GEO series
Baseline Immune State and T cell Clonal Kinetics are Associated with Response to CAR-T Therapy in Large B-cell Lymphoma
GSE273170
Homo sapiens (human)
Single-cell RNA-seq
81 samples
Submitted 2024/08/12
Platform GPL24676
At a glance
Single-cell RNA-seq · human · 81 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 81 samples: 12 conditions, mostly with about 5 replicates eachGroups 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
- Baseline immune state and T-cell clonal kinetics are associated with durable response to CAR-T therapy in large B-cell lymphomaBlood · 2024
Summary (written by the submitters)
Engineered cellular therapy with CD19-targeting chimeric antigen receptor T-cells (CAR-T) has revolutionized outcomes for patients with relapsed/refractory Large B-Cell Lymphoma (LBCL), but the cellular and molecular features associated with response remain largely unresolved.
Read the full summary ↓
We analyzed serial peripheral blood samples ranging from day of apheresis (day -28/baseline) to 28 days after CAR-T infusion from 50 patients with LBCL treated with axicabtagene ciloleucel (axi-cel) by integrating single cell RNA and TCR sequencing (scRNA-seq/scTCR-seq), flow cytometry, and mass cytometry (CyTOF) to characterize features associated with response to CAR-T. Pretreatment patient characteristics associated with response included presence of B cells and increased lymphocyte-to-monocyte ratio (ALC/AMC). Infusion products from responders were enriched for clonally expanded, highly activated CD8+ T cells. We expanded these observations to 99 patients from the ZUMA-1 cohort and identified a subset of patients with elevated baseline B cells, 80% of whom were complete responders. We integrated B cell proportion and ALC/AMC into a two-factor predictive model and applied this model to the ZUMA-1 cohort. Estimated progression free survival (PFS) at 1 year in patients meeting one or both criteria was 65% versus 31% for patients meeting neither criterion. Our results suggest that patients’ immunologic state at baseline affects likelihood of response to CAR-T through both modulation of the T cell apheresis product composition and promoting a more favorable circulating immune compartment prior to therapy. These baseline immunologic features, measured readily in the clinical setting prior to CAR-T, can be applied to predict response to therapy.
Published in
Maurer K, Grabski IN, Houot R et al.
· Blood 2024
· PMID 39241199
· doi:10.1182/blood.2024024381
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 GSE273170_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1140521. Searching any of these in the dataset finder brings you back here.
Study design
12 conditions, mostly with about 5 replicates each
PBMCs, RNA, Day 7, CA ×10
PBMCs, RNA, Day 14, CA ×10
PBMCs, TCR, Day 7, CA ×9
PBMCs, TCR, Day 14, CA ×9
PBMCs, ADT, Day 7, CA ×8
PBMCs, ADT, Day 14, CA ×8
Infusion product, RNA, CA ×5
Infusion product, TCR, CA ×5
+4 more
Supports a between-group comparison across 81 samples.
