Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets.

Recent breakthroughs in creating induced pluripotent stem cells (iPS cells) provide alternative means to obtain embryonic stem (ES) cell-like cells without destroying embryos by introducing four reprogramming factors (Oct3/4, Sox2, and Klf4/c-Myc or Nanog/Lin28) into somatic cells. However, the molecular basis of reprogramming is largely unknown. To address this question, we employed microRNAs, small molecules, and conducted genome-wide RNAi screen, to investigate the regulatory mechanisms of reprogramming. First we showed that depleting miR-21 and miR-29a enhances reprogramming in mouse embryonic fibroblasts (MEFs). We also showed that p53 and ERK1/2 pathways are regulated by miR-21 and miR-29a and function in reprogramming. Second, we showed that computational chemical biology combined with genomic analysis can be used to identify small molecules regulating reprogramming. We discovered that the NSAID Nabumetone and the anti-cancer drug OHTM could replace Sox2 during reprogramming. Nabumetone could also replace c-Myc or Sox2 without compromising self-renewal and pluripotency of derived iPS cells. To identify the cell-fate determinants during reprogramming, we integrated a genome-wide RNAi screen with transcriptome analysis to dissect the molecular requirements in reprogramming. We found that extensive interactions of embryonic stem cell core circuitry regulators are established in mature iPS cells, including Utf1, Nr6a1, Tdgf1, Gsc, Fgf10, T, Chrd, Dppa3, Fgf17, Eomes, Foxa2. Remarkably, genes with non-differential change play the most critical roles in the transitions of reprogramming. Functional validation showed that some genes act as essential or barrier roles to reprogramming. We also identified several genes required for maintaining ES cell properties. Altogether, our results demonstrate the significance of miRNA function in regulating multiple signaling networks involved in reprogramming. And our work further advanced the reprogramming field by identifying several new key modulators.

No / BMP signaling has a crucial role in skin development and homeostasis, whereas molecular mechanisms underlying its involvement in regulating gene expression programs in keratinocytes and fibroblasts remain largely unknown. We show here that several BMP ligands, all BMP receptors, and BMP-associated Smad1/5/8 are expressed in human primary epidermal keratinocytes and dermal fibroblasts. Treatment of both cell types by BMP-4 resulted in the activation of the BMP-Smad, but not BMP-MAPK pathways. Global microarray analysis revealed that BMP-4 treatment induces distinct and cell type-specific changes in gene expression programs in keratinocytes and fibroblasts, which are far more complex than the effects of BMPs on cell proliferation/differentiation described earlier. Furthermore, our data suggest that the potential modulation of cell adhesion, extracellular matrix remodeling, motility, metabolism, signaling, and transcription by BMP-4 in keratinocytes and fibroblasts is likely to be achieved by the distinct and cell-type-specific sets of molecules. Thus, these data provide an important basis for delineating mechanisms that underlie the distinct effects of the BMP pathway on different cell populations in the skin, and will be helpful in further establishing molecular signaling networks regulating skin homeostasis in health and disease.

As interações epitélio-mesênquima podem influenciar o desenvolvimento do tumor no sítio primário e no linfonodo comprometido de pacientes com câncer de mama. Nosso objetivo foi avaliar a taxa de proliferação e perfil gênico de fibroblastos de linfonodos comprometidos e não comprometidos obtidos de pacientes com câncer de mama e determinar a influência de células epiteliais mamárias normais (MCF10A) ou malignas (MDA-MB-231) na expressão gênica destes fibroblastos. Foram estabelecidas culturas primárias de fibroblastos de linfonodos (3 comprometidos e 3 não comprometidos) de 6 diferentes pacientes com câncer de mama e não houve diferença na taxa de proliferação destes fibroblastos. Co-culturas de células MCF10A ou MDA-MB-231 com fibroblastos, separadas fisicamente por membranas porosas, foram realizadas por 72 horas. O RNA total dos fibroblastos foi extraído, amplificado e o perfil gênico foi analisado usando-se uma lâmina de cDNA microarray. Fibroblastos de linfonodos comprometidos e não comprometidos apresentaram perfil gênico similar, pois apenas 13 genes foram modulados, sendo que maior expressão de PGBD3 e PTBP2 em fibroblastos de linfonodos comprometidos foi confirmada em ensaios de RT-PCR em tempo real. Em fibroblastos, a cocultura com células MCF10A alterou a expressão de maior número de genes que a co-cultura com células MDA-MB-231. Em fibroblastos originários de linfonodos não comprometidos mantidos em co-cultura com células MDA-MB-231 foram modulados 151 genes, em relação aos mesmos fibroblastos cultivados na ausência de células epiteliais, sendo que oito deles apresentaram variação de expressão superior a três vezes (BET1, ENTPD1, USP7, DAPK1, ERBB2 e NCF2). As células MDA-MB-231 modularam algumas vias de sinalização em fibroblastos não comprometidos, como vias do cálcio, insulina, hormônio liberador de gonadotrofina (GnRH) e da regulação do citoesqueleto de actina, mas o mesmo não ocorreu em fibroblastos de linfonodos comprometidos. Duzentos e quarenta e nove genes foram diferencialmente expressos em fibroblastos originários de linfonodos comprometidos mantidos em co-cultura com células MDA-MB-231 e quatro genes apresentaram variação superior a três vezes (ACLY, AXUD1, CLCN5 e PDE6D). Nestes fibroblastos, algumas funções biológicas foram reguladas apenas por influência da célula MDA-MB-231, entre as quais metabolismo de aminoácidos, excreção, transporte intra Golgi e regulação da forma celular. As vias de sinalização e funções biológicas reguladas em fibroblastos pela interação com células epiteliais malignas podem estar implicadas no desenvolvimento de metástases regionais no câncer de mama. / Tumor development may be influenced by epithelial-mesenchimal interactions in the primary site as well as in the involved lymph node from breast cancer patients. Our aim was to evaluate the proliferation rate and gene profile of fibroblasts obtained from involved and uninvolved lymph nodes from breast câncer patients and to determine the influence of normal (MCF10A) or malignant (MDA-MB-231) mammary epithelial cells on the gene expression of these fibroblasts. Primary culture from fibroblasts obtained from 3 involved and 3 uninvolved lymph nodes (ILF and NILF) from 6 different breast cancer patients was established and no difference in their proliferation rate was detected. These fibroblasts were co-cultured with MCF10A or MDA-MB-231 cells, physically separated by a porous membrane for 72 hours. Total RNA was extracted from the cells, amplified and the gene profile from fibroblasts cultured alone or with epithelial cells was analyzed by cDNA microarray slides. Fibroblasts from involved and uninvolved lymph nodes present a similar gene profile as only 13 genes were differentially expressed between them, including PGBD3 and PTBP2, which higher expression in fibroblasts from involved lymph nodes was confirmed by real time RT-PCR. In fibroblasts, more genes seem to be regulated upon co-cultured with MCF10A than with MDA-MB-231 cells. In fibroblasts from uninvolved lymph nodes co-cultured with MDA-MB-231 cells, 151 genes were modulated as compared with fibroblasts cultured alone, and eight of them, presented an expression variation superior to three times (BET1, ENTPD1, USP7, DAPK1, ERBB2 e NCF2). In these fibroblasts, MDA-MB-231 could modulate some signaling pathways as calcium, insulin, gonadotrophin releasing hormone (GnRH) and actin cytoskeleton regulation signaling pathways. Two hundred forty nine genes were differentially expressed by fibroblasts from involved lymph nodes co-cultured with MDA-MB-231 cells, four of which with an expression variation superior to three times (ACLY, AXUD1, CLCN5 e PDE6D). In the last condition, fibroblasts had some biological functions regulated upon MDA-MB-231 cells influence, among which amino acid metabolism, excretion, intra-Golgi transport and regulation of cell shape. Signaling pathways and biological functions regulated in fibroblasts after interaction with malignant epithelial cells might be implicated in the development of regional metastasis in breast cancer.

