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DSRT, affinity proteomics, and single-cell surface spatial proteomics in patient with acute myeloid leukemia at diagnosis

Functional and molecular drivers of therapy response in FLT3-mutant leukemia
https://doi.org/10.48723/n3h9-wr71
The purpose of this study was to investigate the molecular and functional mechanisms underlying resistance to FLT3 inhibitors in FLT3-mutant acute myeloid leukemia, with the goal of identifying predictive markers of response and potential combination strategies to overcome resistance. This repository contains multi-omic data generated on FLT3 mutant and wild-type AML patients. The datasets consist of selective drug sensitivity scores, soluble protein levels, and spatial proteomics data, along with annotation files linking patient IDs across datasets and drug classifications. Data processing methods and software dependencies are specified for each dataset. File List: - sDSS.csv : sDSS table with response to 528 drug perturbations in FLT3 mutant patients. - sDSS_FLT3i.csv : sDSS table with response to 8 FLT3i in FLT3 mutant and wild type patients. - olink_NPX.csv : Soluble protein data table for 17 FLT3 mutant patients. - pixelgen.RData : RData file containing a merged Seurat object with single-cell spatial proteomics data for 6 FLT3 mutant patients. - annotation.csv : Annotation file for all samples. Included is also a list of drug classes: - drug_class.csv Total size of the dataset is approximately 1.4 GB.
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Documentation files

  • README.txt
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Citation and access

Data access level:

Creator/Principal investigator(s):

Research principal:

Data contains personal data:

Yes

Type of personal data:

Data contains pseudonymised identifiers

Code key exists:

Yes

Sensitive personal data:

Yes

Citation:

Language:

Method and outcome

Unit of analysis:

Population:

The population consists of 175 acute myeloid leukemia (AML) patients of which 63 have a FLT3 mutation. The proteomic datasets only contain FLT3 mutant patient samples while the drug testing data contains both.

Time method:

Study design:

  • Experimental study
  • Preclinical study

Description of study design:

Functional and molecular multi-omics study of treatment-naive AML to define systems biology linked to treatments.

Sampling procedure:

Description of sampling:

Bone marrow aspirates or peripheral blood were obtained in parallel with clinical routine diagnostics. Mononuclear cells (MNCs) were isolated with lymphoprep. Following MNC isolation, red blood cells were removed with ACK lysis buffer and the cells were directly used for experiments.

Time period(s) investigated:

Data format/data structure:

Samples/material Collected from scientific collection/biobank

Name:

Nationella akutleukemibiobanken

Type(s) of sample:

Bone marrow mononuclear cells

Samples/material Existing from scientific collection/biobank

Name:

Nationella akutleukemibiobanken

Type(s) of sample:

Bone marrow mononuclear cells

Data collection Biological tests

Mode of collection:

Biological tests

Description of the mode of collection:

Drug sensitivity and resistance testing, FIMM FO5A library, CellTiter Glo

Time period(s) for data collection:

2018 - 2021

Data collector:

  • Karolinska Institute

Data collection Biological tests

Mode of collection:

Biological tests

Description of the mode of collection:

Single cell spatial proteomics kit (Pixelgen, immunology panel I), sequenced using a NovaSeq X Plus system

Data collector:

  • Karolinska Institute

Data collection Biological tests

Mode of collection:

Biological tests

Description of the mode of collection:

Olink 96 Immuno-Oncology panel (Olink Proteomics) measured with a BioMarkTM HD System (Fluidigm)

Data collector:

  • Karolinska Institute

Geographic coverage

Geographic location:

Administrative information

Responsible department/unit:

Department of Oncology-Pathology [K7]

Contributor(s):

  • Olli Kallioniemi - Karolinska Institute
  • Sören Lehmann - Karolinska Institute
  • Henrik Gezelius - Uppsala University
  • Anders Lundmark - Uppsala University
  • Jessica Nordlund - Uppsala University

Commissioning organisation:

Ethics Review:

Stockholm - 2017/2085-31/2

Funding

Funding agency:

  • Swedish childhood cancer fund

Award number:

TJ2021-0080

Funding agency:

  • Karolinska Institute

Award number:

2024-00304, 2020-01091, 2018-02283

Funding agency:

  • Swedish foundation for strategic research

Award number:

SB16-0058

Funding agency:

  • Swedish research council

Award number:

2017-06095

Funding agency:

  • Knut and Alice Wallenberg foundation

Award number:

2015.0291

Award title:

Systems Precision Medicine Platform to Optimize Therapies for Cancer Patients: Acute Myeloid Leukemia (AML) and Beyond

Topic and keywords

CESSDA Topic Classification:

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Contact

Tom Erkerstom.erkers@ki.seOpens in a new tab

Metadata

Version 1
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ki
Published: