Proteomic changes in Trypanosoma cruzi epimastigotes treated with the proapoptotic compound PAC-1.

Apoptosis is a highly regulated process of cell death in metazoans. Therefore, understanding the biochemical changes associated with apoptosis-like death in Trypanosoma cruzi is key to drug development. PAC-1 was recently shown to induce apoptosis in T. cruzi; with this as motivation, we used quantitative proteomics to unveil alterations of PAC-1-treated versus untreated epimastigotes. The PAC-1 treatment reduced the abundance of putative vesicle-associated membrane protein, putative eukaryotic translation initiation factor 1 eIF1, coatomer subunit beta, putative amastin, and a putative cytoskeleton-associated protein. Apoptosis-like signaling also increases the abundance of proteins associated with actin cytoskeleton remodeling, cell polarization, apoptotic signaling, phosphorylation, methylation, ergosterol biosynthesis, vacuolar proteins associated with autophagy, and flagellum motility. We shortlist seventeen protein targets for possible use in chemotherapy for Chagas disease. Almost all differentially abundant proteins belong to a family of proteins previously associated with apoptosis in metazoans, suggesting that the apoptotic pathway's key functions have been preserved from trypanosomatids and metazoans. SIGNIFICANCE: Approximately 8 million people worldwide are infected with Trypanosoma cruzi. The treatment of Chagas disease comprises drugs with severe side effects, thus limiting their application. Thus, developing new pharmaceutical solutions is relevant, and several molecules targeting apoptosis are therapeutically efficient for parasitic, cardiac, and neurological diseases. Apoptotic processes lead to specific morphological features that have been previously observed in T. cruzi. Here, we investigate changes in epimastigotes' proteomic profile treated with the proapoptotic compound PAC-1, providing data concerning the regulation of both metabolic and cellular processes in nonmetazoan apoptotic cells. We shortlist seventeen protein target candidates for use in chemotherapy for Chagas disease.

Comparing intestinal versus diffuse gastric cancer using a PEFF-oriented proteomic pipeline.

Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue. Thus, failing to consider the anatomical region could lead to differential proteins that are not disease specific. With this as motivation, we compared the proteomic profiles of intestinal and diffuse adenocarcinoma from the same anatomical region, the corpus. To achieve this, we used isobaric labeling (iTRAQ) of peptides, a 10-step HILIC fractionation, and reversed-phase nano-chromatography coupled online with a Q-Exactive Plus mass spectrometer. We updated PatternLab to take advantage of the new Comet-PEFF search engine that enables identifying post-translational modifications and mutations included in neXtProt's PSI Extended FASTA Format (PEFF) metadata. Our pipeline then uses a text-mining tool that automatically extracts PubMed IDs from the proteomic result metadata and drills down keywords from manuscripts related with the biological processes at hand. Our results disclose important proteins such as apolipoprotein B-100, S100 and 14-3-3 proteins, among many others, highlighting the different pathways enriched by each cancer type. SIGNIFICANCE: Gastric cancer is a heterogeneous and multifactorial disease responsible for a significant number of deaths every year. Despite the constant improvement of surgical techniques and multimodal treatments, survival rates are low, mostly due to limited diagnostic techniques and late symptoms. Intestinal and diffuse types of gastric cancer have distinct clinical and pathological characteristics; yet little is known about the molecular mechanisms regulating these two types of gastric tumors. Here we compared the proteomic profile of diffuse and intestinal types of gastric cancer from the same anatomical location, the corpus, from four male patients. This methodological design aimed to eliminate proteomic variations resulting from comparison of tumors from distinct anatomical regions. Our PEFF-tailored proteomic pipeline significantly increased the identifications as when compared to previous versions of PatternLab.

Considerations about gastric cancer proteomics.

The frequency of molecular studies aimed to analyze promoter methylation of tumor suppressor genes and global proteomics in gastric carcinogenesis is increasing. Nonetheless, only a few considered the different types of stomach cells, the tumor location and the influence of Helicobacter pylori and Epstein Barr virus infection (EBV). Molecular differences relating to anatomical and histological tumor areas were also recently described. The authors propose a molecular classification of gastric cancer, dividing it into four subtypes: tumors positive for EBV; microsatellite unstable tumors; genomically stable tumors and tumors with chromosomal instability. RESUMO A frequência de estudos moleculares visando a analisar os promotores de metilação de genes supressores de tumor e proteômica globais na carcinogênese gástrica está aumentando. No entanto, apenas alguns consideraram os diferentes tipos de células do estômago, a localização do tumor e a influência da infecção por Helicobacter pylori e pelo vírus Epstein-Barr (EBV). Diferenças moleculares relacionadas com áreas tumorais anatômicas e histológicas também foram recentemente descritas. Os autores propõem uma classificação molecular de câncer gástrico, dividindo-o em quatro subtipos: tumores positivos para o EBV; tumores microssatélite instáveis; tumores genomicamente estáveis ​​e tumores com instabilidade cromossômica.