O desenvolvimento da metástase depende, entre outros fatores de um microambiente propício e é possível que as células do câncer de mama influenciem o perfil da expressão gênica das células estromais, tanto no tumor primário como no linfonodo regional. Para estudar este último evento obtivemos fibroblastos de linfonodos comprometidos (n=3) ou não (n=3) de pacientes com câncer de mama, os quais foram co-cultivados com células de câncer de mama MDA-MB-231, separados fisicamente por membranas porosas por 72 horas. O perfil da expressão gênica foi determinado utilizando-se uma plataforma de cDNA microarray. A presença de células MDA-MB231 modulou a expressão de 415 genes em fibroblastos de linfonodos não comprometidos e 779 genes em fibroblastos de linfonodos comprometidos, em relação a células mantidas em mono-cultura, sendo que 120 genes tiveram sua expressão reguladas em ambas comparações. A expressão destes genes determinou a separação dos fibroblastos mantidos em co-cultura daqueles mantidos isoladamente em cultura por análise de agrupamento hierárquico, indicando que a presença das células de câncer de mama influencia o perfil da expressão gênica das células. Entre as funções reguladas pela presença de células MDA-MB231 encontramse tradução e receptor de superfície ligado à transmissão de sinal, em fibroblastos de linfonodos não comprometidos e autofosforilação de proteína e ciclo celular, em fibroblastos de linfonodos comprometidos. Para determinar se a expressão gênica diferencial é um fenômeno que pode ser generalizado para o câncer de mama, realizamos ensaios utilizando outras amostras de fibroblastos obtidos de linfonodos comprometidos de 5 pacientes e de linfonodos não comprometidos de outras 5 pacientes (incluindo as 6 amostras de fibroblastos previamente analisadas), as quais foram co-cultivadas com três linhagens celulares de câncer de mama (MDA-MB231, MDA-MB435 e MCF-7). A expressão relativa de MAP2K3, AKAP8L e CREG1, inicialmente identificados como diferencialmente expressos em análise de cDNA microarray, foi então determinada por RT-PCR em tempo real. Observamos que nenhuma das três linhagens celulares influenciou a expressão de AKAP8L e CREG1 tanto em fibroblastos de linfonodos comprometidos quanto não comprometidos. MAP2K3 foi hiperexpresso tanto em fibroblastos de linfonodos comprometidos quanto em não comprometidos co-cultivados com células MDA-MB231, mas não com células MDA-MB435 ou MCF-7. Nossos resultados indicam que a presença de células MDA-MB231 influencia o perfil de expressão gênica de fibroblastos originário tanto de linfonodos comprometidos quanto de não comprometidos. Alguns genes comumente regulados em fibroblastos de linfonodo comprometido ou não comprometidos, incluindo MAP2K3, podem estar envolvidos no estabelecimento de metástase regional. / Metastasis development may depend on a favorable microenvironment and breast cancer cells may influence stromal cells gene expression profile not only in the primary site but also in the lymph nodes. To study the latter event, fibroblasts were obtained from involved or uninvolved lymph nodes from six breast cancer patients and co-cultivated with breast cancer MDA-MB-231 cells, physically separated by porous membranes, for 72 hours. The gene expression profile was determined utilizing a cDNA microarray platform. The presence of MDA-MB231 cells modulated the expression of 415 genes in fibroblasts from uninvolved nodes and 779 genes in fibroblasts from involved nodes, as compared to fibroblasts cultured isolated, including 120 genes, which were regulated in fibroblasts from both origins. Unsupervised hierarchical clustering allowed a correct segregation of fibroblasts co-cultured with MDA-MB231 cells from fibroblasts cultured alone, indicating that the gene expression profile gene is influenced by the presence of breast cancer cells. Functions, which were regulated by presence of MDA-MB231 cells included translation and cell surface receptor linked signal transduction in fibroblasts from uninvolved nodes and protein autophosphorylation and cell cycle in fibroblasts from involved nodes. To determine whether this differential gene expression was a general process influenced by breast cancer cells, further assays were performed utilizing samples of fibroblasts from involved (n=5) and uninvolved nodes (n=5) from breast cancer patients (including the 6 samples of fibroblasts previously analyzed), which were co-cultured with three breast cancer cell lines (MDAMB231, MDA-MB435 and MCF-7). Relative expression of MAP2K3, AKAP8L and CREG1, initially identified as differentially expressed in co-cultured fibroblasts upon cDNA microarray analysis, was determined by RT-PCR real time. AKAP8L and CREG1 expression in fibroblasts from involved or uninvolved nodes was not influenced by the presence of any of the three cell lines. MAP2K3 was over-expressed in fibroblasts from both involved and uninvolved nodes when co-cultured with MDA-MB231 cells, but not with MDA-MB435 or MCF-7 cells. Our results indicate that the gene expression profile of fibroblasts from involved and uninvolved lymph nodes are influenced by the presence of MDA-MB231. Some genes commonly regulated in fibroblasts from both involved and uninvolved nodes, as MAP2K3, may be involved in regional metastasis establishment.

