Comparative proteomic analysis of patients with acute myeloid leukemia before and after induction therapy.

BACKGROUND: Acute myeloid leukemia (AML) is a malignant disorder of hematopoietic stem and progenitor cells, characterized by accumulation of immature blasts in the bone marrow and peripheral blood of affected patients. Response to chemotherapy treatment in patients with AML is wide-ranging, and to date there are no adequate molecular biomarkers used to predict clinical outcome. OBJECTIVE: The aim of this study was to identify potential protein biomarkers which could help predict response to induction treatment in AML patients. METHODS: Peripheral blood samples were obtained from 15 AML patients both before and after treatment. A comparative proteomic analysis was performed using 2D gel electrophoresis followed by Mass Spectrometry. RESULTS: This comparative proteomic study, combined with a protein network analysis, revealed several proteins that could be considered potential biomarkers of poor prognosis in AML: GAPDH which favors increased glucose metabolism; eEF1A1 and Annexin A1 that promote proliferation and migration, cofilin 1 which plays a role in the activation of apoptosis; and GSTP1 which is involved in the processes of detoxification and chemoresistance. CONCLUSIONS: This study gives an insight into a panel of protein biomarkers with prognostic potential that should be further investigated.

Modulation of the Canonical Wnt Signaling Pathway by Dietary Polyphenols, an Opportunity for Colorectal Cancer Chemoprevention and Treatment.

In the last few decades there has been a rise in the worldwide incidence of colorectal cancer which can be traced back to the influence of well-known modifiable risk factors such as lifestyle, diet and obesity. Conversely, the consumption of fruits, vegetables and fiber decreases the risk of CRC, which is why dietary polyphenols have aroused interest in recent years as potentially anti-carcinogenic compounds. One of the driving forces of colorectal carcinogenesis, in both sporadic and hereditary CRC, is the aberrant activation/regulation of the Wnt/ß-catenin pathway. This review discusses reports of modulation of the Wnt/ß-Catenin signaling pathway by dietary polyphenols (resveratrol, avenanthramides, epigallocatechinin, curcumin, quercetin, silibinin, genistein and mangiferin) specifically focusing on CRC, and proposes a model as to how this modulation occurs. There is potential for implementing these dietary polyphenols into preventative and therapeutic therapies for CRC as evidenced by some clinical trials that have been carried out with promising results.

Interaction network of proteins associated with unfavorable prognosis in acute myeloid leukemia.

Acute myeloid leukemia (AML) is a malignant disorder of hematopoietic stem and progenitor cells, characterized by accumulation of immature blasts in the bone marrow and peripheral blood of affected patients. Standard induction therapy leads to complete remission in approximately 50% to 75% of patients. In spite of favorable primary response rates, only 20% to 30% of patients enjoy long-term disease free survival. Identifying proteins involved in prognosis is important for proposing biomarkers that can aid in the clinical management of the disease. The aim of this study was to construct a protein-protein interaction (PPI) network based on serum proteins associated with unfavorable prognosis of AML, and analyze the biological pathways underlying molecular complexes in the network. We identified 16 candidate serum proteins associated with unfavorable prognosis (in terms of poor response to treatment, poor overall survival, short complete remission, and relapse) in AML via a search in the literature: IL2RA, FTL, HSP90AA1, D2HGDH, PLAU, COL18A1, FGF19, SPP1, FGA, PF4, NME1, TNF, ANGPT2, B2M, CD274, LGALS3. The PPI network was constructed with Cytoscape using association networks from String and BioGRID, and Gene Ontology enrichment analysis using the ClueGo pluggin was performed. The central protein in the network was found to be PTPN11 which is involved in modulating the RAS-ERK, PI3K-AKT and JAK-STAT pathways, as well as in hematopoiesis, and in the regulation of apoptotic genes. Therefore, a dysregulation of this protein and/or of the proteins connected to it in the network leads to the defective activation of these signaling pathways and to a reduction in apoptosis. Together, this could cause an increase in the frequency of leukemic cells and a resistance to apoptosis in response to treatment.

Joint pre-processing framework for two-dimensional gel electrophoresis images based on nonlinear filtering, background correction and normalization techniques.

