cDNA microarrays used in the analysis of the gene expression of tumorigenic adrenocortical lineages treated with FGF2 and ACTH

Uma premissa da Biologia Molecular atual estabelece a ativação de programas de transcrição voltados a processos biológicos específicos. Neste trabalho o objetivo é descrever genes regulados que, uma vez agrupados, são capazes de indicar os programas disparados na linhagem corticoadrenal murina Y1 quando tratada com o fator de crescimento de fibroblasto 2 (FGF2) ou pelo hormônio adrenocorticotrópico (ACTH). O papel de ACTH em células Y1 ainda não está bem estabelecido quanto ao seu potencial mitogênico, uma vez que este hormônio é capaz de agir por diferentes vias de sinalização, apresentando um comportamento dual. Ao traçar o perfil de genes regulados por este hormônio, comparando com o padrão observado por tratamentos de indutores clássicos, espera-se determinar o papel de ACTH frente ao ciclo celular. FGF2 é classicamente conhecido por sua atividade mitogênica, de forma que, em células Y1, é capaz de induzir a passagem G0?G1?S do ciclo celular. Recentemente foi descrita uma nova e surpreendente ação de FGF2, como um indutor de morte seletivo, agindo apenas em células potencialmente tumorigênicas (Costa e Armelin, dados não publicados). Foram feitos estudos de expressão gênica com ensaios de microarray, observando-se o padrão de transcrição da linhagem Y1, bem como de sub-linhagens de Y1 resistentes a morte desencadeada por FGF2, submetidas a tratamentos de FGF2, ACTH e soro. Os resultados indicam que a) o padrão de expressão gênica observado quando a linhagem Y1 é submetida a tratamentos de ACTH é diferente daqueles desencadeados por mitógenos clássicos; b) o tratamento de FGF2 regula genes envolvidos na via de MAPK, controle do ciclo celular e genes relacionados a processos de adesão, comunicação intercelular e sinalização a partir da matriz extracelular (ECM); c) o comportamento de morte induzida por FGF2 está relacionado a alterações na estrutura da célula, envolvendo mecanismos de adesão, remodelagem de citoesqueleto e transdução de sinais a partir da ECM.Nowadays, a molecular biology premise establishes the activation of transcription programs related to specific biological processes. At this work the objective is to describe regulated genes that, once clustered, are able to indicate the running programs when murine adrenocortical lineage Y1 is treated with fibroblast growth factor (FGF2) or by adrenocorticotropin hormone (ACTH). The mitogenic potential of ACTH treatments in Y1 cells is not well established since this hormone acts by different signaling pathways, presenting a dual behavior. By tracing the profile of genes regulated by this hormone and comparing it to the transcription patterns observed in response to classic mitogens it is expected to determine the ACTH role in the cell cycle. FGF2 is known by its mitogenic activity, inducting the G0? G1?S cell cycle transitions in Y1 cells. Recently it has been described a new and surprising feat of FGF2, acting as a selective death inductor, only in potentially tumorigenic cells (Costa and Armelin, unpublished data). Microarray assays were used to determine the transcription patterns observed in Y1 lineage, as well as in FGF2 death-resistant Y1 sub-lineages, submitted to FGF2, ACTH and serum treatments. The results indicate that a) the gene expression profile displayed when Y1 cells are under ACTH treatments is different from the patterns observed when this lineage is submitted to classic mitogens; b) FGF2 treatment regulates genes involved in the MAPK pathway, cell cycle control and genes related to adhesion processes, intercellular communication and signaling from the extra cellularmatrix (ECM); c) the death behavior initiated by FGF2 is related to structural alterations in the cell, involving adhesion mechanisms, citoskeleton remodeling and signal transduction from the ECM

A straightforward assay to evaluate DNA integrity and optimize next-generation sequencing for clinical diagnosis in oncology