Cylindrospermopsin (CYN) is a toxic alkaloid produced by several freshwater cyanobacterial species, the most prevalent in Australian waters being Cylindrospermopsis raciborskii. The occurrence of CYN-producing cyanobacteria in drinking water sources worldwide poses a potential human health risk, with one well-documented case of human poisoning attributed to the toxin. While extensive characterisation of CYN-induced toxicity has been conducted in rodents both in vivo and in primary cell cultures, little is known about mechanisms of toxicity in human cell types. This thesis describes studies undertaken to further define the molecular mechanisms of CYN toxicity in human cells. Concentration-response relationships were determined in various cultured human cell types using standard toxicity assays. As expected, CYN caused dose-dependent decreases in the growth of three cell lines, HepG2, Caco-2 and HeLa, and one primary cell type, human dermal fibroblasts, according to tetrazolium reduction assays. CYN treatment did not disrupt cellular membranes according to the lactate dehydrogenase release assay in HepG2 or Caco-2 cells after 24, 48 or 72 h exposure, but did cause membrane disruption in fibroblasts after 72 h exposure to relatively high concentrations of the toxin. Apoptosis occurred more readily in HeLa cells than HepG2 cells or fibroblasts, with 72 h exposure to 1 &mug/mL required before statistically significant rates of apoptosis occurred in the latter cell types. CYN did not appear to directly affect the structure of actin filaments or microtubules under the conditions used in the present study. The major portion of the work presented in this thesis comprises a large-scale interrogation of changes in gene expression induced by the toxin in cultured cells. To assess the effects of CYN on global gene expression, relative messenger RNA (mRNA) levels in human dermal fibroblasts and HepG2 cells after 6 h and 24 h exposure to 1 &mug/mL CYN were determined using oligonucleotide microarrays representing approximately 19 000 genes. Overall, the number of transcripts significantly altered in abundance was greater in fibroblasts than in HepG2 cells. In both cell types, mRNA levels for genes related to amino acid biosynthesis, carbohydrate metabolism, and protein folding and transport were reduced after CYN treatment, while transcripts representing genes for apoptosis, RNA biosynthesis and RNA processing increased in abundance. More detailed data analyses revealed the modulation of a number of stress response pathways—genes regulated by NF-&kappaB were induced, DNA damage response pathways were up-regulated, and a large number of genes involved in endoplasmic reticulum stress were strongly down-regulated. Genes for the synthesis and processing of mRNA, tRNA and rRNA were strongly up-regulated, indicating that CYN treatment may increase the turnover of all forms of cellular RNA. A small group of genes were differentially expressed in HepG2 cells and fibroblasts, revealing cell-specific responses to the toxin. Selected changes in transcript level were validated using real-time quantitative reverse transcriptase PCR (qRT-PCR). The modulation of stress response pathways by CYN, indicated by microarray analysis, was further investigated using other methods. The role of tumour suppressor protein p53 in CYN-mediated gene expression was confirmed by measuring the expression of known p53-regulated genes following CYN treatment of HepG2 cells and human dermal fibroblasts using qRT-PCR. Western blotting of protein extracts from CYNtreated cells showed that p53 protein accumulation occurred in HepG2 cells, providing additional evidence of the activation of the p53 pathway by CYN in this cell line. The immediate-early genes JUN and FOS were found to be induced by CYN in a concentration-dependent manner, and MYC was induced to a lesser extent. The mitogen-activated protein kinase c-Jun NH2-terminal kinase, implicated in the ribotoxic stress response initiated by damage to ribosomal RNA, appeared to become phosphorylated in HeLa cells after CYN exposure, suggesting that ribotoxic stress may occur in response to CYN in at least some cell types. The expression of a reporter gene under the control of a response element specific for NF-&kappaB was induced at the mRNA level but inhibited at the protein level. This shows that while transcription factors such as p53 and NF-&kappaB are apparently activated in response to the toxin, transactivation of target genes may not necessarily manifest a corresponding increase at the protein level. The current work contributes significantly to the current understanding of cylindrospermopsin toxicity in human-derived cell types, and provides further insight into putative modes of action.