Genetic predisposition to papillary thyroid cancer

Około 5% zróżnicowanych raków tarczycy wykazuje predyspozycję dziedziczną. Dziedziczny nierdzeniasty rak tarczycy może występować jako składowa niektórych dziedzicznych zespołów nowotworowych, na przykład rodzinnej polipowatości jelit oraz jako rodzinny zróżnicowany rak tarczycy (FNMTC, familial non-medullary thyroid cancer), gdzie najczęściej obserwuje się raka brodawkowatego. Choć predyspozycja dziedziczna do nierdzeniastych raków tarczycy jest dobrze znana, to jednak geny warunkujące jej występowanie nie zostały jeszcze poznane. Wykonane jak dotąd badania zidentyfikowały kilka loci - 1q21, 6q22, 8p23.1-p22 oraz 8q24, jednak wyniki te nie zawsze były jednoznaczne. W niniejszej pracy omówiono rezultaty badań sprzężenia oraz ostatnio uzyskane wyniki badań związku całego genomu (GWAS, genome wide association study) wykonano przez badania polimorfizmu pojedynczego nukleotydu (SNP, single nucleotide polymorphism) z wykorzystaniem techniki mikromacierzy wysokiej gęstości. (Endokrynol Pol 2010; 61 (5): 486-489)Approximately 5% of differentiated thyroid cancers are hereditary. Hereditary non-medullary thyroid cancer may occur as a minor component of familial cancer syndromes (e.g. familial adenomatous polyposis) or as a primary feature (familial non-medullary thyroid cancer [FNMTC]). Among FNMTC, PTC is the most common. Although a hereditary predisposition to non-medullary thyroid cancer is well established, the susceptibility genes are poorly known. Up to now, by linkage analysis using microsatellite markers, several putative loci have been described - 1q21, 6q22, 8p23.1-p22, and 8q24; however, validation studies have been unsuccessful. In the present review we discuss the results of linkage analysis and the most recent results of genome wide association studies (GWAS) with high resolution SNP (single nucleotide polymorphism) arrays. (Pol J Endocrinol 2010; 61 (5): 486-489

Epidermal differentiation complex (locus 1q21) gene expression in head and neck cancer and normal mucosa

Epidermal differentiation complex (EDC) comprises a number of genes associated with human skin diseases including psoriasis, atopic dermatitis and hyperkeratosis. These genes have also been linked to numerous cancers, among them skin, gastric, colorectal, lung, ovarian and renal carcinomas. The involvement of EDC components encoding S100 proteins, small proline-rich proteins (SPRRs) and other genes in the tumorigenesis of head and neck squamous cell cancer (HNSCC) has been previously suggested. The aim of the study was to systematically analyze the expression of EDC components on the transcript level in HNSCC. Tissue specimens from 93 patients with HNC of oral cavity and 87 samples from adjacent or distant grossly normal oral mucosawere analyzed. 48 samples (24 tumor and 24 corresponding surrounding tissue) were hybridized to Affymetrix GeneChip Human 1.0 ST Arrays. For validation by quantitative real-time PCR (QPCR) the total RNA from all 180 samples collected in the study was analyzed with Real-Time PCR system and fluorescent amplicon specific-probes. Additional set of samples from 14 patients with laryngeal carcinoma previously obtained by HG-U133 Plus 2.0 microarray was also included in the analyses. The expression of analyzed EDC genes was heterogeneous. Two transcripts (S100A1 and S100A4) were significantly down-regulated in oral cancer when compared to normal mucosa (0.69 and 0.36-fold change, respectively), showing an opposite pattern of expression to the remaining S100 genes. Significant up-regulation in tumors was found for S100A11, S100A7, LCE3D, S100A3 and S100A2 genes. The increased expression of S100A7 was subsequently validated by QPCR, confirming significant differences. The remaining EDC genes, including all encoding SPRR molecules, did not show any differences between oral cancer and normal mucosa. The observed differences were also assessed in the independent set of laryngeal cancer samples, confirming the role of S100A3 and LCE3D transcripts in HNC. In HNC of oral cavity only one family of EDC genes (S100 proteins) showed significant cancer-related differences. A number of other transcripts which showed altered expression in HNC require further validation.

Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling

Wstęp: Rak pęcherzykowy tarczycy (FTC) jest nowotworem którego podłoże molekularne jest mało zbadane. W podjętej analizie transkryptomuoceniono możliwość dyskryminacji raka i gruczolaka pęcherzykowego tarczycy (FTA) na podstawie badań profilu ekspresjigenów metodą tzw. nienadzorowaną (tzn. na podstawie dominujących źródeł zmienności). Analizę tę prowadzono by sprawdzić czyzłośliwość guza jest rzeczywiście czynnikiem dominującym dla profilu ekspresji genów w nowotworach pęcherzykowych.Materiał i metody: Podstawowy zbiór guzów pęcherzykowych obejmował 52 próbki (27 FTC i 25 FTA), z których wyizolowano całkowityRNA i poddano badaniu na mikromacierzach HG-U133 Plus 2.0. Otrzymany zbiór normalizowano za pomocą RMA i GC-RMA. Identyfikacjigłównych źródeł zmienności dokonano metodą analizy głównych składowych (PCA).Wyniki: Analizę funkcji biologicznej genów przeprowadzono dla pierwszych 6 składowych głównych. Geny skorelowane z pierwsząskładową pozwalały wyodrębnić 2 klastry próbek: jeden złożony głównie z gruczolaków, z wysoką ekspresją między innymi transkryptówtarczycowo-swoistych, drugi zaś, zawierający większość raków, wykazywał zwiększoną, ale heterogenną ekspresję genów związanychz odpowiedzią immunologiczną, a obniżoną ekspresję genów tarczycowych. Geny odpowiedzi immunologicznej stwierdzono wśród transkryptów skorelowanych przebiegiem pierwszej, trzeciej i szóstej głównej składowej; w istotny sposób wpływały one na rozróżnieniemiędzy FTC i FTA.Wnioski: W analizie nienadzorowanej stwierdzono, że złośliwość (inwazyjność) nowotworu pęcherzykowego może być jednymz głównych źródeł zmienności w transkryptomie tych guzów. Jednak, genomiczna odległość między grupami FTC i FTA jest niewielka,a wyodrębnione w analizie nienadzorowanej klastry nakładają się, stąd sama analiza nienadzorowana nie jest wystarczającym narzędziemdo celów klasyfikacji tych guzów.(Endokrynol Pol 2013; 64 (5): 329–334)Introduction: Mechanisms driving the invasiveness of follicular thyroid cancer (FTC) are not fully understood. In our study, we undertookan unsupervised analysis of the set of follicular thyroid tumours (adenomas (FTA) and carcinomas) to verify whether the malignantphenotype influences major sources of variability in our dataset.Material and methods: The core set of samples consisted of 52 tumours (27 FTC, 25 FTA). Total RNA was analysed by oligonucleotidemicroarray (HG-U133 Plus 2.0). Principal Component Analysis (PCA) was applied as a main method of unsupervised analysis.Results: An analysis of biological character of genes correlated to the first six PCs was performed. When genes correlated to the first PCwere used to cluster FTC and FTA, they appeared in two branches; one, relatively enriched in adenomas, with homogenous expressionof subset of genes, and the other containing mainly carcinomas, with down-regulation of these genes and heterogeneous up-regulationin a smaller cluster of transcripts. Genes highly up-regulated in adenomas included some thyroid-specific transcripts. The second clusterof genes, up-regulated in carcinomas, contained mainly immunity-related transcripts. Immune response genes were found in the first,third and sixth principal components, improving the discrimination between carcinomas and adenomas.Conclusions: Our unsupervised analysis indicates that invasiveness of follicular tumours might be considered as the major source of variabilityin transcriptome analysis. However, the distance between both groups is small and the clusters are overlapping, thus, unsupervisedanalysis is not sufficient to properly classify them. (Endokrynol Pol 2013; 64 (5): 328–334

