# Drug resistant pathways in relapsed acute lymphoblastic leukemia (ALL)

> **NIH NIH R01** · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · 2020 · $417,172

## Abstract

ABSTRACT
The outcome for children with relapsed acute lymphoblastic leukemia is dismal especially if relapse occurs
while on therapy. While the cure rate for newly diagnosed ALL continues to climb there has been no
improvement in outcome for relapsed ALL (survival 20% to 45% depending on interval from diagnosis).
Relapsed ALL is one of the most common cancer diagnosis in children making relapsed ALL a leading cause
of cancer mortality. Thus the discovery of the biological pathways that mediate drug resistance and relapse is a
top priority. Over the last funding cycle we have used matched diagnosis and relapse samples from patients
enrolled on Children’s Oncology Group (COG) clinical protocols to discover unique relapse-specific somatic
lesions that indicate the clonal outgrowth of the relapsed clone(s). We have identified a number of lesions
(TBL1XR1 deletions and NT5C2 mutations) and/or activation of biological pathways (Wnt and MAP kinase)
that have been validated in preclinical models to result in resistance to one class of agents (e.g. glucocorticoids
or purine nucleosides) and pan-resistance (e.g. MEK2 activation). Our work has led to two clinical trials with an
additional one in the planning stages. Our results have also indicated that the epigenome has a considerable
impact in shaping the resistant phenotype. A fundamental gap in the extensive characterization of the relapsed
genome we have completed to date is insight into shifts in promoter and enhancer activation mediated by
mutations in gene regulatory regions and/or mutations in epigenetic readers/writers. Given the explosion of
evidence that implicates the epigenome in cancer initiation and progression as well as many new agents in
clinical trials that modulate epigenetic pathways our proposal is timely. We propose to map major shifts in the
histone code (promoters and enhancers) and mutations in regulatory regions between diagnosis and relapse
by using ChIP seq/ATAC seq on paired samples already characterized for gene expression (arrays or
RNAseq), DNA methylation, copy number and next generation sequencing (Aim1). We will discover the roles
and long range interactions of dynamic enhancers and super-enhancers shared by the majority of patients by
chromosome capture (Aim 2). Finally we will validate the role of genes and pathways identified in Aims 1 and 2
in a variety of preclinical models. Our ultimate goal is to complete a comprehensive genomic and epigenomic
portrait of clonal evolution in a common hematological malignancy and to use this information to structure
novel therapeutic approaches to the prevention and treatment of relapse.

## Key facts

- **NIH application ID:** 9981483
- **Project number:** 5R01CA140729-10
- **Recipient organization:** NEW YORK UNIVERSITY SCHOOL OF MEDICINE
- **Principal Investigator:** William L. Carroll
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $417,172
- **Award type:** 5
- **Project period:** 2010-07-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9981483

## Citation

> US National Institutes of Health, RePORTER application 9981483, Drug resistant pathways in relapsed acute lymphoblastic leukemia (ALL) (5R01CA140729-10). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9981483. Licensed CC0.

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