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. It is a molecular and prognostic heterogeneous disease. Three main genetic subtypes are called germinal center-like DLBCL (GC-like DLBCL), non-germinal center-like DLBCL (nonGC-like DLBCL) and primary mediastinal B-cell lymphoma (PMBL). These subtypes can be reliably distinguished only with usage of gene expression profiling (GEP). The GEP method can be applied only when fresh frozen tissue is available. The method is technically difficult and expensive. Thus, it is not used routinely. Since the DLBCL subtypes differ in prognosis, it is extremely important to be able to distinguish them. The presented thesis is focused on distinguishing of PMBL diagnosis in the group of DLBCL. Easily stored formalin-fixed, paraffin-embedded tissue (FFPE) and gene expression analysis using real-time quantitative polymerase chain reaction (RTqPCR) are used. In the first step, PMBL and DLBCL cases were distinguished with an internationally accepted clinical-pathological method. The agreement between clinical-pathological diagnosis and GEP is only 76%. In the presented text a genetic algorithm for PMBL/DLBCL distinguishing is suggested. It uses three carefully chosen genes and their expression is measured with RTqPCR. Both, the...

O desenvolvimento da metástase depende, entre outros fatores de um microambiente propício e é possível que as células do câncer de mama influenciem o perfil da expressão gênica das células estromais, tanto no tumor primário como no linfonodo regional. Para estudar este último evento obtivemos fibroblastos de linfonodos comprometidos (n=3) ou não (n=3) de pacientes com câncer de mama, os quais foram co-cultivados com células de câncer de mama MDA-MB-231, separados fisicamente por membranas porosas por 72 horas. O perfil da expressão gênica foi determinado utilizando-se uma plataforma de cDNA microarray. A presença de células MDA-MB231 modulou a expressão de 415 genes em fibroblastos de linfonodos não comprometidos e 779 genes em fibroblastos de linfonodos comprometidos, em relação a células mantidas em mono-cultura, sendo que 120 genes tiveram sua expressão reguladas em ambas comparações. A expressão destes genes determinou a separação dos fibroblastos mantidos em co-cultura daqueles mantidos isoladamente em cultura por análise de agrupamento hierárquico, indicando que a presença das células de câncer de mama influencia o perfil da expressão gênica das células. Entre as funções reguladas pela presença de células MDA-MB231 encontramse tradução e receptor de superfície ligado à transmissão de sinal, em fibroblastos de linfonodos não comprometidos e autofosforilação de proteína e ciclo celular, em fibroblastos de linfonodos comprometidos. Para determinar se a expressão gênica diferencial é um fenômeno que pode ser generalizado para o câncer de mama, realizamos ensaios utilizando outras amostras de fibroblastos obtidos de linfonodos comprometidos de 5 pacientes e de linfonodos não comprometidos de outras 5 pacientes (incluindo as 6 amostras de fibroblastos previamente analisadas), as quais foram co-cultivadas com três linhagens celulares de câncer de mama (MDA-MB231, MDA-MB435 e MCF-7). A expressão relativa de MAP2K3, AKAP8L e CREG1, inicialmente identificados como diferencialmente expressos em análise de cDNA microarray, foi então determinada por RT-PCR em tempo real. Observamos que nenhuma das três linhagens celulares influenciou a expressão de AKAP8L e CREG1 tanto em fibroblastos de linfonodos comprometidos quanto não comprometidos. MAP2K3 foi hiperexpresso tanto em fibroblastos de linfonodos comprometidos quanto em não comprometidos co-cultivados com células MDA-MB231, mas não com células MDA-MB435 ou MCF-7. Nossos resultados indicam que a presença de células MDA-MB231 influencia o perfil de expressão gênica de fibroblastos originário tanto de linfonodos comprometidos quanto de não comprometidos. Alguns genes comumente regulados em fibroblastos de linfonodo comprometido ou não comprometidos, incluindo MAP2K3, podem estar envolvidos no estabelecimento de metástase