Expression analysis of long non-coding RNAs in a renal ischemia-reperfusion injury model

Abstract Purpose: To investigate the long non-coding RNAs (lncRNAs) profile on renal ischemia reperfusion in a mouse model. Methods: Microarray analysis was used to study the expression of misregulated lncRNA in a mouse model of renal ischemia reperfusion(I/R) with long ischemia time. Quantitative real-time PCR (qPCR) was used to verify the expression of selected lncRNAs and mRNAs.The potential functions of the lncRNA was analyzed by bioinformatics tools and databases. Results: Kidney function was impaired in I/R group compared to the normal group. Analysis showed that a total of 2267 lncRNAs and 2341 messenger RNAs (mRNAs) were significantly expressed in I/R group (≥2.0-fold, p < 0.05).The qPCR result showed that lncRNAs and mRNAs expression were consistent with the microarray analysis. The co-expression network profile analysis based on five validated lncRNAs and 203 interacted mRNAs showed it existed a total of 208 nodes and 333 connections. The GO and KEEG pathway analysis results showed that multiple lncRNAs are involved the mechanism of I/R. Conclusion: Multiple lncRNAs are involved in the mechanism of I/R.These analysis results will help us to further understand the mechanism of I/R and promote the new methods targeted at lncRNA to improve I/R injury.

Carbonic Anhydrase IX is Not a Predictor of Outcomes in Non-Metastatic Clear Cell Renal Cell Carcinoma - A Digital Analysis of Tissue Microarray

Introduction The knowledge about the molecular biology of clear cell renal cell carcinoma (ccRCC) is evolving, and Carbonic Anhydrase type IX (CA-IX) has emerged as a potential prognostic marker in this challenging disease. However, most of the literature about CA-IX on ccRCC comes from series on metastatic cancer, with a lack of series on non-metastatic cancer. The objective is to evaluate the expression of CA-IX in a cohort of non-metastatic ccRCC, correlating with 1) overall survival, and 2) with established prognostic parameters (T stage, tumor size, Fuhrman nuclear grade, microvascular invasion and peri-renal fat invasion). Materials and Methods This is a retrospective cohort study. We evaluated 95 patients with non-metastatic clear cell renal cell carcinoma, as to the expression of CA-IX. The analyzed parameters where: overall survival (OS), TNM stage, tumor size (TS), Fuhrman nuclear grade (FNG), microvascular invasion (MVI), peri-renal fat invasion (PFI). We utilized a custom built tissue microarray, and the immunoexpression was digitally quantified using the Photoshop® software. Results: Th e mean follow-up time was 7.9 years (range 1.9 to 19.5 years). The analysis of CA-IX expression against the selected prognostic parameters showed no correlation. The results are as follows: Overall survival (p = 0.790); T stage (p = 0.179); tumor size (p = 0.143); grouped Fuhrman nuclear grade (p = 0.598); microvascular invasion (p = 0.685), and peri-renal fat invasion (p = 0.104). Conclusion Carbonic anhydrase type IX expression does not correlate with overall survival and conventional prognostic parameters in non-metastatic clear cell renal cell carcinoma. .

A novel tissue microarray instrumentation:The HT-1 tissue microarrayer.

Background: Tissue microarray (TMA) is a novel and useful tool to efficiently analyze gene expression in histological tissues. Aim: Cost-efficient and easy to use automated tissue arrayers will provide a better instrumentation to generate TMAs. Thus, we designed and produced our tissue microarrayer to meet these needs. Materials and Methods: The HT-1 tissue microarrayer we designed and manufactured consists primarily of four parts, including an instrument to make array pores for the recipient paraffin blocks, a punch needle, an instrument for negative-pressure embedding, and a special manipulator. By using the HT-1, 14 different TMAs were made to accommodate 312 cases of tissues and TMA sections were tested by hematoxylin-eosin (H&E) staining, in situ hybridization, and immunohistochemistry. Results: Expand: Hematoxylin and eosin staining showed that the tissue cylinders were similar, even, and in order on the slides. Most importantly, the HT-1 microarrayer can make array pores in the recipient paraffin block with a single application in seconds. The HT-1 also contains a unique negative pressure system for embedding TMA blocks. In addition, HT-1 can make tissue cylinders with the same levels and depth for equally embedded and sectioning. Conclusions: The HT-1 tissue microarrayer is a device that is simple, economical and easy to use.

