Gut microbiota in PD-1-treated melanoma patients, Pittsburgh
94 samples from Pittsburgh, USA, from melanoma and other patients, studying gut microbiota signatures linked to anti-PD-1 immunotherapy outcomes and immune-related adverse events, in a case-control design. machine-written summary
94 samples · 94 runs · US · Elderly · 2022 · 8.90 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,492 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, intervention, intervention detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10246505, PMC10654443, PMC10799412, PMC10957474, PMC10957475, PMC12475161, PMC13384208, PMC13387006 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 105 sample values (health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: sequence archive and curatedMetagenomicData disagree for 1 sample (e.g. 70.0 vs 25567.5) — withheld.
The sources disagree on 1 sample. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN21886420 | age | 70.0 (sequence archive) | 25567.5 (curatedMetagenomicData) | withheld: neither value published |
Genera, mean relative abundance over 88 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 94 | 100% | ||||
| country | 94 | 100% | 94 | |||
| health_condition | 94 | 100% | 83 | 11 | ||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 94 | 100% | 94 | |||
| bmi | 94 | 100% | 94 | |||
| collection_date | 94 | 100% | 94 | |||
| detailed_location | 94 | 100% | ||||
| health_condition_detail | 94 | 100% | 94 | |||
| intervention | 94 | 100% | 94 | |||
| intervention_detail | 94 | 100% | 94 | |||
| latitude | 94 | 100% | 94 | |||
| location_locality | 94 | 100% | 94 | |||
| location_region | 94 | 100% | 94 | |||
| longitude | 94 | 100% | 94 | |||
| medication | 94 | 100% | 94 | |||
| medication_detail | 94 | 100% | 94 | |||
| sex | 94 | 100% | 94 | |||
| timepoint_label | 94 | 100% | 94 | |||
| age_at_collection_days | 93 | 99% | 93 |
- <i>Blautia coccoides</i>-derived acetate potentiates anti-PD-1 immunotherapy in melanoma by activating cytotoxic CD8<sup>+</sup> T cells. 2026 PMID 42463281 PMC13384208 own_data
- Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. 2022 PMID 35228752 PMC10246505 unsure
- Predicting cancer immunotherapy response from gut microbiomes using machine learning models. 2022 PMID 35875611 PMC9295706 unsure
- The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer. 2022 PMID 36083892 PMC9925043 unsure
- Gut microbial structural variation associates with immune checkpoint inhibitor response. 2023 PMID 37973916 PMC10654443 unsure
12 more
- Gut microbiome for predicting immune checkpoint blockade-associated adverse events. 2024 PMID 38243343 PMC10799412
- Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. 2024 PMID 38365950 PMC10957474
- A gut microbial signature for combination immune checkpoint blockade across cancer types. 2024 PMID 38429524 PMC10957475
- Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial. 2024 PMID 39486411 PMC11560503
- PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts. 2025 PMID 39753565 PMC11698977
- Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses. 2025 PMID 39929976 PMC11879847
- Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types. 2025 PMID 40151642 PMC11937697
- Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis. 2025 PMID 41006325 PMC12475161
- Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts. 2025 PMID 41304278 PMC12654497
- Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types. 2026 PMID 42146906 PMC13173278
- Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis. 2026 PMID 42189287 PMC13388844
- Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data. 2026 PMID 42262136 PMC13387006
Archive description