Next generation sequencing (NGS) has become an informative tool to guide cancer treatment and conduce a personalized approach in oncology. The biopsy collected for pathologic analysis is usually stored as formalin fixed paraffin-embedded (FFPE) blocks and then availed for molecular diagnostic, resulting in DNA molecules that are invariably fragmented and chemically modified. In an attempt to improve NGS based diagnostics in oncology we developed a straightforward DNA integrity assessment assay based on qPCR, defining clear parameters to whether NGS sequencing results is accurate or when it should be analyzed with caution. We performed DNA extraction from 12 tumor samples from diverse tissues and accessed DNA integrity by straightforward qPCR assays. In order to perform a cancer panel NGS sequencing, DNA library preparation was performed using RNA capture baits. Reads were aligned to the reference human genome and mutation calls were further validated by Sanger sequencing. Results obtained by the DNA integrity assays correlated to the efficiency of the pre-capture library preparation in up to 0.94 (Pearson's test). Moreover, sequencing results showed that poor integrity DNA leads to high rates of false positive mutation calls, specially C:G > T:A and C:G > A:T. Poor quality FFPE DNA samples are prone to generating false positive mutation calls. These are especially perilous in cases in which subclonal populations are expected, such as in advance disease, since it could lead clinicians to erroneous conclusions and equivocated conduct

Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas

Thyroid cancer incidences have been steadily increasing worldwide and are projected to become the fourth leading cancer diagnosis by 2030. Improved diagnosis and prognosis predictions for this type of cancer depend on understanding its genetic bases and disease biology. RAS mutations have been found in a wide range of thyroid tumors, from benign to aggressive thyroid carcinomas. Based on that and in vivo studies, it has been suggested that RAS cooperates with other driver mutations to induce tumorigenesis. This study aims to identify genetic alterations or pathways that cooperate with the RAS mutation in the pathogenesis of thyroid cancer. From a cohort of 120 thyroid carcinomas, 11 RAS-mutated samples were identified. The samples were subjected to RNA-Sequencing analyses. The mutation analysis in our eleven RAS-positive cases uncovered that four genes that belong to the Hippo pathway were mutated. The gene expression analysis revealed that this pathway was dysregulated in the RAS-positive samples. We additionally explored the mutational status and expression profiling of 60 RAS-positive papillary thyroid carcinomas (PTC) from The Cancer Genome Atlas (TCGA) cohort. Altogether, the mutational landscape and pathway enrichment analysis (gene set enrichment analysis (GSEA) and Kyoto Encyclopedia of Genes and Genome (KEGG)) detected the Hippo pathway as dysregulated in RAS-positive thyroid carcinomas. Finally, we suggest a crosstalk between the Hippo and other signaling pathways, such as Wnt and BMP

A straightforward assay to evaluate DNA integrity and optimize next-generation sequencing for clinical diagnosis in oncology

Next generation sequencing (NGS) has become an informative tool to guide cancer treatment and conduce a personalized approach in oncology. The biopsy collected for pathologic analysis is usually stored as formalin fixed paraffin-embedded (FFPE) blocks and then availed for molecular diagnostic, resulting in DNA molecules that are invariably fragmented and chemically modified. In an attempt to improve NGS based diagnostics in oncology we developed a straightforward DNA integrity assessment assay based on qPCR, defining clear parameters to whether NGS sequencing results is accurate or when it should be analyzed with caution. We performed DNA extraction from 12 tumor samples from diverse tissues and accessed DNA integrity by straightforward qPCR assays. In order to perform a cancer panel NGS sequencing, DNA library preparation was performed using RNA capture baits. Reads were aligned to the reference human genome and mutation calls were further validated by Sanger sequencing. Results obtained by the DNA integrity assays correlated to the efficiency of the pre-capture library preparation in up to 0.94 (Pearson's test). Moreover, sequencing results showed that poor integrity DNA leads to high rates of false positive mutation calls, specially C:G > T:A and C:G > A:T. Poor quality FFPE DNA samples are prone to generating false positive mutation calls. These are especially perilous in cases in which subclonal populations are expected, such as in advance disease, since it could lead clinicians to erroneous conclusions and equivocated conduct