Reconnecting Practicing Hygienists with the Nation's Leading Educators and Researchers.

Human Proteome Mapping in Dentistry

Proteomics may soon be used to predict, diagnose, and monitor a number of oral and systemic diseases.

This course was published in the June 2021 issue and expires June 2024. The author has no commercial conflicts of interest to disclose. This 2 credit hour self-study activity is electronically mediated.



After reading this course, the participant should be able to:

  1. Describe the role of proteomics in disease detection, prevention, diagnosis, and monitoring.
  2. Discuss the role of proteomics in dentistry.
  3. Identify the protein biomarkers associated with oral diseases.

Genomic information has improved the knowledge base of disease pathogenesis; however, genes do not fully reflect the status of a cell. The genome is essentially the operating manual that gives cells instructions for making specific proteins to carry out bodily functions.1 As such, proteins provide essential functional information and our “proteome identity.”2 Paradoxically, proteins can be the cause of disease, known as biomarkers, or used to cure disease such as the use of antibodies as therapeutics. Proteins—such as hormones, antibodies, enzymes, and cytokines—secreted in saliva by pathological cells serve as biomarkers for noninvasive disease screening. Therefore, the study of protein structure, function, and interaction, known as proteomics, is crucial for the early detection of and improved diagnosis, prognosis, monitoring of diseases, as well as for developing highly effective and precise therapies. In the future, accurate diagnosis of most diseases will not come from measuring the genetic blueprint, but rather from measuring proteins in their original and modified forms as well as their interactions that determine cell and tissue status or stage of disease. The ability of proteomics and genomics to examine human disease on a molecular level and determine individual response to disease and treatment has opened the door for a new approach to therapeutics and disease treatment called precision medicine.2–5

Beadle and Tatum4 suggested a link between genes, proteins, and disease in 1941. However, the term proteome, which blends the words protein and genome, was not coined until 1994 by Marc Wilkins, PhD. In 2020, the Human Proteome Organization (HUPO) marked the 10th anniversary of the Human Proteome Project by reporting the identification of 17,874 proteins, representing 90% of the predicted 19,773 proteins coded in the human genome. Of the proteins identified so far, only 1,254 do not have a known function. The missing 10% represents 1,899 proteins without sufficient evidence of their existence.1 The goal of HUPO is two-fold. First, it aims to map all human proteins present in health and disease, and second to determine all functions and interactions in original and modified forms. 

Identifying the human proteome is more complicated than identifying the human genome because protein structure is more complex, subject to chemical modifications, may only be expressed at certain times or under certain conditions, and not all proteins are found in nearly every human cell such as DNA.1 In-depth knowledge of the proteome will allow the comparison of proteins expressed by one person to those of another and under different conditions and disease states. Tests used to detect pregnancy, high cholesterol, strep throat, influenza, human immunodeficiency virus, and prostate cancer are examples of medical tests that look for the presence of a single protein. 

In the future, the patient’s proteome will be analyzed to identify abnormalities and treat them by modifying proteins and allowing the body to heal itself.6 With more than 99.9% of DNA being shared by every human, proteomics holds the key to answering how 0.1% of genes in each individual controls the countless phenotypes from eye color to risk for developing disease.4,5 Already, the study of the genome and proteome has led to the development of new drugs through the identification of numerous protein biomarkers associated with disease and using software to create and analyze three-dimensional models of proteins to design drugs to interfere with the action of the proteins.7 Molecular corrector drugs, such as elexacaftor/​​tezacaftor/​​ivacaftor which were launched in late 2019 for the treatment of cystic fibrosis, demonstrate how a drug can correct a defective amino acid in a protein chain and restore normal protein function.8


Precision medicine promotes customized healthcare with decisions and treatments tailored to the needs of the individual. To implement precision medicine in dentistry, dentists and dental hygienists must be knowledgeable about genomics, proteomics, and the relationship between oral and systemic health, in addition to being proficient in the use of new diagnostic tools. Analysis of a patient’s genome, proteome, environmental factors, and cultural influences is used to develop personalized therapy, prescribe more rationally, dose more appropriately, and predict patient response.9

