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
Empty strings are not accepted.
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 carcinoma
- 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
Curated date: 2022/09/04
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Signature 2
Curated date: 2022/09/04
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Experiment 2
Empty strings are not accepted.
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
Curated date: 2022/09/04
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Signature 2
Curated date: 2022/09/04
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Experiment 3
Empty strings are not accepted.
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
Curated date: 2022/09/13
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Signature 2
Curated date: 2022/09/14
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Experiment 4
Empty strings are not accepted.
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
Curated date: 2022/09/15
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Signature 2
Curated date: 2022/09/15
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Experiment 5
Empty strings are not accepted.
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, WikiWorks
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, WikiWorks
Experiment 6
Empty strings are not accepted.
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
Curated date: 2022/09/17
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
Signature 2
Curated date: 2022/09/17
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks
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, WikiWorks
