Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics

Abstract

Blood malignancies provide unique opportunities for longitudinal tracking of disease evolution following therapeutic bottlenecks and for the monitoring of changes in anti-tumor immunity. The expanding development of multi-modal single-cell sequencing technologies affords newer platforms to elucidate the mechanisms underlying these processes at unprecedented resolution. Furthermore, the identification of molecular events that can serve as in-vivo barcodes now facilitate the tracking of the trajectories of malignant and of immune cell populations over time within primary human samples, as these permit unambiguous identification of the clonal lineage of cell populations within heterogeneous phenotypes. Here, we provide an overview of the potential for chromosomal copy number changes, somatic nuclear and mitochondrial DNA mutations, single nucleotide polymorphisms, and T and B cell receptor sequences to serve as personal natural barcodes and review technical implementations in single-cell analysis workflows. Applications of these methodologies include the study of acquired therapeutic resistance and the dissection of donor- and host cellular interactions in the context of allogeneic hematopoietic stem cell transplantation.

Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease

“…1D). 31 Donor and recipient single nucleotide polymorphisms (SNPs) provided us with an opportunity to definitively distinguish malignant (recipient) from normal (donor) myeloid cells in cohort A (total 145,595 cells) 33 . By applying souporcell 34 (Fig.…”

Single-cell lineage tracing with endogenous markers

“…Multiple lineage tracing integrated with CNV states, SNV states and viral lineage barcoding using a colon cancer organoid model over 100 generations allowed the construction of highly detailed evolutionary trees and demonstrated sequential loss of chromosomes 18 and 4 correlates with fitness advantage in tumour evolution (Kester et al 2022 ). The high prevalence of CNV changes in blood malignancies permits unambiguous identification of the clonal lineage of cell populations within heterogeneous phenotypes and facilitates the tracking of the trajectories of malignant and of immune cell populations in acute myeloid leukaemia and chronic lymphocytic leukaemia (Penter et al 2021 , 2022 ).…”

Single-cell genomics-based immune and disease monitoring in blood malignancies

“…For the detection of such natural genetic barcodes with single-cell sequencing, the choices are DNA-and RNAbased platforms which come with their individual strengths and advantages. 51 In general, DNA-based single-cell sequencing, especially amplicon-based strategies, can obtain genetic information in thousands of cells and may be combined with protein detection that can distinguish immune and cancer cell populations. 20,52 On the other hand, RNAbased detection of natural barcodes is more challenging, and has varying degrees of success, as it is dependent on the expression levels of genes that harbor a genetic marker or are part of a region with structural chromosomal changes.…”