Researchers are looking to map proteins expressed in teeth and dental structures to gain an in-depth understanding of how the proteome can be used to monitor health status, disease onset, treatment response, and outcomes. Once known, a complete list of proteins for the oral cavity and their functions will include thousands of entries.4,5 To date, the primary focus of dental proteomic research has been identification of proteins and their differential expression between disease and health in an effort to zero in on specific and predictable biomarkers.10 Although many of the identified biomarkers are awaiting further validation and have not been adopted in the clinical setting, further research and commercialization are likely to revolutionize dentistry by making early diagnosis the treatment of choice. Traditional biomarkers used to identify dental diseases will soon be replaced by those enabling mitigation of disease and administration of targeted therapeutics.4,9

Proteomic research has identified more than 1,000 salivary protein biomarkers including secretory immunoglobin A, lactoperoxidase, statherin, proline rich glycoprotein, truncated cystatin S, cystatins, lysozyme, and histatin-5. Saliva proteomics offers convenient monitoring of the patient’s physiology and prognostic and diagnostic biomarkers that may improve quality of life and reduce the financial burden associated with chronic disease treatment. In addition to traditional saliva testing, the oral fluid nanosensor test (OFNASET) or lab-on-a-chip nanotechnology is a handheld device capable of detecting up to eight salivary biomarkers in less than 15 minutes using a detector probe to signal the presence of the biomarker.11–14 Research indicates this technology effectively identifies biomarkers, but additional evidence is needed to confirm sensitivity, specificity, reproducibility, and correlation with existing disease diagnostic criteria. Although the intended use of OFNASET is detection of salivary biomarkers for oral cancer, this technology shows promise in facilitating a wide range of in-office real-time disease detection using saliva.14 Another emerging and affordable point-of-care technology is a test for periodontal diseases that analyzes saliva for  matrix metalloproteinase-8 (MMP-8) inflammation biomarkers in less than 1 minute using a digital reader. The analysis report gives patients simple insight into treatment needs and provides assessment data corresponding to 2018 American Academy of Periodontology grading classifications.15 

Current challenges for proteomics in dentistry include identifying disease-specific biomarkers, establishing sensitivity and specificity of tests, standardizing collection and storage of saliva samples, and lack of approval by the United States Food and Drug Administration.16 Barriers to implementation of precision dentistry include several inadequacies in reimbursement, lack of an integrated electronic health record, protection of genetic information, disparities in access by marginalized populations, and lack of patient interest.17,18 As precision dentistry progresses, public awareness and acceptance of personal genome sequencing and continued proteomic research focusing on prevention, treatment, and prognosis are essential for success.18,19 


Proteins associated with enamel, cementum, pulp, and dentin give insight into the regenerative ability of dental tissues. Research indicates 72 proteins have been identified in enamel, 510 in cementum, 5,097 in pulp, and 813 in dentin.20–23 Enamel-specific proteins are critical for proper enamel formation, yet proteomics is still determining the roles of the numerous proteins involved and the exact protein composition of healthy tooth enamel in all stages of development.24 Researchers propose 40% to 60% of susceptibility to dental caries is genetically determined.9 This includes defects in the following genes: amelogenin X-linked is responsible for production of amelogenin, which ensures normal enamel development; kallikrein-related peptidase-4 (KLK4) involved in enamel maturation; Lysozyme Like 2, which produces lysozyme-2 protein involved in antibacterial defenses; and adherens junctions associated protein 1 associated with tooth development.9 Major enamel proteins that have been identified are amelogenin, ameloblastin, enamelin, and tuftelin. Additional proteins associated with enamel formation include endoplasmic reticulum protein 29, calbindin, MMP-20, and KLK4.12,24 The identification of proteins exclusive to caries-free vs caries-prone individuals may aid in understanding the mechanism of caries, predicting risk, and advancing the science of caries control and prevention. One proposed caries prevention strategy aims to block or weaken enzymes that enable associated bacteria to form biofilm or attach to the tooth surface.25 Early detection of biomarkers associated with dental caries gives oral health professionals the insight to diagnose and treat patients based on specific findings and better determine prognosis.19 Furthermore, caries risk factors can be used to stratify patients and personalize therapy.25 Researchers have found a mechanism, associated with the delta like non-canonical notch ligand 1 gene, that offers a potential solution for tooth repair by enhancing stem cell activation and tissue regeneration. In the future, this mechanism, targeted at stem cells, may provide a means to repair teeth damaged by caries or trauma.26 

Differences have been found between cementum proteomes of deciduous and permanent teeth. Of the 510 proteins identified in cementum, 123 are exclusive to deciduous teeth, including myeloperoxidase. Whereas, decorin and osteocalcin are two of the 128 proteins exclusive to permanent teeth; an additional 259 are expressed by both. These findings provide a greater understanding of differences between deciduous and permanent cementum, as well as insight into physio­logical/​​pathological events such as root resorption.21

The dentin and pulp function as a complex with odontoblasts from peripheral pulp tissue extending into the dentin. Dentin is a unique connective tissue with specific proteins, such as dentin sialophosphoprotein, and proteins also found in bone such as glycoprotein and osteonectin. Proteins mapped in dentin include dentin sialophosphoprotein, biglycan, osteopontin, and osteocalcin. Their functions include cytoskeletal protein binding, immune transport, calcium and ion binding, and formation of extracellular matrix.22 Proteins mapped in dental pulp vary between health, inflammation, and necrosis. An inflammatory process occurs when pulp disease advances as evidenced by an abundance of immunoglobulins including annexin A1, A2, and A5, and peroxiredoxin 1 and 2. Concomitantly, a repair process triggers upregulation of 14-3-3 protein ζΔ and collagen-α1 which may be associated with platelet activation and odontogenesis.27 

Mapping the proteome dentin-pulp complex will aid in understanding its regenerative potential in response to disease and trauma, the stages of pathology, and define biomarkers for new regenerative therapies for endodontics.22,27 


The one-size-fits-all approach of traditional assessments and nonsurgical periodontal therapy may not adequately treat those at greatest risk for periodontal diseases, and may over-treat those at low risk for periodontal disease progression. Proteomics aims to identify specific biomarkers that enable decision making based on hard data rather than subjective assessments.

Current research shows genetic factors play a role in the clinical variability of periodontal diseases by affecting host-bacterial interactions.9 Considered a polygenic disease, periodontitis is linked to a number of proteins.13 Research is focused on the proinflammatory cytokine interleukin-1 (IL-1) and MMP-8.9,15,28 Approximately 30% of the population is positive for the IL-1 genetic marker.29 Individuals who carry the IL-1 gene experience higher incidence and increased severity of periodontal diseases.9 Currently, MMP-8 is considered the most promising biomarker for early diagnosis of periodontitis and peri-implantitis.15 A recent study showed that MMP-8 had a stronger correlation to bleeding on probing than plaque levels, thereby making it less susceptible to confounding effects of oral hygiene.28 

Alveolar bone, with an identified proteome of 2,625, is critical for tooth retention. Currently, bone grafts are commonly used for alveolar bone regeneration therapy. Therefore, developing techniques that do not require surgery is critical. Transfer of the bone morphogenetic protein2/​​7 gene into periodontal tissues may cause stem cells in periodontal tissue to differentiate into osteogenic cells, enabling generation of new alveolar bone.30,31 This represents a promising, nonsurgical option.

