Cellular barcoding to decipher clonal dynamics in disease

Abstract

Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.

Fig. 1.. An overview of strategies for lineage tracing.

(Left) Some strategies for prospective lineage tracing. These approaches rely on engineered barcodes that are introduced through integration of the barcode into DNA, recombination of modified alleles that can evolve over time, or genome editing–mediated scar formation that can either occur at a single time point or evolve over time. This enables all the descendants of a particular marked cell to be tracked. (Right) The concept of retrospective lineage tracing, which uses the detection of natural barcodes in cells (such as single-nucleotide variants or other types of mutations) to track back and generate phylogenetic relationships between different cells. Such approaches can be made even more powerful by combining this barcoding with measurements of the cell state at single-cell resolution.

Fig. 2.. A simplified example of the use and value of evolving cellular barcoding.

Advances in cell barcoding now enable the use of evolving barcodes. In the simplified example shown, there are three independent integrated barcode regions that can each be modified at every cell division (for example, through genome editing–mediated scar formation). The combination of these different barcodes allows cellular hierarchies to be reconstructed. At the same time, other measurements of cell state can be obtained (such as the transcriptome or epigenome), providing rich information into the evolution of tissues in healthy and disease states.

Fig. 3.. Nonmalignant clonal expansions can be found across a range of human tissues and organs.

A variety of human tissues and organs, including those highlighted here, have been shown to have age-related clonal expansions that are often driven by somatic mutations found in cancer. Examples of the affected tissues and some genes frequently mutated in these expansions are highlighted. The majority of these studies have relied on the use of bulk sequencing approaches, and with improved resolution of barcoding approaches, the implications of such clonal dynamics and its impact on disease will likely become clearer. IBD, inflammatory bowel disease.