RESUMEN

PURPOSE: We describe the outcome of the Biomarkers Consortium CSF Proteomics Project (where CSF is cerebral spinal fluid), a public-private partnership of government, academia, nonprofit, and industry. The goal of this study was to evaluate a multiplexed MS-based approach for the qualification of candidate Alzheimer's disease (AD) biomarkers using CSF samples from the AD Neuroimaging Initiative. EXPERIMENTAL DESIGN: Reproducibility of sample processing, analytic variability, and ability to detect a variety of analytes of interest were thoroughly investigated. Multiple approaches to statistical analyses assessed whether panel analytes were associated with baseline pathology (mild cognitive impairment (MCI), AD) versus healthy controls or associated with progression for MCI patients, and included (i) univariate association analyses, (ii) univariate prediction models, (iii) exploratory multivariate analyses, and (iv) supervised multivariate analysis. RESULTS: A robust targeted MS-based approach for the qualification of candidate AD biomarkers was developed. The results identified several peptides with potential diagnostic or predictive utility, with the most significant differences observed for the following peptides for differentiating (including peptides from hemoglobin A, hemoglobin B, and superoxide dismutase) or predicting (including peptides from neuronal pentraxin-2, neurosecretory protein VGF (VGF), and secretogranin-2) progression versus nonprogression from MCI to AD. CONCLUSIONS AND CLINICAL RELEVANCE: These data provide potential insights into the biology of CSF in AD and MCI progression and provide a novel tool for AD researchers and clinicians working to improve diagnostic accuracy, evaluation of treatment efficacy, and early diagnosis.

Asunto(s)

Enfermedad de Alzheimer/líquido cefalorraquídeo , Bioensayo/métodos , Biomarcadores/líquido cefalorraquídeo , Espectrometría de Masas/métodos , Neuroimagen/métodos , Anciano , Enfermedad de Alzheimer/patología , Secuencia de Aminoácidos , Apolipoproteínas E/líquido cefalorraquídeo , Área Bajo la Curva , Disfunción Cognitiva/líquido cefalorraquídeo , Disfunción Cognitiva/patología , Progresión de la Enfermedad , Femenino , Humanos , Masculino , Datos de Secuencia Molecular , Péptidos/líquido cefalorraquídeo , Péptidos/química , Análisis de Componente Principal , Control de Calidad , Reproducibilidad de los Resultados , Estadística como Asunto

RESUMEN

Each year, millions of pulmonary nodules are discovered by computed tomography and subsequently biopsied. Because most of these nodules are benign, many patients undergo unnecessary and costly invasive procedures. We present a 13-protein blood-based classifier that differentiates malignant and benign nodules with high confidence, thereby providing a diagnostic tool to avoid invasive biopsy on benign nodules. Using a systems biology strategy, we identified 371 protein candidates and developed a multiple reaction monitoring (MRM) assay for each. The MRM assays were applied in a three-site discovery study (n = 143) on plasma samples from patients with benign and stage IA lung cancer matched for nodule size, age, gender, and clinical site, producing a 13-protein classifier. The classifier was validated on an independent set of plasma samples (n = 104), exhibiting a negative predictive value (NPV) of 90%. Validation performance on samples from a nondiscovery clinical site showed an NPV of 94%, indicating the general effectiveness of the classifier. A pathway analysis demonstrated that the classifier proteins are likely modulated by a few transcription regulators (NF2L2, AHR, MYC, and FOS) that are associated with lung cancer, lung inflammation, and oxidative stress networks. The classifier score was independent of patient nodule size, smoking history, and age, which are risk factors used for clinical management of pulmonary nodules. Thus, this molecular test provides a potential complementary tool to help physicians in lung cancer diagnosis.

Asunto(s)

Algoritmos , Proteómica , Nódulo Pulmonar Solitario/sangre , Nódulo Pulmonar Solitario/metabolismo , Biomarcadores de Tumor/sangre , Femenino , Humanos , Modelos Logísticos , Neoplasias Pulmonares/sangre , Neoplasias Pulmonares/metabolismo , Masculino , Persona de Mediana Edad , Análisis Multivariante , Proteínas de Neoplasias/sangre , Reproducibilidad de los Resultados

RESUMEN

We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.