Foxp3 expression is associated with aggressiveness in differentiated thyroid carcinomas

OBJECTIVES: Forkhead box P3 (FoxP3) expression has been observed in human cancer cells but has not yet been reported in thyroid cells. We investigated the prognostic significance of both FoxP3 expression and intratumoral FoxP3+ lymphocyte infiltration in differentiated thyroid carcinoma cells. METHODS: We constructed a tissue microarray with 385 thyroid tissues, including 266 malignant tissues (from 253 papillary thyroid carcinomas and 13 follicular carcinomas), 114 benign lesions, and 5 normal thyroid tissues. RESULTS: We determined the expression of FoxP3 in both tumor cells and tumor-infiltrating lymphocytes using immunohistochemical techniques. Cellular expression of FoxP3 was evident in 71% of benign and 91.9% of malignant tissues. The nuclear and cytoplasmic expression patterns were quantified separately. A multivariate logistic regression analysis indicated that cytoplasmic FoxP3 expression is an independent risk factor for thyroid malignancy. Cytoplasmic FoxP3 staining was inversely correlated with patient age. Nuclear FoxP3 staining was more intense in younger patients and in tumors presenting with metastasis at diagnosis. FoxP3+ lymphocytes were more frequent in tumors smaller than 2 cm, those without extrathyroidal invasion, and in patients with concurrent chronic lymphocytic thyroiditis. CONCLUSIONS: We demonstrated FoxP3 expression in differentiated thyroid carcinoma cells and found evidence that this expression may exert an important influence on several features of tumor aggressiveness.

Utilização de brocas trefina para a confecção de tissue microarray / Use of trephine drills for the production of tissue microarray

Objetivos: Descrever e validar uma técnica alternativa econômica e eficiente para a confecção de amostras teciduais com arranjo matricial (tissue microarrays, TMA). Materiais e métodos: Utilizou-se um motor, um micromotor, um contra-ângulo redutor 16:1 e brocas trefina de aço inoxidável para osso. Análise histomorfométrica do volume das células acinares de glândulas parótidas foi realizada. Para testar marcadores imunoistoquímicos para células mioepiteliais, acinares e ductais das parótidas foram utilizados calponina e PCNA. Resultados: Na análise macroscópica e microscópica das lâminas, não foi encontrada perda total do tissue e nem mesmo deslocamento (parcial e/ou total) deste, sendo as perdas teciduais observadas apenas parciais. Das 90 lâminas analisadas, 59 (65%) obtiveram de 50% a 100% do tissue com ausência de artefato, deslocamento ou perda de tecido. Conclusão: O equipamento proposto pelos autores para a confecção deamostras teciduais com arranjo matricial representa uma alternativa econômica e eficiente.

Objectives: To describe and validate an inexpensive and efficient alternative for the production of tissue microarrays (TMA). Materials and methods: An electric-motor, a hand-piece, a reducing contra-angle hand-piece 16:1 and trephine stainless steel drills for bones were used in this study. A histomorphometric assessment of the volume of the acinar cells of parotid glands was performed. Calponin and PCNA were used to test the immunohistochemical markers for myoepithelial, acinar and ductal cells of parotid glands. Results: During the macroscopic and microscopic analysis, total loss of sections was not observed in any slide as well as artifactual ungluing (total and/or partial) of the sections. The loss of sections was partial. Fifty nine (65%) out of 90 slides showed 50%-100% of the tissue without technical artifact, artifactual ungluing or loss of the section. Conclusion: The equipment proposed by the authors for the production of arrays represents an inexpensive and efficient alternative.

Perda de amostras em tissue microarray: comparação entre técnicas com uso de fita adesiva comercial, lâminas silanizadas pelo método tradicional ou por método modificado / Loss of tissue samples in the tissue microarray: comparison between techniques using commercial adhesive tape, silane-coated microslides by the conventional method and by a modified technique

