Interrogation of clonal tracking data using barcodetrackR

Espinoza, Diego A.; Mortlock, Ryland D.; Koelle, Samson; Wu, Chuanfeng; Dunbar, Cynthia E.

doi:10.1038/s43588-021-00057-4

Cited by 17 publications

(24 citation statements)

References 48 publications

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“…Barcode sequencing fastq output files were processed using custom Python code to identify barcoded clones contributing above sequencing error and sampling thresholds ( 54 , 55 ). Data analysis, Pearson correlations and plot generation were performed using R (Foundation for Statistical Computing) and Prism (GraphPad Software).…”

Section: Methodsmentioning

confidence: 99%

“…Data analysis, Pearson correlations and plot generation were performed using R (Foundation for Statistical Computing) and Prism (GraphPad Software). Custom R code is available on GitHub at and and the various analytical approaches and visualizations employed were described previously ( 54 ). Flow plots were generated by FlowJo V10 (FlowJo, LLC).…”

Section: Methodsmentioning

confidence: 99%

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Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells

Liang

Brenchley

et al. 2022

Front. Immunol.

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Tissue resident (TR) immune cells play important roles in facilitating tissue homeostasis, coordinating immune responses against infections and tumors, and maintaining immunological memory. While studies have shown these cells are distinct phenotypically and functionally from cells found in the peripheral blood (PB), the clonal relationship between these populations across tissues has not been comprehensively studied in primates or humans. We utilized autologous transplantation of rhesus macaque hematopoietic stem and progenitor cells containing high diversity barcodes to track the clonal distribution of T, B, myeloid and natural killer (NK) cell populations across tissues, including liver, spleen, lung, and gastrointestinal (GI) tract, in comparison with PB longitudinally post-transplantation, in particular we focused on NK cells which do not contain endogenous clonal markers and have not been previously studied in this context. T cells demonstrated tissue-specific clonal expansions as expected, both overlapping and distinct from blood T cells. In contrast, B and myeloid cells showed a much more homogeneous clonal pattern across various tissues and the blood. The clonal distribution of TR NK was more heterogenous between individual animals. In some animals, as we have previously reported, we observed large PB clonal expansions in mature CD56-CD16+ NK cells. Notably, we found a separate set of highly expanded PB clones in CD16-CD56- (DN) NK subset that were also contributing to TR NK cells in all tissues examined, both in TR CD56-CD16+ and DN populations but absent in CD56+16- TR NK across all tissues analyzed. Additionally, we observed sets of TR NK clones specific to individual tissues such as lung or GI tract and sets of TR NK clones shared across liver and spleen, distinct from other tissues. Combined with prior functional data that suggests NK memory is restricted to liver or other TR NK cells, these clonally expanded TR NK cells may be of interest for future investigation into NK cell tissue immunological memory, with implications for development of NK based immunotherapies and an understanding of NK memory.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells

Liang

Brenchley

et al. 2022

Front. Immunol.

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“…To standardize the analytical procedure, two R-based programs were developed. genBaRcode focuses on basic error-correction and routine visualization of barcodes, while barcodetrackR steps further to interrogate the different aspects of clonal tracing by offering convenient functions to show pairwise lineage relationship, illustrate longitudinal clonal dynamics and infer lineage bias (Thielecke et al, 2020 ; Adair and Enstrom, 2021 ; Espinoza et al, 2021 ). As for polylox barcoding, an in-house algorithm was created to extract unique barcodes from long reads generated by third-generation sequencing (Pei et al, 2019 ).…”

Section: Technical Considerations and Limitationsmentioning

confidence: 99%

Connecting past and present: single-cell lineage tracing

2022

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Central to the core principle of cell theory, depicting cells’ history, state and fate is a fundamental goal in modern biology. By leveraging clonal analysis and single-cell RNA-seq technologies, single-cell lineage tracing provides new opportunities to interrogate both cell states and lineage histories. During the past few years, many strategies to achieve lineage tracing at single-cell resolution have been developed, and three of them (integration barcodes, polylox barcodes, and CRISPR barcodes) are noteworthy as they are amenable in experimentally tractable systems. Although the above strategies have been demonstrated in animal development and stem cell research, much care and effort are still required to implement these methods. Here we review the development of single-cell lineage tracing, major characteristics of the cell barcoding strategies, applications, as well as technical considerations and limitations, providing a guide to choose or improve the single-cell barcoding lineage tracing.

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“…There is therefore a need for tools that permit the exploration of lineage tracing datasets, without needing to write computer code. Increasing the availability of open-source tools will make lineage-tracing analysis more reproducible, transparent, and accessible—as well as permitting meta-analyses across independent studies ( 31 , 32 ).…”

Section: Introductionmentioning

confidence: 99%

“…Xcalibr is also a pre-processing toolkit, that focuses only on the extraction and demultiplexing of barcodes from sequencing data ( 18 , 19 ). With regards to analysis toolkits, barcodetrackR has been developed for the analysis of clonal tracking data over time ( 31 ) ( Figure 1 ). BarcodetrackR is a versatile tool that places an emphasis on longitudinal analyses.…”

Section: Introductionmentioning

confidence: 99%

CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

et al. 2022

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Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.

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Interrogation of clonal tracking data using barcodetrackR

Cited by 17 publications

References 48 publications

Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells

Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells

Connecting past and present: single-cell lineage tracing

CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data

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