The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers

Study information

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study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30123780

DOI Digital object identifier for electronic documents.

10.3389/fcimb.2018.00267

URI

Authors

Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M, Punyadeera C

Journal

Frontiers in cellular and infection microbiology

Year

2018

Keywords:

biomarker, oral cancer, oral microbiome, oral rinse, saliva

The oral microbiome can play a role in the instigation and progression of oral diseases that can manifest into other systemic conditions. These associations encourage the exploration of oral dysbiosis leading to the pathogenesis of cancers. In this study, oral rinse was used to characterize the oral microbiome fluctuation associated with oral cavity cancer (OCC) and oropharyngeal cancers (OPC). The study cohort consists of normal healthy controls (n = 10, between 20 and 30 years of age; n = 10, above 50 years of age), high-risk individuals (n = 11, above 50 years of age with bad oral hygiene and/or oral diseases) and OCC and OPC patients (n = 31, HPV-positive; n = 21, HPV-negative). Oral rinse samples were analyzed using 16S rRNA gene amplicon sequencing on the MiSeq platform. Kruskal-Wallis rank test was used to identify genera associated with OCC and OPC. A logistic regression analysis was carried out to determine the performance of these genera as a biomarker panel to predict OCC and OPC. In addition, a two-fold cross-validation with a bootstrap procedure was carried out in R to investigate how well the panel would perform in an emulated clinical scenario. Our data indicate that the oral microbiome is able to predict the presence of OCC and OPC with sensitivity and specificity of 100 and 90%, respectively. With further validation, the panel could potentially be implemented into clinical diagnostic and prognostic workflows for OCC and OPC.

Experiment 1

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Curated date: 2021/01/10

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Subjects

Location of subjects: Australia

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: head and neck carcinoma carcinoma of craniocervical region,carcinoma of head and neck,carcinoma of neck,carcinoma of the head and neck,carcinoma of the neck,craniocervical region carcinoma,head and neck cancer,head and neck carcinoma,neck carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: High-risk individuals
Group 1 name Corresponds to the case (exposed) group for case-control studies: OCC & OPC
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer)
Group 0 sample size Number of subjects in the control (unexposed) group: 11
Group 1 sample size Number of subjects in the case (exposed) group: 32

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V6-V8

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Kruskall-Wallis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

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Curated date: 2021/01/10

Curator: Utsav Patel

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Source: Figure 1B, Supp. Table 2, Text

Description: The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers

Abundance in Group 1: decreased abundance in OCC & OPC

NCBI	Quality Control	Links
Paludibacter
Corynebacterium
Porphyromonas
Actinomyces
Actinobacillus
Capnocytophaga
Fusobacterium
Aggregatibacter
Lautropia

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Experiment 2

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Normal Healthy Controls
Group 0 sample size Number of subjects in the control (unexposed) group: 20
Group 1 sample size Number of subjects in the case (exposed) group: 31