1
|
Jin Y, Xue J. Lipid kinases PIP5Ks and PIP4Ks: potential drug targets for breast cancer. Front Oncol 2023; 13:1323897. [PMID: 38156113 PMCID: PMC10753794 DOI: 10.3389/fonc.2023.1323897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023] Open
Abstract
Phosphoinositides, a small group of lipids found in all cellular membranes, have recently garnered heightened attention due to their crucial roles in diverse biological processes and different diseases. Among these, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), the most abundant bis-phosphorylated phosphoinositide within the signaling system, stands notably connected to breast cancer. Not only does it serve as a key activator of the frequently altered phosphatidylinositol 3-kinase (PI3K) pathway in breast cancer, but also its conversion to phosphatidylinositol-3,4,5-triphosphate (PI(3,4,5)P3) is an important direction for breast cancer research. The generation and degradation of phosphoinositides intricately involve phosphoinositide kinases. PI(4,5)P2 generation emanates from the phosphorylation of PI4P or PI5P by two lipid kinase families: Type I phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and Type II phosphatidylinositol-5-phosphate 4-kinases (PIP4Ks). In this comprehensive review, we focus on these two lipid kinases and delineate their compositions and respective cellular localization. Moreover, we shed light on the expression patterns and functions of distinct isoforms of these kinases in breast cancer. For a deeper understanding of their functional dynamics, we expound upon various mechanisms governing the regulation of PIP5Ks and PIP4Ks activities. A summary of effective and specific small molecule inhibitors designed for PIP5Ks or PIP4Ks are also provided. These growing evidences support PIP5Ks and PIP4Ks as promising drug targets for breast cancer.
Collapse
Affiliation(s)
- Yue Jin
- Department of Molecular Diagnosis, Northern Jiangsu People’s Hospital, Yangzhou University Clinical Medical College, Yangzhou, China
| | - Jian Xue
- Department of Emergency Medicine, Yizheng People’s Hospital, Yangzhou University Clinical Medical College, Yangzhou, China
| |
Collapse
|
2
|
Haqani MI, Nakano M, Nagano AJ, Nakamura Y, Tsudzuki M. Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Sci Rep 2023; 13:21307. [PMID: 38042890 PMCID: PMC10693557 DOI: 10.1038/s41598-023-48293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 10/10/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023] Open
Abstract
This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1-13, 15, 17-20, 24, 26-28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.
Collapse
Affiliation(s)
- Mohammad Ibrahim Haqani
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
| | - Michiharu Nakano
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi, 783-8502, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0017, Japan
| | - Yoshiaki Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan
| | - Masaoki Tsudzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
| |
Collapse
|
3
|
Ghosh A, Venugopal A, Shinde D, Sharma S, Krishnan M, Mathre S, Krishnan H, Saha S, Raghu P. PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase. Life Sci Alliance 2023; 6:e202301920. [PMID: 37316298 PMCID: PMC10267561 DOI: 10.26508/lsa.202301920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023] Open
Abstract
Phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) are low-abundance phosphoinositides crucial for key cellular events such as endosomal trafficking and autophagy. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is an enzyme that regulates PI5P in vivo but can act on both PI5P and PI3P in vitro. In this study, we report a role for PIP4K in regulating PI3P levels in Drosophila Loss-of-function mutants of the only Drosophila PIP4K gene show reduced cell size in salivary glands. PI3P levels are elevated in dPIP4K 29 and reverting PI3P levels back towards WT, without changes in PI5P levels, can rescue the reduced cell size. dPIP4K 29 mutants also show up-regulation in autophagy and the reduced cell size can be reverted by depleting Atg8a that is required for autophagy. Lastly, increasing PI3P levels in WT can phenocopy the reduction in cell size and associated autophagy up-regulation seen in dPIP4K 29 Thus, our study reports a role for a PIP4K-regulated PI3P pool in the control of autophagy and cell size.
Collapse
Affiliation(s)
- Avishek Ghosh
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | | | - Dhananjay Shinde
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Sanjeev Sharma
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Meera Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Swarna Mathre
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Harini Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Sankhanil Saha
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| |
Collapse
|
4
|
Takeuchi K, Senda M, Ikeda Y, Okuwaki K, Fukuzawa K, Nakagawa S, Sasaki M, Sasaki AT, Senda T. Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. FEBS J 2023; 290:4419-4428. [PMID: 36856076 PMCID: PMC10471773 DOI: 10.1111/febs.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/02/2023]
Abstract
Over 4 billion years of evolution, multiple mutations, including nucleotide substitutions, gene and genome duplications and recombination, have established de novo genes that translate into proteins with novel properties essential for high-order cellular functions. However, molecular processes through which a protein evolutionarily acquires a novel function are mostly speculative. Recently, we have provided evidence for a potential evolutionary mechanism underlying how, in mammalian cells, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) evolved into a GTP sensor from ATP-utilizing kinase. Mechanistically, PI5P4Kβ has acquired the guanine efficient association (GEA) motif by mutating its nucleotide base recognition sequence, enabling the evolutionary transition from an ATP-dependent kinase to a distinct GTP/ATP dual kinase with its KM for GTP falling into physiological GTP concentrations-the genesis of GTP sensing activity. Importantly, the GTP sensing activity of PI5P4Kβ is critical for the manifestation of cellular metabolism and tumourigenic activity in the multicellular organism. The combination of structural, biochemical and biophysical analyses used in our study provides a novel framework for analysing how a protein can evolutionarily acquire a novel activity, which potentially introduces a critical function to the cell.
Collapse
Affiliation(s)
- Koh Takeuchi
- Graduate School of Pharmacological Sciences, The University of Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan
| | - Koji Okuwaki
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Kaori Fukuzawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, OH, USA
- Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH, USA
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan
- Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Ibaraki, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, Ibaraki, Japan
| |
Collapse
|
5
|
Wei L, Xu M, Liu Z, Jiang C, Lin X, Hu Y, Wen X, Zou R, Peng C, Lin H, Wang G, Yang L, Fang L, Yang M, Zhang P. Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study. J Chem Inf Model 2023; 63:5341-5355. [PMID: 37549337 DOI: 10.1021/acs.jcim.3c00543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Computer-aided drug design (CADD), especially artificial intelligence-driven drug design (AIDD), is increasingly used in drug discovery. In this paper, a novel and efficient workflow for hit identification was developed within the ID4Inno drug discovery platform, featuring innovative artificial intelligence, high-accuracy computational chemistry, and high-performance cloud computing. The workflow was validated by discovering a few potent hit compounds (best IC50 is ∼0.80 μM) against PI5P4K-β, a novel anti-cancer target. Furthermore, by applying the tools implemented in ID4Inno, we managed to optimize these hit compounds and finally obtained five hit series with different scaffolds, all of which showed high activity against PI5P4K-β. These results demonstrate the effectiveness of ID4inno in driving hit identification based on artificial intelligence, computational chemistry, and cloud computing.
Collapse
Affiliation(s)
- Lin Wei
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Min Xu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Zhiqiang Liu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Chongguo Jiang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Xiaohua Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Yaogang Hu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Xiaoming Wen
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Rongfeng Zou
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Hongrui Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Guo Wang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Lijun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Lei Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| | - Peiyu Zhang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Shenzhen 518000, China
| |
Collapse
|
6
|
Burke JE, Triscott J, Emerling BM, Hammond GRV. Beyond PI3Ks: targeting phosphoinositide kinases in disease. Nat Rev Drug Discov 2023; 22:357-386. [PMID: 36376561 PMCID: PMC9663198 DOI: 10.1038/s41573-022-00582-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
Lipid phosphoinositides are master regulators of almost all aspects of a cell's life and death and are generated by the tightly regulated activity of phosphoinositide kinases. Although extensive efforts have focused on drugging class I phosphoinositide 3-kinases (PI3Ks), recent years have revealed opportunities for targeting almost all phosphoinositide kinases in human diseases, including cancer, immunodeficiencies, viral infection and neurodegenerative disease. This has led to widespread efforts in the clinical development of potent and selective inhibitors of phosphoinositide kinases. This Review summarizes our current understanding of the molecular basis for the involvement of phosphoinositide kinases in disease and assesses the preclinical and clinical development of phosphoinositide kinase inhibitors.