Over time, the etiology of periodontitis has moved from biofilm to host-bacterial interaction and host-immune response. The next shift will involve proteomics and precision medicine. Proteomics offers hope that someday periodontitis risk can be determined early and prevented. At present, tests are available to screen for IL-1 and MMP-8. By integrating the precision medicine model into preventive care for periodontitis, time and resources can be allocated efficiently to patients at the highest risk.9,13 


Proteomics is helping to predict which oral cancer lesions are likely to become malignant. A number of protein biomarkers for oral cancer have been studied including, but not limited to, complement proteins (serum proteins activated by pathogens) and inflammatory cytokines.13,32–34 The direct contact between saliva and oral cancer lesions allows for detection of biomarkers.3 In head and neck cancer, specific proteins show promise in predicting the biomarkers used to determine drug targets and therapeutic response, as well as assess risk for cancer recurrence.9 A prime example of how proteomics is changing drug therapies is the biologic drug, cetuximab, which is approved for treatment of oral squamous cell carcinoma. As a monoclonal antibody, cetuximab competitively inhibits receptor binding of a protein responsible for cell growth in tumor cells.35 


Application of proteomics will soon become reality as evidenced by recent milestones in the field. Research suggests proteomics can be a means to predict, diagnosis, and monitor a number of oral and systemic diseases. Proteomics aims to augment or replace traditional clinical and radiographic assessments with low sensitivity and low positive predictive values that only assess history, extent, and severity of disease. Precision medicine shows promise in oral disease such as periodontitis, dental caries, and oral cancer, as well as systemic conditions, such as diabetes, that affect the oral cavity. Pinpointing exact biomarkers associated with various diseases and ensuring high sensitivity and specificity are vital to application in a clinical setting. In the near future, point-of-care saliva tests or other devices will assess the patient’s “proteome identity” quickly, aiding oral health professionals in treatment planning. 

table 1
*click to view full-size


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  2. Alaaeddine R, Favad M, Nehme E, et al. The emerging role of proteomics in precision medicine: applications in neurodegenerative diseases and neurotrauma. Adv Exp Med Biol. 2017;1007:59–70.
  3. Li Q, Ouyang X, Chen J, et al. A review on salivary proteomics for oral cancer screening. Curr Issues Mol Biol. 2020;37:47–56. 
  4. Yoithapprabhunath TR, Nirmal NM, Santhadevy A, et al. Role of proteomics in physiologic and pathologic conditions of dentistry: overview. J Pharm Bioallied Sci. 2015;7(Suppl 2):S344–S349.
  5. Overall C. The HUPO high stringency inventory of humanity’s shared human proteome revealed. J Proteome Res. 2020;19:4211–4314.
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  7. The National Human Genome Research Institute. Introduction to Genomics. Available at:​About-Genomics/​Introduction-to-Genomics#:~:text=What’s%20a%20Genome%3F,that%20organism%20throughout%20its%20life. Accessed May 12, 2021.
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  9. Reddy MS, Shetty SR, Vannala V, et al. Embracing personalized medicine in dentistry. J Pharm Bioall Sci. 2019;11:S92–S96.
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  21. Giovani PA, Martins L, Salmon CR, et al. Comparative proteomic analysis of dental cementum from deciduous and permanent teeth. J Periodont Res. 2021;56:173–185. 
  22. Abbey SR, Eckhard U, Solis N, et al. The human odontoblast cell layer and dental pulp proteomes and N-terminomes. J Dent Res. 2018;97:338–346.
  23. Widbiller M, Schweikl H, Bruckmann A, et al. Shotgun proteomics of human dentin with different prefractionation methods. Sci Rep. 2019;9:1-8.
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  25. Guedes. Saliva proteomics from children with caries at different severity stages. Oral Dis. 2019;26: 1219-1229.
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  31. Kawai M, Kataoka Y-H, Sonobe J, et al. Nonsurgical model for alveolar bone regeneration by bone morphogenetic protein2/​7 gene therapy. J Periodontol. 2018;89:85–92.
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From Dimensions of Dental Hygiene. June 2021;19(6):26-28,31.

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