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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M, Punyadeera C
Journal
Frontiers in cellular and infection microbiology
Year
2018
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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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
31

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

Needs review

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

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 Links
Paludibacter
Corynebacterium
Porphyromonas
Actinomyces
Actinobacillus
Capnocytophaga
Fusobacterium
Aggregatibacter
Lautropia

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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
Normal Healthy Controls
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
20
Group 1 sample size Number of subjects in the case (exposed) group
31

Lab analysis

Sequencing type
16S
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

Needs review

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

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: increased abundance in OCC & OPC

NCBI Links
Oribacterium

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

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 Links
Rothia
Haemophilus
Corynebacterium
Paludibacter
Porphyromonas
Capnocytophaga

Revision editor(s): WikiWorks