Identification of Structural Variation in Pediatric B-Cell Acute Lymphoblastic Leukemia and its Role in Health Disparity
Restricted (Penn State Only)
- Author:
- Budurlean, Laura
- Graduate Program:
- Biomedical Sciences
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- May 29, 2024
- Committee Members:
- James Broach, Chair & Dissertation Advisor
Amanda Nelson, Outside Field Member
Todd Schell, Outside Unit Member
Joshua I Warrick, Special Member
Sinisa Dovat, Major Field Member
Joshua I Warrick, Special Member
Lisa M Shantz, Program Head/Chair - Keywords:
- B-ALL
structural variation
bionano
optical genome mapping
wgs
SVs
b-cell acute lymphoblastic leukemia - Abstract:
- The following dissertation integrates whole genome sequencing (WGS), Bionano optical genome mapping (OGM), and RNA-sequencing to investigate somatic structural variants (SVs) in pediatric B-cell acute lymphoblastic leukemia (B-ALL). Pediatric hematological malignancies comprise 40% of all pediatric cancers, and acute lymphoblastic leukemia (ALL) is the most common type of childhood cancer, with 3,200 new cases per year. Although the mortality of pediatric ALL is steadily decreasing, ALL is the leading cause of death among pediatric cancers, highlighting the unmet medical need for novel treatments for this disease. Children of Hispanic origin have a higher incidence of B-ALL than those of non-Hispanic ancestry, and their mortality rate is 39% higher than that of non-Hispanic individuals. Understanding the pathogenesis of B-ALL, identifying SVs in Hispanic and non-Hispanic children, and developing novel therapies to target specific regulatory mechanisms may reduce health disparities in Hispanic children with B-ALL. Previous studies have failed to consider an integrative approach for SV detection, particularly in the context of genetic ancestry. The aim of this study was to broaden our knowledge of SVs in pediatric B-ALL and their resulting effects on gene expression using a new genome-wide integrated framework that combines short-read WGS with large DNA fragment OGM and RNA sequencing. Using this platform, our research highlights structural variants in pediatric B-ALL that are not captured by traditional cytogenetic techniques or WGS alone and identifies new potential therapeutic targets that may aid in reducing the health disparity in pediatric Hispanic and non-Hispanic B-ALL. The first study examined the methodology and computational challenges of integrating OGM and WGS for SV detection. We introduce a computational pipeline for integrating WGS, OGM and RNA-Seq and filtering for somatic mutations in pediatric B-ALL in the absence of control DNA. We identified that only 11.6% of SVs were detected by both methods and examined the areas and reasons for non-concurrence. These results suggest that integrating OGM with WGS has a higher sensitivity for SV detection and may aid clinical diagnostics. The subsequent study focused on the health disparities between Hispanic and non-Hispanic children with B-ALL. We determined the genetic ancestry of 57 children with the disease and examined the structural variant differences between the two cohorts. We observed SVs in 88% of leukemia driver genes and additional genes involved in DNA repair, transcription factors, and cell cycle and signaling. Further we curated 72 gene fusions including 50 novel fusions, many of which were also expressed. We also showed genes dysregulated in canonical cancer pathways unique to Hispanic individuals. These results suggest how SVs can impact leukemogenesis and may differ between different ethnicities. The final study examined the WGS single nucleotide variation (SNV) to uncover impactful mutations and genes that may be differentially mutated between Hispanic and non-Hispanic children. We showed that tumor mutation burden is not a good predictor of health disparities between ethnicities and further found mutations enriched in each ethnicity. We also found mutations in 59% of genes used in a clinical panel for pediatric cancer and examined co-occurring and mutually exclusive genes. Finally, we found that the NRF2 signaling pathway was affected exclusively in Hispanics. The results suggest how SNVs can also impact prognosis and affect various leukemogenic pathways.