Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-15

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

Subjects

Location of subjects: France

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: Non-small cell lung carcinoma , Renal cell carcinoma , Disease progression measurement non-small cell cancer of lung,non-small cell cancer of the lung,non-small cell carcinoma of lung,non-small cell carcinoma of the lung,non-small cell lung cancer,non-small cell lung carcinoma,non-small cell lung carcinoma (disease),NSCLC,NSCLC - non-small cell lung cancer,Non-small cell lung carcinoma,hypernephroma,kidney adenocarcinoma,RCC,renal cell adenocarcinoma,renal cell carcinoma,renal cell carcinoma (disease),Renal cell carcinoma,Disease progression measurement,disease progression measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Responders (progression or death)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Responders (partial response or stable disease)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease

Group 0 sample size Number of subjects in the control (unexposed) group: 36

Group 1 sample size Number of subjects in the case (exposed) group: 42

Lab analysis

Sequencing type: WMS

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: Mass spectrometry

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

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-13

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): WikiWorks, Folakunmi

Source: Figure 2b

Description: Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment

Abundance in Group 1: increased abundance in Responders (partial response or stable disease)

NCBI	Quality Control	Links
Akkermansia muciniphila
Alistipes
Alistipes finegoldii
Alistipes indistinctus
Bacteroides
Bacteroides sp.
Cloacibacillus porcorum
Enterococcus faecium
Erysipelotrichaceae
Eubacterium sp.
Intestinimonas
Lachnospiraceae
Prevotella
unclassified Bacillota

Revision editor(s): WikiWorks, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-13

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): Atrayees, WikiWorks, Folakunmi

Source: Figure 2b

Description: Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment

Abundance in Group 1: decreased abundance in Responders (partial response or stable disease)

NCBI	Quality Control	Links
Bacillota bacterium
Bacteroides clarus
Bacteroides nordii
Blautia
Clostridiales bacterium
Clostridium sp.
Enterocloster bolteae
Parabacteroides distasonis
Prevotella
Pseudomonadota
unclassified Eubacteriales

Revision editor(s): Atrayees, WikiWorks, Folakunmi

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Progressive- Free- Survival more less than 30 days

Group 1 name Corresponds to the case (exposed) group for case-control studies: Progressive -Free- Survival more than 30 days

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months

Group 0 sample size Number of subjects in the control (unexposed) group: 100

Group 1 sample size Number of subjects in the case (exposed) group: 100

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): none

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-15

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): Atrayees, WikiWorks, Folakunmi

Source: Figure 2C

Description: Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment

Abundance in Group 1: increased abundance in Progressive -Free- Survival more than 30 days

NCBI	Quality Control	Links
Akkermansia muciniphila
Alistipes
Bacillota
Bacillota bacterium
Bacteroides caccae
Bacteroides nordii
Bacteroides xylanisolvens
Blautia
Clostridium sp.
Eubacteriales
Eubacterium sp.
Firmicutes bacterium CAG:110
Flavonifractor
Flavonifractor plautii
Intestinimonas
Lachnospiraceae
Oscillospiraceae
Ruminococcus
Ruminococcus sp.
unclassified Bacillota
unclassified Eubacteriales

Revision editor(s): Atrayees, WikiWorks, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-15

Curated date: 2021/01/10

Curator: William Lam

Revision editor(s): Atrayees, WikiWorks, Folakunmi

Source: Figure 2C

Description: Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment

Abundance in Group 1: decreased abundance in Progressive -Free- Survival more than 30 days

NCBI	Quality Control	Links
Anaerotruncus colihominis
Bacillota bacterium
Erysipelotrichaceae
Eubacteriales
Lachnospiraceae
Parabacteroides distasonis
unclassified Eubacteriales

Revision editor(s): Atrayees, WikiWorks, Folakunmi

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-2-16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Responders

Group 1 name Corresponds to the case (exposed) group for case-control studies: Responders

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Group 1 sample size Number of subjects in the case (exposed) group: 16

Lab analysis

Statistical Analysis

Signature 1