Wiek zachorowania i płeć jako czynniki modyfikujące związek polimorfizmów zlokalizowanych na chromosomie 9q22 i 14q13 z rakiem brodawkowatym tarczycy

Introduction: Papillary thyroid cancer (PTC) shows familial occurrence, and some susceptibility single nucleotide polymorphisms (SNPs) have been identified in FOXE1 and near the NKX2-1 locus. The aim of our study was to analyse the association of PTC risk with SNPs in FOXE1 (rs965513, rs1867277, rs1443434) and near the NKX2-1 locus (rs944289) in a Polish population, and, in the second step, the interac­tion between SNPs and patient-related factors (age at diagnosis and gender). Material and methods: A total of 2243 DNA samples from PTC patients and 1160 controls were included in the study. The SNP analysis was performed with the allelic discrimination technique. Results: There were significant associations of all SNPs with PTC (rs965513 odds ratio [OR] = 1.72, p = 8 × 10-7; rs1867277 OR = 1.59, p = 1 × 10-6; rs1443434 OR = 1.53, p = 1 × 10-5; rs944289 OR = 1.52, p = 4 × 10-5). Logistic regression analysis revealed an increased PTC risk in the interaction of rs944289 with age at diagnosis (OR = 1.01 per year, p = 6 × 10-4) and a decreased PTC risk in the interaction of male gender with the GGT FOXE1 protective haplotype (OR = 0.69, p = 0.01). Conclusions: the association between PTC and all analysed SNPs was confirmed. It was also shown that patient-related factors modify the predisposition to PTC by increasing the risk for rs944289 per year of age, and by enhancing the protective effect of the FOXE1 GGT haplotype in men.Wstęp: Brodawkowaty rak tarczycy należy do grupy nowotworów litych, w których uwarunkowanie genetyczne ogrywa istotną rolę. Geny odpowiedzialne za predyspozycje do raka brodawkowatego nie są dobrze znane, choć polimorfizmy rs965513 i rs944289 obecnie są uznanymi czynnikami ryzyka. Celem pracy była analiza związku polimorfizmów znajdujących się w 9q22 w locus genu FOXE1 (rs965513, rs1867277, rs1443434) oraz w 14q13 w pobliżu genu NKX2-1 (rs944289) z rakiem brodawkowatym tarczycy oraz ocena wpływu czynników zależnych od pacjenta (wieku zachorowania i płci). Materiał i metody. Materiał obejmował 2243 próbek DNA izolowanych z limfocytów krwi obwodowej pacjentów z rakiem brodawkowatym i 1160 próbek DNA pochodzących od osób zdrowych, stanowiących grupę kontrolną (liczba analizowanych próbek różniła się w zależności od polimorfizmu). Badania wykonano w aparacie 7900HT Fast Real-Time PCR System firmy Applied Biosystems techniką dyskryminacji alleli. Wyniki. Znamienny związek z rakiem brodawkowatym wykazywały wszystkie analizowane polimorfizmy (dla rs965513 wartość OR wynosiła 1,72, p = 8 × 10-7; dla rs1867277 OR = 1,58, p = 1 × 10-6; dla rs1443434 OR = 1,53, p = 1 × 10-5; rs944289 OR = 1,52, p = 4 × 10-5). Analiza regresji logistycznej wykazała wzrost ryzyka raka brodawkowatego wraz z wiekiem dla polimorfizmu rs944289 (OR = 1.01 na rok, p = 6 × 10-4) oraz obniżenie ryzyka zachorowania dla haplotypu GGT genu FOXE1 u mężczyzn (OR = 0,69, p = 0,01). Wnioski. Potwierdzony został związek badanych polimorfizmów z rakiem brodawkowatym tarczycy w populacji polskiej. Wykazano modyfikujący wpływ wieku zachorowania i płci męskiej na ryzyko zachorowania uwarunkowane genetycznie

Ratio of proliferation markers and HSP90 gene expression as a predictor of pathological complete response in breast cancer neoadjuvant chemotherapy

Introduction. Prediction of response to preoperative breast cancer chemotherapy may offer a substantial optimization of medical management of this disease. The most efficient prediction would be done a priori, before the start of chemotherapy and based on the biological features of patient and tumor. Numerous markers have been proposed but none of them has been applied as a routine. The role of MKI67 and HSP90 expression has been recently suggested to predict treatment sensitivity in HER2-positive breast cancer. The aim of this study was to validate the utility of proliferation based markers (MKI67 and CDK1) and heat shock proteins (namely HSP90) to predict response to chemotherapy in cohort of breast cancer patients treated preoperatively. Material and methods. Ninety-three patients with breast cancer, all females, mean age 42.2 years, among them 32% T1-T2 patients, 49% T3 patients and 13% with T4 tumor stage, 27% N0, 42% N1, 16% N2, 15% N3 were subjected to initial chemotherapy. The majority of patients (86%) received anthracycline and taxane chemotherapy. Among the patients there were 9 individuals with metastatic disease (M1) at initial presentation, and 11 patients were not treated surgically after initial chemotherapy (no sufficient disease response). From 82 patients operated on, 20 patients (24%) showed pathological complete response (pCR), while in 62 patients there was no pCR. 42% of patients were hormone-sensitive HER2-negative, 20% hormone-sensitive HER2-positive, 9% only HER-positive and 29% with triple negative breast cancer. Four gene transcripts (MKI67, cyclin-dependent kinase 1 [CDK1], heat shock proteins HSP90AA1 and HSP- 90AB1) were analyzed in total RNA isolated from single core obtained during preoperative core needle biopsy by quantitative real-time PCR with fluorescent probes (Universal Probe Library, Roche). Results were normalized to the panel of reference genes. Results. There were no statistically significant differences in MKI67 and CDK1 expression between pCR and no pCR groups (p = 0.099 and 0.35, respectively), although the median expression of both genes was slightly higher in pCR group. In contrast, both HSP90AA1 and HSP90AB1 transcripts showed decreased expression in pCR group (medians 0.77 and 0.55) when compared to no p CR group (median 0.86 and 0.73), statistically significant for HSP90AA1 (p = 0.031) and of borderline significance for HSP90AB1 (p = 0.054). The most significant predictor of pCR was the ratio of CDK1 transcript to HSP90AA transcript. This ratio was significantly higher in CR group (median 0.99) than in no CR group (median 0.68, p = 0.0023), and showed a potential diagnostic utility (area under receiver operating characteristic [ROC] curve 0.72). Conclusions. HSP90AA1 and AB1 genes exhibit low expression in breast cancers highly sensitive to chemotherapy and may indicate the patients with higher probability of pathological complete response. The ratio of HSP90AA1 to proliferation-related markers (CDK1 or MKI67) may be even better predictor of pCR chance, with higher expression of proliferation genes and lower stress response in patients sensitive to chemotherapy

Experimental design.

<p>Cells were subjected to cycling (interchanging periods of 1% and ambient oxygen), chronic hypoxia (constant 1% oxygen) or control conditions (ambient oxygen) for 72 hours. The scheme predominantly shows the time scale of cycling hypoxia, which consisted of the following periods of hypoxia (1% oxygen) and reoxygenation (21% oxygen): 1%–4 hours, 21%–4 hours, followed by two cycles of 1%–12 hours, 21%–4 hours, 1%–4 hours, 21%–4 hours, followed by 4 hours of reoxygenation.</p

Global Gene Expression Profiling in Three Tumor Cell Lines Subjected to Experimental Cycling and Chronic Hypoxia