Collapse
Affiliation(s)
- John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Joanna Triscott
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| |
Collapse
|
7
|
Teng M, Jiang J, Wang ES, Geng Q, Toenjes ST, Donovan KA, Mageed N, Yue H, Nowak RP, Wang J, Manz TD, Fischer ES, Cantley LC, Gray NS. Targeting the Dark Lipid Kinase PIP4K2C with a Potent and Selective Binder and Degrader. Angew Chem Int Ed Engl 2023; 62:e202302364. [PMID: 36898968 PMCID: PMC10150580 DOI: 10.1002/anie.202302364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/12/2023]
Abstract
Phosphatidylinositol 5-phosphate 4-kinase, type II, gamma (PIP4K2C) remains a poorly understood lipid kinase with minimal enzymatic activity but potential scaffolding roles in immune modulation and autophagy-dependent catabolism. Achieving potent and selective agents for PIP4K2C while sparing other lipid and non-lipid kinases has been challenging. Here, we report the discovery of the highly potent PIP4K2C binder TMX-4102, which shows exclusive binding selectivity for PIP4K2C. Furthermore, we elaborated the PIP4K2C binder into TMX-4153, a bivalent degrader capable of rapidly and selectively degrading endogenous PIP4K2C. Collectively, our work demonstrates that PIP4K2C is a tractable and degradable target, and that TMX-4102 and TMX-4153 are useful leads to further interrogate the biological roles and therapeutic potential of PIP4K2C.
Collapse
Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Eric S. Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 (USA)
| | - Qixiang Geng
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305 (USA)
| | - Sean T. Toenjes
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305 (USA)
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Theresa D. Manz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Lewis C. Cantley
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 (USA)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA)
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305 (USA)
| |
Collapse
|
8
|
Wang H, Wang X, Li M, Sun H, Chen Q, Yan D, Dong X, Pan Y, Lu S. Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population. Front Genet 2023; 14:1001352. [PMID: 36814900 PMCID: PMC9939654 DOI: 10.3389/fgene.2023.1001352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07-0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.
Collapse
Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,Faculty of Animal Science, Xichang University, Xichang, Sichuan, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Sun
- Faculty of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuchun Pan
- Faculty of Animal Science, Zhejiang University, Hangzhou, Zhejiang, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
| |
Collapse
|
9
|
Ji W, Wang ES, Manz TD, Jiang J, Donovan KA, Abulaiti X, Fischer ES, Cantley LC, Zhang T, Gray NS. Development of potent and selective degraders of PI5P4Kγ. Eur J Med Chem 2023; 247:115027. [PMID: 36584631 PMCID: PMC10150581 DOI: 10.1016/j.ejmech.2022.115027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks), a family of three members in mammals (α, β and γ), have emerged as potential therapeutic targets due to their role in regulating many important cellular signaling pathways. In comparison to the PI5P4Kα and PI5P4Kβ, which usually have similar expression profiles across cancer cells, PI5P4Kγ exhibits distinct expression patterns, and pathological functions for PI5P4Kγ have been proposed in the context of cancer and neurodegenerative diseases. PI5P4Kγ has very low kinase activity and has been proposed to inhibit the PI4P5Ks through scaffolding function, providing a rationale for developing a selective PI5P4Kγ degrader. Here, we report the development and characterization of JWZ-1-80, a first-in-class PI5P4Kγ degrader. JWZ-1-80 potently degrades PI5P4Kγ via the ubiquitin-proteasome system and exhibits proteome-wide selectivity and is therefore a useful tool compound for further dissecting the biological functions of PI5P4Kγ.
Collapse
Affiliation(s)
- Wenzhi Ji
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Eric S Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Theresa D Manz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xianmixinuer Abulaiti
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY, USA
| | - Tinghu Zhang
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA.
| | - Nathanael S Gray
- Chemical and Systems Biology, Chem-H, Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
10
|
Triscott J, Reist M, Küng L, Moselle FC, Lehner M, Gallon J, Ravi A, Arora GK, de Brot S, Lundquist M, Gallart-Ayala H, Ivanisevic J, Piscuoglio S, Cantley LC, Emerling BM, Rubin MA. PI5P4Kα supports prostate cancer metabolism and exposes a survival vulnerability during androgen receptor inhibition. SCIENCE ADVANCES 2023; 9:eade8641. [PMID: 36724278 PMCID: PMC9891700 DOI: 10.1126/sciadv.ade8641] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/03/2023] [Indexed: 05/07/2023]
Abstract
Phosphatidylinositol (PI)regulating enzymes are frequently altered in cancer and have become a focus for drug development. Here, we explore the phosphatidylinositol-5-phosphate 4-kinases (PI5P4K), a family of lipid kinases that regulate pools of intracellular PI, and demonstrate that the PI5P4Kα isoform influences androgen receptor (AR) signaling, which supports prostate cancer (PCa) cell survival. The regulation of PI becomes increasingly important in the setting of metabolic stress adaptation of PCa during androgen deprivation (AD), as we show that AD influences PI abundance and enhances intracellular pools of PI-4,5-P2. We suggest that this PI5P4Kα-AR relationship is mitigated through mTORC1 dysregulation and show that PI5P4Kα colocalizes to the lysosome, the intracellular site of mTORC1 complex activation. Notably, this relationship becomes prominent in mouse prostate tissue following surgical castration. Finally, multiple PCa cell models demonstrate marked survival vulnerability following stable PI5P4Kα inhibition. These results nominate PI5P4Kα as a target to disrupt PCa metabolic adaptation to castrate resistance.
Collapse
Affiliation(s)
- Joanna Triscott
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Matthias Reist
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Lukas Küng
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Francielle C. Moselle
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Institute of Biosciences, São Paulo State University, São Paulo, Brazil
| | - Marika Lehner
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Archna Ravi
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Gurpreet K. Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Mark Lundquist
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Brooke M. Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Mark A. Rubin
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Bern Center for Precision Medicine, University of Bern and Inselspital, Bern 3008, Switzerland
| |
Collapse
|
11
|
Llorente A, Arora GK, Grenier SF, Emerling BM. PIP kinases: A versatile family that demands further therapeutic attention. Adv Biol Regul 2023; 87:100939. [PMID: 36517396 PMCID: PMC9992244 DOI: 10.1016/j.jbior.2022.100939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are membrane-localized phospholipids that regulate a plethora of essential cellular processes. These lipid signaling molecules are critical for cell homeostasis and therefore their levels are strictly regulated by the coordinated action of several families of lipid kinases and phosphatases. In this review, we provide a focused perspective on the phosphatidylinositol phosphate kinase (PIPK) family and the three subfamilies that compose it: Type I PIPKs or phosphatidylinositol-4-phosphate 5-kinases (PI4P5Ks), Type II PIPKs or phosphatidylinositol-5-phosphate 4-kinases (PI5P4Ks), and Type III PIPKs or phosphatidylinositol-3-phosphate 5-kinases (PIKfyve). Each subfamily is responsible for catalyzing a hydroxyl phosphorylation on specific phosphoinositide species to generate a double phosphorylated lipid, therefore regulating the levels of both substrate and product. Here, we summarize our current knowledge about the functions and regulation of each PIPK subfamily. Further, we highlight the roles of these kinases in various in vivo genetic models and give an overview of their involvement in multiple pathological conditions. The phosphoinositide field has been long focused on targeting PI3K signaling, but growing evidence suggests that it is time to draw attention to the other phosphoinositide kinases. The discovery of the involvement of PIPKs in the pathogenesis of multiple diseases has prompted substantial efforts to turn these enzymes into pharmacological targets. An increasingly refined knowledge of the biology of PIPKs in a variety of in vitro and in vivo models will facilitate the development of effective approaches for therapeutic intervention with the potential to translate into meaningful clinical benefits for patients suffering from cancer, immunological and infectious diseases, and neurodegenerative disorders.
