Gut microbiome in pediatric ALL patients on pegaspargase, Canada
47 gut metagenome samples from pediatric Acute Lymphoblastic Leukemia patients in Canada, in a longitudinal cohort study examining microbial gene changes related to amino acid metabolism during pegaspargase drug therapy. machine-written summary
47 samples · 47 runs · CA · Infant / toddler · 2021 · 1.00 Gbp / sample · cohort Dalhousie pediatric leukemia/lymphoma gut microbio
One study deposited as 2 BioProjects (114 catalog samples together): PRJEB46214 · PRJEB53954 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 141 sample values (country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 94 sample values (location region, location site) · PMC9363618, PMC9998685 |
| ✓ Supplementary tables | 62 sample values (antibiotic exposure, subject id) |
| – 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 not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population other_cancer · Pegaspargase chemotherapy treatment in pediatric ALL patients, sampled over treatment
“Treatment of pediatric acute lymphoblastic leukemia (ALL) with pegaspargase” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
10 of 16 people sampled more than once (32 samples; median 2, up to 7 per person). Schedule stated by the source: “Stool samples collected from patients over the course of pegaspargase treatment; no fixed schedule or timepoints stated” (time origin: treatment_start).
Genera, mean relative abundance over 41 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 | 0 | 0% | ||||
| country | 47 | 100% | 47 | |||
| health_condition | 47 | 100% | 47 | |||
| subject_id | 38 | 81% | 38 | |||
| detailed_location | 47 | 100% | ||||
| health_condition_detail | 47 | 100% | 47 | |||
| location_region | 47 | 100% | 47 | |||
| location_site | 47 | 100% | 47 | |||
| antibiotic_exposure | 24 | 51% | 24 |
- Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia. 2021 PMID 34279176 own_data
- Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense. 2022 PMID 35967843 PMC9363618 own_data
- The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients. 2023 PMID 36909730 PMC9998685 own_data
Archive description
Treatment of pediatric acute lymphoblastic leukemia (ALL) with pegaspargase exploits ALL cells dependency on asparagine. Pegaspargase depletes asparagine, consequentially affecting aspartate, glutamine and glutamate. The gut as a confounding source of these amino acids (AAs) and the role of gut microbiome metabolism of AAs has not been examined. Understanding how microbial gene-products, which interact with these AAs change over treatment were examined. Understanding pathways that change AA availability, including by microbes in the gut, could be useful in optimizing pegaspargase therapy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Gut bacterial gene changes”
- body site study.description · “and glutamate. The gut as a confounding”
- life stage study.title · “pegaspargase treatment in pediatric patients with Acute”
- life stage study.description · “Treatment of pediatric acute lymphoblastic leukemia”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8963594 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.DataSheet_1.docx[table3!β-lactam multiuse/courses dataset] | ERR6281455 | 3+ courses |
| SAMEA8963589 | country | CA | R1 | 0.90 | biosample_attr | Canada |
| SAMEA8963589 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:title | Shotgun metagenomic sequences from stool samples of pediatric patients with Acute Lymphoblastic Leukemia |
| SAMEA8963589 | health_condition_detail | Shotgun metagenomic sequences from stool samples of pediatric patients with Acute Lymphoblastic Leukemia | R1 | 0.85 | biosample.attribute:title | Shotgun metagenomic sequences from stool samples of pediatric patients with Acute Lymphoblastic Leukemia |
| SAMEA8963589 | location_region | Nova Scotia | R3 | 0.70 | paper.body.text | from the Atlantic Maritime provinces of Canada, undergoing care at the IWK Health Centre in Nova Scotia, Canada |
| SAMEA8963589 | location_site | IWK Health Centre | R3 | 0.70 | paper.body.text | from the Atlantic Maritime provinces of Canada, undergoing care at the IWK Health Centre in Nova Scotia, Canada |
| SAMEA8963589 | subject_id | MALL-010 | R2 | 0.75 | paper.supp.DataSheet_1.docx[table3!Sample ID] | ERR6281450 | MALL-010-ST06 |
Sequencing
47 runs over 47 samples · mean 0.95 Gbp per run (median 1.00 Gbp, total 44.57 Gbp; 47 runs with a base count) · layout SINGLE 47 · platform ILLUMINA 47 · models NextSeq 500 (47) · 87% of runs with a Sandpiper profile · first public 2021-07-13 – 2022-06-29
Authors (0)
No author record.
Downloads
PRJEB46214.csv.gz (2.3 KB) · parquet (72.0 KB) — all 47 samples, every field with route and confidence · PRJEB46214_determinations.csv.gz (3.2 KB) — 297 evidence rows