Asunto(s)

Redes Reguladoras de Genes , Hipoxia/genética , Redes y Vías Metabólicas/genética , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/metabolismo , Adaptación Fisiológica , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Inmunoprecipitación de Cromatina , Perfilación de la Expresión Génica , Redes Reguladoras de Genes/genética , Genómica , Hipoxia/metabolismo , Metabolismo de los Lípidos/genética , Modelos Biológicos , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/fisiología , Oxígeno/farmacología , Proteolisis , ARN Mensajero/genética , ARN Mensajero/metabolismo , Reproducibilidad de los Resultados , Análisis de Secuencia de ADN , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Tuberculosis/metabolismo , Tuberculosis/microbiología

RESUMEN

Grounded theory served to develop a model of the family caregiver decision-making process regarding placement of a cognitively impaired elderly relative. Eighteen caregivers were interviewed every 6 months over an average 20 months. Results show the process is activated when the caregiver or a health care professional introduces the possibility of placement. The caregiver's assessment of the pros and cons of placement is modulated primarily by interactions with the formal and informal social network. Three types of longitudinal trajectory emerged from the data suggesting avenues of intervention to support caregivers during this painful process.

Asunto(s)

Cuidadores/psicología , Toma de Decisiones , Demencia , Institucionalización , Casas de Salud , Anciano , Familia , Femenino , Servicios de Atención de Salud a Domicilio , Humanos , Masculino , Persona de Mediana Edad , Modelos Teóricos , Investigación Cualitativa , Quebec

RESUMEN

OBJECTIVES: The objectives of the study were to identify the adjustments made during the implantation and the conditions favouring or limiting the SMAF utilisation. METHODS: A multiqualitative quote was developed. The Functional autonomy measurement system (SMAF) was implanted in 11 French medico-social establishments. Analyses were made with the mixed type thematic method from Miles and Huberman. RESULTS: Principal adjustments that have been made during implantation concern the informatics assistance and clinical support. Strategic, organizational and individual factors explained adhesion level of actors and the subsequent flow of implantation. CONCLUSION: Establishment of SMAF and of the software eSMAF® in the medico-social establishments rests on a certain number of conditions which could be identified during the study. These conditions made it possible to work out structured recommendations for future implementations.

Asunto(s)

Actividades Cotidianas/clasificación , Evaluación Geriátrica , Implementación de Plan de Salud/organización & administración , Anciano , Anciano de 80 o más Años , Evaluación de la Discapacidad , Documentación/métodos , Femenino , Predicción , Implementación de Plan de Salud/tendencias , Humanos , Masculino , Proyectos Piloto , Quebec , Programas Informáticos

RESUMEN

The elderly in palliative care are confronted with difficult decisions relating to treatments. The philosophy of palliative care, namely, including the patient and his/her family right away, leads the doctor to consult with the two parties involved when choosing a treatment. As no theoretical model allows us to understand how the decision-making process hinges on the trio (a capable elderly person, a family caregiver, and the doctor) in a context of palliative care, we propose one which was developed from three strategies of document analysis: theoretical synthesis, theoretical analysis, and theoretical derivation. According to our model, the decision-making process depends on individual factors influencing the decision of the participant, expectations and attitudes as to the role, the level of confidence amongst the parties involved, the manner in which they communicate with each other, their mutual understanding of the clinical and ethical issues, and, finally, their ability to cooperate.

Asunto(s)

Toma de Decisiones , Familia , Modelos Teóricos , Cuidados Paliativos , Anciano , Comunicación , Relaciones Familiares , Humanos , Relaciones Médico-Paciente , Relaciones Profesional-Familia

RESUMEN

BACKGROUND: Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data. RESULTS: The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes. CONCLUSIONS: An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.