Collapse
Affiliation(s)
- Alicia Llorente
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Shea F Grenier
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA.
| |
Collapse
|
12
|
Wang YH, Sheetz MP. When PIP 2 Meets p53: Nuclear Phosphoinositide Signaling in the DNA Damage Response. Front Cell Dev Biol 2022; 10:903994. [PMID: 35646908 PMCID: PMC9136457 DOI: 10.3389/fcell.2022.903994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The mechanisms that maintain genome stability are critical for preventing tumor progression. In the past decades, many strategies were developed for cancer treatment to disrupt the DNA repair machinery or alter repair pathway selection. Evidence indicates that alterations in nuclear phosphoinositide lipids occur rapidly in response to genotoxic stresses. This implies that nuclear phosphoinositides are an upstream element involved in DNA damage signaling. Phosphoinositides constitute a new signaling interface for DNA repair pathway selection and hence a new opportunity for developing cancer treatment strategies. However, our understanding of the underlying mechanisms by which nuclear phosphoinositides regulate DNA damage repair, and particularly the dynamics of those processes, is rather limited. This is partly because there are a limited number of techniques that can monitor changes in the location and/or abundance of nuclear phosphoinositide lipids in real time and in live cells. This review summarizes our current knowledge regarding the roles of nuclear phosphoinositides in DNA damage response with an emphasis on the dynamics of these processes. Based upon recent findings, there is a novel model for p53's role with nuclear phosphoinositides in DNA damage response that provides new targets for synthetic lethality of tumors.
Collapse
Affiliation(s)
| | - Michael P. Sheetz
- Biochemistry and Molecular Biology Dept., University of Texas Medical Branch, Galveston, TX, United States
| |
Collapse
|
13
|
Boffey H, Rooney TPC, Willems HMG, Edwards S, Green C, Howard T, Ogg D, Romero T, Scott DE, Winpenny D, Duce J, Skidmore J, Clarke JH, Andrews SP. Development of Selective Phosphatidylinositol 5-Phosphate 4-Kinase γ Inhibitors with a Non-ATP-competitive, Allosteric Binding Mode. J Med Chem 2022; 65:3359-3370. [PMID: 35148092 PMCID: PMC9097471 DOI: 10.1021/acs.jmedchem.1c01819] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 12/31/2022]
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are emerging as attractive therapeutic targets in diseases, such as cancer, immunological disorders, and neurodegeneration, owing to their central role in regulating cell signaling pathways that are either dysfunctional or can be modulated to promote cell survival. Different modes of binding may enhance inhibitor selectivity and reduce off-target effects in cells. Here, we describe efforts to improve the physicochemical properties of the selective PI5P4Kγ inhibitor, NIH-12848 (1). These improvements enabled the demonstration that this chemotype engages PI5P4Kγ in intact cells and that compounds from this series do not inhibit PI5P4Kα or PI5P4Kβ. Furthermore, the first X-ray structure of PI5P4Kγ bound to an inhibitor has been determined with this chemotype, confirming an allosteric binding mode. An exemplar from this chemical series adopted two distinct modes of inhibition, including through binding to a putative lipid interaction site which is 18 Å from the ATP pocket.
Collapse
Affiliation(s)
- Helen
K. Boffey
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Timothy P. C. Rooney
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Henriette M. G. Willems
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Simon Edwards
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Christopher Green
- UK
Dementia Research Institute, University
of Cambridge, Island
Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Tina Howard
- Peak
Proteins, Alderley Park, Macclesfield SK10 4TG, Cheshire, U.K.
| | - Derek Ogg
- Peak
Proteins, Alderley Park, Macclesfield SK10 4TG, Cheshire, U.K.
| | - Tamara Romero
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Duncan E. Scott
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - David Winpenny
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - James Duce
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - John Skidmore
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Jonathan H. Clarke
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| | - Stephen P. Andrews
- The
ALBORADA Drug Discovery Institute, University
of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K.
| |
Collapse
|
14
|
Arora GK, Palamiuc L, Emerling BM. Expanding role of PI5P4Ks in cancer: A promising druggable target. FEBS Lett 2022; 596:3-16. [PMID: 34822164 PMCID: PMC9154051 DOI: 10.1002/1873-3468.14237] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Cancer cells are challenged by a myriad of microenvironmental stresses, and it is their ability to efficiently adapt to the constantly changing nutrient, energy, oxidative, and/or immune landscape that allows them to survive and proliferate. Such adaptations, however, result in distinct vulnerabilities that are attractive therapeutic targets. Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are a family of druggable stress-regulated phosphoinositide kinases that become conditionally essential as a metabolic adaptation, paving the way to targeting cancer cell dependencies. Further, PI5P4Ks have a synthetic lethal interaction with the tumor suppressor p53, the loss of which is one of the most prevalent genetic drivers of malignant transformation. PI5P4K's emergence as a crucial axis in the expanding landscape of phosphoinositide signaling in cancer has already stimulated the development of specific inhibitors. Thus, a better understanding of the biology of the PI5P4Ks will allow for targeted and effective therapeutic interventions. Here, we attempt to summarize the mounting roles of the PI5P4Ks in cancer, including evidence that targeting them is a therapeutic vulnerability and promising next-in-line treatment for multiple cancer subtypes.
Collapse
Affiliation(s)
- Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| |
Collapse
|
15
|
Wortmann L, Bräuer N, Holton SJ, Irlbacher H, Weiske J, Lechner C, Meier R, Karén J, Siöberg CB, Pütter V, Christ CD, Ter Laak A, Lienau P, Lesche R, Nicke B, Cheung SH, Bauser M, Haegebarth A, von Nussbaum F, Mumberg D, Lemos C. Discovery and Characterization of the Potent and Highly Selective 1,7-Naphthyridine-Based Inhibitors BAY-091 and BAY-297 of the Kinase PIP4K2A. J Med Chem 2021; 64:15883-15911. [PMID: 34699202 DOI: 10.1021/acs.jmedchem.1c01245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PIP4K2A is an insufficiently studied type II lipid kinase that catalyzes the conversion of phosphatidylinositol-5-phosphate (PI5P) into phosphatidylinositol 4,5-bisphosphate (PI4,5P2). The involvement of PIP4K2A/B in cancer has been suggested, particularly in the context of p53 mutant/null tumors. PIP4K2A/B depletion has been shown to induce tumor growth inhibition, possibly due to hyperactivation of AKT and reactive oxygen species-mediated apoptosis. Herein, we report the identification of the novel potent and highly selective inhibitors BAY-091 and BAY-297 of the kinase PIP4K2A by high-throughput screening and subsequent structure-based optimization. Cellular target engagement of BAY-091 and BAY-297 was demonstrated using cellular thermal shift assay technology. However, inhibition of PIP4K2A with BAY-091 or BAY-297 did not translate into the hypothesized mode of action and antiproliferative activity in p53-deficient tumor cells. Therefore, BAY-091 and BAY-297 serve as valuable chemical probes to study PIP4K2A signaling and its involvement in pathophysiological conditions such as cancer.
Collapse
Affiliation(s)
- Lars Wortmann
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Nico Bräuer
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Simon J Holton
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Horst Irlbacher
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Jörg Weiske
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Christian Lechner
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Robin Meier
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Jakob Karén
- Pelago Bioscience AB, Banvaktsvägen 20, 171 48 Solna, Sweden
| | | | - Vera Pütter
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Clara D Christ
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Antonius Ter Laak
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Philip Lienau
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Ralf Lesche
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Barbara Nicke
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Shing-Hu Cheung
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Marcus Bauser
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Andrea Haegebarth
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Franz von Nussbaum
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Clara Lemos
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| |
Collapse
|
16
|
Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells. Proc Natl Acad Sci U S A 2021; 118:2002486118. [PMID: 34001596 DOI: 10.1073/pnas.2002486118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Most human cancer cells harbor loss-of-function mutations in the p53 tumor suppressor gene. Genetic experiments have shown that phosphatidylinositol 5-phosphate 4-kinase α and β (PI5P4Kα and PI5P4Kβ) are essential for the development of late-onset tumors in mice with germline p53 deletion, but the mechanism underlying this acquired dependence remains unclear. PI5P4K has been previously implicated in metabolic regulation. Here, we show that inhibition of PI5P4Kα/β kinase activity by a potent and selective small-molecule probe disrupts cell energy homeostasis, causing AMPK activation and mTORC1 inhibition in a variety of cell types. Feedback through the S6K/insulin receptor substrate (IRS) loop contributes to insulin hypersensitivity and enhanced PI3K signaling in terminally differentiated myotubes. Most significantly, the energy stress induced by PI5P4Kαβ inhibition is selectively toxic toward p53-null tumor cells. The chemical probe, and the structural basis for its exquisite specificity, provide a promising platform for further development, which may lead to a novel class of diabetes and cancer drugs.
