Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding.
CRISPR
Clonal heterogeneity
Genome editing
Screening
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
06 Feb 2019
06 Feb 2019
Historique:
received:
09
04
2018
accepted:
24
01
2019
entrez:
8
2
2019
pubmed:
8
2
2019
medline:
21
5
2019
Statut:
epublish
Résumé
While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells. Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. The first level of barcoding allows monitoring growth kinetics and treatment responses of multiplexed clonal cell lines under identical conditions while the second level enables in-sample replication and tracing of sub-clonal lineages of cells expressing the same sgRNA. Using our approach, we illustrate how heterogeneity in growth kinetics and treatment response of clonal cell lines impairs the results of pooled genetic screens.
Sections du résumé
BACKGROUND
BACKGROUND
While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells.
RESULTS
RESULTS
Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. The first level of barcoding allows monitoring growth kinetics and treatment responses of multiplexed clonal cell lines under identical conditions while the second level enables in-sample replication and tracing of sub-clonal lineages of cells expressing the same sgRNA.
CONCLUSION
CONCLUSIONS
Using our approach, we illustrate how heterogeneity in growth kinetics and treatment response of clonal cell lines impairs the results of pooled genetic screens.
Identifiants
pubmed: 30727954
doi: 10.1186/s12864-019-5480-0
pii: 10.1186/s12864-019-5480-0
pmc: PMC6364396
doi:
Substances chimiques
RNA, Guide
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
107Subventions
Organisme : NHLBI NIH HHS
ID : K25 HL121295
Pays : United States
Organisme : NIH HHS
ID : 1U01MH105028
Pays : United States
Organisme : NIH HHS
ID : U01CA168370
Pays : United States
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