A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme.

Tumors consist of cells in different stages of transformation with molecular and cellular heterogeneity. By far, heterogeneity is the hallmark of glioblastoma multiforme (GBM), the most malignant and aggressive type of glioma. Most proteomic studies aim in comparing tumors from different patients, but here we dive into exploring the intratumoral proteome diversity of a single GBM. For this, we profiled tumor fragments from the profound region of the same patient's GBM but obtained from two surgeries a year's time apart. Our analysis also included GBM's fragments from different anatomical regions. Our quantitative proteomic strategy employed 4-plex iTRAQ peptide labeling followed by a four-step strong cation chromatographic separation; each fraction was then analyzed by reversed-phase nano-chromatography coupled on-line with an Orbitrap-Velos mass spectrometer. Unsupervised clustering grouped the proteomic profiles into four major distinct groups and showed that most changes were related to the tumor's anatomical region. Nevertheless, we report differentially abundant proteins from GBM's fragments of the same region but obtained 1 year apart. We discuss several key proteins (e.g., S100A9) and enriched pathways linked with GBM such as the Ras pathway, RHO GTPases activate PKNs, and those related to apoptosis, to name a few. As far as we know, this is the only report that compares GBM fragments proteomic profiles from the same patient. Ultimately, our results fuel the forefront of scientific discussion on the importance in exploring the richness of subproteomes within a single tissue sample for a better understanding of the disease, as each tumor is unique.

Colorectal cancer DNA methylation patterns from patients in Manaus, Brazil

BACKGROUND: DNA methylation is commonly linked with the silencing of the gene expression for many tumor suppressor genes. As such, determining DNA methylation patterns should aid, in times to come, in the diagnosis and personal treatment for various types of cancers. Here, we analyzed the methylation pattern from five colorectal cancer patients from the Amazon state in Brazil for four tumor suppressor genes, viz.: DAPK, CDH1, CDKN2A, and TIMP2 by employing a polymerase chain reaction (PCR) specific to methylation. Efforts in the study of colorectal cancer are fundamental as it is the third most of highest incidence in the world. RESULTS: Tumor biopsies were methylated in 1/5 (20 %), 2/5 (40 %), 4/5 (80 %), and 4/5 (80 %) for CDH1, CDKN2A, DAPK, and TIMP2 genes, respectively. The margin biopsies were methylated in 3/7 (43 %), 2/7 (28 %), 7/7 (100 %), and 6/7 (86 %) for CDH1, CDKN2A, DAPK, and TIMP2, respectively. CONCLUSIONS: Our findings showed DAPK and TIMP2 to be methylated in most samples from both tumor tissues and adjacent non-neoplastic margins; thus presenting distinct methylation patterns. This emphasizes the importance of better understanding of the relation of these patterns with cancer in the context of different populations.

Proteomic profiling of the influence of iron availability on Cryptococcus gattii.

Iron is essential and ubiquitous in living organisms. The competition for this micronutrient between the host and its pathogens has been related to disease establishment. Cryptococcus gattii is an encapsulated yeast that causes cryptococcosis mainly in immunocompetent individuals. In this study, we analyzed the proteomic profile of the C. gattii R265 Vancouver Island isolate under iron-depleted and -repleted conditions by multidimensional protein identification technology (MudPIT) and by 2D-GE. Proteins and key mechanisms affected by alteration of iron levels such as capsule production, cAMP-signaling pathway, response to stress, and metabolic pathways related to mitochondrial function were identified. Our results also show both proteomic methodologies employed to be complementary.

Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol.

Perillyl alcohol (POH) is a naturally occurring terpene and a promising chemotherapeutic agent for glioblastoma multiform; yet, little is known about its molecular effects. Here we present results of a semi-quantitative proteomic analysis of A172 cells exposed to POH for different time-periods (1', 10', 30', 60', 4h, and 24h). The analysis identified more than 4000 proteins; which were clustered using PatternLab for proteomics and then linked to Ras signaling, tissue homeostasis, induction of apoptosis, metallopeptidase activity, and ubiquitin-protein ligase activity. Our results make available one of the most complete protein repositories for the A172. Moreover, we detected the phosphorylation of GSK3beta (Glycogen synthase kinase) and the inhibition of ERK's (extracellular signal regulated kinase) phosphorylation after 10', which suggests a new mechanism of POH's activation for apoptosis.

