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[PMID]:28452485
[Au] Autor:Li H; Park J; Kim H; Hwang KB; Paek E
[Ad] Endereço:School of Computer Science and Engineering, Soongsil University , Seoul 06978, Republic of Korea.
[Ti] Título:Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments.
[So] Source:J Proteome Res;16(6):2231-2239, 2017 Jun 02.
[Is] ISSN:1535-3907
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Proteogenomic searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated, however, mainly due to the difficulty in confirming the existence of identified novel peptides. We simulated a proteogenomic search using a controlled, spike-in proteomic data set. After confirming that the results of the simulated proteogenomic search were similar to those of a real proteogenomic search using a human cell line data set, we evaluated the performance of six FDR control methods-global, separate, and multistage FDR estimation, respectively, coupled to a target-decoy search and a mixture model-based method-on novel peptide identification. The multistage approach showed the highest accuracy for FDR estimation. However, global and separate FDR estimation with the mixture model-based method showed higher sensitivities than others at the same true FDR. Furthermore, the mixture model-based method performed equally well when applied without or with a reduced set of decoy sequences. Considering different prior probabilities for novel and known protein identification, we recommend using mixture model-based methods with separate FDR estimation for sensitive and reliable identification of novel peptides from proteogenomic searches.
[Mh] Termos MeSH primário: Peptídeos/análise
Proteogenômica/métodos
[Mh] Termos MeSH secundário: Linhagem Celular
Simulação por Computador
Reações Falso-Positivas
Seres Humanos
Métodos
Modelos Teóricos
Espectrometria de Massas em Tandem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Peptides)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jproteome.7b00033


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[PMID]:29258473
[Au] Autor:Wu X; Liu Z; Zhang X; Wang D; Long E; Wang J; Li W; Lai W; Cao Q; Hu K; Chen W; Lin H; Liu Y
[Ad] Endereço:State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54# Xianlie Road, Guangzhou, Guangdong, 510060, China.
[Ti] Título:Proteomics analysis and proteogenomic characterization of different physiopathological human lenses.
[So] Source:BMC Ophthalmol;17(1):253, 2017 Dec 19.
[Is] ISSN:1471-2415
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The aim of the present study was to identify the proteomic differences among human lenses in different physiopathological states and to screen for susceptibility genes/proteins via proteogenomic characterization. METHODS: The total proteomes identified across the regenerative lens with secondary cataract (RLSC), congenital cataract (CC) and age-related cataract (ARC) groups were compared to those of normal lenses using isobaric tagging for relative and absolute protein quantification (iTRAQ). The up-regulated proteins between the groups were subjected to biological analysis. Whole exome sequencing (WES) was performed to detect genetic variations. RESULTS: The most complete human lens proteome to date, which consisted of 1251 proteins, including 55.2% previously unreported proteins, was identified across the experimental groups. Bioinformatics functional annotation revealed the common involvement of cellular metabolic processes, immune responses and protein folding disturbances among the groups. RLSC-over-expressed proteins were characteristically enriched in the intracellular immunological signal transduction pathways. The CC groups featured biological processes relating to gene expression and vascular endothelial growth factor (VEGF) signaling transduction, whereas the molecular functions corresponding to external stress were specific to the ARC groups. Combined with WES, the proteogenomic characterization narrowed the list to 16 candidate causal molecules. CONCLUSIONS: These findings revealed common final pathways with diverse upstream regulation of cataractogenesis in different physiopathological states. This proteogenomic characterization shows translational potential for detecting susceptibility genes/proteins in precision medicine.
[Mh] Termos MeSH primário: Catarata/metabolismo
Proteínas do Olho/metabolismo
Cristalino/metabolismo
Proteoma/análise
[Mh] Termos MeSH secundário: Adulto
Pré-Escolar
Cromatografia Líquida
Feminino
Seres Humanos
Masculino
Meia-Idade
Proteogenômica
Proteoma/genética
Proteômica
Espectrometria de Massas em Tandem
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Eye Proteins); 0 (Proteome)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180105
[Lr] Data última revisão:
180105
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171221
[St] Status:MEDLINE
[do] DOI:10.1186/s12886-017-0642-9


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[PMID]:28759593
[Au] Autor:Swearingen KE; Lindner SE; Flannery EL; Vaughan AM; Morrison RD; Patrapuvich R; Koepfli C; Muller I; Jex A; Moritz RL; Kappe SHI; Sattabongkot J; Mikolajczak SA
[Ad] Endereço:Institute for Systems Biology, Seattle, Washington, United States of America.
[Ti] Título:Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites.
[So] Source:PLoS Negl Trop Dis;11(7):e0005791, 2017 Jul.
[Is] ISSN:1935-2735
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Plasmodium falciparum and Plasmodium vivax cause the majority of human malaria cases. Research efforts predominantly focus on P. falciparum because of the clinical severity of infection and associated mortality rates. However, P. vivax malaria affects more people in a wider global range. Furthermore, unlike P. falciparum, P. vivax can persist in the liver as dormant hypnozoites that can be activated weeks to years after primary infection, causing relapse of symptomatic blood stages. This feature makes P. vivax unique and difficult to eliminate with the standard tools of vector control and treatment of symptomatic blood stage infection with antimalarial drugs. Infection by Plasmodium is initiated by the mosquito-transmitted sporozoite stage, a highly motile invasive cell that targets hepatocytes in the liver. The most advanced malaria vaccine for P. falciparum (RTS,S, a subunit vaccine containing of a portion of the major sporozoite surface protein) conferred limited protection in Phase III trials, falling short of WHO-established vaccine efficacy goals. However, blocking the sporozoite stage of infection in P. vivax, before the establishment of the chronic liver infection, might be an effective malaria vaccine strategy to reduce the occurrence of relapsing blood stages. It is also thought that a multivalent vaccine comprising multiple sporozoite surface antigens will provide better protection, but a comprehensive analysis of proteins in P. vivax sporozoites is not available. To inform sporozoite-based vaccine development, we employed mass spectrometry-based proteomics to identify nearly 2,000 proteins present in P. vivax salivary gland sporozoites. Analysis of protein post-translational modifications revealed extensive phosphorylation of glideosome proteins as well as regulators of transcription and translation. Additionally, the sporozoite surface proteins CSP and TRAP, which were recently discovered to be glycosylated in P. falciparum salivary gland sporozoites, were also observed to be similarly modified in P. vivax sporozoites. Quantitative comparison of the P. vivax and P. falciparum salivary gland sporozoite proteomes revealed a high degree of similarity in protein expression levels, including among invasion-related proteins. Nevertheless, orthologs with significantly different expression levels between the two species could be identified, as well as highly abundant, species-specific proteins with no known orthologs. Finally, we employed chemical labeling of live sporozoites to isolate and identify 36 proteins that are putatively surface-exposed on P. vivax salivary gland sporozoites. In addition to identifying conserved sporozoite surface proteins identified by similar analyses of other Plasmodium species, our analysis identified several as-yet uncharacterized proteins, including a putative 6-Cys protein with no known ortholog in P. falciparum.
[Mh] Termos MeSH primário: Proteínas de Membrana/análise
Plasmodium vivax/isolamento & purificação
Processamento de Proteína Pós-Traducional
Proteoma/análise
Proteínas de Protozoários/análise
[Mh] Termos MeSH secundário: Animais
Anopheles/parasitologia
Malária Vivax/metabolismo
Espectrometria de Massas
Proteogenômica
Glândulas Salivares/parasitologia
Esporozoítos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Membrane Proteins); 0 (Proteome); 0 (Protozoan Proteins)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170827
[Lr] Data última revisão:
170827
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170801
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pntd.0005791


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[PMID]:28712153
[Au] Autor:Manchala NR; Dungdung R; Pilankatta R
[Ad] Endereço:Department of Biochemistry and Molecular Biology, School of Biological Sciences, Central University of Kerala, Padannakkad, Kerala, India.
[Ti] Título:Proteomic analysis reveals the enhancement of human serum apolipoprotein A-1(APO A-1) in individuals infected with multiple dengue virus serotypes.
[So] Source:Trop Med Int Health;22(10):1334-1342, 2017 Oct.
[Is] ISSN:1365-3156
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:OBJECTIVES: Human serum protein profiling of the individual infected with multiple dengue virus serotypes for identifying the potential biomarkers and to investigate the cause for the severity of dengue virus infection. METHODS: Dengue virus NS1-positive serum samples were pooled into two groups (S2 and S3) based on the molecular serotyping and number of heterotypic infections. The pooled serum samples were subjected to two-dimensional gel electrophoresis (2DGE) to identify the differentially expressed proteins. The peptide masses of upregulated protein were detected by matrix-assisted laser desorption-ionisation time-of-flight MALDI-TOF mass spectrometry and analysed by MASCOT search engine. The results were compared with the control group (S1). The commonly upregulated protein was validated by quantitative ELISA and compared with control as well as single serotypic infected samples. RESULTS: Based on 2DGE, total thirteen proteins were differentially upregulated in S2 and S3 groups as compared to control. Some of the upregulated proteins were involved in mediating the complement activation of immune response. The apolipoprotein A-1 (APO A-1) was upregulated in S2 and S3 groups. Upon validation, APO A-1 levels were increased in line with the number of heterotypic infection of dengue viruses. CONCLUSION: Heterotypic infection of dengue viruses upregulate the serum proteins involved in the complement pathway in the early phase of infection. There was a significant increase in the level of APO A-1 in three different serotypic infections of dengue virus as compared to control. Further, the role of APO-A1 can be explored in elucidating the mechanism of dengue pathogenesis.
[Mh] Termos MeSH primário: Vírus da Dengue/classificação
Dengue/virologia
Proteogenômica
[Mh] Termos MeSH secundário: Biomarcadores/sangue
Dengue/sangue
Dengue/imunologia
Vírus da Dengue/imunologia
Ensaio de Imunoadsorção Enzimática/métodos
Seres Humanos
Sorotipagem/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171012
[Lr] Data última revisão:
171012
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170717
[St] Status:MEDLINE
[do] DOI:10.1111/tmi.12931


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[PMID]:28528867
[Au] Autor:Zhang Y; Kwok-Shing Ng P; Kucherlapati M; Chen F; Liu Y; Tsang YH; de Velasco G; Jeong KJ; Akbani R; Hadjipanayis A; Pantazi A; Bristow CA; Lee E; Mahadeshwar HS; Tang J; Zhang J; Yang L; Seth S; Lee S; Ren X; Song X; Sun H; Seidman J; Luquette LJ; Xi R; Chin L; Protopopov A; Westbrook TF; Shelley CS; Choueiri TK; Ittmann M; Van Waes C; Weinstein JN; Liang H; Henske EP; Godwin AK; Park PJ; Kucherlapati R; Scott KL; Mills GB; Kwiatkowski DJ; Creighton CJ
[Ad] Endereço:Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
[Ti] Título:A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations.
[So] Source:Cancer Cell;31(6):820-832.e3, 2017 Jun 12.
[Is] ISSN:1878-3686
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Molecular alterations involving the PI3K/AKT/mTOR pathway (including mutation, copy number, protein, or RNA) were examined across 11,219 human cancers representing 32 major types. Within specific mutated genes, frequency, mutation hotspot residues, in silico predictions, and functional assays were all informative in distinguishing the subset of genetic variants more likely to have functional relevance. Multiple oncogenic pathways including PI3K/AKT/mTOR converged on similar sets of downstream transcriptional targets. In addition to mutation, structural variations and partial copy losses involving PTEN and STK11 showed evidence for having functional relevance. A substantial fraction of cancers showed high mTOR pathway activity without an associated canonical genetic or genomic alteration, including cancers harboring IDH1 or VHL mutations, suggesting multiple mechanisms for pathway activation.
[Mh] Termos MeSH primário: Neoplasias/genética
Fosfatidilinositol 3-Quinases/metabolismo
Proteogenômica
Proteínas Proto-Oncogênicas c-akt/metabolismo
Serina-Treonina Quinases TOR/metabolismo
[Mh] Termos MeSH secundário: Bases de Dados Genéticas
Perfilação da Expressão Gênica
Seres Humanos
Mutação
Neoplasias/metabolismo
Transdução de Sinais
Análise de Sobrevida
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.7.1.- (Phosphatidylinositol 3-Kinases); EC 2.7.1.1 (MTOR protein, human); EC 2.7.1.1 (TOR Serine-Threonine Kinases); EC 2.7.11.1 (Proto-Oncogene Proteins c-akt)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170825
[Lr] Data última revisão:
170825
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170523
[St] Status:MEDLINE


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[PMID]:28515099
[Au] Autor:Chan MY; Neely ML; Roe MT; Goodman SG; Erlinge D; Cornel JH; Winters KJ; Jakubowski JA; Zhou C; Fox KAA; Armstrong PW; White HD; Prabhakaran D; Ohman EM; Huber K; TRILOGY ACS Investigators
[Ad] Endereço:Department of Medicine, National University of Singapore; Singapore; mark_chan@nuhs.edu.sg.
[Ti] Título:Temporal Biomarker Profiling Reveals Longitudinal Changes in Risk of Death or Myocardial Infarction in Non-ST-Segment Elevation Acute Coronary Syndrome.
[So] Source:Clin Chem;63(7):1214-1226, 2017 Jul.
[Is] ISSN:1530-8561
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: There are conflicting data on whether changes in N-terminal pro-B-type natriuretic peptide (NT-proBNP) and high-sensitivity C-reactive protein (hs-CRP) concentrations between time points (delta NT-proBNP and hs-CRP) are associated with a change in prognosis. METHODS: We measured NT-proBNP and hs-CRP at 3 time points in 1665 patients with non-ST-segment elevation acute coronary syndrome (NSTEACS). Cox proportional hazards was applied to the delta between temporal measurements to determine the continuous association with cardiovascular events. Effect estimates for delta NT-proBNP and hs-CRP are presented per 40% increase as the basic unit of temporal change. RESULTS: Median NT-proBNP was 370.0 (25th, 75th percentiles, 130.0, 996.0), 340.0 (135.0, 875.0), and 267.0 (111.0, 684.0) ng/L; and median hs-CRP was 4.6 (1.7, 13.1), 1.9 (0.8, 4.5), and 1.8 (0.8, 4.4) mg/L at baseline, 30 days, and 6 months, respectively. The deltas between baseline and 6 months were the most prognostically informative. Every +40% increase of delta NT-proBNP (baseline to 6 months) was associated with a 14% greater risk of cardiovascular death (adjusted hazard ratio (HR) 1.14, 95% CI, 1.03-1.27) and with a 14% greater risk of all-cause death (adjusted HR 1.14, 95% CI, 1.04-1.26), while every +40% increase of delta hs-CRP (baseline to 6 months) was associated with a 9% greater risk of the composite end point (adjusted HR 1.09, 95% CI, 1.02-1.17) and a 10% greater risk of myocardial infarction (adjusted HR 1.10, 95%, CI 1.00-1.20). CONCLUSIONS: Temporal changes in NT-proBNP and hs-CRP are quantitatively associated with future cardiovascular events, supporting their role in dynamic risk stratification of NSTEACS. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT00699998.
[Mh] Termos MeSH primário: Síndrome Coronariana Aguda/complicações
Síndrome Coronariana Aguda/mortalidade
Biomarcadores/análise
Infarto do Miocárdio/etiologia
Proteogenômica
[Mh] Termos MeSH secundário: Síndrome Coronariana Aguda/diagnóstico
Síndrome Coronariana Aguda/genética
Idoso
Biomarcadores/sangue
Proteína C-Reativa/análise
Feminino
Seres Humanos
Masculino
Meia-Idade
Infarto do Miocárdio/diagnóstico
Infarto do Miocárdio/mortalidade
Peptídeo Natriurético Encefálico/sangue
Fatores de Risco
Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers); 114471-18-0 (Natriuretic Peptide, Brain); 9007-41-4 (C-Reactive Protein)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170713
[Lr] Data última revisão:
170713
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170519
[St] Status:MEDLINE
[do] DOI:10.1373/clinchem.2016.265272


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[PMID]:28513289
[Au] Autor:Ruiz Orduna A; Husby E; Yang CT; Ghosh D; Beaudry F
[Ad] Endereço:a Département de biomédecine vétérinaire, Faculté de médecine vétérinaire , Université de Montréal , Saint-Hyacinthe , QC , Canada.
[Ti] Título:Detection of meat species adulteration using high-resolution mass spectrometry and a proteogenomics strategy.
[So] Source:Food Addit Contam Part A Chem Anal Control Expo Risk Assess;34(7):1110-1120, 2017 Jul.
[Is] ISSN:1944-0057
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Due to the internationalisation of food production and distribution, there has been a significant increase of food fraud in recent years. Food fraud can have serious health implications, and it occurs when food manufacturers implement unethical practices such as making false label claims as well as using additives and fillers within their products to increase profitability. This has been a serious concern. Meat adulteration was examined using a well-defined proteogenomic annotation, carefully selected surrogate tryptic peptides and high-resolution mass spectrometry. Selected mammalian meat samples were homogenised and the proteins extracted and digested with trypsin. Chromatography was achieved using a 30-min linear gradient along with a BioBasic C8 100 × 1 mm column at a flow rate of 75 µl min . The mass spectrometer was operated in full-scan high-resolution and accurate mass using resolving powers of 140,000 and 17,500 (FWHM) in full-scan MS and MS/MS respectively. Data independent acquisition (DIA) mode was used including 12 DIA MS/MS scans to cover the mass range 600-1200 m/z. Methodically in silico analyses of myoglobin, myosin-1, myosin-2 and ß-haemoglobin sequences allow for the identification of a species-specific tryptic peptide mass lists and theoretical MS/MS spectra. Following comprehensive MS, MS/MS or DIA analyses, the method was capable of the detection and identification of very specific tryptic peptides for all four targeted proteins for each animal species tested with observed m/z below 3 ppm compared with the theoretical m/z. The analyses were successfully performed with raw and cooked meat. Specifically, the method was capable of detecting 1% (w/w) of pork or horse meat in a mixture before and after cooking (71°C internal temperature).
[Mh] Termos MeSH primário: Contaminação de Alimentos/análise
Espectrometria de Massas
Carne/análise
Proteogenômica/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171016
[Lr] Data última revisão:
171016
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170518
[St] Status:MEDLINE
[do] DOI:10.1080/19440049.2017.1329951


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[PMID]:28276747
[Au] Autor:Fu S; Liu X; Luo M; Xie K; Nice EC; Zhang H; Huang C
[Ad] Endereço:a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.
[Ti] Título:Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification.
[So] Source:Expert Rev Proteomics;14(4):351-362, 2017 Apr.
[Is] ISSN:1744-8387
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:INTRODUCTION: Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment. Areas covered: In this review, we will present recent advances in proteogenomic investigations of cancer drug resistance with an emphasis on integrative proteogenomic pipelines and the biomarker discovery which contributes to achieving the goal of using precision/personalized medicine for cancer treatment. Expert commentary: The discovery and comprehensive understanding of potential biomarkers help identify the cohort of patients who may benefit from particular treatments, and will assist real-time clinical decision-making to maximize therapeutic efficacy and minimize adverse effects. With the development of MS-based proteomics and NGS-based sequencing, a growing number of proteogenomic tools are being developed specifically to investigate cancer drug resistance.
[Mh] Termos MeSH primário: Biomarcadores Tumorais/genética
Resistência a Medicamentos Antineoplásicos/genética
Neoplasias/genética
Proteogenômica
[Mh] Termos MeSH secundário: Genoma Humano
Seres Humanos
Neoplasias/tratamento farmacológico
Neoplasias/patologia
Proteoma/genética
Proteômica
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Biomarkers, Tumor); 0 (Proteome)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171030
[Lr] Data última revisão:
171030
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170310
[St] Status:MEDLINE
[do] DOI:10.1080/14789450.2017.1299006


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[PMID]:28187513
[Au] Autor:Fiore LD; Rodriguez H; Shriver CD
[Ad] Endereço:Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), Veterans Affairs Boston Healthcare System, Department of Veterans Affairs Office of Research and Development-Cooperative Studies Program, Washington, DC, USA.
[Ti] Título:Collaboration to Accelerate Proteogenomics Cancer Care: The Department of Veterans Affairs, Department of Defense, and the National Cancer Institute's Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) Network.
[So] Source:Clin Pharmacol Ther;101(5):619-621, 2017 May.
[Is] ISSN:1532-6535
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A tri-federal initiative arising out of the Cancer Moonshot has resulted in the formation of a program to utilize advanced genomic and proteomic expression platforms on high-quality human biospecimens in near-real-time in order to identify potentially actionable therapeutic molecular targets, study the relationship of molecular findings to cancer treatment outcomes, and accelerate novel clinical trials with biomarkers of prognostic and predictive value.
[Mh] Termos MeSH primário: Oncologia
National Cancer Institute (U.S.)
Proteogenômica
United States Department of Defense
United States Department of Veterans Affairs
[Mh] Termos MeSH secundário: Sistemas de Liberação de Medicamentos
Seres Humanos
Estados Unidos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1704
[Cu] Atualização por classe:170425
[Lr] Data última revisão:
170425
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:170211
[St] Status:MEDLINE
[do] DOI:10.1002/cpt.658


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[PMID]:28157690
[Au] Autor:Dimitrakopoulos L; Prassas I; Berns EMJJ; Foekens JA; Diamandis EP; Charames GS
[Ad] Endereço:.
[Ti] Título:Variant peptide detection utilizing mass spectrometry: laying the foundations for proteogenomic identification and validation.
[So] Source:Clin Chem Lab Med;55(9):1291-1304, 2017 Aug 28.
[Is] ISSN:1437-4331
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Proteogenomics is an emerging field at the intersection of genomics and proteomics. Many variant peptides corresponding to single nucleotide variations (SNVs) are associated with specific diseases. The aim of this study was to demonstrate the feasibility of proteogenomic-based variant peptide detection in disease models and clinical specimens. METHODS: We sought to detect p53 single amino acid variant (SAAV) peptides in breast cancer tumor samples that have been previously subjected to sequencing analysis. Initially, two cancer cell lines having a cellular tumor antigen p53 (TP53) mutation and one wild type for TP53 were analyzed by selected reaction monitoring (SRM) assays as controls. One pool of wild type and one pool of mutated for TP53 cytosolic extracts were assayed with a shotgun proteogenomic workflow. Furthermore, 18 individual samples having a mutation in TP53 were assayed by SRM. RESULTS: Two mutant p53 peptides were successfully detected in two cancer cell lines as expected from their DNA sequence. Wild type p53 peptides were detected in both cytosolic pools, however, none of the mutant p53 peptides were identified. Mutations at the protein level were detected in two cytosolic extracts and whole tumor lysates from the same patients by SRM analysis. Six thousand and six hundred and twenty eight non-redundant proteins were identified in the two cytosolic pools, thus greatly improving a previously reported cytosolic proteome. CONCLUSIONS: In the current study we show the great potential of using proteogenomics for the direct identification of cancer-associated mutations in clinical samples and we discuss current limitations and future perspectives.
[Mh] Termos MeSH primário: Peptídeos/análise
Peptídeos/genética
Proteogenômica
Proteína Supressora de Tumor p53/genética
[Mh] Termos MeSH secundário: Linhagem Celular Tumoral
Cromatografia Líquida
Citosol/química
Ensaio de Imunoadsorção Enzimática
Seres Humanos
Espectrometria de Massas
Mutação
Neoplasias/genética
Peptídeos/química
Reprodutibilidade dos Testes
Espectrometria de Massas em Tandem
Proteína Supressora de Tumor p53/análise
Proteína Supressora de Tumor p53/química
Estudos de Validação como Assunto
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Peptides); 0 (TP53 protein, human); 0 (Tumor Suppressor Protein p53)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170821
[Lr] Data última revisão:
170821
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170204
[St] Status:MEDLINE



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