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J Periodont Res 2012; 47: 214  2011 John Wiley & Sons A/S

All rights reserved


JOURNAL OF PERIODONTAL RESEARCH
doi:10.1111/j.1600-0765.2011.01387.x

Review Article

What do omic technologies


M. M. Grant
Periodontal Research Group, School of
Dentistry, University of Birmingham, St Chads
Queensway, Birmingham, UK

have to offer periodontal


clinical practice in the
future?
Grant MM. What do omic technologies have to oer periodontal clinical practice in
the future? J Periodont Res 2012; 47: 214.  2011 John Wiley & Sons A/S

Background and Objective: Periodontal diseases are the most common chronic
inammatory diseases of humans and a major cause of tooth loss. Inammatory
periodontitis is also a complex multifactorial disease involving many cell types, cell
products and interactions. It is associated with a dysregulated inammatory
response, which fails to resolve, and which also fails to re-establish a benecial
periodontal microbiota. There is a rich history of biomarker research within the
eld of periodontology, but exemplary improvements in analytical platform
technologies oer exciting opportunities for discovery. These include the omic
technologies, such as genomics, transcriptomics, proteomics and metabolomics,
which provide information on global scales that can match the complexity of the
disease. This narrative review focuses on the recent advances made in in vivo
human periodontal research by use of omic technologies.
Material and Methods: The Medline database was searched to identify articles
currently available on omic technologies with regard to periodontal research. Dr Melissa M. Grant, Periodontal Research
Group, School of Dentistry, University of
Results: One hundred and sixty-one articles focusing on biomarkers of and omic Birmingham, St Chads Queensway,
Birmingham B4 6NN, UK
advances in periodontal research were analysed for their contributions to the Tel: +44 121 237 2884
understanding of periodontal diseases. Fax: +44 121 237 2882
e-mail: m.m.grant@bham.ac.uk
Conclusion: The data generated by the use of omic technologies have huge
Key words: genomics; transcriptomics; proteo-
potential to inform paradigm shifts in our understanding of periodontal diseases, mics; metabolomics; systems biology; periodon-
but data management, analysis and interpretation require a thoughtful and sys- tology
tematic bioinformatics approach, to ensure meaningful conclusions can be made. Accepted for publication May 5, 2011

Periodontal diseases are the most to help identify patients with peri- upon systemic inammatory diseases,
common chronic inammatory dis- odontitis. These would help in early where periodontitis is recognized as a
eases of humans and a major cause of diagnosis of disease onset, progression, risk factor. The identication of bio-
tooth loss (1). Diagnosis requires or indeed resolution following treat- markers using omic technologies, such
training, knowledge and dedicated ment and may reduce both the health- as genomics, transcriptomics, proteo-
clinical facilities, creating a need for care and economic burdens arising mics and metabolomics, could deliver
those in nonspecialist and/or nonden- from periodontitis, estimated as such diagnostic tests.
tal environments (e.g. medical practice) 2.78 billion in the UK in 2008 (2). The ocial National Institutes of
for simple, objective diagnostic tools, Moreover, they may positively impact Health (NIH, USA) denition of a
Omic technologies and periodontal research 3

biomarker is a characteristic that is 10s Increasing sample numbers required 1000s


