Clonal tracking of haematopoietic cells: insights and clinical implications

Abstract

Summary Recent advances in high‐throughput genomics have enabled the direct tracking of outputs from many cell types, greatly accelerating the study of developmental processes and tissue regeneration. The capacity for long‐term self‐renewal with multilineage differentiation potential characterises the cellular dynamics of a special set of developmental states that are critical for maintaining homeostasis. In haematopoiesis, the archetypal model for development, lineage‐tracing experiments have elucidated the roles of haematopoietic stem cells to ongoing blood production and the importance of long‐lived immune cells to immunological memory. An understanding of the biology and clonal dynamics of these cellular fates and states can provide clues to the response of haematopoiesis to ageing, the process of malignant transformation, and are key to designing more efficacious and durable clinical gene and cellular therapies.

Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques

“…We performed autologous transplantation of rhesus macaques with CD34 + HSPCs transduced with lentiviral vectors expressing copepod green fluorescent protein (GFP) and containing a high diversity library of genetic barcodes (Cordes et al ., 2021; Wu et al ., 2014)(Figure 1A). This vector design allows utilization of GFP as a marker gene demonstrating derivation of various cell lineages in tissues from transplanted HSPCs, as well as lineage tracing of HSPC output at a clonal level via quantitative barcode retrieval.…”

“…To explore the ontogeny and longevity of tissue macrophages in outbred populations of NHPs with high relevance to human biology and disease based on life span and characteristics of both HSPC and immune cells, we performed autologous HSPC transplantation after genetically modifying the HSPCs with a lentiviral vector expressing green fluorescent protein and a bar-coded genetic marker (Cordes et al, 2021; Koelle et al, 2017; Wu et al, 2014). As the HSPCs were transduced with lentiviral vectors containing a library of individual bar-coded genetic markers, this approach allowed us to explore the clonal composition of individual leukocyte subsets, including tissue-resident macrophages, in multiple anatomic sites, relative to their clonal composition in peripheral blood (Koelle et al ., 2017; Wu et al ., 2014).…”

Clonal abundance patterns in hematopoiesis: Mathematical modeling and parameter estimation

“…The downstream progenitor and mature cells that derive from proliferation of HSCs of a particular tag will form a clone of cells that share the same tag. Clonal tracking of cell tags is thus a powerful tool for interrogating the differentiation process during hematopoiesis (Lyne et al, 2018;Challen and Goodell, 2020;Cordes et al, 2021). For example, the abundances of the different tags that appear in the different types of mature cells can shed light on the branching structure of differentiation and on proliferation dynamics, particularly when coupled with mathematical models and/or simulations (Stiehl and Marciniak-Czochra, 2011;Sun and Komarova, 2012;Székely et al, 2014;Höfer and Rodewald, 2016;Xu J. et al, 2018).…”

Increasing Complexity of Molecular Landscapes in Human Hematopoietic Stem and Progenitor Cells during Development and Aging

“…Here and with these inherent biases in mind, we review recent molecular advances in single-cell (sc) omics analyses of human HSPCs, set against huge historical efforts spanning more than five decades that have aimed to identify and characterize human HSCs, their lineage-committed progeny during development and aging, and that provide mechanistic insights. Additional sophisticated technological advances over these decades include the discovery of monoclonal antibodies, the development of flow cytometry and cell sorting, of enhanced in situ imaging and single-cell capture technologies for the immunophenotypic identification and isolation of specific human HSPC subsets, of single-cell barcoding, lineage tracing, fate mapping and gene editing, and of sophisticated gene regulatory and three-dimensional genome organizational analyses, coupled with surrogate models in vivo and/or in vitro to assess the function of HSCs and their progeny, or following transplantation into human recipients as exemplified in some of our own and other studies [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. Not only have these approaches provided insights into human hematopoiesis during development and aging, but they have also identified significant heterogeneity in HSCs and their progeny, led to newer concepts of lineage commitment and differentiation, and contributed to an understanding of the cell of origin for hematological disorders and diseases.…”