regional. / Metastasis development may depend on a favorable microenvironment and breast cancer cells may influence stromal cells gene expression profile not only in the primary site but also in the lymph nodes. To study the latter event, fibroblasts were obtained from involved or uninvolved lymph nodes from six breast cancer patients and co-cultivated with breast cancer MDA-MB-231 cells, physically separated by porous membranes, for 72 hours. The gene expression profile was determined utilizing a cDNA microarray platform. The presence of MDA-MB231 cells modulated the expression of 415 genes in fibroblasts from uninvolved nodes and 779 genes in fibroblasts from involved nodes, as compared to fibroblasts cultured isolated, including 120 genes, which were regulated in fibroblasts from both origins. Unsupervised hierarchical clustering allowed a correct segregation of fibroblasts co-cultured with MDA-MB231 cells from fibroblasts cultured alone, indicating that the gene expression profile gene is influenced by the presence of breast cancer cells. Functions, which were regulated by presence of MDA-MB231 cells included translation and cell surface receptor linked signal transduction in fibroblasts from uninvolved nodes and protein autophosphorylation and cell cycle in fibroblasts from involved nodes. To determine whether this differential gene expression was a general process influenced by breast cancer cells, further assays were performed utilizing samples of fibroblasts from involved (n=5) and uninvolved nodes (n=5) from breast cancer patients (including the 6 samples of fibroblasts previously analyzed), which were co-cultured with three breast cancer cell lines (MDAMB231, MDA-MB435 and MCF-7). Relative expression of MAP2K3, AKAP8L and CREG1, initially identified as differentially expressed in co-cultured fibroblasts upon cDNA microarray analysis, was determined by RT-PCR real time. AKAP8L and CREG1 expression in fibroblasts from involved or uninvolved nodes was not influenced by the presence of any of the three cell lines. MAP2K3 was over-expressed in fibroblasts from both involved and uninvolved nodes when co-cultured with MDA-MB231 cells, but not with MDA-MB435 or MCF-7 cells. Our results indicate that the gene expression profile of fibroblasts from involved and uninvolved lymph nodes are influenced by the presence of MDA-MB231. Some genes commonly regulated in fibroblasts from both involved and uninvolved nodes, as MAP2K3, may be involved in regional metastasis establishment.

As interações epitélio-mesênquima podem influenciar o desenvolvimento do tumor no sítio primário e no linfonodo comprometido de pacientes com câncer de mama. Nosso objetivo foi avaliar a taxa de proliferação e perfil gênico de fibroblastos de linfonodos comprometidos e não comprometidos obtidos de pacientes com câncer de mama e determinar a influência de células epiteliais mamárias normais (MCF10A) ou malignas (MDA-MB-231) na expressão gênica destes fibroblastos. Foram estabelecidas culturas primárias de fibroblastos de linfonodos (3 comprometidos e 3 não comprometidos) de 6 diferentes pacientes com câncer de mama e não houve diferença na taxa de proliferação destes fibroblastos. Co-culturas de células MCF10A ou MDA-MB-231 com fibroblastos, separadas fisicamente por membranas porosas, foram realizadas por 72 horas. O RNA total dos fibroblastos foi extraído, amplificado e o perfil gênico foi analisado usando-se uma lâmina de cDNA microarray. Fibroblastos de linfonodos comprometidos e não comprometidos apresentaram perfil gênico similar, pois apenas 13 genes foram modulados, sendo que maior expressão de PGBD3 e PTBP2 em fibroblastos de linfonodos comprometidos foi confirmada em ensaios de RT-PCR em tempo real. Em fibroblastos, a cocultura com células MCF10A alterou a expressão de maior número de genes que a co-cultura com células MDA-MB-231. Em fibroblastos originários de linfonodos não comprometidos mantidos em co-cultura com células MDA-MB-231 foram modulados 151 genes, em relação aos mesmos fibroblastos cultivados na ausência de células epiteliais, sendo que oito deles apresentaram variação de expressão superior a três vezes (BET1, ENTPD1, USP7, DAPK1, ERBB2 e NCF2). As células MDA-MB-231 modularam algumas vias de sinalização em fibroblastos não comprometidos, como vias do cálcio, insulina, hormônio liberador de gonadotrofina (GnRH) e da regulação do citoesqueleto de actina, mas o mesmo não ocorreu