objectively measured and evaluated as
an indicator of normal biologic pro- Discovery: Validation: Cohort Clinical use:
cesses, pathogenic processes, or phar- biomarkers and efficacy in validation: diagnosis and
macologic responses to a therapeutic pathway secondary efficacy in an prognosis
intervention. Although this could be a elucidation population at-risk population
physical trait, such as hair colour, for
the purpose of this focused review of in
Increasing analyte numbers
vivo biomarkers of human periodonti-
tis only molecular biomarkers and Fig. 1. The path through which biomarkers must travel to be useful for the clinician. Omic
those determined in a genetic, proteo- technologies can be used at all stages, but have most impact on the initial stages.
mic or metabolomic prole will be
discussed. As Bensalah et al. (3) have
recently documented, six dierent cannot be established solely by statis- cuss these samples for targeted
types of biomarker can be dierenti- tics; there needs to be an evaluation approaches to biomarker discovery
ated, as follows: akin to structured, phased trial testing (5,710). In particular, Loos & Tjoa (5)
early detection of disease; (3,6). Such independent validation and undertook a critical review of biomar-
diagnosis of presence or absence of ecacy determination in large com- kers in gingival crevicular uid and
disease; munity-dwelling populations, in the found that only eight of 94 in the
prognosis of disease outcome equivalent of phase 2 and 3 trials, is literature of the time fullled any of
and possible patient stratication even scarcer than phase 1 studies. Thus, the criteria for biomarker status.
allowing for personalized medical to mine the proverbial biomarker ice- These eight biomarkers were alka-
interventions (particularly in peri- berg using these novel biomarker tech- line phosphatase (1117), b-glucuroni-
odontology for those at elevated risk nologies, larger multicentre multi-omic dase (15,1826), cathepsin B (2732),
of disease recurrence); systems biology trials need to be per- MMP-8 and MMP-9 (15,3345), dip-
prediction of treatment outcome; formed. eptidyl peptidase II and IV (28,29,
identication of patients who will Samples available for in vivo studies 31,46) and neutrophil elastase (15,24,
respond well to a particular treat- of periodontal diseases include gingival 2629,39,4766). Potential novel bio-
ment; and crevicular uid, plaque, saliva, biop- markers that have been described more
surrogate end-points. sies, peripheral blood cells and plasma recently using omics-driven discoveries
In addition, for a biomarker or a panel (Fig. 2). Several excellent reviews dis- are discussed below.
of biomarkers to be successfully
employed within the clinical environ-
ment, they must also be objective,
reproducible, easy to use, cheaper and
Transcriptomics
with greater sensitivity, specicity and Gingival tissues Genomics
diagnostic accuracy than existing tests
(35). These hurdles are made higher
still by the need for potential biomar-
kers to achieve a status akin to the rig-
orous governance processes through
which drugs must pass for licensing; Saliva Blood:
there is, however, currently no such
Periodontal Cells and fluid
mechanism in place for such evalua-
tions(3). Also in parallel to drug dis- disease
covery is the process of validation
through which biomarkers pass (Fig. 1).
In the past, the most useful biomar-
kers have either been found serendipi-
tously or through careful evaluation of
candidates generated through hypoth-
Micro-organisms Gingival crevicular
esis-driven research (6). Many potential
fluid
biomarkers are developed using pre- Proteomics
clinical in vitro models, and a few go
onto the development of assays used in Metabolomics
the evaluation of a small number of
patients in the equivalent of phase 1 Fig. 2. The compartments available for studying periodontal disease using omic
trials. Proof of biomarker ecacy technologies.
4 Grant