Collapse
|
17
|
Ravi A, Palamiuc L, Loughran RM, Triscott J, Arora GK, Kumar A, Tieu V, Pauli C, Reist M, Lew RJ, Houlihan SL, Fellmann C, Metallo C, Rubin MA, Emerling BM. PI5P4Ks drive metabolic homeostasis through peroxisome-mitochondria interplay. Dev Cell 2021; 56:1661-1676.e10. [PMID: 33984270 DOI: 10.1016/j.devcel.2021.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/29/2021] [Accepted: 04/21/2021] [Indexed: 12/16/2022]
Abstract
PI5P4Ks are a class of phosphoinositide kinases that phosphorylate PI-5-P to PI-4,5-P2. Distinct localization of phosphoinositides is fundamental for a multitude of cellular functions. Here, we identify a role for peroxisomal PI-4,5-P2 generated by the PI5P4Ks in maintaining energy balance. We demonstrate that PI-4,5-P2 regulates peroxisomal fatty acid oxidation by mediating trafficking of lipid droplets to peroxisomes, which is essential for sustaining mitochondrial metabolism. Using fluorescent-tagged lipids and metabolite tracing, we show that loss of the PI5P4Ks significantly impairs lipid uptake and β-oxidation in the mitochondria. Further, loss of PI5P4Ks results in dramatic alterations in mitochondrial structural and functional integrity, which under nutrient deprivation is further exacerbated, causing cell death. Notably, inhibition of the PI5P4Ks in cancer cells and mouse tumor models leads to decreased cell viability and tumor growth, respectively. Together, these studies reveal an unexplored role for PI5P4Ks in preserving metabolic homeostasis, which is necessary for tumorigenesis.
Collapse
Affiliation(s)
- Archna Ravi
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ryan M Loughran
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Joanna Triscott
- Department of Biomedical Research and Bern Center for Precision Medicine, University of Bern and Inselspital Bern, Bern 3008, Switzerland
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Avi Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vivian Tieu
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Chantal Pauli
- Institute of Pathology and Molecular Pathology, University Hospital Zürich and the University of Zurich (UZH), Zurich 8006, Switzerland
| | - Matthias Reist
- Department of Biomedical Research and Bern Center for Precision Medicine, University of Bern and Inselspital Bern, Bern 3008, Switzerland
| | - Rachel J Lew
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Shauna L Houlihan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christof Fellmann
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christian Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark A Rubin
- Department of Biomedical Research and Bern Center for Precision Medicine, University of Bern and Inselspital Bern, Bern 3008, Switzerland
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
18
|
Raghu P. Emerging cell biological functions of phosphatidylinositol 5 phosphate 4 kinase. Curr Opin Cell Biol 2021; 71:15-20. [PMID: 33677148 DOI: 10.1016/j.ceb.2021.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/19/2021] [Accepted: 01/30/2021] [Indexed: 12/22/2022]
Abstract
The generation of phosphoinositides (PIs) with spatial and temporal control is a key mechanism in cellular organization and signaling. The synthesis of PIs is mediated by PI kinases, proteins that are able to phosphorylate unique substrates at specific positions on the inositol headgroup to generate signaling molecules. Phosphatidylinositol 5 phosphate 4 kinase (PIP4K) is one such lipid kinase that is able to specifically phosphorylate phosphatidylinositol 5 phosphate, the most recently discovered PI to generate the well-known and abundant PI, phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2]. PIP4K appears to be encoded only in metazoan genomes, and several genetic studies indicate important physiological functions for these enzymes in metabolism, immune function, and growth control. PIP4K has recently been reported to localize to multiple cellular compartments, including the nucleus, plasma membrane, endosomal systems, and autophagosome. However, the biochemical activity of these enzymes that is relevant to these physiological functions remains elusive. We review recent developments in this area and highlight emerging roles for these enzymes in cellular organization.
Collapse
Affiliation(s)
- Padinjat Raghu
- Cellular Organization and Signaling, National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore, 560065, India.
| |
Collapse
|
19
|
Winiarczyk D, Winiarczyk M, Winiarczyk S, Michalak K, Adaszek Ł. Proteomic Analysis of Tear Film Obtained from Diabetic Dogs. Animals (Basel) 2020; 10:ani10122416. [PMID: 33348610 PMCID: PMC7766195 DOI: 10.3390/ani10122416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Canine diabetes is a serious disease, which can lead to severe complications, eventually even death. Currently, all the diagnostic procedures are the invasive ones, with blood collection remaining as a golden standard for both initial diagnosis, and later follow-up. Tears can be obtained in a non-invasive manner, which makes them a perfect candidate for a screening tool in canine diabetes. In this study we aimed to analyze the protein composition of the tears collected from the healthy animals and compared it to the diabetic group. There are significant differences between these two groups, and we believe that the identified proteins hold promise as a potential diagnostic tool, which can be later on used both in clinical practice, and for better understanding of the disease. Abstract Canine diabetes mellitus is a significant health burden, followed with numerous systemic complications, including diabetic cataracts and retinopathy, leading to blindness. Diabetes should be considered as a disease damaging all the body organs, including gastrointestinal tract, through a complex combination of vascular and metabolic pathologies, leading to impaired gut function. Tear film can be obtained in a non-invasive way, which makes it a feasible biomarker source. In this study we compared proteomic changes ongoing in tear film of diabetic dogs. The study group consisted of 15 diabetic dogs, and 13 dogs served as a control group. After obtaining tear film with Schirmer strips, we performed 2-dimensional electrophoresis, followed by Delta2D software analysis, which allowed to select statistically significant differentially expressed proteins. After their identification with MALDI-TOF (matrix assisted laser desorption and ionisation time of flight) spectrometry we found one up-regulated protein in tear film of diabetic dogs—SRC kinase signaling inhibitor 1 (SRCIN1). Eight proteins were down-regulated: phosphatidylinositol-4 kinase type 2 alpha (PI4KIIα), Pro-melanin concentrating hormone (Pro-MCH), Flotillin-1, Protein mono-ADP ribosyltransferase, GRIP and coiled coil domain containing protein 2, tetratricopeptide repeat protein 36, serpin, and Prelamin A/C. Identified proteins were analyzed by Panther Gene Ontology software, and their possible connections with diabetic etiopathology were discussed. We believe that this is the first study to target tear film proteome in canine diabetes. We believe that combined with traditional examination, the tear film proteomic analysis can be a new source of biomarkers both for clinical practice, and experimental research.
Collapse
Affiliation(s)
- Dagmara Winiarczyk
- Department of Internal Diseases of Small Animals, University of Life Sciences of Lublin, 20-950 Lublin, Poland;
| | - Mateusz Winiarczyk
- Department of Vitreoretinal Surgery, Medical University of Lublin, 20-950 Lublin, Poland;
| | - Stanisław Winiarczyk
- Department of Epizootiology, University of Life Sciences of Lublin, 20-950 Lublin, Poland; (S.W.); (K.M.)
| | - Katarzyna Michalak
- Department of Epizootiology, University of Life Sciences of Lublin, 20-950 Lublin, Poland; (S.W.); (K.M.)
| | - Łukasz Adaszek
- Department of Epizootiology, University of Life Sciences of Lublin, 20-950 Lublin, Poland; (S.W.); (K.M.)