Anti-thrombin as a prognostic biomarker candidate for patients with recurrent glioblastoma multiform under treatment with perillyl alcohol.

Perillyl alcohol (POH) is a naturally occurring monoterpene with antiangiogenic and anti-tumoral properties. This chemotherapeutic agent has proven effectiveness in several clinical trials, including an ongoing phase I, comprising patients with recurrent glioblastoma multiform (GBM) under treatment with POH by intranasal administration. Proteomics offers tools to distinguish states of biological systems according to protein expression differences and therefore, can be used to gain pathological insights and to search for disease follow-up biomarkers. In this work, a differential gel electrophoresis (DIGE) proteomic approach was used to search for plasma proteins that correlated with the disease progression in 10 of these patients. Our results pointed antithrombin (down) and fibrinogen (up) regulated after a four months treatment deserving to be further verified as prognostic markers for this treatment. Possible links between tumor progression and anti-thrombin expression level are also discussed.

Oligodendrogliomas: a genética molecular e o desenvolvimento estratégia terapêutica adjuvante / Oligodendrogliomas: molecular genetics and development of adjuvant therapeutic strategies

A incidência dos oligodendrogliomas tem aumentado provavelmente em razão do progresso na precisão de diagnóstico. Aproximadamente dois terços dos pacientes com a forma mais agressiva, oligodendroglioma anaplásico, mostram resposta substancial à quimioterapia com a associação procarbazina/lomustina/vincristina (PCV). Entretanto, os resultados da quimuiterapia anaplásica dos oligodendrogliomas resulta em grande número de células com ERK/MAPK ativadas. O monoterpeno álcool perílico demonstra atividades quimiopreventiva e quimioterápica em diversos modelos de tumores e sugere-se que estas possam estar associadas com a capacidade de inibir a farmesilação pós-traducional e a sinalização da Ras, assim como a cascata de sinalização por meio da RAF-MEK-ERK. Estudo do nosso grupo observou que pode estar atuando mediante a inibição da fosforilação da extracellular regulated kinase (ERK), uma proteína envolvida na cascata de transdução de sinal através da membrana e proliferação celular induzida pela proteína Ras. Este artigo discute a redução de oligodendroglioma anaplásico recidivado em paciente tratado durante nove meses com álcool perílico por via intranasal.

Marcadores sérios e espectrometria de massa no diagnótico do câncer / Serum markers and mass spectrometry in the diagnosis of cancer

Esta revisão abrange as principais técnicas, limitações e utilidades da espectrometria de massa aplicada à análise de fluidos biológicos para buscar biomarcadores com potencialidade de diagnóstico médico. Atualmente esse método é capaz de discernir, em segundos, padrões moleculares diferencialmente expressos entre indivíduos controles e com câncer. Resultados da literatura apontam a espectrometria de massa como metodologia promissora no futuro do diagnóstico.

This manuscript reviews mass spectrometry methods and limitations for analisys of biological fluids in the search for biomarkers that can aid medical diagnosis. Currently, mass spectrometry has the ability to discriminate differentially expressed molecular patterns among cancer patients and control subjects. Results in the literature point mass spectrometry as having a major role in the future of medical diagnosis.

Effects of perillyl alcohol and heat shock treatment in gene expression of human lung adenocarcinoma cell line A549.

The K-Ras protein is found mutated in 42.4% of lung adenocarcinoma cases, evidencing its importance as a chemotherapeutic target. The Ras protein becomes functional after farnesylation, a post-transduction modification, allowing its attachment to the cellular membrane permitting signal transduction. Perillyl alcohol (POH) has been shown to inhibit the farnesylation of small G-proteins such as Ras. HSP70, a protein known to appear after heat shock (HS), is found over expressed in lung cancer and modifies chemotherapeutic effects. In this work, the effect of POH and HS in the gene expression of human adenocarcinoma lung cells (A549) is studied. Cells incubated with POH followed by 42 degrees C HS presented a 20.7% cellular viability decrease compared to the ones kept at 37 degrees C. A different pattern synthesis was observed for each sequences of cell treatment. Independent of the heat treatment, the amount of HSP70 was decrease by POH without modification in the amount of p53. Here it is shown that HS modified the POH effects in the ERK activation pathway by altering the phosphorylation of p44/42 in human adenocarcinoma lung cells.

Efeito do álcool perílico na expressão gênica de células de adenocarcinoma de pulmão humano / Effect of perillyl alcohol on gene expression of human pulmonary adenocarcinoma cells

OBJETIVO: Estudar a ação do álcool perílico na expressão gênica de células de adenocarcinoma de pulmão humano. MÉTODOS: Incubaram-se células de adenocarcinoma de pulmão com álcool perílico em diluições que variaram entre 0,03 por cento e 0,0003 por cento por 48 horas. Observaram-se as alterações na morfologia celular e quantificou-se a viabilidade celular pelo método do MTT (3-(4,5-dimetiltiazol-2-yl)-2,5 difeniltertrazolim brometo). Analisou-se a síntese de proteínas das amostras previamente marcadas radioativamente com 35S, através de eletroforese em gel de poliacrilamida. Determinou-se a expressão das proteínas p53 e p42/44 através do método de Western Blot. RESULTADOS: Após 48 horas de incubação, observaram-se alterações na morfologia celular para a diluição de 0,03 por cento de álcool perílico, as quais foram pouco verificadas em diluições superiores a 0,003 por cento. A inibição da viabilidade celular foi de 60,17 por cento (p < 0,001), 15,62 por cento (p < 0,001) e 11,53 por cento (p < 0,05) para as diluições de 0,03 por cento, 0,003 por cento e 0,0003 por cento de álcool perílico, respectivamente. Os resultados mostram a indução de proteínas de 110 kDa, 42 kDa e 28 kDa. Não se observou variação estatisticamente significativa para a expressão da proteína p53. Em comparação com a expressão de alfa-tubulina, a diluição de 0,003 por cento de álcool perílico provocou uma diminuição marcante da fosforilação da p44 e um aumento da fosforilação da p42. CONCLUSÃO: Os resultados apresentados sugerem novos caminhos metabólicos da ação do álcool perílico em células de adenocarcinoma de pulmão humano.

OBJECTIVE: To study the effect of perillyl alcohol on the gene expression of human pulmonary adenocarcinoma cells. METHODS: Pulmonary adenocarcinoma cells were incubated with perillyl alcohol in dilutions ranging from 0.03 percent to 0.0003 percent for 48 hours. Alterations were observed in the cell morphology, and cell viability was quantified using [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assays. Protein synthesis of samples previously targeted with S35 was analyzed using electrophoresis on a polyacrylamide gel. Expression of the proteins p53 and p44/42 was determined using the Western blot method. RESULTS: After 48 hours of incubation, greater nsumbers of morphological alterations were observed in cells treated with the 0.03 percent perillyl alcohol dilution than in those treated with perillyl alcohol diluted to 0.003 percent or further. Treatment with perillyl alcohol dilutions of 0.03 percent, 0.003 percent and 0.0003 percent inhibited cellular viability by 60.17 percent (p < 0.001), 15.62 percent (p < 0.001) and 11.53 percent (p < 0.05), respectively. The results show that 28-kDa, 42-kDa and 110-kDa proteins were induced. No statistically significant effect on p53 expression was observed. In comparison with the expression of alpha-tubulin, the 0.003 percent perillyl alcohol dilution induced an increase in p42 phosphorylation and a marked decrease in p44 phosphorylation. CONCLUSION: The results suggest that there are other, previously undescribed, metabolic pathways for perillyl alcohol effects in human pulmonary adenocarcinoma cells.

Detecção de potenciais marcadores moleculares séricos da doença de Hodgkin / Detection of potential serum molecular markers for Hodgkin's disease

MOTIVAÇAO: Neste trabalho foi analisado o perfil de proteínas séricas de pacientes com doença de Hodgkin (DH) localizada e avançada em busca de novos e potenciais biomarcadores para o diagnóstico médico. MATERIAIS E MÉTODOS: O perfil de proteínas presentes no soro de 14 indivíduos saudáveis, 14 pacientes com DH avançada e 15 pacientes com DH localizada, assim como pools de soro dos respectivos grupos, foi analisado em gel desnaturante de poliacrilamida a 12 por cento corado pela prata. A densitometria e a intensidade média das bandas de interesse foram estudadas utilizando-se o Kodak 1D Scientific Imaging System. RESULTADOS E CONCLUSÕES: O perfil protéico apresentou acentuada variação entre os pacientes examinados; entretanto foi observada a indução predominante de determinadas proteínas (aproximadamente 26kDa e 18kDa), cuja expressão foi substancialmente diferente quando em comparação com os controles (p < 0,01). Estas proteínas podem potencialmente constituir-se em marcadores moleculares de acompanhamento da evolução e do tratamento da doença.