The omic technologies include of molecular species in each of the mask less obvious biological pertur-
genomics, transcriptomics, proteomics areas also challenges the investigator, bations, but can be overcome with
and metabolomics (Fig. 2), and each is because there may be over 30,000 genes much larger study populations where
discussed in a separate section below. and transcripts, over 100,000 proteins, general noise can be removed and
Genes, transcripts, proteins and meta- including post-translational modica- small changes can gain statistical sig-
bolites will all feed into the overall tions, and over 6500 metabolites in the nicance due to increasing study
phenotype of periodontal disease human (67); not one of these areas power.
(Fig. 3). It should be noted that, in should be singled out as easier than The following sections summarize
contrast to genomics, transcriptomics, any other, and it should be noted that the data already published using omics
proteomics and metabolomics assess each level can be inuenced by the technologies. Table 1 summarizes the
the temporal expression of genes rather others through feedback loops and data-rich studies. Following the anal-
than the static encoding of the genome. regulatory mechanisms (Fig. 3). All ysis by Loos & Tjoa (5) of the eld of
Thus, they take into account environ- these technologies and assessments can biomarkers, an attempt was made to
mental inuences, i.e. nurture as well be applied to both the host and the stratify these studies according to their
as nature. As we progress from microbiota in periodontitis. Here, only use in detection, classication, plan-
genomics to transcriptomics, proteo- the host contributions are discussed; ning of treatment or monitoring of
mics and metabolomics, we also pro- for excellent and recent reviews on patients. However, though many show
gress from what might happen to what microbiome advances please see work promise, none of the studies has yet
really did happen, with transcriptomics by Parahitiyawa et al.(68), Dewhirst matured to that level of usage, as most
being inuenced by translation and et al.(69), Wade (70) and Pozhitkov are still early though potentially valu-
activation, proteomics elucidating et al.(71). So far, a lot of ground has able reports.
changes to global protein expression, been made on the microbiome associ-
splice variants of proteins and post- ated with health, while advances com-
Genomics
translational modications, and meta- paring health and disease, such as
bolomics demonstrating end-products those published in the eld of gut Genomics is the study of whole
of reactions. There are further dier- microora (72), are eagerly awaited. genomes, i.e. all the DNA of a single
ences between these elds of study; the Drawbacks of all the functional organism. With improvements in
DNA, RNA and proteins studied in genomics technologies include con- sequencing, the dawn of genome-dri-
genomics, transcriptomics and proteo- founding issues such as age, gender, ven individualized medicine has
mics, respectively, are very regular diet, smoking and probably many arrived, where changes to multiple
in structure, and this has greatly aided more. Where dynamic range is a genes may be taken into account for
the discovery in these elds. In problem, the technology may be diagnosis and treatment. With dier-
contrast, metabolomics encompasses aected by the usual suspects phe- ences in more than 3 million nucleo-
many small chemicals with varying nomenon (73), where similar chemical tides (0.1% of the whole genome)
hydrophobicityhydrophilicity, acid- species are found in a variety of unre- evident when comparing two individ-
itybasicity and other physicochemical lated studies and reect the fact that ual genomes, it will, however, probably
properties. This means that the level of some situations/treatments aect cen- take many years before such dier-
complexity and analytical challenges tral signalling or metabolic hubs within ences can be mapped to disease corre-
are increased in metabolomics. How- cells, for example aecting energy lations (74,75). However, for some
ever, taking into account the number generation. This is a problem that can time the changes in individual genes
(gene polymorphisms) have been
studied with reference to disease risk,
phenotype severity and therapeutic outcome.
These gene polymorphisms are highly
Genome prevalent in the population (76), and the
most common type is the single nucle-
otide polymorphism (SNP), where an
Transcripome
individual base pair is aected, by
alteration within, insertion into or
deletion from the DNA sequence.
Proteome
Where these changes fall in promoter
regions, exons, introns or untranslated
regions, will dierentially aect gene
Metabolome
products (75).
environment The inuence of SNPs on peri-
odontal disease was reviewed in 2006
by Takashiba & Naruishi (75). They
Fig. 3. The interplay of the dierent compartments studied by omic technologies. highlighted that nearly half of the
Table 1. Summary of data-rich omics studies

Platform of Number of chemical Source of biological Number of subjects in


Approach Study population(s) evaluation species investigated samples study Conclusion References