- Correspondence:
| |
Collapse
|
20
|
Wang DG, Paddock MN, Lundquist MR, Sun JY, Mashadova O, Amadiume S, Bumpus TW, Hodakoski C, Hopkins BD, Fine M, Hill A, Yang TJ, Baskin JM, Dow LE, Cantley LC. PIP4Ks Suppress Insulin Signaling through a Catalytic-Independent Mechanism. Cell Rep 2020; 27:1991-2001.e5. [PMID: 31091439 PMCID: PMC6619495 DOI: 10.1016/j.celrep.2019.04.070] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/06/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
Insulin stimulates the conversion of phosphatidylino-sitol-4,5-bisphosphate (PI(4,5)P2) to phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3), which mediates downstream cellular responses. PI(4,5)P2 is produced by phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and by phosphatidylinositol-5-phos-phate 4-kinases (PIP4Ks). Here, we show that the loss of PIP4Ks (PIP4K2A, PIP4K2B, and PIP4K2C) in vitro results in a paradoxical increase in PI(4,5)P2 and a concomitant increase in insulin-stimulated production of PI(3,4,5)P3. The reintroduction of either wild-type or kinase-dead mutants of the PIP4Ks restored cellular PI(4,5)P2 levels and insulin stimulation of the PI3K pathway, suggesting a catalytic-independent role of PIP4Ks in regulating PI(4,5)P2 levels. These effects are explained by an increase in PIP5K activity upon the deletion of PIP4Ks, which normally suppresses PIP5K activity through a direct binding interaction mediated by the N-terminal motif VMLϕFPDD of PIP4K. Our work uncovers an allosteric function of PIP4Ks in suppressing PIP5K-mediated PI(4,5)P2 synthesis and insulin-dependent conversion to PI(3,4,5)P3 and suggests that the pharmacological depletion of PIP4K enzymes could represent a strategy for enhancing insulin signaling. PI(4,5)P2 is produced by both phosphatidylinositol-4-phosphate 5-kinases (PIP5Ks) and by phosphatidylinositol-5-phosphate 4-kinases (PIP4Ks). Wang et al. report an allosteric function of a conserved N-terminal motif of PIP4Ks in suppressing PIP5K-mediated PI(4,5)P2 synthesis and insulin-dependent conversion to PI(3,4,5) P3. This non-catalytic role has implications for the development of PIP4K targeted therapies.
Collapse
Affiliation(s)
- Diana G Wang
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell Medicine/Rockefeller University/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Marcia N Paddock
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Hematology and Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Mark R Lundquist
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Janet Y Sun
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Oksana Mashadova
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Solomon Amadiume
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Timothy W Bumpus
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Cindy Hodakoski
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Matthew Fine
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Amanda Hill
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - T Jonathan Yang
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Hematology and Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
| |
Collapse
|
21
|
Sharma S, Mathre S, Ramya V, Shinde D, Raghu P. Phosphatidylinositol 5 Phosphate 4-Kinase Regulates Plasma-Membrane PIP 3 Turnover and Insulin Signaling. Cell Rep 2020; 27:1979-1990.e7. [PMID: 31091438 PMCID: PMC6591132 DOI: 10.1016/j.celrep.2019.04.084] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/06/2019] [Accepted: 04/17/2019] [Indexed: 01/25/2023] Open
Abstract
Phosphatidylinositol 3,4,5-trisphosphate (PIP3) generation at the plasma membrane is a key event during activation of receptor tyrosine kinases such as the insulin receptor required for normal growth and metabolism. We report that in Drosophila, phosphatidylinositol 5 phosphate 4-kinase (PIP4K) is required to limit PIP3 levels during insulin receptor activation. Depletion of PIP4K increases the levels of PIP3 produced in response to insulin stimulation. We find that PIP4K function at the plasma membrane enhances class I phosphoinositide 3-kinase (PI3K) activity, although the catalytic ability of PIP4K to produce phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the plasma membrane is dispensable for this regulation. Animals lacking PIP4K show enhanced insulin signaling-dependent phenotypes and are resistant to the metabolic consequences of a high-sugar diet, highlighting the importance of PIP4K in normal metabolism and development. Thus, PIP4Ks are key regulators of receptor tyrosine kinase signaling with implications for growth factor-dependent processes including tumor growth, T cell activation, and metabolism.
Collapse
Affiliation(s)
- Sanjeev Sharma
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Swarna Mathre
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Visvanathan Ramya
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Dhananjay Shinde
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India.
| |
Collapse
|
22
|
Noch EK, Yim I, Milner TA, Cantley LC. Distribution and localization of phosphatidylinositol 5-phosphate, 4-kinase alpha and beta in the brain. J Comp Neurol 2020; 529:434-449. [PMID: 32449185 DOI: 10.1002/cne.24956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
Phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2 ) is critical for synaptic vesicle docking and fusion and generation of the second messengers, diacylglycerol and inositol-1,4,5-trisphosphate. PI-4,5-P2 can be generated by two families of kinases: type 1 phosphatidylinositol-4-phosphate 5-kinases, encoded by PIP5K1A, PIP5K1B and PIP5K1C, and type 2 phosphatidylinositol-5-phosphate 4-kinases, encoded by PIP4K2A, PIP4K2B, and PIP4K2C. While the roles of the type 1 enzymes in brain function have been extensively studied, the roles of the type 2 enzymes are poorly understood. Using selective antibodies validated by genetic deletion of pip4k2a or pip4k2b in mouse brain, we characterized the location of the enzymes, PI5P4Kα and PI5P4Kβ, encoded by these genes. In mice, we demonstrate that PI5P4Kα is expressed in adulthood, whereas PI5P4Kβ is expressed early in development. PI5P4Kα localizes to white matter tracts, especially the corpus callosum, and at a low level in neurons, while PI5P4Kβ is expressed in neuronal populations, especially hippocampus and cortex. Dual labeling studies demonstrate that PI5P4Kα co-localizes with the oligodendrocyte marker, Olig2, whereas PI5P4Kβ co-localizes with the neuronal marker, NeuN. Ultrastructural analysis demonstrates that both kinases are contained in axon terminals and dendritic spines adjacent to the synaptic membrane, which support a potential role in synaptic transmission. Immunoperoxidase analysis of macaque and human brain tissue demonstrate a conserved pattern for PI5P4Kα and PI5P4Kβ. These results highlight the diverse cell-autonomous expression of PI5P4Kα and PI5P4Kβ and support further exploration into their role in synaptic function in the brain.
Collapse
Key Words
- PIP4K
- RRID:AB_1,127,270
- RRID:AB_10,622,025
- RRID:AB_10,711,040
- RRID:AB_1904103
- RRID:AB_2,164,572
- RRID:AB_2,223,210
- RRID:AB_2096811
- RRID:AB_2269374
- RRID:AB_2300649
- RRID:AB_353,929
- RRID:AB_561,049
- brain
- neuron
- oligodendrocyte
- phosphatidylinositol-5-phosphate 4-kinase
- phosphoinositide
Collapse
Affiliation(s)
- Evan K Noch
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA.,Department of Neurology, Weill Cornell Medicine, New York, New York, USA
| | - Isaiah Yim
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA.,Harold and Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, New York, USA
| | - Lewis C Cantley
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| |
Collapse
|
23
|
Sivakumaren SC, Shim H, Zhang T, Ferguson FM, Lundquist MR, Browne CM, Seo HS, Paddock MN, Manz TD, Jiang B, Hao MF, Krishnan P, Wang DG, Yang TJ, Kwiatkowski NP, Ficarro SB, Cunningham JM, Marto JA, Dhe-Paganon S, Cantley LC, Gray NS. Targeting the PI5P4K Lipid Kinase Family in Cancer Using Covalent Inhibitors. Cell Chem Biol 2020; 27:525-537.e6. [PMID: 32130941 PMCID: PMC7286548 DOI: 10.1016/j.chembiol.2020.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 11/14/2019] [Accepted: 02/13/2020] [Indexed: 12/12/2022]
Abstract
The PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here, we present the discovery and characterization of a pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K's reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.
Collapse
Affiliation(s)
- Sindhu Carmen Sivakumaren
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hyeseok Shim
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark R Lundquist
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - Christopher M Browne
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Marcia N Paddock
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - Theresa D Manz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbruecken, Germany
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ming-Feng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Pranav Krishnan
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Diana G Wang
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - T Jonathan Yang
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA
| | - Nicholas P Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - James M Cunningham
- Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY 10065, USA.
