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Protein proximity networks and functional evaluation of the Casein Kinase 1 γ family reveals unique roles for CK1 γ 3 in WNT signaling
Open accessPreprint — published as 10.1016/j.jbc.2022.101986
Abstract
The WNT/ β -catenin signaling pathway is evolutionarily conserved and controls normal embryonic development, adult tissue homeostasis and regeneration. Aberrant activation or suppression of WNT signaling contributes to cancer initiation and progression, developmental disorders, neurodegeneration, and bone disease. Despite great need and more than 40 years of research, targeted therapies for the WNT pathway have yet to be fully realized. Kinases are exceptionally druggable and occupy key nodes within the WNT signaling network, but several pathway-relevant kinases remain understudied and ‘dark’. Here we studied the function of the CSNK1 γ subfamily of human kinases. miniTurbo-based proximity biotinylation and mass spectrometry analysis of CSNK1 γ 1, CSNK1 γ 2, and CSNK1 γ 3 revealed numerous established components of the β -catenin- dependent and independent WNT signaling pathway, as well as novel interactors. In gain-of- function experiments leveraging a panel of transcriptional reporters, CSNK1 γ 3 but not CSNK1 γ 1 or CSNK1 γ 2 activated β -catenin-dependent WNT signaling and the Notch pathway. Within the family, CSNK1 γ 3 expression uniquely induced LRP6 phosphorylation. Conversely, siRNA- mediated silencing of CSNK1 γ 3 alone had no impact on WNT signaling, though co-silencing of all three family members decreased WNT pathway activity. We characterized two moderately selective and potent small molecule inhibitors of the CSNK1 γ family. These inhibitors and a CSNK1 γ 3 kinase dead mutant suppressed but did not eliminate WNT-driven LRP6 phosphorylation and β -catenin stabilization. Our data suggest that while CSNK1 γ 3 expression uniquely drives pathway activity, potential functional redundancy within the family necessitates loss of all three family members to suppress the WNT signaling pathway.
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![Figure 2 Low-throughput reporter screen identifies CK1γ3 as an activator of WNT signaling.A, HEK293T cells were transiently transfected for 30 h with 100 ng of indicated positive control (β-catenin, NRF2, and NICD) construct or pGUS negative control or the indicated CK1γ construct. About 40 ng TK-Renilla and 40 ng of the indicated Response Element–Luciferase construct was included. Where indicated, cells were treated with (TGFβ 10 ng/ml, TNFα 10 ng/ml, and retinoic acid [RA] 10 ng/ml) for 6 h (TGFβ and TNFα) or 16 h (RA). Inset W. blot demonstrates protein overexpression for the BAR luciferase assay. Each condition was normalized to pGUS control. Error bars represent standard deviation, and statistics are compared to pGUS control. B, BAR luciferase assay from HEK293T B/R (stable BAR-firefly luciferase, TK-Renilla–expressing cell line) cells transfected for 24 h with indicated DNA mass. Statistics are compared to pGUS control. Inset blot is confirmation of overexpression for luciferase assay in B. Dashed line represents cropped blot for removal of redundant untreated sample. C, HEK293T B/R cells were transfected with the indicated construct for 14 h and then treated with Lcell or WNT3A CM for 16 h. All statistics are compared to FLAG-Control Lcell sample. D, HEK293T B/R cells were transfected with the indicated construct for 24 h before luciferase quantitation. Statistics are compared to pGUS control. E, HEK293T B/R cells were transfected with the indicated construct for 14 h and then treated with 10 μM C59 for 18 h. F, WT, LRP5/6 DKO, DVL TKO HEK293T cells transfected with 20 ng BAR-luciferase, 10 ng TK-Renilla, and 70 ng of indicated constructs for 14 h, and then treated with either Lcell CM or WNT3A CM for 18 h. Statistical significance presented is compared with Lcell-treated FLAG-Control cells for each cell type. For all panels: ∗∗∗p < 0.0005, ∗∗p < 0.005, and ∗p < 0.05. All data are plotted as box-and-whisker plots, with the boxes representing the median and the interquartile range. All biological replicates are averaged across three technical replicates. Statistical significance was evaluated by Student’s t test. CK1γ3, casein kinase 1γ3; CM, conditioned media; DKO, double KO; DVL, disheveled; HEK293T, human embryonic kidney 293T cell line; LRP, low-density lipoprotein receptor–related protein; NICD, Notch intracellular domain; NRF2, nuclear factor erythroid 2–related factor 2; TGFβ, transforming growth factor beta; TKO, triple KO; TNFα, tumor necrosis factor alpha; W. blot, Western blot.](/paper-figures/46a0bc87e69146a5ad56c15a240666b8/protein-proximity-networks-and-functional-evaluation-of-the-casein-kinase-1-i-i-figure-2.jpg)






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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Agajanian, M. J., Potjewyd, F. M., Bowman, B. M., Solomon, S., LaPak, K. M., Bhatt, D. P., Smith, J. L., Goldfarb, D., Axtman, A. D., & Major, M. B.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Washington University in St. Louis (US)
- Corresponding author
- Major, Michael B.
- ORCID
- Venue
- Journal of Biological Chemistry
- Publisher
- openRxiv
- Published
- 2021-11-30
- Volume
- 298
- Issue
- 6
- Pages
- 101986-101986
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC9157009
- OpenAlex
- W4224939721
- Cited by
- 12
- References
- 1
- Citations by year
- 2026: 6 · 2025: 1 · 2024: 1 · 2023: 4
- FWCI
- 0.49
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, cc-by)
- Funders
- Howard Hughes Medical Institute
- Boehringer Ingelheim
- Pfizer
- North Carolina Biotechnology Center (2018-IDG-1030)
- Meso Scale Diagnostics
- Takeda Pharmaceuticals U.S.A.
- Genome Canada (115766)
- Merck KGaA
- Wellcome Trust (106169/ZZ14/Z)
- European Federation of Pharmaceutical Industries and Associations (115766)
- Ontario Ministry of Economic Development and Innovation
- Canada Foundation for Innovation
- Fundação de Amparo à Pesquisa do Estado de São Paulo (106169/ZZ14/Z)
- Ministero dello Sviluppo Economico
- Innovative Medicines Initiative
- National Institutes of Health (5f99ca245724-02, 1097737, F99/K00)
- Genentech
- Novartis Pharma
- National Institute on Aging (U54AG065187)
- National Cancer Institute (F99 CA245724, K00CA245724, F99/K00, T32CA009547)
- National Institute of Diabetes and Digestive and Kidney Diseases (U24DK116204)
- Janssen Pharmaceuticals
- Eshelman Institute for Innovation, University of North Carolina at Chapel Hill
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Wnt/β-catenin signaling in development and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Signaling Pathways in Disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Keywords
- Wnt/β-catenin signaling, protein-protein interaction network, LRP6 phosphorylation, β-catenin stabilization, kinase inhibitors, functional redundancy, kinase families, cancer signaling
- MeSH terms
- Humans, Phosphorylation, Casein Kinase I, Wnt Proteins, beta Catenin, Wnt Signaling Pathway, Low Density Lipoprotein Receptor-Related Protein-6
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- Agajanian, M. J., Potjewyd, F. M., Bowman, B. M., Solomon, S., LaPak, K. M., Bhatt, D. P., Smith, J. L., Goldfarb, D., Axtman, A. D., & Major, M. B. (2021). Protein proximity networks and functional evaluation of the Casein Kinase 1 γ family reveals unique roles for CK1 γ 3 in WNT signaling. Journal of Biological Chemistry. https://doi.org/10.1101/2021.11.30.470617