Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry
- Peking University, China
- Southern University of Science and Technology, China
- Beijing Normal University, China
- Zhejiang University, China
Abstract
The dual-specificity tyrosine phosphorylation-regulated kinase DYRK2 has emerged as a critical regulator of cellular processes. We took a chemical biology approach to gain further insights into its function. We developed C17, a potent small-molecule DYRK2 inhibitor, through multiple rounds of structure-based optimization guided by several cocrystallized structures. C17 displayed an effect on DYRK2 at a single-digit nanomolar IC50 and showed outstanding selectivity for the human kinome containing 467 other human kinases. Using C17 as a chemical probe, we further performed quantitative phosphoproteomic assays and identified several novel DYRK2 targets, including eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) and stromal interaction molecule 1 (STIM1). DYRK2 phosphorylated 4E-BP1 at multiple sites, and the combined treatment of C17 with AKT and MEK inhibitors showed synergistic 4E-BP1 phosphorylation suppression. The phosphorylation of STIM1 by DYRK2 substantially increased the interaction of STIM1 with the ORAI1 channel, and C17 impeded the store-operated calcium entry process. These studies collectively further expand our understanding of DYRK2 and provide a valuable tool to pinpoint its biological function.
Data availability
The structural coordinates of DYRK2 in complex with compounds 5, 6, 7, 8, 10, 13, 14, 17, 18, 19, and 20 have been deposited in the Protein Data Bank with accession codes 7DH3, 7DG4, 7DH9, 7DHV, 7DHC, 7DHK, 7DHO, 7DJO, 7DL6, 7DHH, and 7DHN, respectively.All the raw mass spectrometry data as well as the identified and significantly regulated phosphosites tables have been deposited in the public proteomics repository MassIVE and are accessible at ftp://massive.ucsd.edu/MSV000087106/.
Article and author information
Author details
Funding
National Key Research and Development Plan (2017YFA0505200)
- Tiantian Wei
- Jue Wang
- Ruqi Liang
- Wendong Chen
- Yilan Chen
- Mingzhe Ma
- An He
- Yifei Du
- Wenjing Zhou
- Zhiying Zhang
- Xin Zeng
- Chu Wang
- Jin Lu
- Xing Guo
- Xiao-Wei Chen
- Youjun Wang
- Junyu Xiao
- Xiaoguang Lei
National Natural Science Foundation of China (91853202,21625201,21961142010,21661140001,and 21521003)
- Tiantian Wei
- Jue Wang
- Ruqi Liang
- Wendong Chen
- Yilan Chen
- Mingzhe Ma
- An He
- Yifei Du
- Wenjing Zhou
- Zhiying Zhang
- Xin Zeng
- Chu Wang
- Jin Lu
- Xing Guo
- Xiao-Wei Chen
- Youjun Wang
- Junyu Xiao
- Xiaoguang Lei
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Hening Lin, Cornell University, United States
Version history
- Preprint posted: February 12, 2021 (view preprint)
- Received: February 8, 2022
- Accepted: April 12, 2022
- Accepted Manuscript published: April 19, 2022 (version 1)
- Accepted Manuscript updated: April 21, 2022 (version 2)
- Version of Record published: May 17, 2022 (version 3)
Copyright
© 2022, Wei et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry
eLife 11:e77696.
https://doi.org/10.7554/eLife.77696
Further reading
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- Biochemistry and Chemical Biology
- Cell Biology
The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis, and DNA damage repair, and its de-regulation is linked to neuromuscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97–cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. The two human family members VCP nuclear cofactor family member 1 and 2 (VCF1/2) bind p97 directly via a novel, alpha-helical motif and associate with p97-UFD1-NPL4 and p97-UBXN2B complexes in cells. VCF1/2 localize to the nucleus and promote the nuclear import of p97. Loss of VCF1/2 results in reduced nuclear p97 levels, slow growth, and hypersensitivity to chemical inhibition of p97 in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.
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- Biochemistry and Chemical Biology
- Epidemiology and Global Health
Background: High levels of circulating adiponectin are associated with increased insulin sensitivity, low prevalence of diabetes, and low body mass index (BMI); however, high levels of circulating adiponectin are also associated with increased mortality in the 60-70 age group. In this study, we aimed to clarify factors associated with circulating high-molecular-weight (cHMW) adiponectin levels and their association with mortality in the very old (85-89 years old) and centenarians.
Methods: The study included 812 (women: 84.4%) for centenarians and 1,498 (women: 51.7%) for the very old. The genomic DNA sequence data were obtained by whole genome sequencing or DNA microarray-imputation methods. LASSO and multivariate regression analyses were used to evaluate cHMW adiponectin characteristics and associated factors. All-cause mortality was analyzed in three quantile groups of cHMW adiponectin levels using Cox regression.
Results: The cHMW adiponectin levels were increased significantly beyond 100 years of age, were negatively associated with diabetes prevalence, and were associated with SNVs in CDH13 (p = 2.21 × 10-22) and ADIPOQ (p = 5.72 × 10-7). Multivariate regression analysis revealed that genetic variants, BMI, and high-density lipoprotein cholesterol (HDLC) were the main factors associated with cHMW adiponectin levels in the very old, whereas the BMI showed no association in centenarians. The hazard ratios for all-cause mortality in the intermediate and high cHMW adiponectin groups in very old men were significantly higher rather than those for all-cause mortality in the low level cHMW adiponectin group, even after adjustment with BMI. In contrast, the hazard ratios for all-cause mortality were significantly higher for high cHMW adiponectin groups in very old women, but were not significant after adjustment with BMI.
Conclusions: cHMW adiponectin levels increased with age until centenarians, and the contribution of known major factors associated with cHMW adiponectin levels, including BMI and HDLC, varies with age, suggesting that its physiological significance also varies with age in the oldest old.
Funding: This study was supported by grants from the Ministry of Health, Welfare, and Labour for the Scientific Research Projects for Longevity; a Grant-in-Aid for Scientific Research (No 21590775, 24590898, 15KT0009, 18H03055, 20K20409, 20K07792, 23H03337) from the Japan Society for the Promotion of Science; Keio University Global Research Institute (KGRI), Kanagawa Institute of Industrial Science and Technology (KISTEC), Japan Science and Technology Agency (JST) Research Complex Program 'Tonomachi Research Complex' Wellbeing Research Campus: Creating new values through technological and social innovation (JP15667051), the Program for an Integrated Database of Clinical and Genomic Information from the Japan Agency for Medical Research and Development (No. 16kk0205009h001, 17jm0210051h0001, 19dk0207045h0001); the medical-welfare-food-agriculture collaborative consortium project from the Japan Ministry of Agriculture, Forestry, and Fisheries; and the Biobank Japan Program from the Ministry of Education, Culture, Sports, and Technology.
