You are here

BMC Biol DOI:10.1186/s12915-020-00911-3

CloneSifter: enrichment of rare clones from heterogeneous cell populations.

Publication TypeJournal Article
Year of Publication2020
AuthorsFeldman, D, Tsai, FN, Garrity, AJ, O'Rourke, R, Brenan, L, Ho, P, Gonzalez, E, Konermann, S, Johannessen, CM, Beroukhim, R, Bandopadhayay, P, Blainey, PC
JournalBMC Biol
Date Published2020 11 24

BACKGROUND: Many biological processes, such as cancer metastasis, organismal development, and acquisition of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. While large-scale barcoding with NGS readout has facilitated cellular fitness assessment at the population level, this approach does not support characterization of clones prior to selection. Single-cell genomics methods provide high biological resolution, but are challenging to scale across large populations to probe rare clones and are destructive, limiting further functional analysis of important clones.

RESULTS: Here, we develop CloneSifter, a methodology for tracking and enriching rare clones throughout their response to selection. CloneSifter utilizes a CRISPR sgRNA-barcode library that facilitates the isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrate that CloneSifter can measure clonal fitness of cancer cell models in vitro and retrieve targeted clones at abundance as low as 1 in 1883 in a heterogeneous cell population.

CONCLUSIONS: CloneSifter provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.


Alternate JournalBMC Biol
PubMed ID33234154
PubMed Central IDPMC7687773
Grant ListCA201592-02 / NH / NIH HHS / United States
1U54CA224068-01 / NH / NIH HHS / United States
CA188228 / NH / NIH HHS / United States
CA219943 / NH / NIH HHS / United States
HG009283 / NH / NIH HHS / United States