Introdução/objetivo: O microarranjo tecidual, ou tissue microarray (TMA), permite avaliar múltiplas amostrasde tecido em um único bloco. Um dos problemas do TMA é o descolamento dos cortes teciduais, por isso, para reduzir essa perda, tem-se utilizado fita adesiva especial comercial. Não há relatos comparando o uso dessas fitas adesivas com a técnica de silanização modificada. O objetivo desse estudo foi comparar as perdas de cortes entre lâminas usando fitas adesivas comerciais, lâminas silanizadas por técnica convencional elâminas silanizadas por técnica modificada, com menor consumo de acetona. Material e método: O TMA foiconstruído com blocos de tecido hepático, em dispositivo de base fixa, colocando-se 32 cilindros de 2 mmde diâmetro em duplicata e espaçamento de 2,2 mm. Quinze secções de 4 μm foram colocadas em lâminas silanizadas a 4% por técnica convencional (grupo 1), 15 em lâminas silanizadas com técnica modificada (6%de silano e com uso mínimo de acetona) (grupo 2) e 15 em lâminas com fita adesiva comercial de acordo comas recomendações do fabricante (grupo 3). Todas as lâminas foram processadas por imuno-histoquímica para citoqueratina 18, com recuperação antigênica em tampão citrato pH 6, em microondas. As perdas de amostrasforam quantificadas e expressas como: perda total (≥ 80%), quase total (75% a 79%) ou parcial (50% a 74%).Resultados: A perda de tecidos foi semelhante nos três grupos: com silanização tradicional, modificada oufita adesiva comercial (4,9 vs. 3,1 vs. 8,1, respectivamente) (análise de variância [ANOVA], p = 0,3654). Umadas lâminas com a fita adesiva apresentou descolamento artefatual de todos os tecidos e outra de 20 tecidosem um dos lados. Nenhuma das lâminas silanizadas apresentou tal artefato. Conclusão: Lâminas silanizadas têm resultados satisfatórios, requerem menos treinamento técnico e reduzem os custos da utilização do TMA justificando seu uso em pesquisa...

Introduction/objective: The tissue microarray (TMA) technique allows the evaluation of multiple tissue samplesin a single block. One of the problems of TMA is the ungluing of tissue sections, thus commercial adhesive tape has been used to reduce this loss. There are no reports comparing the use of the commercial adhesive tape with the use of the modified silane-coated technique. The objective of this study was to compare section loss in slides using commercial adhesive tape, silane-coated microslides with the conventional technique or with the modified technique. Material and method: The TMA was constructed with hepatic tissue blocks embedded in paraffin, using a fixed base device, placing 32 cylinders of 2 mm in diameter in duplicate and 2.2 mm apart from each other. Fifteen 4-μm sections were placed on conventional silane-coated microslides at 4% (Group 1), 15 on silane-coated microslides with a modified technique (6% of silane and minimum use of acetone) (Group 2), and 15 on slides using commercial adhesive tape, according to the manufacturer's recommendations (Group 3). All microslides were processed by immunohistochemistry for cytokeratin 18, with antigen retrieval accomplished by incubation with citrate buffer pH 6.0 with microwave enhancement. Samples loss was quantified and expressed as: total (≥ 80%), almost complete (75% to 79%) or partial (50% to 74%). Results: The loss of sections was similar in all three groups (4.9 vs. 3.1 vs. 8.1, respectively) (analysis of variance [ANOVA], p = 0.3654). One slide usingcommercial adhesive tape showed artifactual ungluing of all sections and another one showed loss of 20 sampleson one side of the slide. None of the silane-coated microslides showed such artifact. Conclusions: Silane-coated microslides show adequate results, require less technical training and reduce the cost of TMA procedure, whatjustifies their use in research...

Tissue microarray: a simple technology that has revolutionized research in pathology.

Tissue microarray (TMA) technology is a high-throughput research tool, which has greatly facilitated and accelerated tissue analyses by in-situ technologies. TMAs are amenable to every research method that can be applied on the standard whole sections at enhanced speed. It plays a central role in target verification of results from cDNA arrays, expression profiling of tumors and tissues, and is proving to be a powerful platform for proteomic research. In this review article, primarily meant for students of pathology and oncology, we briefly discuss its basic methodology, applications and merits and limitations.

Construção de arrays de tecido com equipamento alternativo e de baixo custo para estudo imuno-histoquímico de tumores mamários / Construction of low cost tissue microarrays using alternative equipment for immunohistochemical study of breast tumors

