGF-A and VEGF-C and GADPH (reference gene) was assessed in washouts on the mRNA level using the real-time PCR technique. Probes of patients who underwent subsequent thyroidectomy and were diagnosed with differentiated thyroid cancer (DTC; proved by post-surgical histopathology) were analyzed. Similar number of patients with benign cytology were randomly selected to be a control group. Results Thirty one DTCs and 28 benign thyroid lesions were analyzed. Expression of VEGF-A was insignificantly higher in patients with DTCs (p = 0.13). Expression of VEGF-C was significantly higher in patients with DTC. The relative expression of VEGF-C (in comparison with GAPDH) was 0.0049 for DTCs and 0.00070 for benign lesions, medians – 0.0036 and 0.000024 respectively (p<0.0001). Conclusions Measurement of expression VEGF-C on the mRNA level in washouts from FNAB is more useful than more commonly investigated VEGF-A. Measurement of VEGF-C in FNAB washouts do not allow for fully reliable differentiation of benign and malignant thyroid nodules and should be interpreted carefully. Further studies on larger groups are indicated. However, measurement of VEGF-C on mRNA level can bring important information without exposing patient for additional risk and invasive procedures.

CCND1 gene polymorphic variants in patients with differentiated thyroid carcinoma

Alterations in the CCND1 gene affect the cell cycle and are frequently observed in a variety of cancers. While the most frequent mutations that occur in thyroid tumor tissue have been characterized, the genetic factors that predispose individuals to differentiated thyroid cancer (DTC) remain to be elucidated. The present study examined whether the CCND1 c.723G>A (rs9344; p.Pro241=) and c.669C>T (rs3862792; p.Phe223=) variants have an impact on DTC susceptibility. A cohort consisting of 652 patients diagnosed with DTC were analyzed and comapred with a reference group of 799 subjects from the general population. Pyrosequencing was used as the genotyping technique. In order to determine the statistical significance of differences observed in the genotypic and allelic frequencies between the compared groups, GraphPad Prism 4 was used. At the rs9344 locus in the DTC patients, a higher frequency of allele A [P=0.032; odds ratio (OR), 1.18; 95% confidence interval (CI), 1.014–1.361] and the AA homozygous genotype (P=0.028; OR, 1.41; 95% CI, 1.059–1.989) was observed compared with the control population group. The differences were stronger for papillary carcinomas (OR 1.45; 95% CI, 1.059–1.989), but were not significant in follicular tumors. No statistically significant differences were noted in the frequency of genotypes or alleles at the rs3862792 locus in the examined groups. The present findings indicate that the c.723A variant of the CCDN1 gene may be a susceptibility low penetrance allele in the development of papillary thyroid cancer in the population studied, however it does not impact on multifocality, metastatic ability or age at diagnosis. A cumulative effect of the analyzed CCND1 gene variants was also excluded.

RET gene mutations spectrum in patients with medullary thyroid carcinoma (MTC) from Great Poland region

Medullary thyroid carcinoma (MTC) is an epithelial tumor of the thyroid gland, derived from thyroid parafollicular C cells and represents approximately 4% of thyroid carcinomas. In 50 % of patients, MTC is diagnosed at an advanced stage. Due to a lack of TSH receptors on C-cells surface MTC does not respond to suppression therapy with TSH and radio-iodine treatment, and thereby it conferring worse outcomes overall. 5-year survival rates range from 75% for patients with stage III disease to 40% for patients with stage IV disease. MTC is associated with one of three clinically different, inherited endocrine syndromes caused by germline mutations in the RET gene. It encodes a transmembrane receptor tyrosine kinase which is expressed in cells derived from the neural crest. Activating mutations in the RET gene are detected in the majority (95%) patients with an inherited medullary thyroid carcinoma and approximately 30-50% of cases without family history. Familial medullary thyroid carcinomas (FMTCs) are associated with mutations in codons 609, 611, 618, and 620 (exon 10), as well as codon 768 (exon 13) and codon 804 (exon 14). In FMTC patients, MTC is often the only clinical symptom. Multiple endocrine neoplasia (MEN) 2A is associated in the most cases, with RET gene mutations in codons 609, 611, 618, and 620, as well as in codon 634. Patients with MEN2A typically have MTC, pheochromocytoma, and primary hyperparathyroidism (PHPT). Patients diagnosed with MEN 2B present the most aggressive type of MTC, pheochromocytoma but not PHPT, musculoskeletal abnormalities and other developmental defects. This syndrome is associated mostly with mutation in codon 918 in exon 16. Here we report the RET gene mutations spectrum in a group from Great Poland (Wielkopolska) region. Molecular analysis was performed for 304 individuals: patients with diagnosed MTC or apparent MEN 2A syndrome and first and second degree relatives. Studied group included also one family with MEN 2B syndrome. All patients were diagnosed in the Department of Endocrinology, Metabolism, and Internal Diseases of the Poznan University of Medical Sciences. We screened RET gene exons: 10, 11, 13-16 using pyrosequencing for specific codons and HRMA technique followed by Sanger sequencing. Identification of RET gene mutations was possible for 50 patients (32%). This group included 12 family cases and in 6 subjected individuals diagnosis were possible before cancer occurring. In a group of 106 (68%) MTC patients we did not detect mutations in analyzed RET gene regions. The most frequent was missense substitutions occurring in codon 634 (72%): C634R (58%), C634G (10%) and C634Y (4%). Surprisingly, in our group of patients we did not detect mutations in exon 10, as they are frequent in other populations. However, we observed 3 different mutations in exon 13 (18%) and in exon 14 (6%). In four unrelated patients with negative family history we detected missense change Y791F, which is associated with late onset MTC, but interestingly one of patients was homozygous and presented more aggressive course of the disease (characterized with multifocality and onset in the moment of diagnosis at 47 years of age). In MEN 2B family, M918A mutation was detected. Due to the fact, that we observe a different mutational spectrum in our patients, we consider more extensive analysis of the RET gene as reasonable.