Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma
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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
Authors
Pratap Singh R, Kumari N, Gupta S, Jaiswal R, Mehrotra D, Singh S, Mukherjee S, Kumar R
Journal
Microbiology spectrum
Year
2023
Keywords:
OSCC, biomarker, inflammation, microbiome, tumor microenvironment
Characterization of the oral microbiota profile through various studies has shown an association between the microbiome and oral cancer; however, stage-specific determinants of dynamic changes in microbial communities of oral cancer remain elusive. Additionally, the influence of the intratumoral microbiota on the intratumoral immune system remains largely unexplored. Therefore, this study aims to stratify microbial abundance in the early-onset and subsequent stages of oral cancer and analyze their influence on clinical-pathological and immunological features. The microbiome composition of tissue biopsy samples was identified using 16S rRNA amplicon sequencing, while intratumoral and systemic immune profiling was done with flow cytometry and immunohistochemistry-based analysis. The bacterial composition differed significantly among precancer, early cancer, and late cancer stages with the enrichment of genera Capnocytophaga, Fusobacterium, and Treponema in the cancer group, while Streptococcus and Rothia were enriched in the precancer group. Late cancer stages were significantly associated with Capnocytophaga with high predicting accuracy, while Fusobacterium was associated with early stages of cancer. A dense intermicrobial and microbiome-immune network was observed in the precancer group. At the cellular level, intratumoral immune cell infiltration of B cells and T cells (CD4+ and CD8+) was observed with enrichment of the effector memory phenotype. Naive and effector subsets of tumor-infiltrating lymphocytes (TILs) and related gene expression were found to be distinctly associated with bacterial communities; most importantly, highly abundant bacterial genera of the tumor microenvironment were either negatively correlated or not associated with the effector lymphocytes, which led to the conclusion that the tumor microenvironment favors an immunosuppressive and nonimmunogenic microbiota. IMPORTANCE The gut microbiome has been explored extensively for its importance in the modulation of systemic inflammation and immune response; in contrast, the intratumoral microbiome is less studied for its influence on immunity in cancer. Given the established correlation between intratumoral lymphocyte infiltration and patient survival in cases of solid tumors, it was pertinent to explore the extrinsic factor influencing immune cell infiltration in the tumor. Modulation of intratumoral microbiota could have a beneficial effect on the antitumor immune response. This study stratifies the microbial profile of oral squamous cell carcinoma starting from precancer to late-stage cancer and provides evidence for their immunomodulatory role in the tumor microenvironment. Our results suggest combining microbiome study with immunological signatures of tumors for their prognostic and diagnostic application.
Experiment 1
Subjects
- Location of subjects
- India
- 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
- 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,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral cavity carcinoma carcinoma of mouth,carcinoma of oral cavity,carcinoma of the oral cavity,mouth carcinoma,oral cavity cancer,oral cavity carcinoma,Oral cavity carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adjacent normal tissue (AT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor tissue (TT) samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumor tissue (TT) specimens were obtained from the inner part of the tumor
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, sex, Matched on: "risk factor status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.risk factor status
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
Source: Supplementary Figure 3A
Description: Differential abundance of core bacterial genera among adjacent tumor tissue and tumor tissues.
Abundance in Group 1: increased abundance in Tumor tissue (TT) samples
| NCBI | Quality Control | Links |
|---|---|---|
| Brevundimonas |
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 2B, 3A and 3c
Description: Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and tumor tissues.
Abundance in Group 1: decreased abundance in Tumor tissue (TT) samples
| NCBI | Quality Control | Links |
|---|---|---|
| Brevundimonas diminuta | ||
| Neisseria | ||
| Neisseria mucosa | ||
| Neisseria subflava | ||
| Ochrobactrum | ||
| Rothia | ||
| Rothia dentocariosa | ||
| Rothia mucilaginosa | ||
| Veillonella | ||
| Pseudomonadota |
Revision editor(s): MyleeeA
Experiment 2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Precancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and erythroplakia.
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 2C, 3B and 3D
Description: Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and Precancer Samples.
Abundance in Group 1: decreased abundance in Precancer
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 3D
Description: Differential abundances of core bacterial Species among adjacent tumor tissue and Precancer lesions.
Abundance in Group 1: increased abundance in Precancer
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus periodonticum |
Revision editor(s): MyleeeA
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Precancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early Stage Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cancer Samples subdivided into T1 and T2
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3B
Description: Differential abundances of core bacterial species between the precancer group with early (T1 and T2)
Abundance in Group 1: increased abundance in Early Stage Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga ochracea | ||
| Capnocytophaga granulosa | ||
| Capnocytophaga leadbetteri | ||
| Fusobacterium nucleatum | ||
| Fusobacterium canifelinum | ||
| Treponema denticola |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3B
Description: Differential abundances of core bacterial species between the precancer group and early (T1 and T2)
Abundance in Group 1: decreased abundance in Early Stage Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus periodonticum | ||
| Rothia dentocariosa | ||
| Rothia mucilaginosa | ||
| Streptococcus dysgalactiae |
Revision editor(s): MyleeeA
Experiment 4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late Stage Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cancer Samples subdivided into T3 and T4
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3B
Description: Differential abundances of core bacterial species between the precancer group and late cancer (T3 and T4) groups
Abundance in Group 1: increased abundance in Late Stage Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga ochracea | ||
| Capnocytophaga granulosa | ||
| Capnocytophaga sputigena | ||
| Capnocytophaga leadbetteri |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3B
Description: Differential abundances of core bacterial species between the precancer group and late cancer (T3 and T4) groups
Abundance in Group 1: decreased abundance in Late Stage Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus dysgalactiae | ||
| Streptococcus periodonticum | ||
| Rothia mucilaginosa | ||
| Rothia dentocariosa |
Revision editor(s): MyleeeA
Experiment 5
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants at different stages of disease pathogenesis (T1 to T4).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B, 2C, 3A and Supplementary Fig 2D
Description: Differential abundances of core bacterial Phyla, Family, Genera and Species between Precancer and Cancer Samples.
Abundance in Group 1: increased abundance in Cancer
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2B, 2C, 3A and Supplementary Fig 2D
Description: Differential abundances of core bacterial Phyla, Family, Genera and Species between Precancer and Cancer Samples.
Abundance in Group 1: decreased abundance in Cancer
Revision editor(s): MyleeeA
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early Stage Cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late Stage Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cancer Samples subdivided into T3 and T4
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2D and Supplementary Figure 2A
Description: Differential abundances of core bacterial species between the Early stage cancer groups (T1 and T2) and Late Stage cancer (T3 and T4) groups
Abundance in Group 1: increased abundance in Late Stage Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Pedobacter |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2D and Supplementary Figure 2A
Description: Differential abundances of core bacterial species between the Early stage cancer groups (T1 and T2) and Late Stage cancer (T3 and T4) groups
Abundance in Group 1: decreased abundance in Late Stage Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriia | ||
| Leptotrichia | ||
| Desulfovibrionaceae | ||
| Eubacteriales |
Revision editor(s): MyleeeA
Experiment 7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Precancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Early Stage Cancer Patients grouped as T1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Experiment 8
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Early Stage Cancer Patients grouped as T2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Experiment 9
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Late Stage Cancer Patients grouped as T3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Experiment 10
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Late Stage Cancer Patients grouped as T4
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Experiment 11
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Late Stage Cancer Patients grouped as T3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Experiment 12
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Late Stage Cancer Patients grouped as T4
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
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