Genomics Severe periodontitis, TaqMan PCR 637 SNPs Whole peripheral n = 22 severe GNRH1, PIK3R1, DPP4, 114
comparison to blood periodontitis patients, FGL2, and CALCR
healthy subjects n = 19 control signicantly associated with
subjects disease
Aggressive Aymetrix Genome-wide Whole peripheral n = 141, 142, 164 GLT6D1 was signicantly 116
periodontitis Gene Chip Human association study of blood and gingival assessment in two associated with disease
Mapping 500K 500,000 SNPs tissue cohorts by genome-wide
Array Set association study and
validated in a third cohort
(aected teeth 26%)
Transcriptomics Chronic and Aymetrix Human 22,000 transcripts Biopsies of gingival n = 1 localized chronic Patients were clustered by 117
aggressive Genome U-133 A tissue periodontitis, n = 6 pathogen presence rather
periodontitis arrays generalized chronic than by disease type
periodontitis n = 1
localized aggressive
periodontitis, n = 6
generalized aggressive
periodontitis
Chronic and Aymetrix Human 47,000 transcripts Biopsies of gingival n = 90 (63 chronic and Gene ontology groups 118
aggressive Genome U-133 tissue 27 aggressive) increased included
periodontitis Plus 2.0 arrays periodontitis apoptosis, antimicrobial
patients humoral response, antigen
presentation, regulation of
metabolic processes, signal
transduction and
angiogenesis
Chronic and Aymetrix Human 47,000 transcripts Biopsies of gingival n = 120 (65 chronic Commonalities and 119
aggressive Genome U-133 tissue and 55 aggressive) dierences were found
periodontitis Plus 2.0 arrays patients between gene expression
and bacterial species present
Experimental Aymetrix Human 47,000 transcripts Biopsies of gingival n = 14 healthy Dierences in gene ontology groups: 121
gingivitis Genome U-133 tissue volunteers neural processes, epithelial
Plus 2.0 arrays defences, angiogenesis and
wound healing
Periodontal disease Agilent 2100 160 genes Biopsies of gingival n = 12 severe Activation of pathways 122
compared with Bioanalyzer and a tissue generalized chronic regulating tissue damage
control human inammation periodontitis, n = 11 and repair after treatment
microarray control subjects
Refractory Aymetrix Human 22,000 transcripts Subepithelial connective n = 7 refractory Increases in immune re 123
periodontitis Genome U-133 tissue periodontitis and sponse, tissue modelling
A arrays n = 7 periodontally and apoptosis in disease in
Omic technologies and periodontal research

well-maintained refactory patients


patients
5
6
Table 1. (Continued)

Platform of Number of chemical Source of biological Number of subjects in


Approach Study population(s) evaluation species investigated samples study Conclusion References
Grant

Periodontitis Aymetrix Human 47,000 transcripts Peripheral n = 15 patients Changes in innate 124
patients undergoing Genome U-133 monocytes immunity, apoptosis and
treatment Plus 2.0 arrays cell signalling were seen
Periodontitis Aymetrix Human 22,000 transcripts Peripheral n = 19 patients Type-1 interferon-stimulated 127
Genome U-133 A neutrophils genes were increased
arrays
Proteomics Periodontitis in Electrophoresis and Not given Gingival crevicular n = 10 periodontitis S100A8 and S100A9 134
comparison to MS uid, serum and patients, n = 4 control represented major dierences
control saliva subjects between gingival crevicular
uid and saliva
Periodontitis Electrophoresis and 66 proteins identied Gingival crevicular n = 12 patients Identication of serum and 135
patients in MS uid cell-derived proteins
maintenance phase
Aggressive Electrophoresis and Not given Saliva n = 5 aggressive Six proteins were increased in 136
periodontitis in MS periodontitis patients, saliva of periodontitis
comparison to n = 5 control subjects subjects, while ve were
control decreased
Generalized Quantitative MS 154 human, bacterial, Gingival crevicular n = 5 aggressive Human plastin-2 and microbial 137
aggressive fungal and viral uid periodontitis patients, proteins increased in disease,
periodontitis proteins n = 5 control subjects annexin A1 increased in
health
Experimental Quantitative MS 202 human and Gingival crevicular n = 10 healthy Identication of 186 proteins, 138
gingivitis bacterial uid volunteers including serum and
proteins cell-derived species, including
plastin-2. Novel structural
proteins for cilia and ribbon
synapses found.
Metabolomics Chronic MS 103 metabolites Gingival crevicular n = 22 patients; At diseased sites antioxidant, 147
periodontitis identied uid samples collected glutamine, di-and trisaccharide
included diseased and levels decreased; amino acids
healthy sites (except glutamine), choline,
glucose, polyamines, purine
degradation and urea cycle
metabolites increased
Localized aggressive MS Seven diacylglycerol Neutrophils n = 11 localized Increased diacylglycerol species 148
periodontitis species aggressive periodontitis, in disease compared with
n = 4 asymptomatic control
family members
Systems biology Periodontitis Data mining and 61 genes In silico Not relevant Five leader genes (or hubs: 152
cluster analysis NFkB1, CBL, GRB2, PIK3R1
and RELA) identied