<div><p>Hypoxia is one of the most important features of the tumor microenvironment, exerting an adverse effect on tumor aggressiveness and patient prognosis. Two types of hypoxia may occur within the tumor mass, chronic (prolonged) and cycling (transient, intermittent) hypoxia. Cycling hypoxia has been shown to induce aggressive tumor cell phenotype and radioresistance more significantly than chronic hypoxia, though little is known about the molecular mechanisms underlying this phenomenon. The aim of this study was to delineate the molecular response to both types of hypoxia induced experimentally in tumor cells, with a focus on cycling hypoxia. We analyzed <i>in</i><i>vitro</i> gene expression profile in three human cancer cell lines (melanoma, ovarian cancer, and prostate cancer) exposed to experimental chronic or transient hypoxia conditions. As expected, the cell-type specific variability in response to hypoxia was significant. However, the expression of 240 probe sets was altered in all 3 cell lines. We found that gene expression profiles induced by both types of hypoxia were qualitatively similar and strongly depend on the cell type. Cycling hypoxia altered the expression of fewer genes than chronic hypoxia (6,132 <i>vs.</i> 8,635 probe sets, FDR adjusted p<0.05), and with lower fold changes. However, the expression of some of these genes was significantly more affected by cycling hypoxia than by prolonged hypoxia, such as <i>IL8, PLAU,</i> and epidermal growth factor (EGF) pathway-related genes (<i>AREG, HBEGF,</i> and <i>EPHA2</i>). These transcripts were, in most cases, validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Our results indicate that experimental cycling hypoxia exerts similar, although less intense effects, on the examined cancer cell lines than its chronic counterpart. Nonetheless, we identified genes and molecular pathways that seem to be preferentially regulated by cyclic hypoxia.</p></div

Gene expression from bronchoscopy obtained tumour samples as a predictor of outcome in advanced inoperable lung cancer.

BACKGROUND: Several studies have shown the prognostic and predictive potential of molecular markers in combined therapy for lung cancer. Most of them referred, however, to operable early stage NSCLC. The aim of the present study is to correlate the expression of multiple mRNA markers in bronchoscopy obtained cancer specimens with clinical outcome of advanced lung cancer. METHODS: Bronchoscopy cancer specimens were taken from 123 patients with radiological diagnosis of advanced lung tumor. Out of 123 patients 50 were diagnosed with squamous cell cancer, 17 with adenocarcinoma, 12 with NOS, 32 with SCLC and one with large cell neuroendocrinal cancer. In 11 patients other tumours were diagnosed. The group was heterogeneous with respect to clinical stage, performance of the patients and treatment. Quantitative real time PCR was carried out by ABI 7900 HT machine, with Universal Probe Library (Roche) fluorescent probes. The genes selected for the analysis were ERCC1, EGFR, BRCA1, CSF1, CA9, DUSP6, STAT1, ERBB3, MMD, FN1, and CDKN1B. RESULTS: More than 50 ng of RNA (the amount considered sufficient for the analysis) was isolated in 82 out of 112 lung cancer specimens (73%), including 60/80 (75.0%) of NSCLC specimens and 22/32 (68,7%) of SCLC samples. The highest Cohen's κ coefficient for discrimination between small cell, squamous cell and adenocarcinoma was found for CDKN1B, CSF and EGFR1 (κ = 0.177, p = 0.0041). A multivariate Cox regression model has shown a significant impact of clinical stage (p<0.001, RR = 4.19), ERCC1 (p = 0.01, RR = 0.43) and CA9 (p = 0.03, RR = 2.11) expression on overall survival in a group of 60 patients with NSCLC. CONCLUSION: These results show the feasibility of multiple gene expression analysis in bronchoscopy obtained cancer specimens as prognostic markers in radiotherapy and chemotherapy for advanced lung cancer. A limiting factor was relatively high proportion of samples from which sufficient amount of RNA could not be isolated