BACKGROUND: Two-dimensional gel electrophoresis (2-DGE) is a commonly used tool for proteomic analysis. This gel-based technique separates proteins in a sample according to their isoelectric point and molecular weight. 2-DGE images often present anomalies due to the acquisition process, such as: diffuse and overlapping spots, and background noise. This study proposes a joint pre-processing framework that combines the capabilities of nonlinear filtering, background correction and image normalization techniques for pre-processing 2-DGE images. Among the most important, joint nonlinear diffusion filtering, adaptive piecewise histogram equalization and multilevel thresholding were evaluated using both synthetic data and real 2-DGE images. RESULTS: An improvement of up to 46% in spot detection efficiency was achieved for synthetic data using the proposed framework compared to implementing a single technique of either normalization, background correction or filtering. Additionally, the proposed framework increased the detection of low abundance spots by 20% for synthetic data compared to a normalization technique, and increased the background estimation by 67% compared to a background correction technique. In terms of real data, the joint pre-processing framework reduced the false positives up to 93%. CONCLUSIONS: The proposed joint pre-processing framework outperforms results achieved with a single approach. The best structure was obtained with the ordered combination of adaptive piecewise histogram equalization for image normalization, geometric nonlinear diffusion (GNDF) for filtering, and multilevel thresholding for background correction.

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review.

Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image.

Urine protein biomarkers for detection of cardiovascular disease and their use for the clinic.

INTRODUCTION: Cardiovascular disease (CVD) is the leading noncommunicable disease and main cause of death worldwide. Traditionally, blood has been the sample of choice for biomarker discovery, however, urine has roused great interest in recent years as a source of biomarkers. Sample collection is simple, non-invasive, and there is the possibility of implementing minimal cost tests in primary care settings. Areas covered: In this review, we systematically searched PubMed for proteomic studies of CVD, with the criteria that urine was included as a biological sample. Based on these criteria, and after manual curation, 47 research papers were included: 8 for coronary artery disease, 5 for angina, 15 for myocardial infarction, 23 for heart failure, and 4 for cerebrovascular disease. Expert commentary: Urinary biomarkers of early, asymptomatic stages of the disease would have a great impact on CVD morbidity and mortality, as widespread screening could be implemented at a reduced cost, allowing high-risk individuals to be identified and treated in a timely manner. An approach involving multiple biomarkers is necessary, as a single biomarker is unlikely to be sensitive/specific enough. By assessing a range of peptides there is the potential to detect changes in many pathways involved in the pathogenesis of CVDs.

Molecular biomarkers in acute myeloid leukemia.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults. The pathophysiology of this disease is just beginning to be understood at the cellular and molecular level, and currently cytogenetic markers are the most important for risk stratification and treatment of AML patients. However, with the advent of new technologies, the detection of other molecular markers such as point mutations and characterization of epigenetic and proteomic profiles, have begun to play an important role in how the disease is approached. Recent evidence shows that the identification of new AML biomarkers contributes to a better understanding of the molecular basis of the disease, is significantly useful in screening, diagnosis, prognosis and monitoring of AML, as well as the possibility of predicting each individual's response to treatment. This review summarizes the most relevant molecular (genetic, epigenetic, and protein) biomarkers associated with acute myeloid leukemia and discusses their clinical importance in terms of risk prediction, diagnosis and prognosis.

Análisis proteómico del veneno de la abeja africanizada: comparación de métodos de extracción / Proteomic Analysis of Africanized Bee Venom: a Comparison of Protein Extraction Methods

La abeja africanizada es la más común en la apicultura colombiana y a su veneno (apitoxina) se le han atribuido propiedades terapéuticas para diferentes enfermedades, sin mayor soporte científico. Al revisar en la literatura los reportes publicados sobre el análisis proteómico de la apitoxina, se encontraron cuatro métodos distintos para la extracción de proteínas de la apitoxina. El primer método consiste en resuspender la apitoxina en Urea 7 M, precipitar con acetona y finalmente resuspender en Urea 7 M y CHAPS 4 %. Para el segundo método se resuspende la apitoxina en buffer de lisis, se precipita con ácido tricloroacético, y luego se resuspende en Urea 7 M y CHAPS 4 %. El tercer método es igual al anterior, excepto que la precipitación se realiza con acetona en vez de ácido tricloroacético. Finalmente, el cuarto método consiste en resuspender la apitoxina en agua destilada, precipitar con acetona y resuspender en Urea 7 M y CHAPS 4 %. Este trabajo se enfocó en comparar el desempeño de estos cuatro métodos de extracción y determinar el método con el mejor resultado en cuanto a la concentración e integridad obtenida de las proteínas. De los distintos métodos evaluados, se encontró que los mejores resultados en cuanto a concentración de proteínas se obtuvieron con la resuspensión de apitoxina en buffer de lisis y precipitación con acetona (método 3) y con el método de resuspensión de apitoxina en agua destilada y precipitación con acetona (método 4). De estos, el mejor método de extracción en cuanto a integridad de las proteínas y perfil proteómico fue el de resuspensión de apitoxina en buffer de lisis seguido de precipitación con acetona (método 3).

