Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB, Eng C
Journal
Genome medicine
Year
2017
Keywords:
Bacteria, Head and neck squamous cell carcinoma (HNSCC), Microbiome
BACKGROUND: While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamous cell carcinomas. Prior investigations have been limited to comparisons of microbiota obtained from surface swabs of the oral cavity. This study aims to identify microbiomic differences in paired tumor and non-tumor tissue samples in a large group of 121 patients with head and neck squamous cell carcinomas and correlate these differences with clinical-pathologic features. METHODS: Total DNA was extracted from paired normal and tumor resection specimens from 169 patients; 242 samples from 121 patients were included in the final analysis. Microbiomic content of each sample was determined using 16S rDNA amplicon sequencing. Bioinformatic analysis was performed using QIIME algorithms. F-testing on cluster strength, Wilcoxon signed-rank testing on differential relative abundances of paired tumor-normal samples, and Wilcoxon rank-sum testing on the association of T-stage with relative abundances were conducted in R. RESULTS: We observed no significant difference in measures of alpha diversity between tumor and normal tissue (Shannon index: p = 0.13, phylogenetic diversity: p = 0.42). Similarly, although we observed statistically significantly differences in both weighted (p = 0.01) and unweighted (p = 0.04) Unifrac distances between tissue types, the tumor/normal grouping explained only a small proportion of the overall variation in the samples (weighted R2 = 0.01, unweighted R2 < 0.01). Notably, however, when comparing the relative abundances of individual taxa between matched pairs of tumor and normal tissue, we observed that Actinomyces and its parent taxa up to the phylum level were significantly depleted in tumor relative to normal tissue (q < 0.01), while Parvimonas was increased in tumor relative to normal tissue (q = 0.01). These differences were more pronounced among patients with more extensive disease as measured by higher T-stage. CONCLUSIONS: Matched pairs analysis of individual tumor-normal pairs revealed significant differences in relative abundance of specific taxa, namely in the genus Actinomyces. These differences were more pronounced among patients with higher T-stage. Our observations suggest further experiments to interrogate potential novel mechanisms relevant to carcinogenesis associated with alterations of the oral microbiome that may have consequences for the human host.

Experiment 1


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Head and neck squamous cell carcinoma carcinoma of the head and neck,craniocervical region squamous cell carcinoma,head and neck squamous cell carcinoma,HNSCC,SCCHN,squamous cell carcinoma of head and neck,squamous cell carcinoma of the head and neck,squamous cell carcinoma, head and neck,squamous cell carcinomas of head and neck,Head and neck squamous cell carcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
normal adjacent tissues
Group 1 name Corresponds to the case (exposed) group for case-control studies
squamous cell carcinoma tissues
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
tissues with evidence of squamous cell carcinoma
Group 0 sample size Number of subjects in the control (unexposed) group
121
Group 1 sample size Number of subjects in the case (exposed) group
121

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Sanger

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Nidhi Saini

Revision editor(s): WikiWorks

Source: Figure 3 +text

Description: Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.

Abundance in Group 1: increased abundance in squamous cell carcinoma tissues

NCBI Quality ControlLinks
Tissierellaceae
Parvimonas

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 3 +text

Description: Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.

Abundance in Group 1: decreased abundance in squamous cell carcinoma tissues

NCBI Quality ControlLinks
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, LGeistlinger, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
T0-T2 low tumor stages patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
T3-T4 high tumor stages patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Not stated
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified
Group 1 sample size Number of subjects in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Not specified
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No


Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 4 +text

Description: Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.

Abundance in Group 1: increased abundance in T3-T4 high tumor stages patients

NCBI Quality ControlLinks
Parvimonas

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 4 +text

Description: Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.

Abundance in Group 1: decreased abundance in T3-T4 high tumor stages patients

NCBI Quality ControlLinks
Actinomyces
Actinomycetota

Revision editor(s): WikiWorks