Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 4 de 4
Filtrar
Mais filtros








Base de dados
Intervalo de ano de publicação
1.
Nat Commun ; 11(1): 3793, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32732981

RESUMO

Reproducible research is the bedrock of experimental science. To enable the deployment of large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time and across instruments and develop computational methods for improving quantitative accuracy. We perform 1560 data independent acquisition (DIA)-MS runs of eight samples containing known proportions of ovarian and prostate cancer tissue and yeast, or control HEK293T cells. Replicates are run on six mass spectrometers operating continuously with varying maintenance schedules over four months, interspersed with ~5000 other runs. We utilise negative controls and replicates to remove unwanted variation and enhance biological signal, outperforming existing methods. We also design a method for reducing missing values. Integrating these computational modules into a pipeline (ProNorM), we mitigate variation among instruments over time and accurately predict tissue proportions. We demonstrate how to improve the quantitative analysis of large-scale DIA-MS data, providing a pathway toward clinical proteomics.


Assuntos
Espectrometria de Massas/métodos , Proteoma/análise , Proteômica/métodos , Biomarcadores Tumorais/análise , Linhagem Celular Tumoral , Feminino , Células HEK293 , Humanos , Masculino , Neoplasias Ovarianas , Neoplasias da Próstata , Reprodutibilidade dos Testes , Saccharomyces cerevisiae
2.
Proteomics Clin Appl ; 12(3): e1700094, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29227041

RESUMO

PURPOSE: To validate differences in protein levels between good and poor prognosis American Joint Committee on Cancer (AJCC) stage III melanoma patients and compile a protein panel to stratify patient risk. EXPERIMENTAL DESIGN: Protein extracts from melanoma metastases within lymph nodes in patients with stage III disease with good (n = 16, >4 years survival) and poor survival (n = 14, <2 years survival) were analyzed by selected reaction monitoring (SRM). Diagonal Linear Discriminant Analysis (DLDA) was performed to generate a protein biomarker panel. RESULTS: SRM analysis identified ten proteins that were differentially abundant between good and poor prognosis stage III melanoma patients. The ten differential proteins were combined with 22 proteins identified in our previous work. A panel of 14 proteins was selected by DLDA that was able to accurately classify patients into prognostic groups based on levels of these proteins. CONCLUSIONS AND CLINICAL RELEVANCE: The ten differential proteins identified by SRM have biological significance in cancer progression. The final signature of 14 proteins identified by SRM could be used to identify AJCC stage III melanoma patients likely to have poor outcomes who may benefit from adjuvant systemic therapy.


Assuntos
Melanoma/diagnóstico , Melanoma/metabolismo , Proteínas de Neoplasias/metabolismo , Proteômica , Biomarcadores Tumorais/metabolismo , Humanos , Estimativa de Kaplan-Meier , Metástase Linfática , Melanoma/patologia , Estadiamento de Neoplasias , Prognóstico , Fatores de Tempo
3.
Cancers (Basel) ; 8(3)2016 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-26927180

RESUMO

The UPR (unfolded protein response) has been identified as a key factor in the progression and metastasis of cancers, notably melanoma. Several mediators of the UPR are upregulated in cancers, e.g., high levels of GRP78 (glucose-regulator protein 78 kDa) correlate with progression and poor outcome in melanoma patients. The proliferative burden of cancer induces stress and activates several cellular stress responses. The UPR is a tightly orchestrated stress response that is activated upon the accumulation of unfolded proteins within the ER (endoplasmic reticulum). The UPR is designed to mediate two conflicting outcomtes, recovery and apoptosis. As a result, the UPR initiates a widespread signaling cascade to return the cell to homeostasis and failing to achieve cellular recovery, initiates UPR-induced apoptosis. There is evidence that ER stress and subsequently the UPR promote tumourigenesis and metastasis. The complete role of the UPR has yet to be defined. Understanding how the UPR allows for adaption to stress and thereby assists in cancer progression is important in defining an archetype of melanoma pathology. In addition, elucidation of the mechanisms of the UPR may lead to development of effective treatments of metastatic melanoma.

4.
J Neuropathol Exp Neurol ; 74(5): 425-41, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25853691

RESUMO

Glioblastoma multiforme (GBM) tumor invasion is facilitated by cell migration and degradation of the extracellular matrix. Invadopodia are actin-rich structures that protrude from the plasma membrane in direct contact with the extracellular matrix and are proposed to participate in epithelial-mesenchymal transition. We characterized the invasiveness of 9 established GBM cell lines using an invadopodia assay and performed quantitative mass spectrometry-based proteomic analyses on enriched membrane fractions. All GBM cells produced invadopodia, with a 65% difference between the most invasive cell line (U87MG) and the least invasive cell line (LN229) (p = 0.0001). Overall, 1,141 proteins were identified in the GBM membrane proteome; the levels of 49 proteins correlated with cell invasiveness. Ingenuity Pathway Analysis predicted activation "cell movement" (z-score = 2.608, p = 3.94E(-04)) in more invasive cells and generated a network of invasion-associated proteins with direct links to key regulators of invadopodia formation. Gene expression data relating to the invasion-associated proteins ITGA5 (integrin α5), CD97, and ANXA1 (annexin A1) showed prognostic significance in independent GBM cohorts. Fluorescence microscopy demonstrated ITGA5, CD97, and ANXA1 localization in invadopodia assays, and small interfering RNA knockdown of ITGA5 reduced invadopodia formation in U87MG cells. Thus, invasion-associated proteins, including ITGA5, may prove to be useful anti-invasive targets; volociximab, a therapeutic antibody against integrin α5ß1, may be useful for treatment of patients with GBM.


Assuntos
Neoplasias Encefálicas/patologia , Regulação Neoplásica da Expressão Gênica , Glioblastoma/patologia , Proteínas de Membrana/metabolismo , Invasividade Neoplásica/patologia , Anexina A1/genética , Anexina A1/metabolismo , Antígenos CD/genética , Antígenos CD/metabolismo , Linhagem Celular Tumoral , Bases de Dados de Proteínas/estatística & dados numéricos , Humanos , Masculino , Proteínas de Membrana/genética , Pessoa de Meia-Idade , Proteômica/métodos , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Espectrometria de Massas em Tandem , Transfecção
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA