Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G, Dong Q
Journal
Cancer management and research
Year
2020
Keywords:
microbiome, oral squamous cell carcinoma, predicted functions, random forest machine learning
Objective: The aim of this study was to explore the signatures of oral microbiome associated with OSCC using a random forest (RF) model. Patients and Methods: A total of 24 patients with OSCC were enrolled in the study. The oral microbiome was assessed in cancerous lesions and matched paracancerous tissues from each patient using 16S rRNA gene sequencing. Signatures of mucosal microbiome in OSCC were identified using a RF model. Results: Significant differences were found between OSCC lesions and matched paracancerous tissues with respect to the microbial profile and composition. Linear discriminant analysis effect size analyses (LEfSe) identified 15 bacteria genera associated with cancerous lesions. Fusobacterium, Treponema, Streptococcus, Peptostreptococcus, Carnobacterium, Tannerella, Parvimonas and Filifactor were enriched. A classifier based on RF model identified a microbial signature comprising 12 bacteria, which was capable of distinguishing cancerous lesions and paracancerous tissues (AUC = 0.82). The network of the oral microbiome in cancerous lesions appeared to be simplified and fragmented. Functional analyses of oral microbiome showed altered functions in amino acid metabolism and increased capacity of glucose utilization in OSCC. Conclusion: The identified microbial signatures may potentially be used as a biomarker for predicting OSCC or for clinical assessment of oral cancer risk.

Experiment 1


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
China
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 , Skin of cheek , Tongue , Gingiva , Oropharynx 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,Cheek skin,Skin of cheek,Glossus,Tongue,Gingival mucosa,Gum,Gum tissue,Gums,Gingiva,Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity
Group 0 name Corresponds to the control (unexposed) group for case-control studies
paracancerous tissues
Group 1 name Corresponds to the case (exposed) group for case-control studies
cancerous lesions
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients at different stages of OSCC were enrolled in the study
Group 0 sample size Number of subjects in the control (unexposed) group
24
Group 1 sample size Number of subjects in the case (exposed) group
24
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 weeks

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
LEfSe
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

Needs review

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2A

Description: Relative abundance of genera enriched in cancerous tissues

Abundance in Group 1: increased abundance in cancerous lesions

NCBI Quality ControlLinks
Filifactor
Tannerella
Parvimonas
Carnobacterium
Peptostreptococcus
Streptococcus
Treponema
Fusobacterium

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Atrayees, WikiWorks

Source: Figure 2A

Description: Relative abundance of genera enriched in cancerous tissues

Abundance in Group 1: decreased abundance in cancerous lesions

NCBI Quality ControlLinks
Arthrobacter
Brevundimonas
Desulfovibrio
Microbacterium
Mucispirillum
Paenibacillus
Streptophyta

Revision editor(s): Atrayees, WikiWorks