How we read this: 12 replicated groups read from 81 sample titles; they account for 81 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
- GSM8423371 PBMCs, RNA, Day 7, CAR116 PBMCs, RNA, Day 7, CA
- GSM8423372 PBMCs, TCR, Day 7, CAR116 PBMCs, TCR, Day 7, CA
- GSM8423373 PBMCs, ADT, Day 7, CAR116 PBMCs, ADT, Day 7, CA
- GSM8423374 PBMCs, RNA, Day 14, CAR116 PBMCs, RNA, Day 14, CA
- GSM8423375 PBMCs, TCR, Day 14, CAR116 PBMCs, TCR, Day 14, CA
- GSM8423376 PBMCs, ADT, Day 14, CAR116 PBMCs, ADT, Day 14, CA
- GSM8423377 Infusion product, RNA, CAR122 Infusion product, RNA, …
- GSM8423378 Infusion product, TCR, CAR122 Infusion product, TCR, …
- GSM8423379 Infusion product, ADT, CAR122 Infusion product, ADT, …
- GSM8423380 PBMCs, RNA, Baseline, CAR122 PBMCs, RNA, Baseline, CA
- GSM8423381 PBMCs, ADT, Baseline, CAR122 PBMCs, ADT, Baseline, CA
- GSM8423382 PBMCs, RNA, Day 7, CAR122 PBMCs, RNA, Day 7, CA
- GSM8423383 PBMCs, TCR, Day 7, CAR122 PBMCs, TCR, Day 7, CA
- GSM8423384 PBMCs, ADT, Day 7, CAR122 PBMCs, ADT, Day 7, CA
- GSM8423385 PBMCs, RNA, Day 14, CAR122 PBMCs, RNA, Day 14, CA
- GSM8423386 PBMCs, TCR, Day 14, CAR122 PBMCs, TCR, Day 14, CA
- GSM8423387 PBMCs, ADT, Day 14, CAR122 PBMCs, ADT, Day 14, CA
- GSM8423388 PBMCs, RNA, Baseline, CAR147 PBMCs, RNA, Baseline, CA
- GSM8423389 PBMCs, TCR, Baseline, CAR147 PBMCs, TCR, Baseline, CA
- GSM8423390 PBMCs, ADT, Baseline, CAR147 PBMCs, ADT, Baseline, CA
- GSM8423391 PBMCs, RNA, Day 7, CAR147 PBMCs, RNA, Day 7, CA
- GSM8423392 PBMCs, TCR, Day 7, CAR147 PBMCs, TCR, Day 7, CA
- GSM8423393 PBMCs, ADT, Day 7, CAR147 PBMCs, ADT, Day 7, CA
- GSM8423394 PBMCs, RNA, Day 14, CAR147 PBMCs, RNA, Day 14, CA
- GSM8423395 PBMCs, TCR, Day 14, CAR147 PBMCs, TCR, Day 14, CA
- GSM8423396 PBMCs, ADT, Day 14, CAR147 PBMCs, ADT, Day 14, CA
- GSM8423397 Infusion product, RNA, CAR137 Infusion product, RNA, …
- GSM8423398 Infusion product, TCR, CAR137 Infusion product, TCR, …
- GSM8423399 Infusion product, ADT, CAR137 Infusion product, ADT, …
- GSM8423400 PBMCs, RNA, Day 7, CAR137 PBMCs, RNA, Day 7, CA
- GSM8423401 PBMCs, TCR, Day 7, CAR137 PBMCs, TCR, Day 7, CA
- GSM8423402 PBMCs, ADT, Day 7, CAR137 PBMCs, ADT, Day 7, CA
- GSM8423403 PBMCs, RNA, Day 14, CAR137 PBMCs, RNA, Day 14, CA
- GSM8423404 PBMCs, TCR, Day 14, CAR137 PBMCs, TCR, Day 14, CA
- GSM8423405 PBMCs, ADT, Day 14, CAR137 PBMCs, ADT, Day 14, CA
- GSM8423406 PBMCs, RNA, Baseline, CAR142 PBMCs, RNA, Baseline, CA
- GSM8423407 PBMCs, ADT, Baseline, CAR142 PBMCs, ADT, Baseline, CA
- GSM8423408 Infusion product, RNA, CAR128 Infusion product, RNA, …
- GSM8423409 Infusion product, TCR, CAR128 Infusion product, TCR, …
- GSM8423410 Infusion product, ADT, CAR128 Infusion product, ADT, …
+ 41 more — browse all 81 samples with per-sample file links →
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- GSE304878 Single-cell multi-omics profiling of PBMCs from SLE patients pre- and post-dual-target (BCMA/CD19) CAR-T therapy 30 samples shares car-t, therapy
- GSE322796 Persistence of mucosal CAR-T cells and inflammatory remodeling in enterocolitis associated with BCMA CAR-T cell therapy 23 samples shares car-t, therapy
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Share this dataset
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.