Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | Feldman, D, Tsai, FN, Garrity, AJ, O'Rourke, R, Brenan, L, Ho, P, Gonzalez, E, Konermann, S, Johannessen, CM, Beroukhim, R, Bandopadhayay, P, Blainey, PC |
Journal | BMC Biol |
Volume | 18 |
Issue | 1 |
Pages | 177 |
Date Published | 2020 11 24 |
ISSN | 1741-7007 |
Abstract | 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. |
DOI | 10.1186/s12915-020-00911-3 |
Pubmed | |
Alternate Journal | BMC Biol |
PubMed ID | 33234154 |
PubMed Central ID | PMC7687773 |
Grant List | CA201592-02 / 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 |
BMC Biol DOI:10.1186/s12915-020-00911-3
CloneSifter: enrichment of rare clones from heterogeneous cell populations.
Recent Broad Publications
News at the broad
News / 01.4.21
News / 02.25.21