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

Właściwości fizyczne stopów Ti-Zr-X (X=Mn, Co, Ni, Cu)

Promotor: Łukasz Gondek.Recenzent: Andrzej Szytuła, Andrzej Budziak.Niepublikowana praca doktorska.Tyt. z ekranu tyt.Praca doktorska. Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydział Fizyki i Informatyki Stosowanej, 2015.Zawiera bibliogr.Dostępna również w wersji drukowanej.Tryb dostępu: Internet.Synteza materiałów poprzez stapianie mechaniczne, opis metody, uzyskiwane materiały, materiały amorficzne, materiały kwazikrystaliczne, materiały krystaliczne, przegląd właściwości materiałów mielonych, opis aparatury technik badawczych, synteza, proszkowa dyfrakcja rentgenowska, dyfrakcja neutronowa, badania magnetyczne, badanie absorpcji wodoru–aparat Sievertsa, badanie składu metodą XRF, mikroskopia elektronowa, opis wyników, Ti45Zr38Ni17, Ti45Zr38Ni17-xMnx dla x = 2, 4, Ti45Zr38Ni17-xFex dla x = 4, 8, Ti45Zr38Ni13Co4, Ti45Zr38Ni9Cu8, Ti45Zr38Cu1

Electronic nose with polymer-composite sensors for monitoring fungal deterioration of stored rapeseed

Investigations were performed to examine the possibility of using an electronic nose to monitor development of fungal microflora during the first eighteen days of rapeseed storage. The Cyranose 320 device manufactured by Sensigent was used to analyse volatile organic compounds. Each sample of infected material was divided into three parts and the degree of spoilage was measured in three ways: analysis of colony forming units, determination of ergosterol content, and measurement of volatile organic compounds with the e-nose. Principal component analysis was performed on the generated patterns of signals and six groups of different spoilage levels were isolated. An analysis of sensorgrams for a few sensors with a strong signal for each group of rapeseed spoilage was performed. The ratio of the association time to the steady state was calculated. This ratio was different for the low level and the highest level of ergosterol and colony forming units. The results have shown that the e-nose can be a useful tool for quick estimation of the degree of rapeseed spoilage

The Role of CXCL16 in the Pathogenesis of Cancer and Other Diseases

CXCL16 is a chemotactic cytokine belonging to the α-chemokine subfamily. It plays a significant role in the progression of cancer, as well as the course of atherosclerosis, renal fibrosis, and non-alcoholic fatty liver disease (NAFLD). Since there has been no review paper discussing the importance of this chemokine in various diseases, we have collected all available knowledge about CXCL16 in this review. In the first part of the paper, we discuss background information about CXCL16 and its receptor, CXCR6. Next, we focus on the importance of CXCL16 in a variety of diseases, with an emphasis on cancer. We discuss the role of CXCL16 in tumor cell proliferation, migration, invasion, and metastasis. Next, we describe the role of CXCL16 in the tumor microenvironment, including involvement in angiogenesis, and its significance in tumor-associated cells (cancer associated fibroblasts (CAF), microglia, tumor-associated macrophages (TAM), tumor-associated neutrophils (TAN), mesenchymal stem cells (MSC), myeloid suppressor cells (MDSC), and regulatory T cells (Treg)). Finally, we focus on the antitumor properties of CXCL16, which are mainly caused by natural killer T (NKT) cells. At the end of the article, we summarize the importance of CXCL16 in cancer therapy

Studies on water transport in quasi two-dimensional porous systems using neutron radiography

The spontaneous wetting and drying of flat porous samples of linen, cotton and synthetic textiles were studied using dynamic neutron radiography (DNR). The progress of the wetting process of the media was delineated from the obtained neutron dynamical radiography images. The results of the investigation reveal a non-classical behaviour of kinetics of wicking of these materials. The character of the wetting kinetics is discussed in terms of the fractal character of the tortuosity of fabric capillaries

Sub-Perception and Supra-Perception Spinal Cord Stimulation in Chronic Pain Syndrome: A Randomized, Semi-Double-Blind, Crossover, Placebo-Controlled Trial