Abbreviations: MS, mass spectrometry; SNP, single nucleotide polymorphism; GLT6D1, glycosyltransferase 6 domain containin 1; NFkB1, nuclear factor of kappa light polypeptide gene
enhanced in B cells 1; CBL, Cas-Br-M ectropic retroviral transforming sequence; GRB2, growth factor receptor-bound protein 2; RELA,v-rel reticuloendotheliosis viral oncogene homology A;
PIK3R1, phosphoinistidite-3-kinase, regulatory subunit 1.
Omic technologies and periodontal research 7

research in this area has focused upon enzymes are single-pass transmembrane dierent transcriptome proles and
cytokines, with the rest investigating proteins, which contribute to the syn- contribute to the heterogeneity of
human leukocyte antigens, immunore- thesis of histo-blood-related antigens in results. However, it was possible to
ceptors, proteases, structural molecules the Golgi. GLT6D1 was found to be identify genes that have not previously
and other proteins. However, of the highly expressed in the gingival con- been linked with periodontal diseases,
140 papers they used for their review nective tissues and may inuence im- such as CXCL6 (granulocyte chemo-
the majority focused on only six genes: mune responses. Future studies using attractant protein 6; 117,120). In their
interleukin 1 (IL1), tumour necrosis larger numbers of patients and control latest paper, Papapanou et al. (119)
factor a (TNFa), Fcc receptors, subjects may yield more associations; correlated the transcriptomes of
MMPs, cathepsin C and vitamin D however, the acquisition of even one chronic periodontitis patients with the
receptor), indicating that this eld is unknown gene that may predict peri- subgingival microora in those
still in its infancy. Interleukin-1 SNPs odontal disease is potentially of great patients/sites. This interesting study
were suggested to be more associated value. coupled the two key drivers of peri-
with environmental interactions, such odontal disease expression, the host
as with smoking, than with suscepti- and microbial factors, to determine
Transcriptomics
bility to periodontitis, whereas TNFa whether species of bacteria can cluster
showed a lack of association with The eld of transcriptomics involves the large number of genes dierentially
inammatory periodontal disease. the study of mRNA production by expressed in periodontal disease, thus
However, polymorphisms in Fcc cells in particular conditions. Unlike yielding information on how bacterial
receptors tend to be associated with proteomics and metabolomics (see next species might inuence host gene
both aggressive and chronic forms of section), this is typically studied in cell expression. Gingival biopsies were also
periodontitis. For the other genes populations and thus in periodontal taken by Oenbacher et al. (121) to
mentioned above, limited evidence investigations either uses biopsies of investigate the temporal changes in
makes it dicult to relate SNPs to relevant oral tissues or peripheral gene expression during experimental
periodontitis. In the past 5 years since blood leukocytes rather than oral uids gingivitis. Again, large numbers of
the review by Takashiba & Naruishi such as gingival crevicular uid and genes were dierentially expressed and
(75), there have been at least an addi- saliva, which can be studied using novel gene ontology groups were
