Poly (A)+ Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines

We report the first quantitative and qualitative analysis of the poly (A)+ transcriptome of two human mammary cell lines, differentially expressing (human epidermal growth factor receptor) an oncogene over-expressed in approximately 25% of human breast tumors. Full-length cDNA populations from the two cell lines were digested enzymatically, individually tagged according to a customized method for library construction, and simultaneously sequenced by the use of the Titanium 454-Roche-platform. Comprehensive bioinformatics analysis followed by experimental validation confirmed novel genes, splicing variants, single nucleotide polymorphisms, and gene fusions indicated by RNA-seq data from both samples. Moreover, comparative analysis showed enrichment in alternative events, especially in the exon usage category, in ERBB2 over-expressing cells, data indicating regulation of alternative splicing mediated by the oncogene. Alterations in expression levels of genes, such as LOX, ATP5L, GALNT3, and MME revealed by large-scale sequencing were confirmed between cell lines as well as in tumor specimens with different ERBB2 backgrounds. This approach was shown to be suitable for structural, quantitative, and qualitative assessment of complex transcriptomes and revealed new events mediated by ERBB2 overexpression, in addition to potential molecular targets for breast cancer that are driven by this oncogene

Gene expression analysis of human breast epithelial cell lines treated with the combination of rapamycin and doxorubicin

