GEO series
Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia
GSE270185
Homo sapiens (human)
RNA-seq (gene expression)
249 samples
Submitted 2024/08/08
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 249 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Acute myeloid leukemiaThis series is part of our curated briefing on it.
- Samples
- 249 samples: 209 × Bulk RNA-seq of BMMCs from pediatric BCP-ALL patientGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemiaHaematologica · 2024
Summary (written by the submitters)
In contrast to patients with B cell precursor acute lymphoblastic leukemia (BCP-ALL), patients with acute myeloid leukemia (AML) have not yet benefited from recent advances in targeted immunotherapy. Repurposing immunotherapies that have been successfully used to target other hematological malignancies could, in case of a shared target antigen, represent a promising opportunity to expand the immunotherapeutic options for AML.
Read the full summary ↓
Here, we evaluated the expression of CD19 in a large pediatric AML cohort, assessed the ex vivo AML killing efficacy of CD19-directed immunotherapies, and characterized the bone marrow immune microenvironment in pediatric AML, BCP-ALL, and non-leukemic controls. Out of 167 newly diagnosed de novo pediatric AML patients, 18 patients (11%) had CD19+ AML, with 61% carrying the translocation t(8;21)(q22;q22). Among CD19+ samples, we observed a continuum of CD19 expression levels on AML cells. In individuals exhibiting unimodal and high CD19 expression, the antigen was consistently present on nearly all CD34+CD38- and CD34+CD38+ subpopulations. In ex vivo AML-T cell co-cultures, blinatumomab demonstrated substantial AML killing, with an efficacy similar to BCP-ALL. In addition, CAR T cells could effectively eliminate CD19+ AML cells ex vivo. Furthermore, our immunogenomic assessment of the bone marrow immune microenvironment of newly diagnosed pediatric t(8;21) AML revealed that T- and NK cells had a less exhausted and senescent phenotype in comparison to pediatric BCP-ALL. Altogether, our study underscores the promise of CD19-directed immunotherapies for the treatment of pediatric CD19+ AML.
Published in
Barneh F, Koedijk JB, Wijnen NE et al.
· Haematologica 2024
· PMID 39113654
· doi:10.3324/haematol.2024.285707
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE270185_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1125391. Searching any of these in the dataset finder brings you back here.
Study design
209 × Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient
Supports a between-group comparison across 209 samples.
How we read this: 1 replicated groups read from 249 sample titles; they account for 209 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM8336330 Bulk RNA-seq of BMMCs from pediatric AML patient 1 (other genotype group)
- GSM8336331 Bulk RNA-seq of BMMCs from pediatric AML patient 2 (other genotype group)
- GSM8336332 Bulk RNA-seq of BMMCs from pediatric AML patient 3 (other genotype group)
- GSM8336333 Bulk RNA-seq of BMMCs from pediatric AML patient 4 (t(8;21) group)
- GSM8336334 Bulk RNA-seq of BMMCs from pediatric AML patient 5 (t(8;21) group)
- GSM8336335 Bulk RNA-seq of BMMCs from pediatric AML patient 6 (other genotype group)
- GSM8336336 Bulk RNA-seq of BMMCs from pediatric AML patient 7 (t(8;21) group)
- GSM8336337 Bulk RNA-seq of BMMCs from pediatric AML patient 8 (t(8;21) group)
- GSM8336338 Bulk RNA-seq of BMMCs from pediatric AML patient 9 (other genotype group)
- GSM8336339 Bulk RNA-seq of BMMCs from pediatric AML patient 10 (t(8;21) group)
- GSM8336340 Bulk RNA-seq of BMMCs from pediatric AML patient 11 (t(8;21) group)
- GSM8336341 Bulk RNA-seq of BMMCs from pediatric AML patient 12 (t(8;21) group)
- GSM8336342 Bulk RNA-seq of BMMCs from pediatric AML patient 13 (other genotype group)
- GSM8336343 Bulk RNA-seq of BMMCs from pediatric AML patient 14 (other genotype group)
- GSM8336344 Bulk RNA-seq of BMMCs from pediatric AML patient 15 (other genotype group)
- GSM8336345 Bulk RNA-seq of BMMCs from pediatric AML patient 16 (other genotype group)
- GSM8336346 Bulk RNA-seq of BMMCs from pediatric AML patient 17 (other genotype group)
- GSM8336347 Bulk RNA-seq of BMMCs from pediatric AML patient 18 (other genotype group)
- GSM8336348 Bulk RNA-seq of BMMCs from pediatric AML patient 19 (other genotype group)
- GSM8336349 Bulk RNA-seq of BMMCs from pediatric AML patient 20 (other genotype group)
- GSM8336350 Bulk RNA-seq of BMMCs from pediatric AML patient 21 (other genotype group)
- GSM8336351 Bulk RNA-seq of BMMCs from pediatric AML patient 22 (other genotype group)
- GSM8336352 Bulk RNA-seq of BMMCs from pediatric AML patient 23 (t(8;21) group)
- GSM8336353 Bulk RNA-seq of BMMCs from pediatric AML patient 24 (t(8;21) group)
- GSM8336354 Bulk RNA-seq of BMMCs from pediatric AML patient 25 (other genotype group)
- GSM8336355 Bulk RNA-seq of BMMCs from pediatric AML patient 26 (other genotype group)
- GSM8336356 Bulk RNA-seq of BMMCs from pediatric AML patient 27 (other genotype group)
- GSM8336357 Bulk RNA-seq of BMMCs from pediatric AML patient 28 (other genotype group)
- GSM8336358 Bulk RNA-seq of BMMCs from pediatric AML patient 29 (other genotype group)
- GSM8336359 Bulk RNA-seq of BMMCs from pediatric AML patient 30 (other genotype group)
- GSM8336360 Bulk RNA-seq of BMMCs from pediatric AML patient 31 (other genotype group)
- GSM8336361 Bulk RNA-seq of BMMCs from pediatric AML patient 32 (other genotype group)
- GSM8336362 Bulk RNA-seq of BMMCs from pediatric AML patient 33 (other genotype group)
- GSM8336363 Bulk RNA-seq of BMMCs from pediatric AML patient 34 (other genotype group)
- GSM8336364 Bulk RNA-seq of BMMCs from pediatric AML patient 35 (other genotype group)
- GSM8336365 Bulk RNA-seq of BMMCs from pediatric AML patient 36 (other genotype group)
- GSM8336366 Bulk RNA-seq of BMMCs from pediatric AML patient 37 (other genotype group)
- GSM8336367 Bulk RNA-seq of BMMCs from pediatric AML patient 38 (other genotype group)
- GSM8336368 Bulk RNA-seq of BMMCs from pediatric AML patient 39 (other genotype group)
- GSM8336369 Bulk RNA-seq of BMMCs from pediatric AML patient 40 (t(8;21) group)
+ 209 more — browse all 249 samples with per-sample file links →
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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.