Background: The introduction of modern sub-perception modalities has improved the efficacy of spinal cord stimulation (SCS) in refractory pain syndromes of the trunk and lower limbs. The objective of this study was to evaluate the effectiveness of low and high frequency SCS among patients with chronic pain. Material and methods: A randomised, semi-double-blind, placebo controlled, four period (4 × 2 weeks) crossover trial was conducted from August 2018 to January 2020. Eighteen patients with SCS due to failed back surgery syndrome and/or complex regional pain syndrome were randomised to four treatment arms without washout periods: (1) low frequency (40-60 Hz), (2) 1 kHz, (3) clustered tonic, and (4) sham SCS (i.e., placebo). The primary outcome was pain scores measured by visual analogue scale (VAS) preoperatively and during subsequent treatment arms. Results: Pain scores (VAS) reported during the preoperative period was M (SD) = 8.13 (0.99). There was a 50% reduction in pain reported in the low frequency tonic treatment group (M (SD) = 4.18 (1.76)), a 37% reduction in the 1 kHz treatment group (M (SD) = 5.17 (1.4)), a 34% reduction in the clustered tonic settings group (M (SD) = 5.27 (1.33)), and a 34% reduction in the sham stimulation group (M (SD) = 5.42 (1.22)). The reduction in pain from the preoperative period to the treatment period was significant in each treatment group (p < 0.001). Overall, these reductions were of comparable magnitude between treatments. However, the modality most preferred by patients was low frequency (55% or 10 patients). Conclusions: The pain-relieving effects of SCS reached significance and were comparable across all modes of stimulation including sham. Sub-perception stimulation was not superior to supra-perception. SCS was characterised by a high degree of placebo effect. No evidence of carryover effect was observed between subsequent treatments. Contemporary neuromodulation procedures should be tailored to the individual preferences of patients

Gene Expression (mRNA) Markers for Differentiating between Malignant and Benign Follicular Thyroid Tumours

Distinguishing between follicular thyroid cancer (FTC) and follicular thyroid adenoma (FTA) constitutes a long-standing diagnostic problem resulting in equivocal histopathological diagnoses. There is therefore a need for additional molecular markers. To identify molecular differences between FTC and FTA, we analyzed the gene expression microarray data of 52 follicular neoplasms. We also performed a meta-analysis involving 14 studies employing high throughput methods (365 follicular neoplasms analyzed). Based on these two analyses, we selected 18 genes differentially expressed between FTA and FTC. We validated them by quantitative real-time polymerase chain reaction (qRT-PCR) in an independent set of 71 follicular neoplasms from formaldehyde-fixed paraffin embedded (FFPE) tissue material. We confirmed differential expression for 7 genes (CPQ, PLVAP, TFF3, ACVRL1, ZFYVE21, FAM189A2, and CLEC3B). Finally, we created a classifier that distinguished between FTC and FTA with an accuracy of 78%, sensitivity of 76%, and specificity of 80%, based on the expression of 4 genes (CPQ, PLVAP, TFF3, ACVRL1). In our study, we have demonstrated that meta-analysis is a valuable method for selecting possible molecular markers. Based on our results, we conclude that there might exist a plausible limit of gene classifier accuracy of approximately 80%, when follicular tumors are discriminated based on formalin-fixed postoperative material

Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma—Do They Exist?

Molecular mechanisms of distant metastases (M1) in papillary thyroid cancer (PTC) are poorly understood. We attempted to analyze the gene expression profile in PTC primary tumors to seek the genes associated with M1 status and characterize their molecular function. One hundred and twenty-three patients, including 36 M1 cases, were subjected to transcriptome oligonucleotide microarray analyses: (set A—U133, set B—HG 1.0 ST) at transcript and gene group level (limma, gene set enrichment analysis (GSEA)). An additional independent set of 63 PTCs, including 9 M1 cases, was used to validate results by qPCR. The analysis on dataset A detected eleven transcripts showing significant differences in expression between metastatic and non-metastatic PTC. These genes were validated on microarray dataset B. The differential expression was positively confirmed for only two genes: IGFBP3, (most significant) and ECM1. However, when analyzed on an independent dataset by qPCR, the IGFBP3 gene showed no differences in expression. Gene group analysis showed differences mainly among immune-related transcripts, indicating the potential influence of tumor immune infiltration or signal within the primary tumor. The differences in gene expression profile between metastatic and non-metastatic PTC, if they exist, are subtle and potentially detectable only in large datasets

The average tumour size in <i>BRAF</i> positive patients was significantly higher than in the wild-type group (p = 0.04).

<p>The average tumour size in <i>BRAF</i> positive patients was significantly higher than in the wild-type group (p = 0.04).</p