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Mastering the use of cellular barcoding to explore cancer heterogeneity

Nature Reviews Cancer volume 22, pages 609–624 (2022)Cite this article

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Abstract

Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity have a higher chance of leading to patient death. However, clonal fate can be driven by non-genomic features. In this context, new technologies are emerging not only to track the spatiotemporal fate of individual cells and their progeny but also to study their molecular features using various omics analysis. In particular, the recent development of cellular barcoding facilitates the labelling of tens to millions of cancer clones and enables the identification of the complex mechanisms associated with clonal fate in different microenvironments and in response to therapy. In this Review, we highlight the recent discoveries made using lentiviral-based cellular barcoding techniques, namely genetic and optical barcoding. We also emphasize the strengths and limitations of each of these technologies and discuss some of the key concepts that must be taken into consideration when one is designing barcoding experiments. Finally, we suggest new directions to further improve the use of these technologies in cancer research.

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Fig. 1: Workflow of the multistep process involved in genetic and optical barcoding.
Fig. 2: Investigating the stochasticity of clonal fate with clone-splitting experiments.
Fig. 3: Strengths and weaknesses of the genetic and optical barcoding techniques.
Fig. 4: Technical challenges of cellular barcoding experiments.
Fig. 5: Challenges with optical barcoding transduction.
Fig. 6: Other considerations for the optimal design of optical barcoding experiments.
Fig. 7: Biological challenges associated with cellular barcoding.

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Acknowledgements

The authors acknowledge F. El-Saafin and S. Gadipally for their constructive feedback, and T. Weber for useful discussions. A.S. is supported by the Melbourne Research Scholarship. D.M. is supported by Cancer Council Victoria, the Love Your Sister Foundation, the NBCF (Investigator Initiated Research Scheme grant IIRS-19-082), Susan G. Komen and Cancer Australia (CCR19606878), the Victorian Cancer Agency Mid-Career Research Fellowship (MCRF21011) and the Australian National Health and Medical Research Council (Grant 2012196). S.H.N. is supported by the Australian National Health and Medical Research Council (Grants 1062820, 1100033, 1101378, 1124812 and 1145184). The authors and the Olivia Newton-John Cancer Research Institute gratefully acknowledge the generous support of the Love Your Sister Foundation and the contribution of the Victorian Government acting through the Victorian Cancer Agency. The contents of the published material are solely the responsibility of the individual authors and do not reflect the views of Cancer Australia or other funding agencies.

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Authors and Affiliations

  1. Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia

    Antonin Serrano, Jean Berthelet & Delphine Merino

  2. School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia

    Antonin Serrano, Jean Berthelet & Delphine Merino

  3. Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Antonin Serrano, Shalin H. Naik & Delphine Merino

  4. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia

    Antonin Serrano, Shalin H. Naik & Delphine Merino

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D.M. and A.S. researched data for the article. All authors contributed substantially to discussion of the content. D.M. and A.S. wrote the article. All authors reviewed and/or edited the manuscript before submission.

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Correspondence to Delphine Merino.

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Glossary

Clones

Subpopulations of cells derived from a common progenitor and harbouring genomic similitude. By extension, in cellular barcoding studies, ‘clone’ refers to cells harbouring the same barcode, as these cells originate from a unique barcoded cell.

Fitness

The ability of individual clones to survive and proliferate in specific conditions.

Diapause

A reversible cellular state originally observed as a survival mechanism of embryos pausing their development when environmental conditions are unfavourable.

Minimal residual disease

Cancer cells detected in a low quantity after treatment.

Spectral flow cytometry

A type of flow cytometry that enables the full spectrum of fluorescence to be recorded with multiple detectors, as opposed to conventional flow cytometry, which uses a single detector.

Serial dilution experiments

Experiments consisting of successive dilution of a cell suspension to select decreasing amounts of cells or to isolate single cells.

Multiplicity of infection

(MOI). The ratio of the number of viral particles to the number of targeted cells.

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Serrano, A., Berthelet, J., Naik, S.H. et al. Mastering the use of cellular barcoding to explore cancer heterogeneity. Nat Rev Cancer 22, 609–624 (2022). https://doi.org/10.1038/s41568-022-00500-2

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