Orthogonal Comparison of Nuclear and Mitochondrial Clonal Architectures in Hematologic Malignancies

<p>Acute myeloid leukemia (AML) is a hematologic malignancy characterized by accumulation of mutations that disrupt hematopoietic differentiation and promote clonal expansion. Understanding how these mutations arise and evolve is essential for improving diagnosis, prognosis, and treatment stratification. Current methods are limited by either restricted genomic coverage (targeted panels) or low throughput and high cost (in single-cell whole genome sequencing, scWGS). An emerging alternative is the use of mitochondrial DNA (mtDNA) mutations as clonal markers.</p> <p>This study aims to determine whether mitochondrial-derived clonal architectures correlate with nuclear-derived clonal architectures in AML, thereby evaluating mtDNA as a scalable orthogonal tool for lineage reconstruction.</p> <p>Bone marrow and peripheral blood samples were collected from four AML patients. Mononuclear cells were isolated and processed using a custom Mission Bio Tapestri single cell DNA panel to simultaneously capture nuclear driver mutations and full-length mitochondrial variants. Single-cell barcoding was performed, followed by library preparation and sequencing. Data were processed through the Tapestri Pipeline and analyzed using R and Python for quality filtering, UMAP visualization, and clonality inference. Mitochondrial variants were annotated to determine functional impact.</p> <p>In parallel, scWGS data from previously profiled multiple myeloma patient samples were analyzed using Mutect2 to reconstruct nuclear and mitochondrial phylogenies. The concordance between nuclear and mtDNA-based clades was quantified using Jaccard indices and phylogenetic overlap metrics.</p> <p>Preliminary analyses revealed consistent detection of both nuclear driver mutations and heteroplasmic mitochondrial variants across single cells. Distinct subclones defined by nuclear mutations such as DNMT3A, IDH1, and ASXL1 frequently exhibited co-segregating mitochondrial variants, suggesting shared clonal ancestry. Comparison of mtDNAand nDNA-derived phylogenies showed partial concordance, particularly in recent clonal expansions, while older lineages displayed weaker alignment due to stochastic mtDNA mutation drift.</p> <p>These findings demonstrate that mitochondrial DNA variants can serve as informative lineage markers that partially recapitulate nuclear-derived clonal structures in AML. Integrating mtDNA profiling with single-cell nuclear sequencing provides a cost-effective, scalable strategy to dissect clonal evolution. This orthogonal framework offers a new avenue for tracing leukemic evolution, monitoring disease relapse, and exploring hematopoietic dynamics in health and malignancy. </p>

Name thesis:degree_name

Masters of Science (MS)

Level thesis:degree_level

Thesis (MS)

Year dc:date.available

2025

Authors dc:creator

• Shah, Nehali
• <p>https://orcid.org/0009-0009-7163-5429</p>

Contributors dc:contributor

• Koichi Takahashi
• Nicholas Short
• Angela Ting

• Clonal Hematopoiesis
• Leukemia
• single cell DNA sequencing
• mitochondrial DNA
• Bioinformatics
• Genetics and Genomics
• Hematology
• Oncology
• Translational Medical Research

Repository record dc:identifier

https://digitalcommons.library.tmc.edu/utgsbs_dissertations/1504

OAI identifier oai:identifier

oai:digitalcommons.library.tmc.edu:utgsbs_dissertations-2561