Clonal tracking using embedded viral barcoding and high-throughput sequencing

Bramlett, Charles; Du, Jie; Nogalska, Anna; Eerdeng, Jiya; Contreras, Jorge L.; Lu, Rong

doi:10.1038/s41596-019-0290-z

Cited by 28 publications

(29 citation statements)

References 53 publications

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“…As PDX studies generally do not discriminate between samples collected from different disease stages, our data demonstrate that certain samples may be severely biased. The sampling limitations of the PDX model are particularly troubling in the light of the heterogeneity of cancer cells 1-4,8,9 . Our data precisely delineate the heterogenous clonal dynamics of leukemia using robust biological replicate assays that eliminate the influence of rare molecular events, such as random viral integration [36][37][38][39][40] . Using 5 primary patient samples and 15 primary xenograft mice, we showed that dominant clonal expansion in the bone marrow is commonly restricted to confined anatomical sites ( Figs.…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we present an integrated experimental system that directly connects gene expression with cellular behavior at the single cell level by combining synthetic DNA barcode tracking and single cell mRNA sequencing in a PDX model. We have previously demonstrated the high sensitivity and precise quantification of our DNA barcode tracking using hematopoietic stem cells in vivo [36][37][38][39][40] . Here, we adapted the barcode tracking to assay the activities of cancer cells and their gene expression profiles simultaneously in a PDX model xenografted by human B-cell acute lymphoblastic leukemia (B-ALL) samples.…”

Section: Recent Advances In Single Cell Genomic and Transcriptomic Sementioning

confidence: 99%

“…Primary B-ALL cells were genetically barcoded using a GFP-encoding lentiviral vector (Fig. 1a) 36,37 . After barcode labeling, they were transplanted into sub-lethally irradiated NSG or NSG-SGM3 mice.…”

Section: An Integrated Experimental System Connecting Single Cell Tramentioning

confidence: 99%

“…After barcode labeling, they were transplanted into sub-lethally irradiated NSG or NSG-SGM3 mice. Subsequent clonal tracking assays were performed as previously described 36,37 . Our data show that the barcoded leukemia cells expanded proportionally to nonbarcoded leukemia cells in recipient mice ( Fig.…”

Section: An Integrated Experimental System Connecting Single Cell Tramentioning

confidence: 99%

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Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses

Contreras-Trujillo

Eerdeng

et al. 2021

Preprint

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Cellular heterogeneity is a major cause of treatment resistance in cancer. Despite recent advances in single-cell genomic and transcriptomic sequencing, it remains difficult to relate measured molecular profiles to the cellular activities underlying cancer. Here, we present an integrated experimental system that connects single cell gene expression to heterogeneous cancer cell growth, metastasis, and treatment response. Our system integrates single cell transcriptome profiling with DNA barcode based clonal tracking in patient-derived xenograft models. We show that leukemia cells exhibiting unique gene expression signatures respond to different chemotherapies in distinct but consistent manners across multiple mice. In addition, we uncover an unexpected yet common form of leukemia expansion that is spatially confined to the bone marrow of single anatomical sites and driven by cells with distinct gene expression signatures. Our integrated system directly and effectively interrogates the molecular and cellular basis of the intratumoral heterogeneity underlying disease progression and treatment resistance.

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Section: Discussionmentioning

confidence: 99%

Section: Recent Advances In Single Cell Genomic and Transcriptomic Sementioning

confidence: 99%

Section: An Integrated Experimental System Connecting Single Cell Tramentioning

confidence: 99%

Section: An Integrated Experimental System Connecting Single Cell Tramentioning

confidence: 99%

See 2 more Smart Citations

Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses

Contreras-Trujillo

Eerdeng

et al. 2021

Preprint

Self Cite

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“…Given the diversity of labelling and recovery strategies, as well as underlying differences in vector and barcode constructs, a number of approaches for recovery of sequences from raw sequencing data and determination of "true" integration site or genetic tag from sequencing artifacts or other confounders have been developed and are largely approach-dependent (14)(15)(16)(17).…”

Section: Introductionmentioning

confidence: 99%

barcodetrackR: an R package for the interrogation of clonal tracking data

Espinoza

Mortlock

Koelle

et al. 2020

Preprint

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Clonal tracking methods provide quantitative insights into the cellular output of genetically labelled progenitor cells across time and cellular compartments. However, the absence of a toolbox by which to interrogate these data has precluded the development of standardized analytical frameworks within the field. Thus, we developed barcodetrackR, an R package that provides users with tools for the analysis and visualization of clonal dynamics across time and cellular compartments in clonal tracking experiments. Here, we demonstrate the utility of barcodetrackR in exploring longitudinal clonal patterns and lineage relationships in the context of clonal tracking studies of hematopoietic stem and progenitor cells.

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A CRISPR view of hematopoietic stem cells: Moving innovative bioengineering into the clinic

Worthington

Forsberg

2022

American J Hematol

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Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas genome engineering has emerged as a powerful tool to modify precise genomic sequences with unparalleled accuracy and efficiency. Major advances in CRISPR technologies over the last 5 years have fueled the development of novel techniques in hematopoiesis research to interrogate the complexities of hematopoietic stem cell (HSC) biology. In particular, high throughput CRISPR based screens using various “flavors” of Cas coupled with sequencing and/or functional outputs are becoming increasingly efficient and accessible. In this review, we discuss recent achievements in CRISPR‐mediated genomic engineering and how these new tools have advanced the understanding of HSC heterogeneity and function throughout life. Additionally, we highlight how these techniques can be used to answer previously inaccessible questions and the challenges to implement them. Finally, we focus on their translational potential to both model and treat hematological diseases in the clinic.

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Clonal tracking using embedded viral barcoding and high-throughput sequencing

Cited by 28 publications

References 53 publications

Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses

Deciphering intratumoral heterogeneity using integrated clonal tracking and single-cell transcriptome analyses

barcodetrackR: an R package for the interrogation of clonal tracking data

A CRISPR view of hematopoietic stem cells: Moving innovative bioengineering into the clinic

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