Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Slovakia
- 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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer breast cancer,breast tumor,cancer of breast,malignant breast neoplasm,malignant breast tumor,malignant neoplasm of breast,malignant neoplasm of the breast,malignant tumor of breast,malignant tumor of the breast,mammary cancer,mammary neoplasm,mammary tumor,primary breast cancer,Breast cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal breast tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- breast cancer tumor tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients (stage I–III) treated with surgery from April 2012 to February 2015
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Kruskall-Wallis
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 3 (A)
Description: Differentially represented taxa between normal breast tissue samples (from cancer-free donors) and breast tumour tissue. (A) Comparison of the microbiome in primary tumours of Slovak patients and normal breast tissue of Slovak cancer-free donors. Since standard conditions identified too many results, to visualise data, LEfSe was run with parameters (LDA > 3, Kruskal Wallis testp-value < 0.05, Wilcoxon testp-value < 0.05)
Abundance in Group 1: increased abundance in breast cancer tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Rhodobacter | ||
| Micrococcus | ||
| Priestia megaterium | ||
| Priestia | ||
| Mycobacteriales | ||
| Acinetobacter | ||
| Caudoviricetes | ||
| Gorganvirus isfahan | ||
| Gorganvirus | ||
| Uroviricota | ||
| Viruses |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 3 (A)
Description: Differentially represented taxa between normal breast tissue samples (from cancer-free donors) and breast tumour tissue. (A) Comparison of the microbiome in primary tumours of Slovak patients and normal breast tissue of Slovak cancer-free donors. Since standard conditions identified too many results, to visualise data, LEfSe was run with parameters (LDA > 3, Kruskal Wallis testp-value < 0.05, Wilcoxon testp-value < 0.05)
Abundance in Group 1: decreased abundance in breast cancer tumor tissue
Revision editor(s): Ecsharp
Experiment 2
Subjects
- Location of subjects
- China
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Triple-negative breast cancer triple-negative breast cancer,triple-negative breast carcinoma,triple-receptor negative breast cancer,Triple-negative breast cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- triple-negative breast cancer tumor tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- RNA-seq transcriptomic data obtained from triple-negative breast cancer patients in China (Data taken from study PRJNA553096)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 72
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 5.5
Signature 1
Source: Figure 3 (B)
Description: Differentially represented taxa between normal breast tissue samples and breast tumour tissue. (B) Comparison of microbiome in primary tumours of 72 patients from China and 18 normal breast tissues of cancer-free donors from China. For visualisation, LEfSe was run with parameters (LDA > 5.5, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05), for the purpose of visualising the best hits.
Abundance in Group 1: increased abundance in triple-negative breast cancer tumor tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Bacillales | ||
| Bacillaceae | ||
| Achromobacter | ||
| Peptostreptococcaceae | ||
| Alcaligenaceae |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 3 (B)
Description: Differentially represented taxa between normal breast tissue samples and breast tumour tissue. (B) Comparison of microbiome in primary tumours of 72 patients from China and 18 normal breast tissues of cancer-free donors from China. For visualisation, LEfSe was run with parameters (LDA > 5.5, Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05), for the purpose of visualising the best hits.
Abundance in Group 1: decreased abundance in triple-negative breast cancer tumor tissue
Revision editor(s): Ecsharp
Experiment 3
Subjects
- Location of subjects
- Slovakia
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer breast cancer,breast tumor,cancer of breast,malignant breast neoplasm,malignant breast tumor,malignant neoplasm of breast,malignant neoplasm of the breast,malignant tumor of breast,malignant tumor of the breast,mammary cancer,mammary neoplasm,mammary tumor,primary breast cancer,Breast cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BC patients without CTC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BC patients with CTC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients with circulating tumour cells (CTC) in their blood
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 4 (A)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. (A) Comparison of the microbiome in primary tumours of patients with CTC in their blood and primary tumours of patients without CTC detected in their blood (LDA threshold = 3).
Abundance in Group 1: increased abundance in BC patients with CTC
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4 (A)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. (A) Comparison of the microbiome in primary tumours of patients with CTC in their blood and primary tumours of patients without CTC detected in their blood (LDA threshold = 3).
Abundance in Group 1: decreased abundance in BC patients with CTC
Revision editor(s): Ecsharp
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HR- BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HR+ BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients with hormone receptor status (HR+ vs HR-) was defined as positive for either oestrogen receptor or progesterone receptor vs negative for both, 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4 (B)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (B) Comparison of the microbiome in primary tumours of patients positive on HR marker and negative on HR marker.
Abundance in Group 1: increased abundance in HR+ BC patients
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4 (B)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (B) Comparison of the microbiome in primary tumours of patients positive on HR marker and negative on HR marker.
Abundance in Group 1: decreased abundance in HR+ BC patients
Revision editor(s): Ecsharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HER2- BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HER2+ BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients with HER2 status (HER+ vs HER-). 1% of cells positive for hormone receptor was used as the cut-off to define hormone receptor positivity and HER2 status.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4 (C)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (C) Comparison of the microbiome in primary tumours of patients positive on HER2 marker and negative on HER2 marker status.
Abundance in Group 1: increased abundance in HER2+ BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter pylori | ||
| Musicola paradisiaca | ||
| Pseudactinotalea sp. HY158 | ||
| Paraburkholderia fungorum | ||
| Massilia oculi | ||
| Burkholderiales | ||
| Betaproteobacteria |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4 (C)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (C) Comparison of the microbiome in primary tumours of patients positive on HER2 marker and negative on HER2 marker status.
Abundance in Group 1: decreased abundance in HER2+ BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Flavobacteriia | ||
| Flavobacteriales | ||
| Weeksellaceae | ||
| Nocardioides | ||
| Deinococci | ||
| Deinococcota |
Revision editor(s): Ecsharp
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ki67 < 20% BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ki67 > 20% BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Slovakia breast cancer patients were labeled Ki67 > 20% or Ki67 < 20%. Ki-67 labelling index was reported as a percentage of cells with Ki-67 positive nuclear immunostaining.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4 (E)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (E) Comparison of the microbiome in primary tumours of Ki67 > 20% and Ki67 < 20%.
Abundance in Group 1: increased abundance in Ki67 > 20% BC patients
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4 (E)
Description: Differentially represented taxa in primary tumour tissues of Slovak patients between multiple markers statuses. For all comparisons, LEfSe was run with parameters: LDA > 3 (stricter than default LDA > 2 just for purpose of visualisation), Kruskal Wallis test p-value < 0.05, Wilcoxon test p-value < 0.05. (E) Comparison of the microbiome in primary tumours of Ki67 > 20% and Ki67 < 20%.
Abundance in Group 1: decreased abundance in Ki67 > 20% BC patients
Revision editor(s): Ecsharp