Asunto(s)

Proteínas Bacterianas/análisis , Brucella abortus/química , Genoma Bacteriano , Proteoma/análisis , Secuencia de Aminoácidos , Animales , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Secuencia de Bases , Brucella abortus/genética , Línea Celular , Ratones , Datos de Secuencia Molecular , Operón , Proteoma/química , Proteoma/genética , Proteómica

RESUMEN

Macrophages were infected with virulent Brucella abortus strain 2308 or attenuated strain 19. Intracellular bacteria were recovered at different times after infection and their proteomes compared. The virulent strain initially reduced most biosynthesis and altered its respiration; adaptations reversed later in infection. The attenuated strain was unable to match the magnitude of the virulent strain's adjustments. The results provide insight into mechanisms utilized by Brucella to establish intracellular infections.

Asunto(s)

Proteínas Bacterianas/metabolismo , Brucella abortus/metabolismo , Macrófagos/microbiología , Proteoma/metabolismo , Línea Celular , Cromatografía Liquida , Humanos , Espectrometría de Masas en Tándem

RESUMEN

Brucella virulence is linked to components of the cell envelope and tightly connected to the function of the BvrR/BvrS sensory-regulatory system. To quantify the impact of BvrR/BvrS on cell envelope proteins, we performed a label-free mass spectrometry-based proteomic analysis of spontaneously released outer membrane fragments from four strains of Brucella abortus (wild type virulent, avirulent bvrR- and bvrS- mutants as well as reconstituted virulent bvrR+ (bvrR-/pbvrR+)). We identified 167 differentially expressed proteins, of which 25 were assigned to the outer membrane. Approximately half of the outer membrane proteins decreased in abundance, whereas half increased. Notably, expression of five Omp3 family proteins decreased whereas five lipoproteins increased in the mutant strains. In the periplasmic space, by contrast, approximately 80% of the 60 differentially expressed proteins were increased in at least one avirulent mutant. Periplasmic proteins are primarily involved in substrate uptake and transport, and a uniform increase in this class may indicate a nutritional stress response, possibly a consequence of defective outer membrane function. Virtually all proteins reverted to wild type levels in the reconstituted virulent bvrR+ strain. We propose that the wide changes in cell envelope protein expression relate to the markedly avirulent phenotype of bvrR- and bvrS- mutants and that Brucella virulence depends on regulatory networks involving cell envelope and metabolism rather than on discrete virulence factors. This model may be relevant to other alpha-Proteobacteria harboring BvrR/BvrS orthologous systems known to be essential for parasitism or endosymbiosis.

Asunto(s)

Proteínas de la Membrana Bacteriana Externa/análisis , Brucella abortus/metabolismo , Brucella abortus/patogenicidad , Proteínas Periplasmáticas/análisis , Porinas/análisis , Secuencia de Aminoácidos , Proteínas de la Membrana Bacteriana Externa/metabolismo , Brucella abortus/genética , Modelos Biológicos , Datos de Secuencia Molecular , Mutación , Proteínas Periplasmáticas/metabolismo , Porinas/metabolismo , Virulencia

RESUMEN

Conformational conversion of proteins in disease is likely to be accompanied by molecular surface exposure of previously sequestered amino-acid side chains. We found that induction of beta-sheet structures in recombinant prion proteins is associated with increased solvent accessibility of tyrosine. Antibodies directed against the prion protein repeat motif, tyrosine-tyrosine-arginine, recognize the pathological isoform of the prion protein but not the normal cellular isoform, as assessed by immunoprecipitation, plate capture immunoassay and flow cytometry. Antibody binding to the pathological epitope is saturable and specific, and can be created in vitro by partial denaturation of normal brain prion protein. Conformation-selective exposure of Tyr-Tyr-Arg provides a probe for the distribution and structure of pathologically misfolded prion protein, and may lead to new diagnostics and therapeutics for prion diseases.

Asunto(s)

Especificidad de Anticuerpos , Epítopos/inmunología , Proteínas PrPSc/química , Proteínas PrPSc/inmunología , Pliegue de Proteína , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Animales , Anticuerpos/genética , Anticuerpos/inmunología , Anticuerpos/metabolismo , Reacciones Cruzadas , Ensayo de Inmunoadsorción Enzimática , Citometría de Flujo , Humanos , Datos de Secuencia Molecular , Pruebas de Precipitina , Conformación Proteica , Conejos , Sensibilidad y Especificidad , Homología de Secuencia de Aminoácido , Tirosina/química , Tirosina/metabolismo