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
24
|
Manz TD, Sivakumaren SC, Ferguson FM, Zhang T, Yasgar A, Seo HS, Ficarro SB, Card JD, Shim H, Miduturu CV, Simeonov A, Shen M, Marto JA, Dhe-Paganon S, Hall MD, Cantley LC, Gray NS. Discovery and Structure-Activity Relationship Study of ( Z)-5-Methylenethiazolidin-4-one Derivatives as Potent and Selective Pan-phosphatidylinositol 5-Phosphate 4-Kinase Inhibitors. J Med Chem 2020; 63:4880-4895. [PMID: 32298120 DOI: 10.1021/acs.jmedchem.0c00227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Due to their role in many important signaling pathways, phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are attractive targets for the development of experimental therapeutics for cancer, metabolic, and immunological disorders. Recent efforts to develop small molecule inhibitors for these lipid kinases resulted in compounds with low- to sub-micromolar potencies. Here, we report the identification of CVM-05-002 using a high-throughput screen of PI5P4Kα against our in-house kinase inhibitor library. CVM-05-002 is a potent and selective inhibitor of PI5P4Ks, and a 1.7 Å X-ray structure reveals its binding interactions in the ATP-binding pocket. Further investigation of the structure-activity relationship led to the development of compound 13, replacing the rhodanine-like moiety present in CVM-05-002 with an indole, a potent pan-PI5P4K inhibitor with excellent kinome-wide selectivity. Finally, we employed isothermal cellular thermal shift assays (CETSAs) to demonstrate the effective cellular target engagement of PI5P4Kα and -β by the inhibitors in HEK 293T cells.
Collapse
Affiliation(s)
- Theresa D Manz
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States.,Department of Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbruecken, Germany
| | - Sindhu Carmen Sivakumaren
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 United States
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Scott B Ficarro
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, 02215, United States.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Joseph D Card
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, 02215, United States.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hyeseok Shim
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, New York 10065, United States
| | - Chandrasekhar V Miduturu
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 United States
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 United States
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, 02215, United States.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 United States
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine and New York Presbyterian Hospital, New York, New York 10065, United States
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| |
Collapse
|
25
|
Manz T, Sivakumaren SC, Yasgar A, Hall MD, Davis MI, Seo HS, Card JD, Ficarro SB, Shim H, Marto JA, Dhe-Paganon S, Sasaki AT, Boxer MB, Simeonov A, Cantley LC, Shen M, Zhang T, Ferguson FM, Gray NS. Structure-Activity Relationship Study of Covalent Pan-phosphatidylinositol 5-Phosphate 4-Kinase Inhibitors. ACS Med Chem Lett 2020; 11:346-352. [PMID: 32184968 PMCID: PMC7074221 DOI: 10.1021/acsmedchemlett.9b00402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/03/2019] [Indexed: 12/20/2022] Open
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are important molecular players in a variety of diseases, such as cancer. Currently available PI5P4K inhibitors are reversible small molecules, which may lack selectivity and sufficient cellular on-target activity. In this study, we present a new class of covalent pan-PI5P4K inhibitors with potent biochemical and cellular activity. Our designs are based on THZ-P1-2, a covalent PI5P4K inhibitor previously developed in our lab. Here, we report further structure-guided optimization and structure-activity relationship (SAR) study of this scaffold, resulting in compound 30, which retained biochemical and cellular potency, while demonstrating a significantly improved selectivity profile. Furthermore, we confirm that the inhibitors show efficient binding affinity in the context of HEK 293T cells using isothermal CETSA methods. Taken together, compound 30 represents a highly selective pan-PI5P4K covalent lead molecule.
Collapse
Affiliation(s)
- Theresa
D. Manz
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department
of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbruecken, Germany
| | - Sindhu C. Sivakumaren
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Adam Yasgar
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Mindy I. Davis
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Hyuk-Soo Seo
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Joseph D. Card
- Department
of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Oncologic Pathology, Dana-Farber Cancer
Institute, 360 Longwood
Avenue, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department
of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Oncologic Pathology, Dana-Farber Cancer
Institute, 360 Longwood
Avenue, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hyeseok Shim
- Meyer
Cancer Center, Weill Cornell Medicine and
New York Presbyterian Hospital, New York, New York 10065, United States
| | - Jarrod A. Marto
- Department
of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Oncologic Pathology, Dana-Farber Cancer
Institute, 360 Longwood
Avenue, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Sirano Dhe-Paganon
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Atsuo T. Sasaki
- Division
of Hematology and Oncology, University of
Cincinnati, 3125 Eden
Avenue, Cincinnati, Ohio 45267-0508, United States
| | - Matthew B. Boxer
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Lewis C. Cantley
- Meyer
Cancer Center, Weill Cornell Medicine and
New York Presbyterian Hospital, New York, New York 10065, United States
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Tinghu Zhang
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Fleur M. Ferguson
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Nathanael S. Gray
- Department
of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| |
Collapse
|
26
|
Murakami M, Rhayem Y, Kunzke T, Sun N, Feuchtinger A, Ludwig P, Strom TM, Gomez-Sanchez C, Knösel T, Kirchner T, Williams TA, Reincke M, Walch AK, Beuschlein F. In situ metabolomics of aldosterone-producing adenomas. JCI Insight 2019; 4:130356. [PMID: 31484828 DOI: 10.1172/jci.insight.130356] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/01/2019] [Indexed: 12/17/2022] Open
Abstract
Recent genetic examinations and multisteroid profiles have provided the basis for subclassification of aldosterone-producing adenomas (APAs). The objective of the current study was to produce a comprehensive, high-resolution mass spectrometry imaging (MSI) map of APAs in relation to morphometry, immunohistochemical profiles, mutational status, and clinical outcome. The study cohort comprised 136 patients with unilateral primary aldosteronism. Matrix-assisted laser desorption/ionization-Fourier transform-ion cyclotron resonance MSI was conducted, and metabolite profiles were analyzed with genotype/phenotype information, including digital image analysis from morphometry and IHC of steroidogenic enzymes. Distinct molecular signatures between KCNJ5- and CACNA1D-mutated APAs with significant differences of 137 metabolites, including metabolites of purine metabolism and steroidogenesis, were observed. Intratumor concentration of 18-oxocortisol and 18-hydroxycortisol were inversely correlated with the staining intensity of CYP11B1. Lower staining intensity of CYP11B1 and higher levels of 18-oxocortisol were associated with a higher probability of complete clinical success after surgery. The present study demonstrates distinct metabolomic profiles of APAs in relation to tumor genotype. In addition, we reveal an inverse correlation between cortisol derivatives and CYP11B1 and the impact of 18-oxocortisol and CYP11B1 on clinical outcome, which provides unprecedented insights into the pathophysiology, clinical features, and steroidogenesis of APAs.
Collapse
Affiliation(s)
- Masanori Murakami
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yara Rhayem
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Na Sun
- Research Unit Analytical Pathology and
| | | | - Philippe Ludwig
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tim Matthias Strom
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Celso Gomez-Sanchez
- Division of Endocrinology, G.V. (Sonny) Montgomery VA Medical Center, and the University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Thomas Knösel
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tracy Ann Williams
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany.,Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany.,Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Unviersitätsspital Zürich, Zurich, Switzerland
| |
Collapse
|
27
|
Nakada-Tsukui K, Watanabe N, Maehama T, Nozaki T. Phosphatidylinositol Kinases and Phosphatases in Entamoeba histolytica. Front Cell Infect Microbiol 2019; 9:150. [PMID: 31245297 PMCID: PMC6563779 DOI: 10.3389/fcimb.2019.00150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphatidylinositol (PtdIns) metabolism is indispensable in eukaryotes. Phosphoinositides (PIs) are phosphorylated derivatives of PtdIns and consist of seven species generated by reversible phosphorylation of the inositol moieties at the positions 3, 4, and 5. Each of the seven PIs has a unique subcellular and membrane domain distribution. In the enteric protozoan parasite Entamoeba histolytica, it has been previously shown that the PIs phosphatidylinositol 3-phosphate (PtdIns3P), PtdIns(4,5)P2, and PtdIns(3,4,5)P3 are localized to phagosomes/phagocytic cups, plasma membrane, and phagocytic cups, respectively. The localization of these PIs in E. histolytica is similar to that in mammalian cells, suggesting that PIs have orthologous functions in E. histolytica. In contrast, the conservation of the enzymes that metabolize PIs in this organism has not been well-documented. In this review, we summarized the full repertoire of the PI kinases and PI phosphatases found in E. histolytica via a genome-wide survey of the current genomic information. E. histolytica appears to have 10 PI kinases and 23 PI phosphatases. It has a panel of evolutionarily conserved enzymes that generate all the seven PI species. However, class II PI 3-kinases, type II PI 4-kinases, type III PI 5-phosphatases, and PI 4P-specific phosphatases are not present. Additionally, regulatory subunits of class I PI 3-kinases and type III PI 4-kinases have not been identified. Instead, homologs of class I PI 3-kinases and PTEN, a PI 3-phosphatase, exist as multiple isoforms, which likely reflects that elaborate signaling cascades mediated by PtdIns(3,4,5)P3 are present in this organism. There are several enzymes that have the nuclear localization signal: one phosphatidylinositol phosphate (PIP) kinase, two PI 3-phosphatases, and one PI 5-phosphatase; this suggests that PI metabolism also has conserved roles related to nuclear functions in E. histolytica, as it does in model organisms.
