Improved tools for the Brainbow toolbox

Cai, Dawen; Cohen, Kimberly B; Luo, Tuanlian; Lichtman, Jeff W.; Sanes, Joshua R.

doi:10.1038/nmeth.2450

Cited by 380 publications

(400 citation statements)

References 52 publications

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“…1A) are each capable of undergoing a recombination event with a site of the same kind but not with the other type of site (Schlake and Bode, 1994;Senecoff and Cox, 1986). This type of mutually exclusive recombination between different recombinase target variants has been exploited in several genetic systems, such as iMos (Claveria et al, 2013), Brainbow (Cai et al, 2013;Hadjieconomou et al, 2011;Hampel et al, 2011;Livet et al, 2007), recombinase-mediated cassette exchange (RMCE) (Turan et al, 2013) and the flip-excision (FlEx) transgene inversion strategy (Schnutgen et al, 2005).…”

Section: Design and Features Of The Coinflp Systemmentioning

confidence: 99%

CoinFLP: a system for efficient mosaic screening and for visualizing clonal boundaries in Drosophila

2015

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Section: Design and Features Of The Coinflp Systemmentioning

confidence: 99%

CoinFLP: a system for efficient mosaic screening and for visualizing clonal boundaries in Drosophila

2015

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“…Brainbow mice represent a major technical advance with a variety of applications. 7,15,16 However, as with RGB marking, numerous and complex color combinations might impede recovery and subsequent analysis of individual clones.…”

Section: Introductionmentioning

confidence: 99%

Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity

et al. 2017

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Intratumoral heterogeneity has been identified as one of the strongest drivers of treatment resistance and tumor recurrence. Therefore, investigating the complex clonal architecture of tumors over time has become a major challenge in cancer research. We developed a new fluorescent "optical barcoding" technique that allows fast tracking, identification, and quantification of live cell clones in vitro and in vivo using flow cytometry (FC). We optically barcoded two cell lines derived from malignant glioma, an exemplary heterogeneous brain tumor. In agreement with mathematical combinatorics, we demonstrate that up to 41 clones can unambiguously be marked using six fluorescent proteins and a maximum of three colors per clone. We show that optical barcoding facilitates sensitive, precise, rapid, and inexpensive analysis of clonal composition kinetics of heterogeneous cell populations by FC. We further assessed the quantitative contribution of multiple clones to glioblastoma growth in vivo and we highlight the potential to recover individual viable cell clones by fluorescence-activated cell sorting. In summary, we demonstrate that optical barcoding is a powerful technique for clonal cell tracking in vitro and in vivo, rendering this approach a potent tool for studying the heterogeneity of complex tissues, in particular, cancer.

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“…The recently established Br3 offers an improved method for multicolor imaging of neurons. One of the main features of this transcript is that it contains a new set of photostable farnesylated fluorescent proteins, which enable an even staining of the finest neuronal processes 20 .…”

Section: Introductionmentioning

confidence: 99%

A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice

Amitai-Lange

Berkowitz

Altshuler

et al. 2015

JoVE

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Lineage tracing experiments define the origin, fate and behavior of cells in a specific tissue or organism. This technique has been successfully applied for many decades, revealing seminal findings in developmental biology. More recently, it was adopted by stem cell biologists to identify and track different stem cell populations with minimal experimental intervention. The recent developments in mouse genetics, the availability of a large number of mouse strains, and the advancements in fluorescent microscopy allow the straightforward design of powerful lineage tracing systems for various tissues with basic expertise, using commercially available tools. We have recently taken advantage of this powerful methodology to explore the origin and fate of stem cells at the ocular surface using R26R-Confetti mouse. This model offers a multi-color genetic system, for the expression of 4 fluorescent genes in a random manner. Here we describe the principles of this methodology and provide an adaptable protocol for designing lineage tracing experiments; specifically for the corneal epithelium as well as for other tissues.

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Improved tools for the Brainbow toolbox

Cited by 380 publications

References 52 publications

CoinFLP: a system for efficient mosaic screening and for visualizing clonal boundaries in Drosophila

CoinFLP: a system for efficient mosaic screening and for visualizing clonal boundaries in Drosophila

Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity

A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice

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