The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer
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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
- China
- 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
- 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
- Digestive System Carcinoma carcinoma of digestive system,carcinoma of the gastrointestinal system,digestive system carcinoma,gastrointestinal carcinoma,gastrointestinal carcinoma (disease),gastrointestinal system carcinoma,Digestive System Carcinoma,digestive System Carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders to anti–PD-1/PD-L1 immunotherapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders to anti–PD-1/PD-L1 immunotherapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with stage 3 or stage 4 gastrointestinal cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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).
- raw counts
- Statistical test
- Zero-Inflated Negative Binomial Regression
- 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
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 3A, Supp. Table S6
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer
Abundance in Group 1: increased abundance in Responders to anti–PD-1/PD-L1 immunotherapy
Revision editor(s): Hamza, Scholastica
Signature 2
Source: Fig. 3A, Supp. Table S6
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in all 74 patients with Gastrointestinal Cancer
Abundance in Group 1: decreased abundance in Responders to anti–PD-1/PD-L1 immunotherapy
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Catenibacterium | ||
Hungatella | ||
Ruminococcus_2Ruminococcus_2 | ||
Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group | ||
uncultured Oscillospiraceae bacterium |
Revision editor(s): Hamza, Scholastica
Experiment 2
Subjects
- 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-responders (colorectal cancer - CRC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders (colorectal cancer - CRC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with colorectal cancer (CRC) who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.
- 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
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 3B, Supp. Table S7
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Colorectal Cancer (CRC)
Abundance in Group 1: increased abundance in Responders (colorectal cancer - CRC)
Revision editor(s): Scholastica
Signature 2
Source: Fig. 3B, Supp. Table S7
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Colorectal Cancer (CRC)
Abundance in Group 1: decreased abundance in Responders (colorectal cancer - CRC)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Bifidobacterium | ||
Lachnoclostridium | ||
Odoribacter | ||
Oscillibacter | ||
Parabacteroides | ||
Subdoligranulum | ||
Coprococcus_2Coprococcus_2 |
Revision editor(s): Scholastica
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Esophageal carcinoma cancer of esophagus,cancer of oesophagus,cancer of the esophagus,carcinoma of esophagus,carcinoma of oesophagus,carcinoma of the esophagus,esophageal cancer,esophageal cancer, NOS,esophageal carcinoma,esophagus carcinoma,Esophageal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders (esophageal carcinoma)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders (esophageal carcinoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with esophageal carcinoma who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 3C, Supp. Table S8
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in esophageal carcinoma cancer patients
Abundance in Group 1: increased abundance in Responders (esophageal carcinoma)
Revision editor(s): Scholastica
Signature 2
Source: Fig. 3C, Supp. Table S8
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 Immunotherapy in esophageal carcinoma cancer patients
Abundance in Group 1: decreased abundance in Responders (esophageal carcinoma)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Clostridium | ||
Hungatella | ||
Lachnospira | ||
Lactobacillus | ||
Marvinbryantia | ||
Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group | ||
uncultured Oscillospiraceae bacterium |
Revision editor(s): Scholastica
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer,Gastric cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders (gastric cancer)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders (gastric cancer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with gastric cancer who achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 3D, Supp. Table S9
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients
Abundance in Group 1: increased abundance in Responders (gastric cancer)
NCBI | Quality Control | Links |
---|---|---|
Prevotella_9Prevotella_9 | ||
Bifidobacterium | ||
Prevotella_2Prevotella_2 | ||
Lachnospira | ||
Bacteroides | ||
Ruminococcaceae bacterium UCG-005 | ||
Agathobacter |
Revision editor(s): Scholastica
Signature 2
Source: Fig. 3D, Supp. Table S9
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in gastric cancer patients
Abundance in Group 1: decreased abundance in Responders (gastric cancer)
NCBI | Quality Control | Links |
---|---|---|
Agathobacter | ||
Bacteroides | ||
Bifidobacterium | ||
Butyricimonas | ||
Megamonas | ||
uncultured Lachnospiraceae bacterium |
Revision editor(s): Scholastica
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Digestive System Carcinoma carcinoma of digestive system,carcinoma of the gastrointestinal system,digestive system carcinoma,gastrointestinal carcinoma,gastrointestinal carcinoma (disease),gastrointestinal system carcinoma,Digestive System Carcinoma,digestive System Carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Responders to anti–PD-1/PD-L1 immunotherapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-responders to anti–PD-1/PD-L1 immunotherapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with stage 3 or stage 4 gastrointestinal cancer who did not achieved an objective response (Partial Responders/Stable Disease) lasting at least 3 months upon treatment start with anti–PD-1/PD-L1 immunotherapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Supp. Table S10
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Gastrointestinal Cancer (Responders, n=25; Non-responders, n=15)
Abundance in Group 1: increased abundance in Non-responders to anti–PD-1/PD-L1 immunotherapy
NCBI | Quality Control | Links |
---|---|---|
Latilactobacillus curvatus | ||
Catenibacterium mitsuokai | ||
Dialister succinatiphilus | ||
unclassified Yersinia (in: enterobacteria) |
Revision editor(s): Scholastica
Signature 2
Source: Supp. Table S10
Description: Differential abundance between responders and non-responders to Anti–PD-1/PD-L1 immunotherapy in patients with Gastrointestinal Cancer (Responders, n=25; Non-responders, n=15)
Abundance in Group 1: decreased abundance in Non-responders to anti–PD-1/PD-L1 immunotherapy
Revision editor(s): Scholastica