Collapse
Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Natsuki Watanabe
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tomohiko Maehama
- Division of Molecular and Cellular Biology, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
28
|
Lundquist MR, Goncalves MD, Loughran RM, Possik E, Vijayaraghavan T, Yang A, Pauli C, Ravi A, Verma A, Yang Z, Johnson JL, Wong JCY, Ma Y, Hwang KSK, Weinkove D, Divecha N, Asara JM, Elemento O, Rubin MA, Kimmelman AC, Pause A, Cantley LC, Emerling BM. Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy. Mol Cell 2019; 70:531-544.e9. [PMID: 29727621 DOI: 10.1016/j.molcel.2018.03.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/13/2018] [Accepted: 03/29/2018] [Indexed: 01/21/2023]
Abstract
While the majority of phosphatidylinositol-4, 5-bisphosphate (PI-4, 5-P2) in mammalian cells is generated by the conversion of phosphatidylinositol-4-phosphate (PI-4-P) to PI-4, 5-P2, a small fraction can be made by phosphorylating phosphatidylinositol-5-phosphate (PI-5-P). The physiological relevance of this second pathway is not clear. Here, we show that deletion of the genes encoding the two most active enzymes in this pathway, Pip4k2a and Pip4k2b, in the liver of mice causes a large enrichment in lipid droplets and in autophagic vesicles during fasting. These changes are due to a defect in the clearance of autophagosomes that halts autophagy and reduces the supply of nutrients salvaged through this pathway. Similar defects in autophagy are seen in nutrient-starved Pip4k2a-/-Pip4k2b-/- mouse embryonic fibroblasts and in C. elegans lacking the PI5P4K ortholog. These results suggest that this alternative pathway for PI-4, 5-P2 synthesis evolved, in part, to enhance the ability of multicellular organisms to survive starvation.
Collapse
Affiliation(s)
- Mark R Lundquist
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Marcus D Goncalves
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ryan M Loughran
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Metabolism and Signaling Networks Program, La Jolla, CA 92037, USA
| | - Elite Possik
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Tarika Vijayaraghavan
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Annan Yang
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Chantal Pauli
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY 10065, USA
| | - Archna Ravi
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Metabolism and Signaling Networks Program, La Jolla, CA 92037, USA
| | - Akanksha Verma
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhiwei Yang
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jared L Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jenny C Y Wong
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yilun Ma
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Katie Seo-Kyoung Hwang
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David Weinkove
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK
| | - Nullin Divecha
- The Inositide Laboratory, Centre for Biological Sciences, Southampton University, Southampton, SO17 1BJ, UK
| | - John M Asara
- Department of Medicine, Division of Signal Transduction, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Olivier Elemento
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mark A Rubin
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY 10065, USA
| | - Alec C Kimmelman
- Perlmutter Cancer Center, Department of Radiation Oncology, NYU Medical School, New York, NY 10016, USA
| | - Arnim Pause
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Brooke M Emerling
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Metabolism and Signaling Networks Program, La Jolla, CA 92037, USA.
| |
Collapse
|
29
|
Abstract
We recently demonstrated that the circadian clock component CRY2 is an essential cofactor in the SCFFBXL3-mediated ubiquitination of c-MYC. Because our demonstration that CRY2 recruits phosphorylated substrates to SCFFBXL3 was unexpected, we investigated the scope of this role by searching for additional substrates of FBXL3 that require CRY1 or CRY2 as cofactors. Here, we describe an affinity purification mass spectrometry (APMS) screen through which we identified more than one hundred potential substrates of SCFFBXL3+CRY1/2, including the cell cycle regulated Tousled-like kinase, TLK2. Both CRY1 and CRY2 recruit TLK2 to SCFFBXL3, and TLK2 kinase activity is required for this interaction. Overexpression or genetic deletion of CRY1 and/or CRY2 decreases or enhances TLK2 protein abundance, respectively. These findings reinforce the idea that CRYs function as co-factors for SCFFBXL3, provide a resource of potential substrates, and establish a molecular connection between the circadian and cell cycle oscillators via CRY-modulated turnover of TLK2.
Collapse
|
30
|
Zhang S, Li Z, Yan X, Bao L, Deng Y, Zeng F, Wang P, Zhu J, Yin D, Liao F, Zhou X, Zhang D, Xia X, Wang H, Yang X, Zhang W, Gao H, Zhang W, Yang L, Hou Q, Xu H, Zhang Y, Shu Y, Wang Y. Regulatory Network and Prognostic Effect Investigation of PIP4K2A in Leukemia and Solid Cancers. Front Genet 2019; 9:721. [PMID: 30697230 PMCID: PMC6341070 DOI: 10.3389/fgene.2018.00721] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/21/2018] [Indexed: 02/05/2023] Open
Abstract
Germline variants of PIP4K2A impact susceptibility of acute lymphoblastic leukemia (ALL) through inducing its overexpression. Although limited reports suggested the oncogenic role of PIP4K2A in cancers, regulatory network and prognostic effect of this gene remains poorly understood in tumorigenesis and leukemogenesis. In this study, we conducted genome-wide gene expression association analyses in pediatric B-ALL cohorts to discover expression associated genes and pathways, which is followed by the bioinformatics analyses to investigate the prognostic role of PIP4K2A and its related genes in multiple cancer types. 214 candidates were identified to be significantly associated with PIP4K2A expression in ALL patients, with known cancer-related genes rankings the top (e.g., RAC2, RBL2, and TFDP1). These candidates do not only tend to be clustered in the same types of leukemia, but can also separate the patients into novel molecular subtypes. PIP4K2A is noticed to be frequently overexpressed in multiple other types of leukemia and solid cancers from cancer cohorts including TCGA, and associated with its candidates in subtype-specific and cancer-specific manners. Interestingly, the association status varied in tumors compared to their matched normal tissues. Moreover, PIP4K2A and its related candidates exhibit stage-independent prognostic effects in multiple cancers, mostly with its lower expression significantly associated with longer overall survival (p < 0.05). Our findings reveal the transcriptional regulatory network of PIP4K2A in leukemia, and suggest its potentially important role on molecular subtypes of multiple cancers and subsequent treatment outcomes.