The Africanised bee is the most common type of bee in Colombia, and therapeutic properties for different diseases have been attributed to its venom, without much scientific support. A literature search of reports on the proteomic analysis of honeybee venom yielded four different methods for extracting proteins from bee venom. The first method consists in resuspending the venom in 7 M Urea, followed by precipitation with acetone and finally resuspending the pellet in 7 M Urea and 4 % CHAPS. For the second method, the venom is resuspended in lysis buffer, precipitated with trichloroacetic acid, and then resuspended in 7 M Urea and 4 % CHAPS. The third method is similar to the previous one, except that the precipitation step is performed with acetone instead of trichloroacetic acid. Finally, the fourth method is to resuspend the venom in distilled water, precipitate with acetone and resuspend in 7 M Urea and 4 % CHAPS. This work focused on comparing the performance of these four extraction methods, in order to determine the method with the best results in terms of concentration and integrity of the proteins obtained. Of the four methods evaluated, the best results in terms of protein concentration and yield were obtained by resuspending the bee venom in lysis buffer followed by precipitation with acetone (method 3), and by resuspending in distilled water followed by precipitation with acetone (method 4). Of these, the method that maintained protein integrity and yielded the best proteomic profile was that in which the bee venom was resuspended in lysis buffer followed by precipitation with acetone (method 3).

Advances in urinary protein biomarkers for urogenital and non-urogenital pathologies.

The discovery of protein biomarkers that reflect the biological state of the body is of vital importance to disease management. Urine is an ideal source of biomarkers that provides a non-invasive approach to diagnosis, prognosis and prediction of diseases. Consequently, the study of the human urinary proteome has increased dramatically over the last 10 years, with many studies being published. This review focuses on urinary protein biomarkers that have shown potential, in initial studies, for diseases affecting the urogenital tract, specifically chronic kidney disease and prostate cancer, as well as other non-urogenital pathologies such as breast cancer, diabetes, atherosclerosis and osteoarthritis. PubMed was searched for peer-reviewed literature on the subject, published in the last 10 years. The keywords used were "urine, biomarker, protein, and/or prostate cancer/breast cancer/chronic kidney disease/diabetes/atherosclerosis/osteoarthritis". Original studies on the subject, as well as a small number of reviews, were analysed including the strengths and weaknesses, and we summarized the performance of biomarkers that demonstrated potential. One of the biggest challenges found is that biomarkers are often shared by several pathologies so are not specific to one disease. Therefore, the trend is shifting towards implementing a panel of biomarkers, which may increase specificity. Although there have been many advances in urinary proteomics, these have not resulted in similar advancements in clinical practice due to high costs and the lack of large data sets. In order to translate these potential biomarkers to clinical practice, vigorous validation is needed, with input from industry or large collaborative studies.

The dynamin-related protein Vps1 regulates vacuole fission, fusion and tubulation in the fission yeast, Schizosaccharomyces pombe.

Fission yeast cells lacking the dynamin-related protein (DRP) Vps1 had smaller vacuoles with reduced capacity for both fusion and fission in response to hypotonic and hypertonic conditions respectively. vps1Delta cells showed normal vacuolar protein sorting, actin organisation and endocytosis. Over-expression of vps1 transformed vacuoles from spherical to tubular. Tubule formation was enhanced in fission conditions and required the Rab protein Ypt7. Vacuole tubulation by Vps1 was more extensive in the absence of a second DRP, Dnm1. Both dnm1Delta and the double mutant vps1Delta dnm1Delta showed vacuole fission defects similar to that of vps1Delta. Over-expression of vps1 in dnm1Delta, or of dnm1 in vps1Delta failed to rescue this phenotype. Over-expression of dnm1 in wild-type cells, on the other hand, induced vacuole fission. Our results are consistent with a model of vacuole fission in which Vps1 creates a tubule of an appropriate diameter for subsequent scission by Dnm1.