Gut microbiome in melanoma patients on vidutolimod plus nivolumab
113 gut microbiome samples from adult and elderly melanoma patients in Pittsburgh, USA, from a single-arm phase 2 neoadjuvant trial of TLR9 agonist vidutolimod combined with anti-PD-1 nivolumab. machine-written summary
113 samples · 113 runs · US · Age unknown · 2024 · 7.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,356 sample values (age, collection date, country, intervention, intervention detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 226 sample values (health condition, health condition detail) · PMC11560503 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
25 people have samples in more than one arm.
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population other_cancer · Neoadjuvant TLR9 agonist vidutolimod plus anti-PD-1 nivolumab
“neoadjuvant TLR9 agonist vidutolimod combined with anti-PD-1 nivolumab” — abstract:39486411 (study level; per-sample arms are in the intervention column below)
longitudinal
27 of 30 people sampled more than once (110 samples; median 4, up to 5 per person) · follow-up median 11 mo (max 18 mo) · median interval between samples 2 mo (time from collection months (month precision)). Schedule stated by the source: “Repeated fecal sampling per subject across neoadjuvant treatment and follow-up, binned at stated timepoint_days_bin values (1,14,42,63,84,112, etc.), with intermediate timepoints flagged.”.
Each row is one person (26 shown of 27); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 106 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 | 113 | 100% | ||||
| country | 113 | 100% | 113 | |||
| health_condition | 113 | 100% | 113 | |||
| subject_id | 113 | 100% | 113 | |||
| age_at_collection_days | 113 | 100% | 113 | |||
| collection_date | 113 | 100% | 113 | |||
| detailed_location | 113 | 100% | ||||
| health_condition_detail | 113 | 100% | 113 | |||
| intervention | 113 | 100% | 113 | |||
| intervention_detail | 113 | 100% | 113 | |||
| latitude | 113 | 100% | 113 | |||
| location_locality | 113 | 100% | 113 | |||
| location_region | 113 | 100% | 113 | |||
| longitude | 113 | 100% | 113 | |||
| sex | 113 | 100% | 113 | |||
| timepoint_label | 113 | 100% | 113 |
- Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial. 2024 PMID 39486411 PMC11560503 unsure
Archive description
Intratumoral TLR9 agonists and anti-PD-1 therapies provide durable clinical responses and broad immune activation. To evaluate the efficacy and mechanisms of action of this therapeutic combination, we conducted a single-arm phase 2 neoadjuvant study of TLR9 agonist vidutolimod combined with anti-PD-1 nivolumab in patients with high-risk resectable melanoma. In 31 evaluable patients, 55% (17/31) had major pathologic response (MPR), with eight grade 3 treatment-related adverse events. MPR was associated with necrosis, and melanophagocytosis with increased CD8+ tumor-infiltrating lymphocytes and plasmacytoid dendritic cells (pDCs) in the tumor microenvironment, and increased frequencies of Ki67+ CD8+ and CD4+ T cells, pDCs, and monocytes peripherally. Patients with MPR had an enriched pre-treatment gene signature of myeloid cells , and response to therapy was associated with gene signatures of immune cells, pDCs, phagocytosis, and macrophage activation. Patients with MPR also had gut microbial signatures enriched for Gram-negative bacteria belonging to the Bacteroidaceae and Enterobacteriaceae families and the small subgroup of Gram-negative Firmicutes. Our findings support that combined vidutolimod and nivolumab stimulates a broad antitumor immune response and is associated with distinct baseline myeloid gene signature and gut microbiome composition.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “patients with high-risk resectable melanoma”
- body site study.description · “gut microbial signatures enriched for Gram-negative bacteria”
- life stage sample.attr.age · “58 (n=56/113)”
- life stage sample.attr.age · “66 (n=54/113)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41879536 | age_at_collection_days | 21915.0 | R1 | 0.85 | sample.attr.age | 60 |
| SAMN41879536 | collection_date | 2018-11 | R1 | 0.90 | biosample.attribute:collection_date | 2018-11 |
| SAMN41879536 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Pittsburgh |
| SAMN41879536 | health_condition | other_cancer | R3 | 0.70 | paper.fulltext.methods | clinical stage III cutaneous melanoma according to the American Joint Committee |
| SAMN41879536 | health_condition_detail | high-risk resectable stage III cutaneous melanoma | R3 | 0.70 | paper.fulltext.methods | clinical stage III cutaneous melanoma according to the American Joint Committee |
| SAMN41879536 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:Timepoint_days_bin | Timepoint_days_bin: 1 |
| SAMN41879536 | intervention_detail | Timepoint_days_bin = 1 (before intervention start) | R1 | 0.80 | biosample.attribute:Timepoint_days_bin | Timepoint_days_bin: 1 |
| SAMN41879536 | latitude | 40.4540 | R1 | 0.90 | biosample.attribute:lat_lon | 40.454 N 79.933 W |
| SAMN41879536 | location_locality | Pittsburgh | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Pittsburgh |
| SAMN41879536 | location_region | Pennsylvania | R1 | 0.60 | biosample.attribute:lat_lon | 40.454 N 79.933 W |
| SAMN41879536 | longitude | -79.9330 | R1 | 0.90 | biosample.attribute:lat_lon | 40.454 N 79.933 W |
| SAMN41879536 | sex | male | R1 | 0.90 | sample.attr.gender | male |
| SAMN41879536 | subject_id | UOP-004 | R1 | 0.85 | sample.attr.patient_id | UOP-004 |
| SAMN41879536 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:timepoint_days_bin | 1 |
Sequencing
113 runs over 113 samples · mean 7.26 Gbp per run (median 7.24 Gbp, total 820.88 Gbp; 113 runs with a base count) · layout PAIRED 113 · platform ILLUMINA 113 · models Illumina NovaSeq 6000 (113) · 94% of runs with a Sandpiper profile · first public 2024-09-27
Authors (53)
Davar D first · Morrison RM · Dzutsev AK · Karunamurthy A · Chauvin JM · Amatore F · Deutsch JS · Das Neves RX · Rodrigues RR · McCulloch JA · Wang H · Hartman DJ · Badger JH · Fernandes MR · Bai Y · Sun J · Cole AM · Aggarwal P · Fang JR · Deitrick C · Bao R · Duvvuri U · Sridharan SS · Kim SW · A Choudry H · Holtzman MP · Pingpank JF · O'Toole JP · DeBlasio R · Jin Y · Ding Q · Gao W · Groetsch C · Pagliano O · Rose A · Urban C · Singh J · Divarkar P · Mauro D · Bobilev D · Wooldridge J · Krieg AM · Fury MG · Whiteaker JR · Zhao L · Paulovich AG · Najjar YG · Luke JJ · Kirkwood JM · Taube JM · Park HJ · Trinchieri G · Zarour HM last
Downloads
PRJNA1107274.csv.gz (5.0 KB) · parquet (77.3 KB) — all 113 samples, every field with route and confidence · PRJNA1107274_determinations.csv.gz (12.6 KB) — 1,582 evidence rows