tional 37 articles published concerning proteomic and metabolomic platforms. reported, including those of neural
SNPs in cytokines (77113). These There are two major advantages that processes, epithelial defences, angio-
small-scale studies of individual SNPs this technique provides: (i) the ability genesis and wound healing.
are no longer in a position to contrib- to amplify the expressed gene products; Beikler et al. (122) investigated gene
ute anything new to the literature and and (ii) the stability and uniformity of expression changes in periodontal tis-
are of limited value. the platforms employed in identica- sues before and after treatment using a
Moving into wider ranging analysis, tion of interesting and/or novel chem- semi-targeted human inammation
Suzuki et al. (114) examined 637 SNPs ical species. This is reected in the far microarray. They concluded that those
in 19 healthy and 22 severe periodon- greater number of articles reporting gene proles that were altered the most
titis cases, revealing ve previously transcriptomic studies than proteomic indicated an activation of pathways
untargeted genes as potential markers and metabolomic studies. Over the last that regulate tissue damage and repair.
for periodontitis. 5 years, Papapanou et al. have analy- Kim et al. (123) examined subepithelial
Overall, the genetic basis of peri- sed whole-tissue transcriptomes from connective tissues from healthy control
odontitis accounts for approximately the excised papillae of healthy and subjects and periodontal patients. They
half the population variance in chronic diseased patients in an attempt to found that these tissues also demon-
periodontitis (115,116). There is a need reclassify periodontal disease biologi- strated transcriptomic increases in the
to progress to large-scale genome-wide cally rather than clinically (117119). A immune response, tissue remodelling
association studies, and the rst of these pilot study, however, could not dier- and apoptosis genes.
has been published (116). Comparison entiate between chronic and aggressive Looking at how periodontitis aects
of two cohorts of aggressive periodon- forms of periodontitis (117), whereas the peripheral blood system, Papapa-
titis patients independently identied comparison of diseased and healthy nou et al. (124) took monocytes from
197 and 244 quality-controlled SNPs papillae from patients with advanced periodontal patients undergoing treat-
from 141 and 142 patients, respectively, periodontitis did detect dierences in ment and examined mRNA expression
examining 500,568 potential SNPs. gene ontology groups for apoptosis, using Aymetrix arrays. They found
However, when the results from both antimicrobial humoral responses, that a third of patients had substantial
sets were compared, only one remained antigen presentation, regulation of changes in genes relevant to innate
signicant, which was subsequently metabolic groups, signal transduction immunity, apoptosis and cell signalling,
validated in a third set of patients and angiogenesis. The authors com- and concluded that periodontal therapy
(n = 164). The gene identied was mented that the papillae are composed had a systemic anti-inammatory
GLT6D1, which encodes for a glyco- of a variety of cell types, These dier- eect. Matthews et al. (125,126) have
syltransferase 6 family protein. These ences in composition may give rise to previously reported that neutrophils
8 Grant

