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

Livius Penter,Catherine J Wu,Satyen H Gohil

doi:10.3389/fimmu.2021.788891

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.

Highlights

After decades of research, cancer has remained a formidable enemy with relapse as an all too frequent outcome despite advances in treatment approaches
We describe the utility of T or B cell receptor (TCR, BCR) sequences and copy number changes, somatic nuclear and mitochondrial DNA mutations for lineage tracing
While copy number variations (CNV) and somatic nuclear mutations are well-established approaches to lineage tracing, recently it has been recognized that mitochondrial DNA mutations have the potential to serve as phylogenetic barcodes (Figure 1E) [107, 108]

Summary

Introduction

Cancer has remained a formidable enemy with relapse as an all too frequent outcome despite advances in treatment approaches. We describe the utility of T or B cell receptor (TCR, BCR) sequences and copy number changes, somatic nuclear and mitochondrial DNA (mtDNA) mutations for lineage tracing. Chromosomal copy number variations (CNV) can provide robust signals that are detectable with RNA- and DNA-based sequencing platforms (Figure 1C).

Results

Conclusion