Abstract 2532: High-throughput single-cell targeted DNA sequencing from frozen, fixed and preserved solid tumor samples reveals complex genomic variation and clonal propagation

Abstract AML (acute myeloid leukemia) is increasingly being treated with precision medicine. To better inform treatment, the mutational content of patient samples must be determined. However, current tumor sequencing paradigms are inadequate to fully characterize many instances of the disease. A major challenge has been the unambiguous identification of potentially rare and genetically heterogeneous neoplastic cell populations, capable of critically impacting tumor evolution and the acquisition of therapeutic resistance. Standard bulk population sequencing is unable to identify rare alleles and definitively determine whether mutations co-occur within the same cell. Single-cell sequencing has the potential to address these key issues and transform our ability to accurately characterize clonal heterogeneity in AML. Previous single-cell studies examining genetic variation in AML have relied upon laborious, expensive and low-throughput technologies that are not readily scalable for routine analysis of the disease. We applied a newly developed platform technology to perform targeted single-cell DNA sequencing on over 140,000 cells and generated high-resolution maps of clonal architecture from AML tumor samples. Marrow and/or peripheral blood samples were collected prior to, during treatment, and at clinical progression to the FLT3 inhibitor gilteritinib given on a clinical trial for relapsed/refractory AML with FLT3 mutation. Single-cell sequencing of multiple patient samples demonstrated that relapse clones acquired oncogenic RAS mutations. We utilized the high-throughput and sensitivity of our single-cell approach to more definitively assess where in the course of treatment these RAS mutated clones were acquired. Oncogenic RAS harboring clones, comprising between 0.4%, and 0.1% of tumor populations, were identified in patient samples either prior to or shortly after onset of treatment. Significantly, these RAS variant alleles were not detectable with targeted bulk sequencing. Throughout the course of treatment with the FLT3 inhibitor gilteritinib, the RAS mutant clones selectively expanded and were responsible for resistance to therapy and relapse. These findings point to the presence of underlying genetic heterogeneity in AML and demonstrate the utility of sensitively assaying clonal architecture to better inform patient stratification and therapy selection. Disclosures Eastburn: Mission Bio, Inc.: Employment, Equity Ownership. Durruthy-Durruthy:Mission Bio, Inc.: Employment, Equity Ownership. Smith:Astellas Pharma: Research Funding. Perl:Actinium Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; NewLink Genetics: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Daiichi Sankyo: Consultancy; Arog: Consultancy; Novartis: Membership on an entity's Board of Directors or advisory committees; Astellas: Consultancy; AbbVie: Membership on an entity's Board of Directors or advisory committees.

Download Full-text

Abstract 4696: High-throughput single-cell targeted DNA sequencing using an updated TapestriTMPlatform reveals rare clones and clonal evolution for multiple blood cancers

10.1158/1538-7445.sabcs18-4696 ◽

2019 ◽

Author(s):

Nianzhen Li ◽

Daniel Mendoza ◽

Adam Sciambi ◽

Mani Manivannan ◽

Jacob Ho ◽

...

Keyword(s):

Dna Sequencing ◽

Single Cell ◽

High Throughput ◽

Clonal Evolution ◽

Multiple Blood

Download Full-text

Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics

10.1101/2020.02.07.925743 ◽

2020 ◽

Cited By ~ 5

Author(s):

Kiyomi Morita ◽

Feng Wang ◽

Katharina Jahn ◽

Jack Kuipers ◽

Yuanqing Yan ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Dna Sequencing ◽

Single Cell ◽

High Throughput ◽

Myeloid Leukemia ◽

Clonal Evolution ◽

Treatment Resistance ◽

Clonal Diversity ◽

History Of ◽

Acute Myeloid

SummaryOne of the pervasive features of cancer is the diversity of mutations found in malignant cells within the same tumor; a phenomenon called clonal diversity or intratumor heterogeneity. Clonal diversity allows tumors to adapt to the selective pressure of treatment and likely contributes to the development of treatment resistance and cancer recurrence. Thus, the ability to precisely delineate the clonal substructure of a tumor, including the evolutionary history of its development and the co-occurrence of its mutations, is necessary to understand and overcome treatment resistance. However, DNA sequencing of bulk tumor samples cannot accurately resolve complex clonal architectures. Here, we performed high-throughput single-cell DNA sequencing to quantitatively assess the clonal architecture of acute myeloid leukemia (AML). We sequenced a total of 556,951 cells from 77 patients with AML for 19 genes known to be recurrently mutated in AML. The data revealed clonal relationship among AML driver mutations and identified mutations that often co-occurred (e.g., NPM1/FLT3-ITD, DNMT3A/NPM1, SRSF2/IDH2, and WT1/FLT3-ITD) and those that were mutually exclusive (e.g., NRAS/KRAS, FLT3-D835/ITD, and IDH1/IDH2) at single-cell resolution. Reconstruction of the tumor phylogeny uncovered history of tumor development that is characterized by linear and branching clonal evolution patterns with latter involving functional convergence of separately evolved clones. Analysis of longitudinal samples revealed remodeling of clonal architecture in response to therapeutic pressure that is driven by clonal selection. Furthermore, in this AML cohort, higher clonal diversity (≥4 subclones) was associated with significantly worse overall survival. These data portray clonal relationship, architecture, and evolution of AML driver genes with unprecedented resolution, and illuminate the role of clonal diversity in therapeutic resistance, relapse and clinical outcome in AML.

Download Full-text