Construction and characterization of the Korean whole saliva proteome to determine ethnic differences in human saliva proteome

Cho, Ha Ra; Kim, Han Sol; Park, Jun Seo; Park, Seung Cheol; Kim, Kwang Pyo; Wood, Troy D.; Choi, Yong Seok

doi:10.1371/journal.pone.0181765

Cited by 13 publications

(2 citation statements)

References 26 publications

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“…Future studies including a larger breed representation in the various phylogenic groups and a larger number of dogs per breed will help answer this question. Interestingly, a recent study showed unique proteins in the saliva of Korean people when compared to a comprehensive database of human salivary proteins indicating ethnic differences in the human saliva proteome [ 71 ].…”

Section: Discussionmentioning

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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Section: Discussionmentioning

confidence: 99%

Salivary proteomics of healthy dogs: An in depth catalog

et al. 2018

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“…Proteomics. Numerous proteomic studies have provided evidence for the influence of ethnicity on protein expression (Cho et al, 2017;Kim et al, 2010;Nguyen et al, 2019). We are currently in what might be considered the ''golden age'' of proteomics, characterized by the creation of public proteomics databases, the development of structural analysis tools which predict variant effects, such as HUMA and PRIMO (Brown and Tastan Bishop, 2018;Hatherley et al, 2016), and the standardization of data submission under the Proteo-meXchange consortium (Vizcaíno et al, 2014 Egypt).…”

Section: Availability Of Human African Omics Datamentioning

confidence: 99%

Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects

Hamdi

Zass

Othman

et al. 2021

OMICS: A Journal of Integrative Biology

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Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.

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Comparisons of Whole Saliva and Cell Free Saliva by DIA‐Based Proteome Profiling

Jiao,

Dong,

Qin

et al. 2024

Proteomics Clinical Apps

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BackgroundSaliva has emerged as a promising diagnostic resource due to its accessibility, noninvasiveness, and repeatability, enabling early disease detection and timely intervention. However, current studies often overlook the distinction between whole saliva (WS) and cell‐free saliva (CFS).ObjectiveThis study aims to compare the proteomic profiles of WS and CFS.Method and resultThe saliva was detected with and without low‐abundance protein enrichment using nanoparticles, employing DIA‐MS technology. Our findings reveal a substantial enhancement in the detectability of low‐abundance proteins in saliva with utilization of nanoparticles, enabling identification of 12%–15% low‐abundance proteins previously undetectable in WS or CFS. In total, 3817 saliva proteins were identified, with 3413 found in WS and 2340 in CFS. More interestingly, we found that it was not the similarity of the samples that did the clustering, but rather it depended more on the different detection methods and sample types. And the predominant functions of the identified proteins in WS were related to oxidative phosphorylation and neurodegenerations, whereas those in CFS were primarily associated with nitrogen and glycosaminoglycan metabolism. And both exhibited functions in immune response and proteasome.ConclusionThis study represents the first comparison of WS and CFS, providing valuable experimental evidence for guiding the selection of research subjects in future saliva omics studies.

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Construction and characterization of the Korean whole saliva proteome to determine ethnic differences in human saliva proteome

Cited by 13 publications

References 26 publications

Salivary proteomics of healthy dogs: An in depth catalog

Salivary proteomics of healthy dogs: An in depth catalog

Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects

Comparisons of Whole Saliva and Cell Free Saliva by DIA‐Based Proteome Profiling

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