from periodontitis patients are both often not possible to examine the entire illustrating perhaps the need for
hyper-reactive to stimulation by proteome, and it is frequently neces- prefractionation to dissect deeper
Fusobacterium nucleatum or Fcc recep- sary to try and remove or separate the down into the proteome. Quantitative
tors and also show baseline hyperac- most abundant proteins from a sample LC-MS/MS has been used by Bostanci
tivity with respect to production of (e.g. albumin) prior to analysis. How- et al. (137) and by Grant et al. (138) to
reactive oxygen species. Following ever, proteomics does address changes investigate gingival crevicular uid
these discoveries, the same group (127) to proteins, such as splice variants and proles from patients with generalized
used neutrophils from periodontitis post-translational modications. Tar- aggressive periodontitis and volunteers
patients to determine what genes were geted approaches to look at panels of undergoing experimental gingivitis,
aected. They found signicant in- cytokines, such as using the bead-based respectively. Both studies, as with Ngo
creases in type-1 interferon-stimulated Luminex platform, allow examination et al. (135), found proteins of both
genes, and this led to the discovery that of proteins of low concentration, but serum and tissue origins and, more
patients had signicantly greater con- such presumptive approaches are not specically, found changes in com-
centrations of circulating interferon-a, discussed here. mon, previously uninvestigated pro-
which, upon successful periodontal In the study of periodontal diseases, teins, such as neutrophil plastin-2, an
treatment, decreased to the same levels many proteomic approaches have actin-bundling protein involved in Fcc
as in nondiseased control subjects. They been used. Top-down whole-protein receptor stimulation. With the inclusion
concluded that periodontitis is a com- approaches to identify low molecular of a quantitative aspect, these studies
plex disease, where increases in inter- weight proteins have investigated the allow for a more detailed investigation,
feron-a may be one component of a presence of human neutrophil peptides where bioinformatic tools may be able
distinct molecular phenotype in neu- (131133) in gingival crevicular uid. to nd composites of proteins that could
trophils, triggered potentially by viral However, the use of bottom-up be used as biomarkers. To date, how-
priming or autoimmune responses. This approaches, where proteins are ever, these biomarkers have not been
latter concept is new to periodontology digested to individual peptides prior to validated.
and may help explain the association identication by tandem mass spec- Degradomics is a specialized eld of
between periodontitis and rheumatoid trometry techniques, has yielded many proteomics employing all of the tech-
arthritis (128130). more novel insights into the peri- niques previously described. It assesses
Advances have been made using odontitis proteome. Kojima et al. the proteases at work within the tis-
transcriptomic approaches, but there is (134) separated gingival crevicular sues which may be involved in sub-
a need to bring together the established uid proteins by two-dimensional strate processing, yielding activated or
data sets and also to conduct much electrophoresis and then identied inactivated substrates, altering func-
larger, wide-ranging studies that can proteins of interest by mass spec- tionalities or localizations, by looking
take into account possible changes in trometry. The addition of two-dimen- at protease activity and cleaved pro-
cell type within periodontal tissues, to sional electrophoresis introduced a teins. This is of particular interest to
pinpoint genes that may be useful in method to assess protein levels quan- periodontology, where there is a large
dierentiating between disease types titatively between diseased and healthy amount of tissue destruction by either
and address the criteria for biomarker subjects, although intra-individual var- the host or pathogen eorts. Protease
research previously stated. iation swamped the slight trend for more activities have been found in peri-
calprotectin subunits in periodontitis odontitis, for example the cleavage of
patients. Use of liquid chromatogra- interleukin-8 by Porphyromonas gini-
Proteomics
phymass spectrometry techniques to givalis protease gingipains (139,140).
Proteomics, the study of all the pro- study periodontitis has recently been The truncated interleukin-8 increases
teins in a given sample, was revolu- reported. Ngo et al. (135) examined in chemotactic activity and the ability
tionized by advances in mass gingival crevicular uid samples by to stimulate the oxidative burst in
spectrometry in the 1990s. It became electrophoresis and liquid chromato- neutrophils (139). Another protease
possible to identify the constituent graphy tandem mass spectrometry that has been studied is cathepsin K
protein species within biological sam- (LC-MS/MS) to identify 66 proteins, (141), demonstrating a correlation
ples, and now many studies have used which included a large number of with the severity of periodontal dis-
an ever-expanding and complex array serum and cell-derived proteins, ease by dening the targets of this
of techniques that are both qualitative reecting the dual origin of the uid. protease. Large-scale unbiased ap-
and quantitative in their outputs. A Wu et al. (136) compared saliva pro- proaches have yet to be employed for
feature of many biological/clinical teomes from generalized aggressive the evaluation of protease activities or
samples is that they exhibit a very wide periodontitis patients and control substrates in periodontitis, and they
dynamic range of constituent protein subjects using a similar technique. will be of great value when completed.
species, for instance in plasma that Whole saliva yielded dierences in For information of the state of the
range is six orders of magnitude. highly abundant proteins, such as eld, please see recent reviews by
Without the advantages that DNA and albumin and amylase, which were Impens et al. (142) and Morrison
RNA amplication strategies oer, it is increased in the diseased samples, et al. (143).
Omic technologies and periodontal research 9

