Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples

Abstract

Aim To identify possible novel biomarkers in gingival crevicular fluid (GCF) samples from chronic periodontitis (CP) and periodontally healthy individuals by high-throughput proteomic analysis. Materials and Methods GCF samples were collected from twelve CP and twelve periodontally healthy subjects. Samples were trypically digested, eluted using high-performance liquid chromatography, and fragmented using tandem mass spectrometry (MS/MS). MS/MS were analyzed using PILOT_PROTEIN to identify all unmodified proteins within the samples. Results Using the database derived from Homo sapiens taxonomy and all bacterial taxonomies, 432 human (120 new) and 30 bacterial proteins were identified. The human proteins, angiotensinogen, clusterin and thymidine phosphorylase were identified as biomarker candidates based on their high-scoring only in samples from periodontal health. Similarly, neutrophil defensin-1, carbonic anhydrase-1 and elongation factor-1 gamma were associated with CP. Candidate bacterial biomarkers include 33 kDa chaperonin, iron uptake protein A2 and phosphoenolpyruvate carboxylase (health-associated) and ribulose biphosphate carboxylase, a probable succinyl-CoA:3-ketoacid-coenzyme A transferase, or DNA-directed RNA polymerase subunit beta (CP-associated). Most of these human and bacterial proteins have not been previously evaluated as biomarkers of periodontal conditions and require further investigation. Conclusions The proposed methods for large-scale comprehensive proteomic analysis may lead to the identification of novel biomarkers of periodontal disease.

Metabolomic Analysis of Gingival Crevicular Fluid Using Gas Chromatography/Mass Spectrometry

“…It is well known that there are some di erences in the proteins found in GCF collected from clinically healthy sites and sites with chronic periodontitis. [3][4][5] Protein contents in GCF are commonly analyzed by enzyme-linked immunosorbent assay (ELISA), but there is a limitation in the number of proteins that can be analyzed at one time. Also, conventional methods for analyzing non-protein or novel molecules are time-consuming and may require multiple techniques (and also instrumentation for each technique) to gain a complete analyte pro le useful for prediction and diagnosis.…”

Gingival Crevicular Fluid as a Novel Potential Source of Biomarkers Distinguishes Pubertal from Post-Pubertal Subjects

“…GCF is part of saliva that is comprised of complicated protein content and remains more stable regardless of tooth brushing and eating [9], with a characteristic of site-specificity. The total amounts of proteins and peptides that have been identified in GCF in periodontal healthy subjects are reported to be in a range from 88 [29] to 327 [30] that depends on the different sample sizes and methods employed in different studies. Many studies have applied gel-based or gel-free mass spectrometric analysis of GCF proteomic profiling for the detection of novel biomarkers of periodontitis and have successfully discovered several protein biomarkers that have never been investigated before [20,21,31], and some have confirmed the significance of biomarkers that had been proposed in previous studies via conventional research methods [30].…”

Host Genome, Epigenome, and Oral Microbiome Interactions: Toward Personalized Periodontal Therapy

“…51 Another clinical application is the use of proteomics technology to detect protein signatures in periodontitis that can be used for early diagnosis and prevention of disease progression. 52,53 DNA information combined with clinical information, especially medical records, becomes a necessity for highly customized periodontal treatment (Fig. 1).…”