Mastering the use of cellular barcoding to explore cancer heterogeneity

Marusyk, A., Janiszewska, M. & Polyak, K. Intratumor heterogeneity: the Rosetta stone of therapy resistance. Cancer Cell 37, 471–484 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Shembrey, C., Huntington, N. D. & Hollande, F. Impact of tumor and immunological heterogeneity on the anti-cancer immune response. Cancers https://doi.org/10.3390/cancers11091217 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Tabassum, D. P. & Polyak, K. Tumorigenesis: it takes a village. Nat. Rev. Cancer 15, 473–483 (2015).

CAS  PubMed  Article  Google Scholar 

Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kim, C. et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell 173, 879–893 e813 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Jia, Q., Chu, H., Jin, Z., Long, H. & Zhu, B. High-throughput single-cell sequencing in cancer research. Signal. Transduct. Target. Ther. 7, 145 (2022).

PubMed  PubMed Central  Article  Google Scholar 

Nam, A. S., Chaligne, R. & Landau, D. A. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics. Nat. Rev. Genet. 22, 3–18 (2021).

CAS  PubMed  Article  Google Scholar 

Merino, D. et al. Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer. Nat. Commun. 10, 766 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Naik, S. H., Schumacher, T. N. & Perie, L. Cellular barcoding: a technical appraisal. Exp. Hematol. 42, 598–608 (2014).

PubMed  Article  Google Scholar 

Bystrykh, L. V. & Belderbos, M. E. Clonal analysis of cells with cellular barcoding: when numbers and sizes matter. Methods Mol. Biol. 1516, 57–89 (2016).

CAS  PubMed  Article  Google Scholar 

Kebschull, J. M. & Zador, A. M. Cellular barcoding: lineage tracing, screening and beyond. Nat. Methods 15, 871–879 (2018).

CAS  PubMed  Article  Google Scholar 

Lewis, S. M. et al. Spatial omics and multiplexed imaging to explore cancer biology. Nat. Methods https://doi.org/10.1038/s41592-021-01203-6 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Gui, P. & Bivona, T. G. Evolution of metastasis: new tools and insights. Trends Cancer https://doi.org/10.1016/j.trecan.2021.11.002 (2021).

Article  PubMed  Google Scholar 

Klein, C. A. Parallel progression of primary tumours and metastases. Nat. Rev. Cancer 9, 302–312 (2009).

CAS  PubMed  Article  Google Scholar 

Dagogo-Jack, I. & Shaw, A. T. Tumour heterogeneity and resistance to cancer therapies. Nat. Rev. Clin. Oncol. 15, 81–94 (2018).

CAS  PubMed  Article  Google Scholar 

Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56–62 (2007).

CAS  PubMed  Article  Google Scholar 

Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134–144 (2010).

CAS  PubMed  Article  Google Scholar 

Dumas, L., Clavreul, S., Michon, F. & Loulier, K. Multicolor strategies for investigating clonal expansion and tissue plasticity. Cell Mol. Life Sci. 79, 141 (2022).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Baron, C. S. & van Oudenaarden, A. Unravelling cellular relationships during development and regeneration using genetic lineage tracing. Nat. Rev. Mol. Cell Biol. 20, 753–765 (2019).

CAS  PubMed  Article  Google Scholar 

McKenna, A. & Gagnon, J. A. Recording development with single cell dynamic lineage tracing. Development https://doi.org/10.1242/dev.169730 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Wagner, D. E. & Klein, A. M. Lineage tracing meets single-cell omics: opportunities and challenges. Nat. Rev. Genet. 21, 410–427 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Weber, K. et al. RGB marking facilitates multicolor clonal cell tracking. Nat. Med. 17, 504–509 (2011).

CAS  PubMed  Article  Google Scholar 

Coffey, S. E., Giedt, R. J. & Weissleder, R. Automated analysis of clonal cancer cells by intravital imaging. Intravital https://doi.org/10.4161/intv.26138 (2013).

Article  PubMed  Google Scholar 

Caiado, F. et al. Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nat. Commun. 10, 4986 (2019).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Berthelet, J. et al. The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile. Sci. Adv. https://doi.org/10.1126/sciadv.abf4408 (2021). This study uses optical barcoding to map clonal fate and interactions of 31 breast cancer clones in vitro and in vivo, in multiple organs and in response to targeted therapy.

Article  PubMed  PubMed Central  Google Scholar 

Nguyen, L. V. et al. DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts. Nat. Commun. 5, 5871 (2014). This study is one of the first to use genetic barcoding to investigate the frequency of tumour-initiating cells in retransplantation experiments using PDXs.

CAS  PubMed  Article  Google Scholar 

Naik, S. H. et al. Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature 496, 229–232 (2013).

CAS  PubMed  Article  Google Scholar 

Jordan, C. T. & Lemischka, I. R. Clonal and systemic analysis of long-term hematopoiesis in the mouse. Genes Dev. 4, 220–232 (1990).

CAS  PubMed  Article  Google Scholar 

Walsh, C. & Cepko, C. L. Widespread dispersion of neuronal clones across functional regions of the cerebral cortex. Science 255, 434–440 (1992).

CAS  PubMed  Article  Google Scholar 

Elder, A. et al. Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia. Leukemia 31, 2577–2586 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Nguyen, L. V. et al. Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells. Cell Stem Cell 14, 253–263 (2014).

CAS  PubMed  Article  Google Scholar 

Seth, S. et al. Pre-existing functional heterogeneity of tumorigenic compartment as the origin of chemoresistance in pancreatic tumors. Cell Rep. 26, 1518–1532 e1519 (2019).

CAS  PubMed  Article  Google Scholar 

Fennell, K. A. et al. Non-genetic determinants of malignant clonal fitness at single-cell resolution. Nature https://doi.org/10.1038/s41586-021-04206-7 (2021). This article describes the generation of a high-diversity transcribed library, which is used to study, over time, the non-genetic processes influencing clonal fitness in leukaemia.

Article  PubMed  Google Scholar 

Oren, Y. et al. Cycling cancer persister cells arise from lineages with distinct programs. Nature https://doi.org/10.1038/s41586-021-03796-6 (2021). This study describes the development of the Watermelon library, which enables the characterization of drug-resistant clones at single-cell resolution.

Article  PubMed  PubMed Central  Google Scholar 

Biddy, B. A. et al. Single-cell mapping of lineage and identity in direct reprogramming. Nature 564, 219–224 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Gutierrez, C. et al. Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment. Nat. Cancer 2, 758–772 (2021). This study describes the use of a multifunctional library, ClonMapper, to combine lineage tracing, single-cell analysis and lineage recall to study the behaviour of leukaemia clones in response to chemotherapy.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F. D. & Klein, A. M. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science https://doi.org/10.1126/science.aaw3381 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Prasher, D. C., Eckenrode, V. K., Ward, W. W., Prendergast, F. G. & Cormier, M. J. Primary structure of the Aequorea victoria green-fluorescent protein. Gene 111, 229–233 (1992).

CAS  PubMed  Article  Google Scholar 

Chudakov, D. M., Matz, M. V., Lukyanov, S. & Lukyanov, K. A. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol. Rev. 90, 1103–1163 (2010).

CAS 

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