The gut microbiome has been proposed to be a biomarker and a driver of response to immune checkpoint blockade therapy in cancer. However, reported microbial signatures have been inconsistent across cohorts. We hereby analyze a new melanoma patient cohort with the aim of comparing it with four previously published datasets in order to identify signatures of beneficial and detrimental taxa that potentially contribute to the resistance to anti-PD1 therapy and development of immune-related adverse events (irAEs).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Intestinal Microbiota Signatures”
- life stage sample.attr.age · “66 (n=65/94)”
- life stage sample.attr.age · “60 (n=28/94)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21886367 | age_at_collection_days | 13110.0 | R1 | 0.85 | sample.attr.age | 35.5917808219178 |
| SAMN21886367 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | Not_Used |
| SAMN21886439 | antibiotic_exposure | yes | R1 | 0.80 | sample.attr.abx_use | Used; also had MTX use |
| SAMN21886367 | bmi | 33.63 | R1 | 0.90 | sample.attr.bmi | 33.63 |
| SAMN21886367 | collection_date | 2017-05-30 | R1 | 0.90 | biosample.attribute:collection_date | 2017-05-30 |
| SAMN21886367 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Pittsburgh |
| SAMN21886367 | health_condition | other_cancer | R1 | 0.70 | biosample_attr | IV-B |
| SAMN21886408 | health_condition | other_cancer | R2 | 0.75 | external.cmd source | disease: melanoma |
| SAMN21886367 | health_condition_detail | melanoma;colitis | R2 | 0.75 | external.cmd source | disease: melanoma;colitis |
| SAMN21886367 | intervention | drug_therapy | R1 | 0.90 | biosample.attribute:Immunotherapy_Drug | Immunotherapy_Drug: Nivolumab |
| SAMN21886368 | intervention | no_intervention | R1 | 0.90 | biosample.attribute:Timepoint | Timepoint: PreTreatment |
| SAMN21886367 | intervention_detail | nivolumab anti-PD-1 therapy | R1 | 0.90 | biosample.attribute:Immunotherapy_Drug | Immunotherapy_Drug: Nivolumab |
| SAMN21886368 | intervention_detail | baseline sample before anti-PD-1 therapy; assigned arm: pembrolizumab anti-PD-1 therapy | R1 | 0.90 | biosample.attribute:Timepoint | Timepoint: PreTreatment |
| SAMN21886367 | latitude | 40.4540 | R1 | 0.90 | biosample.attribute:lat_lon | 40.454 N 79.933 W |
| SAMN21886367 | location_locality | Pittsburgh | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Pittsburgh |
| SAMN21886367 | location_region | Pennsylvania | R1 | 0.60 | biosample.attribute:lat_lon | 40.454 N 79.933 W |
| SAMN21886367 | longitude | -79.9330 | R1 | 0.90 | biosample.attribute:lat_lon | 40.454 N 79.933 W |
| SAMN21886367 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:immunotherapy_drug | Nivolumab |
| SAMN21886387 | medication | immunosuppressant_or_biologic;ppi | R1 | 0.85 | biosample.attribute:ppi_use | Used |
| SAMN21886367 | medication_detail | Nivolumab | R1 | 0.85 | biosample.attribute:immunotherapy_drug | Nivolumab |
| SAMN21886387 | medication_detail | Pembrolizumab; Pantoprazole | R1 | 0.85 | biosample.attribute:ppi_use | Used |
| SAMN21886367 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN21886367 | timepoint_label | 41 | R1 | 0.85 | sample.attr.timepoint_days | 41 |
Sequencing
94 runs over 94 samples · mean 9.44 Gbp per run (median 8.90 Gbp, total 887.33 Gbp; 94 runs with a base count) · layout PAIRED 94 · platform ILLUMINA 94 · models Illumina NovaSeq 6000 (94) · 94% of runs with a Sandpiper profile · first public 2022-01-06
Authors (45)
Zhang L first · Zhou DD · Feng J · Liao ZJ · Shu XL · Yang RM · Gao YC · Zhou HH · Zhang W · Zou Y · Liu R last · Qiao T first · Zhu Z last · Candeliere F first · Busi E · Cerri S · Sola L · Lombardi M · Greco S · Pedroni S · Amaretti A · Raimondi S · Chiavelli C · Vitale MG · Bertolini F · Depenni R · Franchini G · Dominici M · Rossi M last · Iacovacci J first · Cannon N · McCulloch JA · Rancati T · Trinchieri G last · Zhang Z first · Liang X · Tian Y · Li C · Cao X · Wang D · Xie A · Liu S · Lin K · Li Q · Liang Y last
Downloads
PRJNA762360.csv.gz (5.7 KB) · parquet (79.3 KB) — all 94 samples, every field with route and confidence · PRJNA762360_determinations.csv.gz (17.3 KB) — 1,597 evidence rows