INTRODUÇÂO: Tissue microarrays (TMA) são blocos contendo numerosos cilindros de tecido parafinado organizados em linhas e colunas que permitem analisar muitas amostras numa única lâmina. Equipamentos disponíveis comercialmente são importados e têm alto custo (entre 11 e 24 mil dólares). OBJETIVOS: Descrever uma forma alternativa de construção de arrays de tumores mamários de baixo custo e relatar nossa experiência na sua utilização em estudo imuno-histoquímico (IIQ). METODOLOGIA: Utilizou-se modelo que consiste numa minirretífica com agulha de biópsia hepática de 2mm de diâmetro acoplada à bancada com suporte (Dremel). Inicialmente preparou-se o bloco receptor fazendo o número de furos desejável (55). Cilindros de tecido foram obtidos com o mesmo dispositivo e colocados nos orifícios do bloco receptor. De cada bloco doador, obteve-se dois cilindros de diferentes áreas representativas do tumor. Em cada array foram incluídos cilindros de tumor (controle positivo e negativo) para cada anticorpo testado na IIQ, e cilindro marcador de iniciação da leitura da lâmina (fígado). Cortes sequenciais de 4µm obtidos do array foram submetidos à IIQ. A primeira e a última lâmina foram coradas pela hematoxilina e eosina (HE) para avaliar: número de discos de tecido, preservação tecidual e adequabilidade da amostra. Foi realizada IIQ empregando anticorpos anti-receptores de estrógeno, progesterona, Ki67, p53 e Her2. RESULTADOS: O custo total do equipamento foi apenas US$180,00. Cortes histológicos do array apresentaram boa preservação tecidual, sendo adequados para avaliação morfológica e suficientes para confirmação diagnóstica. A qualidade das realizações IIQ foi semelhante à obtida nos blocos doadores. CONCLUSÃO: Esse equipamento e a técnica representam uma alternativa econômica aos equipamentos comerciais.

BACKGROUND: Tissue microarrays (TMA) are blocks containing numerous cylinders of paraffinized tissue organized in lines and columns allowing analysis of numerous samples in one slide. Commercially available equipment is imported and have high cost (US$ 11,000.00 to 24,000.00). AIM: we describe a low cost breast-tumor TMA and our experience in its use for immunohistochemistry (IHC). MATERIAL AND METHODS: A model that consists of a work station (Dremel) to which a liver biopsy needle of 2mm of diameter was connected. A receptor block was prepared perforating it until the desired number of rows (55) was reached. Then, the cylinders of tissue were obtained using the same equipment and included in the holes of the receptor block. Two samples were obtained from different tumor areas of each donor block. Cylinders of previously tested positive control tumors for each antibody and one marker (liver sample) that indicated the beginning of slide reading were also included. IHC was performed in sequential 4µm sections from the same array using antibodies against estrogen and progesterone receptors, Ki67, p53 and Her2. The first and the last slides were stained by hematoxylin and eosin to evaluate: number of tissue discs, tissue preservation, and adequacy of the tissue sample. RESULTS: The equipment total cost was US$ 180,00. The slides showed fine tissue preservation, adequate for morphologic evaluation, and sufficient to confirm diagnosis. The IHC quality was similar to the donor blocks. CONCLUSION: This equipment and technique represent an economical alternative when compared to commercial equipments.

The Usefulness of CDX-2 for Differentiating Primary and Metastatic Ovarian Carcinoma: An Immunohistochemical Study Using a Tissue Microarray

Distinguishing primary ovarian carcinoma from metastatic carcinoma to the ovary is often difficult by histologic examination alone. Recently an immunohistochemical marker CDX-2 was found to be of considerable diagnostic value in establishing the gastrointestinal origin of metastatic tumors. The aim of this study was to determine whether CDX-2 can distinguish between these malignancies. Paraffin-embedded tissue sections from 57 primary ovarian tumors and 40 metastatic tumors to the ovary were immunostained for CDX-2, and results were compared to the ancillary immunohistochemical results for CK7/CK20, CEA, CA125, and her-2/neu. CDX-2 immunoreactivity was observed in most of metastatic carcinomas with colorectal (91%) and appendiceal (100%) origin, however CDX-2 was negative in all primary ovarian carcinomas, except for the mucinous subtype. Almost all primary ovarian carcinomas including the mucinous subtype showed diffuse and strong immunoexpression for CK7. CEA and CA125 were mainly found in metastatic and primary ovarian carcinoma, respectively. Her-2/neu overexpression was only noted in a small proportion of primary and metastatic ovarian carcinomas. These results suggest that CDX-2 is very useful immunohistochemical marker for distinguishing metastatic colorectal carcinoma to the ovary from primary ovarian carcinoma, including the mucinous subtype. Furthermore, combination with CDX-2 and CK7 strengthen the differential diagnosis between these tumors.