scholarly journals Decision letter: Comparative genetic screens in human cells reveal new regulatory mechanisms in WNT signaling

2016 ◽  
Author(s):  
Andres M. Lebensohn ◽  
Ramin Dubey ◽  
Leif R. Neitzel ◽  
Ofelia Tacchelly ◽  
Caleb D. Marceau ◽  
...  

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Andres M Lebensohn ◽  
Ramin Dubey ◽  
Leif R Neitzel ◽  
Ofelia Tacchelly-Benites ◽  
Eungi Yang ◽  
...  

The comprehensive understanding of cellular signaling pathways remains a challenge due to multiple layers of regulation that may become evident only when the pathway is probed at different levels or critical nodes are eliminated. To discover regulatory mechanisms in canonical WNT signaling, we conducted a systematic forward genetic analysis through reporter-based screens in haploid human cells. Comparison of screens for negative, attenuating and positive regulators of WNT signaling, mediators of R-spondin-dependent signaling and suppressors of constitutive signaling induced by loss of the tumor suppressor adenomatous polyposis coli or casein kinase 1α uncovered new regulatory features at most levels of the pathway. These include a requirement for the transcription factor AP-4, a role for the DAX domain of AXIN2 in controlling β-catenin transcriptional activity, a contribution of glycophosphatidylinositol anchor biosynthesis and glypicans to R-spondin-potentiated WNT signaling, and two different mechanisms that regulate signaling when distinct components of the β-catenin destruction complex are lost. The conceptual and methodological framework we describe should enable the comprehensive understanding of other signaling systems.


2016 ◽  
Author(s):  
Andres M Lebensohn ◽  
Ramin Dubey ◽  
Leif R Neitzel ◽  
Ofelia Tacchelly-Benites ◽  
Eungi Yang ◽  
...  

2019 ◽  
Author(s):  
Kendall R Sanson ◽  
Peter C DeWeirdt ◽  
Annabel K Sangree ◽  
Ruth E Hanna ◽  
Mudra Hegde ◽  
...  

ABSTRACTCas12a enzymes have attractive properties for scalable delivery of multiplexed perturbations, yet widespread usage has lagged behind Cas9-based strategies. Here we describe the optimization of Cas12a from Acidaminococcus (AsCas12a) for use in pooled genetic screens in human cells. By assaying the activity of thousands of guides, we confirm on-target design rules and extend them to an enhanced activity variant, enAsCas12a. We also develop the first comprehensive set of off-target rules for Cas12a, and demonstrate that we can predict and exclude promiscuous guides. Finally, to enable efficient higher-order multiplexing via lentiviral delivery, we screen thousands of direct repeat variants and identify 38 that outperform the wildtype sequence. We validate this optimized AsCas12a toolkit by targeting 12 synthetic lethal gene pairs with up to 400 guide pairs each, and demonstrate effective triple knockout via flow cytometry. These results establish AsCas12a as a robust system for combinatorial applications of CRISPR technology.


PLoS ONE ◽  
2012 ◽  
Vol 7 (6) ◽  
pp. e39651 ◽  
Author(s):  
Lidia M. Duncan ◽  
Richard T. Timms ◽  
Eszter Zavodszky ◽  
Florencia Cano ◽  
Gordon Dougan ◽  
...  

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 439 ◽  
Author(s):  
Dusan Hrckulak ◽  
Lucie Janeckova ◽  
Lucie Lanikova ◽  
Vitezslav Kriz ◽  
Monika Horazna ◽  
...  

T-cell factor 4 (TCF4), together with β-catenin coactivator, functions as the major transcriptional mediator of the canonical wingless/integrated (Wnt) signaling pathway in the intestinal epithelium. The pathway activity is essential for both intestinal homeostasis and tumorigenesis. To date, several mouse models and cellular systems have been used to analyze TCF4 function. However, some findings were conflicting, especially those that were related to the defects observed in the mouse gastrointestinal tract after Tcf4 gene deletion, or to a potential tumor suppressive role of the gene in intestinal cancer cells or tumors. Here, we present the results obtained using a newly generated conditional Tcf4 allele that allows inactivation of all potential Tcf4 isoforms in the mouse tissue or small intestinal and colon organoids. We also employed the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system to disrupt the TCF4 gene in human cells. We showed that in adult mice, epithelial expression of Tcf4 is indispensable for cell proliferation and tumor initiation. However, in human cells, the TCF4 role is redundant with the related T-cell factor 1 (TCF1) and lymphoid enhancer-binding factor 1 (LEF1) transcription factors.


PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e67694 ◽  
Author(s):  
Ângela M. Sousa Costa ◽  
Isabel Pereira-Castro ◽  
Elisabete Ricardo ◽  
Forrest Spencer ◽  
Shannon Fisher ◽  
...  

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