GEO series

Sensitization of non-M3 acute myeloid leukemia blasts to all-trans retinoic acid by the LSD1 inhibitor tranylcypromine: TRANSATRA phase I study

GSE277031 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/05/01 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 3 × TRANSATRA Patient 01-002 day vs 3 × TRANSATRA Patient 05-001 dayGroups 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: Sensitization of Non-M3 Acute Myeloid Leukemia Blasts to All-Trans Retinoic Acid by the LSD1 Inhibitor Tranylcypromine: TRANSATRA Phase I StudyEuropean journal of haematology · 2025

Summary (written by the submitters)

Elderly, non-fit AML/MDS patients relapsed/refractory (R/R) after HMA-based treatment represent a highly unmet clinical need, necessitating the development of age-appropriate therapies with an acceptable safety profile, e.g. with all-trans retinoic acid (ATRA). As histone demethylase LSD1 (KDM1A) is a rational therapeutic target in AML, we conducted a phase I trial with the LSD1 inhibitor tranylcypromine (TCP, dose levels [DL] 20, 40, 60, 80mg p.o.

Read the full summary ↓

d1-28) combined with fixed-dose ATRA (45mg/m2 p.o. d10-28) and low-dose cytarabine (LDAC, 40mg s.c. d1-10). The primary endpoint was dose limiting toxicity (DLT) in the first 28 days of treatment. The aim was the determination of the maximum tolerated dose (MTD). Enrollment into DLs was performed using the rolling six design. Twenty-three patients with R/R AML and 2 with relapsed MDS were accrued, with a median age 75 years (range 62-84), after a median of two prior treatment lines (range, 1-5). Three, 6, 6 and 10 patients were allocated to DL 20, 40, 60, and 80 mg TCP, respectively, with 3, 12, 6 , 4 patients achieving the respective dose of 20, 40, 60, and 80 mg, and 3 patients on each DL being fully evaluable for MTD. TCP was administered for a median of 39.5 days (range 11-228), for >60 days in 30% of patients. No dose-limiting toxicities (DLTs) were observed at any DL, MTD could not be established. Most common adverse events > grade 3 occurring in >10% of patients were: pneumonia (16%) and febrile neutropenia (12%). No differentiation syndrome occurred. Two patients attained a partial remission; stable disease was achieved in 10 of 22 evaluable patients. Median overall survival was 62 days (range 14-325). Accompanying studies included pharmacokinetics, serial determinations of fetal hemoglobin and genes known to be regulated by LSD1 or ATRA, such as CD86, CD38 and GFI1B. Patients’ quality of life, anxiety and depression were determined before and after treatment. In conclusion, the combination of TCP with ATRA and LDAC was well feasible, even at the highest DL. Almost half of the patients attained stable disease, indicating limited cross-resistance with prior HMA treatment. Hence, studies with more potent LSD1 inhibitors appear warranted.

Published in

Sensitization of Non-M3 Acute Myeloid Leukemia Blasts to All-Trans Retinoic Acid by the LSD1 Inhibitor Tranylcypromine: TRANSATRA Phase I Study

Kruszewski M, Schmoor C, Berg T et al. · European journal of haematology 2025 · PMID 40459012 · doi:10.1111/ejh.14426

This dataset

Open GSE277031 in finder → Find more human RNA-seq datasets → Acute myeloid leukemia landscape →

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.

Series matrix ↓

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 GSE277031_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

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.

Raw reads on ENA ↗

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 PRJNA1160257 and SRA study SRP532333. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40459012) ↗

Study design

3 × TRANSATRA Patient 01-002 day vs 3 × TRANSATRA Patient 05-001 day

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 6 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

GSM8512997 TRANSATRA Patient 01-002 screening
GSM8512998 TRANSATRA Patient 01-002 day 10 TRANSATRA Patient 01-00…
GSM8512999 TRANSATRA Patient 01-002 day 20 TRANSATRA Patient 01-00…
GSM8513000 TRANSATRA Patient 01-002 day 28 TRANSATRA Patient 01-00…
GSM8513001 TRANSATRA Patient 01-002 EOT
GSM8513002 TRANSATRA Patient 03-001 screening
GSM8513003 TRANSATRA Patient 03-001 day 28
GSM8513004 TRANSATRA Patient 05-001 screening
GSM8513005 TRANSATRA Patient 05-001 day 20 TRANSATRA Patient 05-00…
GSM8513006 TRANSATRA Patient 05-001 day 28 TRANSATRA Patient 05-00…
GSM8513007 TRANSATRA Patient 05-001 day 56 TRANSATRA Patient 05-00…
GSM8513008 TRANSATRA Patient 05-001 EOT

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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.