Gronert et al. (148) used a lipidomics nantly involved receptor-mediated sig-


Metabolomics
approach to identify and quantify nalling and may reect the stimulation
Metabolomics is a discipline that studies diacylglycerol species in neutrophils of the host inammatoryimmune sys-
the quantities of all chemicals except from localized aggressive periodontitis tem by bacteria in periodontitis.
DNA, RNA and proteins within a patients, following a transcriptomics Use of holistic approaches will have
sample. No one experimental technique analysis that had identied diacylglyc- the advantage that they will address
can analyse all chemical structures. erol kinase from neutrophils as not the synergistic qualities of multiple
Thus, samples need to be analysed by a being expressed, in comparison to dis- bacterial challenges and multiple cell
battery of techniques and separated by ease-free control subjects. Metabolo- types present at the diseased lesion.
their chemical and physical properties mics is an area that could and should The bacterial challenge, in particular,
and identied, principally, by nuclear see intensive research to provide a should not be overlooked, with so
magnetic resonance and mass spec- clearer understanding of periodontitis. many so-called unculturable bacteria
trometry. There is a vast number of It will be able to reveal information being present (153). Microbiome
potential metabolites, and targeted about the host and hostmicroora strategies to study the thousands of
approaches have elucidated some interactions which may yield specic bacteria present will unite with the
changes (22,144146), but there are very small molecule targets that have been omic technologies (154). Nibali et al.
few articles that report on tackling the overlooked by other techniques. (155) have already termed the interac-
global metabolome in periodontal dis- tion between host genetic factors, such
ease. Barnes et al. (147) used gas and as SNPs, and the oral microbiome as
Systems biology
liquid chromatographic separations infectogenomics.
coupled to mass spectrometry to inves- Systems biology is the integration of Even before it was termed systems
tigate gingival crevicular uid samples multiple omics platforms and data biology, scientists were creating net-
from 22 chronic periodontitis patients, through the reconstruction of the com- works, graphs or maps of the inter-
stratied for healthy, gingivitis and plex networks involved (149). These action of genes through regulation,
periodontitis sites. They identied 103 complex networks characterize partic- proteins through proteinprotein
metabolites in comparison to a chemical ular systems, often cells, but in peri- interactions and signalling cascades
reference library, nding that levels of odontitis it would need to address the and metabolites through metabolic
metabolites from gingivitis sites fell whole disease, i.e. interactions not of maps. Systems biology now needs to
between healthy and periodontitis sites. one cell type but of many and also with rely on the computational modelling of
At disease sites, in comparison to the micro-organisms present in the dis- quantitative large-scale data sets that
healthy sites, antioxidant, glutamine ease state. Advances in network infer- can be produced by omic technologies.
and di- and trisacchride levels were ence and analysis in other diseases, such Biological and articial networks can
decreased, whereas amino acids (except as obesity, diabetes and atherosclerosis, be inferred and used to understand
glutamine), choline, glucose, polyam- are already highlighting that it may be dierences between states of systems,
ines and purine degradation and urea necessary to target multiple (1050) for instance, health and disease.
cycle metabolites were increased. This genes, in dierent tissues, simulta- Although many approaches can be
study has expanded our knowledge of neously to treat a disease eectively used, there is now a drive towards
the sources of oxidative stress, which is (150). Such an approach would yield a making these rigorous with challenges
already acknowledged as being of par- holistic overview of the disease milieu. such as those from DREAM (Dialogue
ticular importance in periodontal dis- The complementary information from on Reverse Engineering Assessment
ease by the potential increase in activity the dierent omic technologies needs to and Methods; 156), and problems of
of the xanthine oxidasereactive oxygen be co-ordinated and integrated, and integration of dierent data sets have
species axis (147). Nuclear magnetic several strategies are being progressed in been overcome by advances in the eld
resonance-based approaches have not, other research areas (151). This still (157,158). At the heart of systems
as yet, been described for human gingi- remains a major challenge to the peri- biology is a cycle of data and knowl-
val crevicular uid. This may be due to odontal eld, and there is still the edgein silico modellinghypothesis
the larger concentrations of samples requirement for fundamental under- generationexperimental validation
required. standing of the mechanisms taking that leads back to more data and
Lipidomics is a particular subspeci- place so that the data can be appropri- knowledge (159). In the periodontal
ality of metabolomics that investigates ately modelled. The rst report has been eld we have lots of knowledge, such
the role of lipids in cellular function, published in the eld. Using an ab initio as the investigations into transcripto-
because they integrate signalling and bioinformatic approach, Covani et al. mics data sets that have thrown up
metabolic processes. The most common (152) predicted ve leader genes from an some initial gene ontology information
technique employs mass spectrometry, investigation of 61 genes potentially (117,121,124) that could demonstrate
particularly using MSn where n > 1 involved in periodontitis, using pub- where dislocations in networks might
and multiple sequential mass spectro- lished articles as the source of data. occur. Integration and combination
metry events continue analysis of one These genes were NFkB1, CBL, GRB2, of overlapping data sets and creation
chemical species of interest. Recently, PIK3R1 and RELA, and are predomi- of networks might yield interesting
10 Grant

results, such as those found in other 15. Nakashima K, Giannopoulou C, Ander-


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12 Grant

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