A resistência à quimioterapia, a qual se constitui em um dos maiores desafios a serem superados durante o tratamento do cancer de mama, pode ser modulada por várias cascatas de sinalização cellular que levam ao aumento da sobrevivência celular. A via PI3K/Akt/mTOR é uma importante reguladora desse processo, visto que ela pode favorecer o crescimento tumoral após sua ativação por diversos receptores de fatores de crescimento, incluindo os receptores HER-2. Assim, nossa proposta foi investigar se a inibição dessa via poderia aumentar a sensibilidade de linhagens epiteliais mamárias humanas ao agente quimioterápico doxorrubicina. Também decidimos analisar o perfil de expressão gênica gerado por essa abordagem com o objetivo de compreender os mecanismos moleculares associados à resposta biológica. A rapamicina (um inibidor de mTOR) e a doxorrubicina foram utilizadas individualmente ou em combinação no tratamento de três linhagens epiteliais mamárias humanas: HB4a, C5.2 e SKBR3. A linhagem HB4a, uma linhagem derivada de epitélio mamário normal, expressa níveis basais do receptor HER-2. As outras duas linhagens expressam altos níveis desse receptor: a linhagem SKBR3 (derivada de adenocarcinoma mamário), expressa constitutivamente esse receptor e a linhagem C5.2 foi derivada da linhagem HB4a pela transfecção com o cDNA full-lenght do gene HER-2. A células foram tratadas com 20 nM de rapamicina associada ou não a doses de 30 nM a 1000 nM de doxorrubicina por 24, 48 e 72 horas. Após 24 horas, os resultados de citometria de fluxo mostraram que, enquanto as linhagens SKBR3 e C5.2 apresentaram indução de parada na fase G0/G1 do ciclo celular, a linhagem HB4a não demonstrou alterações significativas na distribuição do ciclo celular pelo tratamento com rapamicina. Esses resultados sugeriram que as linhagens SKBR3 e C5.2 foram mais sensíveis à rapamicina quando comparadas à linhagem HB4a. A doxorrubicina, por sua vez, induziu parada na fase S-G2/M do ciclo celular, a qual foi maior na linhagem HB4a comparada com as demais. De forma similar ao tratamento com doxorrubicina sozinha, o tratamento combinado também induziu parada em S-G2/M nas linhagens HB4a e C5.2. Assim, os efeitos da doxorrubicina foram predominantes aos da rapamicina na distribuição do ciclo celular no tratamento combinado nessas linhagens. Por outro lado, a linhagem SKBR3 mostrou um efeito proeminente da rapamicina, visto que sua associação com doxorrubicina induziu parada na fase G0/G1 do ciclo celular após exposição a 30 nM de doxorrubicina. Os ensaios de viabilidade celular mostraram que o tratamento combinado foi 20% mais eficiente na inibição do crescimento celular quando comparado à doxorrubicina sozinha nas três linhagens celulares, o que foi associado a uma redução de 2 vezes no IC50 da doxorrubicina. Para cada linhagem, os dados de microarray foram analisados usando o SAM (FDR 5%) para comparar os tratamento com doxorrubicina, rapamicina e o tratamento combinado aos seus respectivos controles. Considerando apenas as linhagens C5.2 e SKBR3, a anotação funcional dos genes modulados pelo tratamento combinado mostrou que os genes relacionados ao tratamento combinado estavam relacionados ao rearranjo de RNAs (splicing). Além disso, genes exclusivamente modulados pelo tratamento combinado mostrou funções associadas ao transporte intracellular enquanto que a resposta mediada por HER-2 no tratamento combinado incluiu alterçãoes na via do ubiquitina-proteossomo, glicólise e cadeia trasnportadora de elétrons. Em conjunto, nossos resultados pareceram afetar vias moleculares importantes relacionadas à sobrevivência tumoral em linhagens caracterizadas pela superexpressão de HER-2, o que foi associado a uma supressão de 2 vezes no IC50 da doxorrubicina. Esses dados ressaltam a relevância clínica da terapia combinada no contexto do HER-2, visto que essa associação pode ser capaz de reduzir a toxicidade dos pacientes submetidos à quimioterapiaChemotherapy resistance, which is the major challenge to be overcome during breast cancer treatment, can be modulated by several signaling cascades that lead to increased cell survival. The PI3K/Akt/mTOR pathway is an important regulator of this process, as it can favour the tumor growth after its activation by several growth factor receptors, including HER-2 receptors. Thus, we proposed to investigate whether the inhibition of this pathway could improve the sensitivity of human HER-2-overexpressing breast epithelial cell lines to the chemotherapeutic agent doxorubicin. We also decided to analyze the gene expression profile generated by this approach to better understand the molecular mechanisms associated with the biological response. Rapamycin (a mTOR inhibitor) and doxorubicin were used individually or in combination on three human breast epithelial cell lines: HB4a, C5.2 e SKBR3. The HB4a cell, a normal mammary epithelial cell line, expresses basal levels of HER-2. The two other cell lines express high levels of this receptor: the SKBR3 cell (derived from a mammary adenocarcinoma) expresses constitutively this receptor.and the C5.2 cell was derived from HB4a cells transfected with the cDNA-full length of HER-2. The cells were treated with 20 M of rapamycin with or without 30nM to 1000nM of doxorubicin for 24, 48 and 72 hours. After 24 hours, the flow citometry results showed that while SKBR3 and C5.2 were arrested in G0/G1 phase, HB4a demonstrated no alterations in the cell cycle distribution after rapamycin treatment. These results showed that SKBR3 and C5.2 cells were more sensitive to rapamycin compared to HB4a. Doxorubicin, in turn, led the cells to a S-G2/M arrest which was greater in HB4a cells compared to SKBR3 and C5.2. Similarly to doxorubicin alone, the combined treatment also caused an increase of S-G2/M arrest in HB4a and C5.2 cells. So, doxorubicin effects were predominant to the rapamycin effects on the cell cycle distribution of the combined treatment in these cell lines. Otherwise, SKBR3 showed a predominant effect of rapamycin since its association with doxorubicin caused a G0/G1 arrest after exposure to 30 nM of doxorubicin. The viability assays showed that the combined treatment was 20% more effective in inhibiting cell growth than doxorubicin alone in the three cell lines, which was associated with a reduction in the IC50 of doxorubicin by 2-fold. For each cell line, microarray data were analyzed using SAM (FDR 5%) to compare doxorubicin, rapamycin and the combined treatment to the respective untreated cells. Considering only C5.2 and SKBR3 cells, Gene Ontology (GO) annotations of the genes modulated by the combined treatment showed altered genes related to RNA splicing. Moreover, genes exclusively modulated by the combined treatment showed altered functions related to intracellular trafficking whereas HER-2-mediated response to the combined treatment included changes in the ubiquitin-proteasome pathway, glycolysis and electron transport chain. Altogether, our results seemed to affect important molecular pathways related to tumor survival in HER-2- overexpressing cell lines, which was associated to a 2-fold suppression in the IC50 of doxorubicin. These findings highlight the clinical relevance of the rapamycin/doxorubicin combination therapy in HER-2 context, since this association could be able to decrease toxicity of patients undergoing chemotherap

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data