A proteomic approach to compare saliva from individuals with and without oral leukoplakia

Camisasca, Danielle Resende; Gonçalves, Lorena Da Rós; Soares, Márcia Regina; Sandim, Vanessa; Nogueira, Fábio César Sousa; Saraiva-Garcia, Carlos; Cruz, Raquel Santana da; Oliveira, Silvia Paula De; Buexm, Luisa Aguirre; Faria, Paulo Antônio Silvestre de; Dias, Fernando Luiz; Pereira, Denise de Abreu; Zingali, Russolina B.; Alves, Gilda; Lourenço, Simone de Queiroz Chaves

doi:10.1016/j.jprot.2016.07.029

Cited by 32 publications

(22 citation statements)

References 34 publications

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“…For example, in-solution digestion workflows have recently been applied to the study of other cancer samples such as those from colorectal tumors [35] and from body fluids of head and neck cancer patients [36]. Lately, 2DE has been used to analyze saliva from individuals with and without oral leukoplakia [37]. However, as found in our study on AML patient samples, the FASP procedure and the use of a super-SILAC mix of five cell lines [38] have proved to be excellent methodologies for quantitative proteomics of breast cancer samples [39].…”

Section: Discussionmentioning

confidence: 99%

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

et al. 2016

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Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.

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Section: Discussionmentioning

confidence: 99%

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

et al. 2016

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“…The combination of these three biomarkers could reach 85% sensitivity and 80% specificity for the detection of gastric cancer with accuracy of 0.93 31 . A 2D-electrophoretic analysis coupled off-line with MS identification of the tryptic digest of the spots identified 22 proteins selectively expressed in patients with oral leukoplakia 32 . Immunohistochemical validation suggested that keratin 10 was an interesting potential biomarker of OLK and should be further investigated.…”

Section: Human Saliva As Diagnostic Body Fluidmentioning

confidence: 97%

Salivary biomarkers and proteomics: future diagnostic and clinical utilities

Castagnola

Scarano

Passàli

et al. 2017

Acta Otorhinolaryngol Ital

130

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Lo studio della proteomica salivare, test economico e non invasivo, rappresenta una fonte di numerose informazioni, ed è utile per la diagnosi di svariate malattie. Da quando siamo entrati nellera della tecnologia genomica e delle scienze omiche, la raccolta di campioni salivari è aumentata esponenzialmente. Recenti piattaforme proteomiche hanno analizzato il proteoma salivare umano, caratterizzando circa 3000 peptidi e proteine, espressi in maniera differente: più del 90% in peso deriva dalla secrezione delle tre ghiandole salivari maggiori, mentre la restante parte proviene dalle ghiandole salivari minori, dal fluido crevicolare gengivale, da essudati mucosi e dalla microflora orale. Lobiettivo principale dellanalisi proteomica è discriminare tra condizioni fisiologiche e patologiche. Ad oggi, tuttavia, non esiste un preciso protocollo che permetta di analizzare lintero proteoma salivare, pertanto sono state realizzate svariate strategie. Innanzitutto, è possibile distinguere due tipologie di piattaforme proteomiche: lapproccio top-down prevede lanalisi delle proteine sotto esame come entità intatte; nellapproccio bottom-up la caratterizzazione della proteina avviene mediante lo studio dei peptidi ottenuti dopo digestione enzimatica (con tripsina tipicamente). A causa di questa eterogeneità, per una stessa patologia sono stati proposti differenti biomarkers. Il proteoma salivare è stato caratterizzato in numerose malattie: carcinoma squamoso e leucoplachie orali, malattia del trapianto contro lospite (GVHD) cronica, sindrome di Sjögren e altri disordini autoimmuni come la sindrome SAPHO (sinovite, acne, pustolosi, iperostosi e osteite), schizofrenia e disordine bipolare, malattie genetiche come la sindrome di Down o la malattia di Wilson. In conclusione, i risultati delle ricerche riportate in questa review suggeriscono che nel prossimo futuro la saliva diverrà un fluido di indubbia rilevanza diagnostica utile per fini clinici, sia diagnostici, sia prognostici.

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“…Various mass spectrometry methods are currently available and have been widely used to study the salivary proteins, and smaller, endogenous peptides. However, despite extensive investigation in humans [ 2 , 5 , 8 , 10 – 26 ], much less work has been done in other species [ 3 , 27 – 34 ]. Recently, the protein components of dog saliva were examined using SDS-PAGE-LC coupled to tandem mass spectrometry (MS/MS) [ 3 ], but only one dog sample was analyzed.…”

Section: Introductionmentioning

confidence: 99%

Salivary proteomics of healthy dogs: An in depth catalog

et al. 2018

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ObjectiveTo provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups.Methods36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups). Saliva collected from dogs was pooled by phylogeny group and analyzed using nanoscale liquid chromatography-tandem mass spectrometry. Resulting tandem mass spectra were compared to databases for identification of endogenous peptides and inferred proteins.Results2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups’ saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups.Conclusions and clinical relevanceUsing a sophisticated nanoscale liquid chromatography-tandem mass spectrometry, we were able to identify 10-fold more salivary proteins than previously reported in dogs. Seven of the top 10 most abundant proteins or peptides serve immune functions and many more with various antimicrobial mechanisms were found. This is the most comprehensive analysis of healthy canine saliva to date, and will provide the groundwork for future studies analyzing salivary proteins and endogenous peptides in disease states.

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A proteomic approach to compare saliva from individuals with and without oral leukoplakia

Cited by 32 publications

References 34 publications

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

Salivary biomarkers and proteomics: future diagnostic and clinical utilities

Salivary proteomics of healthy dogs: An in depth catalog

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