Dataset Information

Label-free quantitative proteomics versus antibody-based assays to measure neutrophil derived enzymes in saliva

ABSTRACT: Discovery-based quantitative proteomics identified dozens of novel protein candidates in saliva, yet none are clinically qualified. Mass spectrometry (MS) has been recognized as newer 'gold standard' for the identification and analysis of individual proteins in complex biological samples due to higher sensitivity, specificity and independence of antibody availability. However, whether MS can replace immunoassays for salivary biomarker validation has not been thoroughly studied. Therefore, we aimed to test the potential of label-free quantitative (LFQ) proteomics in comparison to conventional antibody-based methods to quantify ‘candidate biomarkers’ in saliva during experimentally-induced oral inflammation development in humans. Whole unstimulated saliva, collected at five time points, was analyzed by LFQ shotgun proteomics. Salivary levels of ‘candidate biomarkers’ were also assessed by antibody-based immunoassays such as ELISA and time-resolved immunofluorometric assay (IFMA).

INSTRUMENT(S): LCQ Classic, Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Saliva

DISEASE(S): Gingivitis

SUBMITTER: Kai Bao

LAB HEAD: Nagihan Bostanci

PROVIDER: PXD015220 | Pride | 2019-12-20

REPOSITORIES: Pride

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Publications

Label-Free Quantitative Proteomics versus Antibody-Based Assays to Measure Neutrophil-Derived Enzymes in Saliva.

Silbereisen Angelika A Alassiri Saeed S Bao Kai K Grossmann Jonas J Nanni Paolo P Fernandez Claudia C Tervahartiala Taina T Nascimento Gustavo G GG Belibasakis Georgios N GN Heikkinen Anna-Maria AM Lopez Rodrigo R Sorsa Timo T Bostanci Nagihan N

Proteomics. Clinical applications 20200107 3

<h4>Purpose</h4>This study aims to validate label-free quantitative proteomics (LFQ) against antibody-based methods for quantifying established periodontal disease biomarkers in saliva.<h4>Experimental design</h4>In an experimental gingivitis model, healthy volunteers (n = 10) provide saliva at baseline (d0), during the induction (d7, d14, d21) and resolution (d35) of gingival inflammation (total n = 50). Biomarker levels are analyzed by LFQ and time-resolved immunofluorometric assay (IFMA) or e ...[more]

PMID: 31840410

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Project description:This is a pilot study. We are trying to detect potential salivary biomarkers in mice with a pancreatic tumor. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals. Recent studies have demonstrated that discriminatory salivary biomarkers can be readily detected upon the development of systemic diseases such as pancreatic cancer, breast cancer, lung cancer and ovarian cancer. However, the utility of salivary biomarkers for the detection of systemic diseases has been undermined due to the absence of biological and mechanistic rationale why distal diseases from the oral cavity would lead to the development of discriminatory biomarkers in saliva. Here, we examine the hypothesis that pancreatic tumor-derived exosomes are mechanistically involved in the development of pancreatic cancer-discriminatory salivary transcriptomic biomarkers. We first developed a pancreatic cancer mouse model that yielded discriminatory salivary biomarkers by implanting the mouse pancreatic cancer cell line Pan02 into the pancreas of the syngeneic host C57BL/6. The role of pancreatic cancer-derived exosomes in the development of discriminatory salivary biomarkers was then tested by engineered a Pan02 cell line that is suppressed for exosome biogenesis, implanted into the C56BL/6 mouse and examine if the discriminatory salivary biomarker profile was ablated or disrupted. Suppression of exosome biogenesis results in the ablation of discriminatory salivary biomarker development. This study supports that tumor-derived exosomes provide a mechanism in the development of discriminatory biomarkers in saliva and distal systemic diseases. We analyzed saliva from 6 healthy mice and 6 mice with a pancreatic tumor using the Affymetrix Mouse Exon Genome 430 2.0 platform. Array data was processed by dChip. No techinical replicates were performed.

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Dataset Information

Label-free quantitative proteomics versus antibody-based assays to measure neutrophil derived enzymes in saliva

Publications

Label-Free Quantitative Proteomics versus Antibody-Based Assays to Measure Neutrophil-Derived Enzymes in Saliva.

Similar Datasets

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