Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2022/09/04
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Peace Sandy
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-GQD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low-dose GQD (300 mg/kg)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum. Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days. The mouse colorectal carcinoma cell line CT26 (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3c
Description: Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on the Wilcoxon rank-sum test.
Abundance in Group 1: increased abundance in low-dose GQD (300 mg/kg)
Revision editor(s): Mary Bearkland, Claregrieve1
Signature 2
Source: Figure 3c
Description: Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on the Wilcoxon rank-sum test.
Abundance in Group 1: decreased abundance in low-dose GQD (300 mg/kg)
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Saccharimonas | ||
| Peptococcaceae | ||
| Staphylococcus sp. | ||
| Turicibacter | ||
| Tyzzerella | ||
| uncultured Oscillibacter sp. |
Revision editor(s): Mary Bearkland, Claregrieve1
Experiment 2
Curated date: 2022/09/04
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Victoria
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum. Then the mice were orally lavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days. The mouse colorectal carcinoma cell line CT26 (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
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: Figure 3d
Description: Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2)
Abundance in Group 1: increased abundance in low-dose GQD (300 mg/kg)
Revision editor(s): Mary Bearkland, Claregrieve1
Signature 2
Source: Figure 3D
Description: Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2)
Abundance in Group 1: decreased abundance in low-dose GQD (300 mg/kg)
Revision editor(s): Mary Bearkland, Claregrieve1
Experiment 3
Curated date: 2022/09/13
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low-dose GQD (300 mg/kg) + PD-1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum. Then the mice were orally gavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days. The mouse colorectal carcinoma cell line CT26 (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours. When the tumours reached a size of 50mm3, the mice were intraperitoneally (i.p.) injected with 250 μg of anti-mouse PD-1 mAb. The mice in the control group were administered the same volume of PBS. All mice were injected five times at 3-day intervals with antimouse PD-1 mAb or PBS
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
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: Figure 4f
Description: Differential microbial abundance between the GQD (300 mg/kg) + PD-1 group vs. the control group based on the Wilcoxon rank-sum test.
Abundance in Group 1: increased abundance in low-dose GQD (300 mg/kg) + PD-1
Revision editor(s): Mary Bearkland, Claregrieve1
Signature 2
Source: Fig 4f
Description: Differential microbial abundance between GQD(300mg/kg)+PD-1 group and control group
Abundance in Group 1: decreased abundance in low-dose GQD (300 mg/kg) + PD-1
Revision editor(s): Mary Bearkland, Claregrieve1
Experiment 4
Curated date: 2022/09/15
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Victoria
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low-dose GQD (300 mg/kg)
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supp fig S6D
Description: Differential microbial abundance between GQD(300mg/kg) treated mice and controls
Abundance in Group 1: increased abundance in low-dose GQD (300 mg/kg)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Eubacterium xylanophilum | ||
| Hungatella | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| unclassified Coriobacteriaceae |
Revision editor(s): Mary Bearkland, Claregrieve1
Signature 2
Source: supp fig S6
Description: Differential microbial abundance between GQD(300mg/kg) treated mice and controls
Abundance in Group 1: decreased abundance in low-dose GQD (300 mg/kg)
Revision editor(s): Mary Bearkland, Claregrieve1
Experiment 5
Curated date: 2022/09/17
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Victoria
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD-1 group
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
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
Signature 1
Source: supp fig S6
Description: Supplementary Figure S6: (E) LDA scores computed for differentially abundant taxa in the faecal microbiomes of mice from each group.
Abundance in Group 1: increased abundance in PD-1 group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Anaeroplasma | ||
| Anaeroplasmataceae | ||
| Anaeroplasmatales | ||
| Thomasclavelia | ||
| Eubacterium ventriosum | ||
| Hungatella | ||
| Mollicutes | ||
| Mycoplasmatota |
Revision editor(s): Mary Bearkland
Signature 2
Source: supp fig S6
Description: Supplementary Figure S6: (E) LDA scores computed for differentially abundant taxa in the faecal microbiomes of mice from each group.
Abundance in Group 1: decreased abundance in PD-1 group
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter | ||
| Bacillota |
Revision editor(s): Mary Bearkland
Experiment 6
Curated date: 2022/09/17
Curator: Mary Bearkland
Revision editor(s): WikiWorks, Claregrieve1, Mary Bearkland, Victoria
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low dose 300 mg/kg GQD + PD-1 group
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Source: supp fig S6
Description: Differentially abundant taxa between control mice and mice treated with 300mg/kg GQD + PD-1
Abundance in Group 1: increased abundance in low dose 300 mg/kg GQD + PD-1 group
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Candidatus Stoquefichus | ||
| Prevotellaceae | ||
| Rikenellaceae | ||
| Ruminiclostridium | ||
| unclassified Prevotellaceae | ||
| Oscillospiraceae |
Revision editor(s): Mary Bearkland, Claregrieve1
Signature 2
Source: Supp fig S6
Description: Differentially abundant taxa between control mice and mice treated with 300mg/kg GQD + PD-1
Abundance in Group 1: decreased abundance in low dose 300 mg/kg GQD + PD-1 group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Bacteroidales | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Bifidobacterium | ||
| Candidatus Saccharibacteria |
Revision editor(s): Mary Bearkland, Claregrieve1
