Quantitative distribution of patient-derived leukemia clones in murine xenografts revealed by cellular barcodes

Detection of chemotherapy-resistant patient-derived acute lymphoblastic leukemia clones in murine xenografts using cellular barcodes

“…The observation that chemotherapy increases the asymmetric distribution of ALL clones across skeletal locations is in line with our previous work, demonstrating skewed localization of normal hematopoietic stem cells, as well as leukemia clones in untreated recipients 13,14,28 . Collectively, these studies support a model in which any reduction in the number of leukemia clones (e.g.…”

“…Key challenges for lineage tracing studies in highly polyclonal samples, such as ALL, are to reliably discriminate "true" subclones from sequencing noise, and to distinguish between clonal selection and random fluctuations in clonal abundance. In previous work, we have shown that estimation of the number of clones in polyclonal samples is highly dependent on the definitions of clonal complexity and methods for their assessment, with the Shannon approximation being the most reliable 13,14 .…”

“…We and others have previously shown that cellular barcoding is a powerful method to study the competitive dynamics of leukemic [13][14][15][16] and normal hematopoietic stem cell clones [17][18][19] in murine…”

Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion

“…Thus, there have been several approaches to overcome this limitation. Some groups apply various tools depending on the structure of the barcode for semi-random barcodes such as Shannon count [ 28 , 67 , 68 ] or the top 90% of present barcodes identified in the sample [ 32 ], others apply the exact match to the constant fragment of the PCR handle downstream the barcode and recover a barcode sequence (by design random 17 nucleotides) allowing up to 4 mutations within the barcode [ 14 , 16 , 19 , 69 ]. In this manuscript, we have applied the criteria of the top 90% of barcodes present in the sample.…”

A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML

“…In contrast to conventional transplantation assays with a single (e.g., GFP) labeled population, FGB enables the longitudinal characterization of multiple color-coded populations in parallel along with the opportunity to assess population-specific differentiation capacities and phenotypes. In comparison to DNA barcode-based tracking approaches [15][16][17], FGB thus benefits from the opportunity to identify and isolate viable cells of interest for subsequent studies by flow cytometric techniques as demonstrated for LSC and hematopoietic stem cells (HSC), respectively [10,18,19].…”