St. Louis Children’s Hospital Archives - Page 2 of 3

2019

Scholar Grant

Jeffrey Magee

St. Louis, MO

Title: Cooperating mutations and resistance to FLT3-ITD inhibition in pediatric acute myeloid leukemia

Executive Summary:
The overarching goal of this project is to understand how a common acute myeloid leukemia (AML) mutation, called FLT3ITD, interacts with other mutations found within the same leukemia cells. Our preliminary data show that the gene expression profiles of FLT3ITD mutant cells can differ based on which cooperating mutations are simultaneously present. This could affect how the AML cells respond to drugs that block FLT3ITD. We want to understand the mechanisms that cause FLT3ITD to activate different target genes in differ genetic contexts, and we want to leverage this information to augment FLT3ITD-directed therapy.

Aim 1. To test whether cooperating NHD13/Flt3ITD and Runx1DEL/Flt3ITD mutations induce distinct patterns of epigenome remodeling that persist after FLT3ITD inhibition.

Aim 2. To identify genes that are necessary to maintain NUP-translocated, FLT3ITD-positive AML cells after FLT3ITD inactivation.

Restated in lay terms, we will pursue the following goals:

1) We will learn why drugs that inactive a specific mutation found in pediatric acute myeloid leukemia, called the FLT3ITD, can work in one patient but not another. We believe that other mutations found in the leukemia cells can influence drug responses.

2) We will identify new targets for therapies to augment the effects of drugs that block FLT3ITD. Ideally, these therapies will be tailored for specific patients based on the mutations that are present.

This work will improve our ability to treat some of the most highly aggressive leukemias that affect children. It will help make precision therapies more precise and effective. While the proposal focuses on FLT3ITD, the approaches should be valuable for studying leukemias with other mutations.

2019

Young Investigator

Nicole Brossier

St. Louis, MO

Executive Summary: As we enter into an era of precision pediatric oncology, it is becoming increasingly important to identify the factors that underlie the risk of brain tumor development. This challenge is particularly relevant for individuals with cancer predisposition syndromes like Neurofibromatosis type 1 (NF1), where 15-20% of children born with a germline NF1 gene mutation develop optic pathway gliomas (OPGs). Our inability to provide accurate risk assessment information for these young children leads to frequent sedated neuroimaging, suboptimal visual screening, and delays in instituting treatment for those at greatest risk. Leveraging emerging evidence from both human and animal studies suggesting not all NF1 gene mutations confer equal risk for OPG development, I now hypothesize that NF1 gene mutations differently increase the risk of optic glioma formation at the level of the cell of origin for these tumors. In this grant, I propose to perform a detailed analysis of the potential cells of origin for these tumors using a novel collection of Nf1 mutant mice genetically engineered to harbor different NF1 patient germline Nf1 gene mutations. Specifically, I plan to determine:

(a) which cells in the developing brain give rise to mouse optic gliomas and

(b) the differential impact of the Nf1 germline mutation on the capabilities of these cells to generate optic gliomas. Taken together, these experiments aim to determine how the germline NF1 gene mutation functions as a risk factor for pediatric brain tumor formation, relevant to future risk assessment strategies for NF1 and other pediatric brain cancer predisposition syndromes.

2018

Quantum Grant

Todd Druley

St. Louis, MO

Improving pediatric AML survival by implementing RNA-specific error corrected sequencing for residual disease

Acute myeloid leukemia (AML) only accounts for 25% of pediatric leukemia cases, but accounts for 50% of pediatric leukemia deaths. One reason for poor outcomes is the inability to precisely assess genetic differences before and after treatment (minimal residual disease, MRD). The current method for AML MRD is multi-parameter flow cytometry (MPFC), which quantifies exterior cell surface markers to identify AML cells as rare as 0.001 (1:1,000). However, 30% of MPFC-MRD-“negative” patients still relapse and most die, which highlights that detecting residual AML after treatment is not enough. Given the growing cadre of gene-specific precision therapies, sequencing, rather than using cell surface proteins, could provide a unique genetic mutational profile that specifically marks a patient’s leukemia and provides information to tailor molecular therapies. Recently, RNA sequencing studies demonstrated that, compared to adults, pediatric leukemia is far more likely to harbor RNA anomalies. However, standard RNA sequencing lacks adequate quantitation for very rare RNA species, resulting in an incomplete molecular profiling of any AML sample.

The Druley lab has developed, validated and applied error-corrected sequencing mitigating sequencing errors with a limit of detection of 0.0001 (1:10,000), 100-fold better than standard sequencing, to redefine the prevalence of physiologic and AML-associated mutations in blood. RNA-ECS can quantitatively detect very rare allele(mutation)-specific gene expression, cryptic fusions and aberrant splice isoforms from any AML patient before, during and after treatment. Preliminary studies find previously undetectable AML-related RNA fusions and splice variants in over 65% of pediatric cases studied to date. This proposal leverages a multi-disciplinary team of pediatric AML experts and will apply RNA-ECS to more than 1,800 specimens from the largest pediatric AML trial ever completed. These results will improve detection of residual, clonal AML, which will improve future therapeutic selection and survival for children with AML.