Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G, Dong Q
Journal
Cancer management and research
Year
2020
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
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
Source: Figure 2A
Description: Relative abundance of genera enriched in cancerous tissues
Abundance in Group 1: increased abundance in cancerous lesions
NCBI | Links |
---|---|
Filifactor ⚠ | |
Tannerella | |
Parvimonas | |
Carnobacterium | |
Peptostreptococcus | |
Streptococcus | |
Treponema | |
Fusobacterium |
Revision editor(s): WikiWorks743
Signature 2
Needs review
Source: Figure 2A
Description: Relative abundance of genera enriched in cancerous tissues
Abundance in Group 1: decreased abundance in cancerous lesions
NCBI | Links |
---|---|
Arthrobacter ⚠ | |
Brevundimonas ⚠ | |
Desulfovibrio | |
Microbacterium ⚠ | |
Mucispirillum | |
Paenibacillus ⚠ | |
Streptophyta |
Revision editor(s): WikiWorks743, Atrayees
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