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1449 Mapping Chemo-Resistance Profiles of Pediatric Acute Leukemia through Integration of Ex-Vivo Drug Screens with Molecular Data

Program: Oral and Poster Abstracts
Session: 605. Molecular Pharmacology and Drug Resistance: Lymphoid Neoplasms: Poster I
Hematology Disease Topics & Pathways:
Lymphoid Leukemias, ALL, pediatric, Diseases, Lymphoid Malignancies, Human, Study Population
Saturday, December 9, 2023, 5:30 PM-7:30 PM

Anna Pia Enblad1,2*, Olga Krali2*, Kristin Blom2*, Claes Andersson2*, Britt-Marie Frost1*, Josefine Palle1*, Arja Harila1*, Erik Forestier3,4*, Jukka Kanerva4,5*, Trond Flægstad4,6*, Ólafur G Jónsson4,7*, Kjeld Schmiegelow, MD4,8,9, Mats Heyman4,10,11, Peter Nygren12*, Rolf Larsson2*, Gudmar Lönnerholm1* and Jessica Nordlund2*

1Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
2Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
3Department of Medical Biosciences, Umeå University, Umeå, Sweden
4For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
5Division of Hematology, Oncology and Stem Cell Transplantation, Helsinki University Central Hospital, Helsinki, Finland
6Department of Pediatrics, Tromsø University and University Hospital, Tromsø, Norway
7Pediatric Hematology-Oncology, Children’s Hospital, Barnaspitali Hringsins, Landspitali University Hospital, Reykjavík, Iceland
8Medical Faculty, Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
9Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
10Childhood Cancer Research Unit, Karolinska Institute, Stockholm, Sweden
11Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
12Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden


While novel approaches for treatment of acute lymphoblastic leukemia (ALL) in children have resulted in significant improvements in survival rates, survivors are faced with potentially life-long challenges as a result of the highly toxic treatment and the outcome for patients who relapse remains poor. The current risk-adapted treatment for ALL in children includes multiple drugs administered sequentially or in combination, with little variation in timing or intensity. Factors that affect varying treatment response between patients and cellular mechanisms that underly response to individual drugs are still under exploration. In this study, we investigate the relationship between ex-vivo drug resistance, transcriptomes, epigenomes and clinical outcome, with the aim of better understanding underlying determinants of treatment response.


Pediatric patients diagnosed with B-ALL between 1992 and 2008 in the Nordic countries were included in the study (n = 598). For these patients, ex-vivo drug response to ten clinically used drugs was determined using the fluorometric microculture cytotoxicity assay (FMCA). Clinical data, including follow-up information (overall survival and relapse free survival) was available for all patients. Additionally, DNA-methylation (450K array, n = 383) and gene expression profiling (RNA-seq, n = 119) was performed on a subset of diagnostic patient samples. The patients were stratified into low, medium and high resistance groups based on ex-vivo drug response. The low and high resistance groups were compared with regard to differentially methylated CpG sites or expressed genes associated with individual drug response profiles.


Overall survival was significantly lower for patients with higher ex-vivo drug resistance to dexamethasone, doxorubicin and thioguanine compared to patients that displayed sensitivity to these drugs (p < 0.05). Similarly, relapse free survival was significantly lower for patients with ex-vivo resistance to cytarabine, dexamethasone, doxorubicin, prednisolone and thioguanine (p < 0.05). After adjusting for sex and risk group, according to the Nordic Society of Pediatric Hematology and Oncology (NOPHO) protocol, in a Cox proportional hazards model, higher hazard ratios for relapse were observed in the highly resistant group across all drugs. We identified distinct DNA methylation and gene expression patterns in patients with low and high resistance, indicating the presence of predetermined molecular resistance fates. These resistance patterns included 665 genes that were differentially expressed (absolute log2FC > 1, Benjamini-Hochberg adjusted p value < 0.05) and 1 422 CpG sites with differential methylation status (absolute mean β-value difference > 0.2, Benjamini-Hochberg adjusted p value < 0.05) in resistant compared to sensitive groups, for one or multiple drugs. With the aim of identifying the genes with the largest impact on drug resistance, we selected the most differentially expressed genes and the genes with the largest difference in methylation status between resistant and sensitive samples. Among these, we identified ~20 putative genes of interest for future studies into resistance mechanisms based on potential functional prioritization.


Our findings confirm that drug response profiles are associated with outcome in pediatric ALL, reflecting response in vivo. We show molecular evidence for differentiating low- and high-resistant types based on diagnostic gene expression and DNA methylation profiles, suggesting contribution of certain molecular signatures to drug response. Our data integrating molecular data with drug response profiles may help identifying such changes of importance in drug resistance mechanisms.

Disclosures: Schmiegelow: Novo Nordisk Foundation: Current holder of stock options in a privately-held company, Research Funding; Illumina, Jazz Pharmaceuticals, Servier, Amgen, Medscape: Honoraria.

*signifies non-member of ASH