em fibroblastos de linfonodos comprometidos. Duzentos e quarenta e nove genes foram diferencialmente expressos em fibroblastos originários de linfonodos comprometidos mantidos em co-cultura com células MDA-MB-231 e quatro genes apresentaram variação superior a três vezes (ACLY, AXUD1, CLCN5 e PDE6D). Nestes fibroblastos, algumas funções biológicas foram reguladas apenas por influência da célula MDA-MB-231, entre as quais metabolismo de aminoácidos, excreção, transporte intra Golgi e regulação da forma celular. As vias de sinalização e funções biológicas reguladas em fibroblastos pela interação com células epiteliais malignas podem estar implicadas no desenvolvimento de metástases regionais no câncer de mama. / Tumor development may be influenced by epithelial-mesenchimal interactions in the primary site as well as in the involved lymph node from breast cancer patients. Our aim was to evaluate the proliferation rate and gene profile of fibroblasts obtained from involved and uninvolved lymph nodes from breast câncer patients and to determine the influence of normal (MCF10A) or malignant (MDA-MB-231) mammary epithelial cells on the gene expression of these fibroblasts. Primary culture from fibroblasts obtained from 3 involved and 3 uninvolved lymph nodes (ILF and NILF) from 6 different breast cancer patients was established and no difference in their proliferation rate was detected. These fibroblasts were co-cultured with MCF10A or MDA-MB-231 cells, physically separated by a porous membrane for 72 hours. Total RNA was extracted from the cells, amplified and the gene profile from fibroblasts cultured alone or with epithelial cells was analyzed by cDNA microarray slides. Fibroblasts from involved and uninvolved lymph nodes present a similar gene profile as only 13 genes were differentially expressed between them, including PGBD3 and PTBP2, which higher expression in fibroblasts from involved lymph nodes was confirmed by real time RT-PCR. In fibroblasts, more genes seem to be regulated upon co-cultured with MCF10A than with MDA-MB-231 cells. In fibroblasts from uninvolved lymph nodes co-cultured with MDA-MB-231 cells, 151 genes were modulated as compared with fibroblasts cultured alone, and eight of them, presented an expression variation superior to three times (BET1, ENTPD1, USP7, DAPK1, ERBB2 e NCF2). In these fibroblasts, MDA-MB-231 could modulate some signaling pathways as calcium, insulin, gonadotrophin releasing hormone (GnRH) and actin cytoskeleton regulation signaling pathways. Two hundred forty nine genes were differentially expressed by fibroblasts from involved lymph nodes co-cultured with MDA-MB-231 cells, four of which with an expression variation superior to three times (ACLY, AXUD1, CLCN5 e PDE6D). In the last condition, fibroblasts had some biological functions regulated upon MDA-MB-231 cells influence, among which amino acid metabolism, excretion, intra-Golgi transport and regulation of cell shape. Signaling pathways and biological functions regulated in fibroblasts after interaction with malignant epithelial cells might be implicated in the development of regional metastasis in breast cancer.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. It is a molecular and prognostic heterogeneous disease. Three main genetic subtypes are called germinal center-like DLBCL (GC-like DLBCL), non-germinal center-like DLBCL (nonGC-like DLBCL) and primary mediastinal B-cell lymphoma (PMBL). These subtypes can be reliably distinguished only with usage of gene expression profiling (GEP). The GEP method can be applied only when fresh frozen tissue is available. The method is technically difficult and expensive. Thus, it is not used routinely. Since the DLBCL subtypes differ in prognosis, it is extremely important to be able to distinguish them. The presented thesis is focused on distinguishing of PMBL diagnosis in the group of DLBCL. Easily stored formalin-fixed, paraffin-embedded tissue (FFPE) and gene expression analysis using real-time quantitative polymerase chain reaction (RTqPCR) are used. In the first step, PMBL and DLBCL cases were distinguished with an internationally accepted clinical-pathological method. The agreement between clinical-pathological diagnosis and GEP is only 76%. In the presented text a genetic algorithm for PMBL/DLBCL distinguishing is suggested. It uses three carefully chosen genes and their expression is measured with RTqPCR. Both, the...