Collapse
Affiliation(s)
- Shouyue Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Zhaozhi Li
- Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinyu Yan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Li Bao
- Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yun Deng
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Feier Zeng
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Peiqi Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jianhui Zhu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dandan Yin
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Fei Liao
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xueyan Zhou
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Duyu Zhang
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xuyang Xia
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Hong Wang
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Xue Yang
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wanhua Zhang
- Department of Hematology and Hematology Research Laboratory, Sichuan University, Chengdu, China
| | - Hu Gao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu
| | - Wei Zhang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, China
| | - Li Yang
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qianqian Hou
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Heng Xu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Shu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yuelan Wang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| |
Collapse
|
31
|
Choi S, Houdek X, Anderson RA. Phosphoinositide 3-kinase pathways and autophagy require phosphatidylinositol phosphate kinases. Adv Biol Regul 2018; 68:31-38. [PMID: 29472147 PMCID: PMC5955796 DOI: 10.1016/j.jbior.2018.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 01/10/2023]
Abstract
Phosphatidylinositol phosphate kinases (PIPKs) generate a lipid messenger phosphatidylinositol 4,5-bisphosphate (PI4,5P2) that controls essentially all aspects of cellular functions. PI4,5P2 rapidly diffuses in the membrane of the lipid bilayer and does not greatly change in membrane or cellular content, and thus PI4,5P2 generation by PIPKs is tightly linked to its usage in subcellular compartments. Based on this verity, recent study of PI4,5P2 signal transduction has been focused on investigations of individual PIPKs and their underlying molecular regulation of cellular processes. Here, we will discuss recent advances in the study of how PIPKs control specific cellular events through assembly and regulation of PI4,5P2 effectors that mediate specific cellular processes. A focus will be on the roles of PIPKs in control of the phosphoinositide 3-kinase pathway and autophagy.
Collapse
Affiliation(s)
- Suyong Choi
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Xander Houdek
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Richard A Anderson
- University of Wisconsin-Madison, School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA.
| |
Collapse
|
32
|
Dual blockade of the lipid kinase PIP4Ks and mitotic pathways leads to cancer-selective lethality. Nat Commun 2017; 8:2200. [PMID: 29259156 PMCID: PMC5736559 DOI: 10.1038/s41467-017-02287-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 11/17/2017] [Indexed: 12/04/2022] Open
Abstract
Achieving robust cancer-specific lethality is the ultimate clinical goal. Here, we identify a compound with dual-inhibitory properties, named a131, that selectively kills cancer cells, while protecting normal cells. Through an unbiased CETSA screen, we identify the PIP4K lipid kinases as the target of a131. Ablation of the PIP4Ks generates a phenocopy of the pharmacological effects of PIP4K inhibition by a131. Notably, PIP4Ks inhibition by a131 causes reversible growth arrest in normal cells by transcriptionally upregulating PIK3IP1, a suppressor of the PI3K/Akt/mTOR pathway. Strikingly, Ras activation overrides a131-induced PIK3IP1 upregulation and activates the PI3K/Akt/mTOR pathway. Consequently, Ras-transformed cells override a131-induced growth arrest and enter mitosis where a131’s ability to de-cluster supernumerary centrosomes in cancer cells eliminates Ras-activated cells through mitotic catastrophe. Our discovery of drugs with a dual-inhibitory mechanism provides a unique pharmacological strategy against cancer and evidence of cross-activation between the Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways via a Ras˧PIK3IP1˧PI3K signaling network. The Ras/Raf/MEK/ERK and PI3K/Akt/mTOR signaling pathways are essential for cancer cell survival. Here, the authors describes a molecule a131 with dual-inhibitory properties, which targets PI5P4K and mitosis, and it is involved in Ras/Raf/MEK/ERK and PI3K/Akt/mTOR crosstalk, thereby causing reversible growth arrest in normal cells and cell death of tumor cells.
Collapse
|
33
|
MANF regulates hypothalamic control of food intake and body weight. Nat Commun 2017; 8:579. [PMID: 28924165 PMCID: PMC5603516 DOI: 10.1038/s41467-017-00750-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 07/25/2017] [Indexed: 12/30/2022] Open
Abstract
The hypothalamus has a vital role in controlling food intake and energy homeostasis; its activity is modulated by neuropeptides and endocrine factors. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a neurotrophic factor that is also localized in the endoplasmic reticulum (ER) in neurons. Here we show that MANF is highly enriched in distinct nuclei of the mouse hypothalamus, and that MANF expression in the hypothalamus is upregulated in response to fasting. Increasing or decreasing hypothalamic MANF protein levels causes hyperphagia or hypophagia, respectively. Moreover, MANF triggers hypothalamic insulin resistance by enhancing the ER localization and activity of PIP4k2b, a kinase known to regulate insulin signaling. Our findings indicate that MANF influences food intake and body weight by modulating hypothalamic insulin signaling.MANF is a neurotrophic factor that is secreted but also mediates the unfolded protein response acting intracellularly. Here, the authors show that MANF expression in the brain is influenced by nutritional cues, and hypothalamic MANF influences food intake and systemic energy homeostasis.
Collapse
|
34
|
Kriebs A, Jordan SD, Soto E, Henriksson E, Sandate CR, Vaughan ME, Chan AB, Duglan D, Papp SJ, Huber AL, Afetian ME, Yu RT, Zhao X, Downes M, Evans RM, Lamia KA. Circadian repressors CRY1 and CRY2 broadly interact with nuclear receptors and modulate transcriptional activity. Proc Natl Acad Sci U S A 2017; 114:8776-8781. [PMID: 28751364 PMCID: PMC5565439 DOI: 10.1073/pnas.1704955114] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nuclear hormone receptors (NRs) regulate physiology by sensing lipophilic ligands and adapting cellular transcription appropriately. A growing understanding of the impact of circadian clocks on mammalian transcription has sparked interest in the interregulation of transcriptional programs. Mammalian clocks are based on a transcriptional feedback loop featuring the transcriptional activators circadian locomotor output cycles kaput (CLOCK) and brain and muscle ARNT-like 1 (BMAL1), and transcriptional repressors cryptochrome (CRY) and period (PER). CRY1 and CRY2 bind independently of other core clock factors to many genomic sites, which are enriched for NR recognition motifs. Here we report that CRY1/2 serve as corepressors for many NRs, indicating a new facet of circadian control of NR-mediated regulation of metabolism and physiology, and specifically contribute to diurnal modulation of drug metabolism.
Collapse
Affiliation(s)
- Anna Kriebs
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sabine D Jordan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Erin Soto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Emma Henriksson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
- Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö 20502, Sweden
| | - Colby R Sandate
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Megan E Vaughan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Alanna B Chan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Drew Duglan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Stephanie J Papp
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Anne-Laure Huber
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Megan E Afetian
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Ruth T Yu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Xuan Zhao
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Michael Downes
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Ronald M Evans
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037
- Center for Circadian Biology, University of California, San Diego, CA 92161
| | - Katja A Lamia
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037;
- Center for Circadian Biology, University of California, San Diego, CA 92161
| |
Collapse
|
35
|
Jordan SD, Kriebs A, Vaughan M, Duglan D, Fan W, Henriksson E, Huber AL, Papp SJ, Nguyen M, Afetian M, Downes M, Yu RT, Kralli A, Evans RM, Lamia KA. CRY1/2 Selectively Repress PPARδ and Limit Exercise Capacity. Cell Metab 2017; 26:243-255.e6. [PMID: 28683290 PMCID: PMC5546250 DOI: 10.1016/j.cmet.2017.06.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/31/2017] [Accepted: 06/07/2017] [Indexed: 01/18/2023]
Abstract
Cellular metabolite balance and mitochondrial function are under circadian control, but the pathways connecting the molecular clock to these functions are unclear. Peroxisome proliferator-activated receptor delta (PPARδ) enables preferential utilization of lipids as fuel during exercise and is a major driver of exercise endurance. We show here that the circadian repressors CRY1 and CRY2 function as co-repressors for PPARδ. Cry1-/-;Cry2-/- myotubes and muscles exhibit elevated expression of PPARδ target genes, particularly in the context of exercise. Notably, CRY1/2 seem to repress a distinct subset of PPARδ target genes in muscle compared to the co-repressor NCOR1. In vivo, genetic disruption of Cry1 and Cry2 enhances sprint exercise performance in mice. Collectively, our data demonstrate that CRY1 and CRY2 modulate exercise physiology by altering the activity of several transcription factors, including CLOCK/BMAL1 and PPARδ, and thereby alter energy storage and substrate selection for energy production.
Collapse
Affiliation(s)
- Sabine D Jordan
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anna Kriebs
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Megan Vaughan
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Drew Duglan
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Weiwei Fan
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emma Henriksson
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Clinical Sciences, CRC, Lund University, Malmö 20502, Sweden
| | - Anne-Laure Huber
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stephanie J Papp
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Madelena Nguyen
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Megan Afetian
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael Downes
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ruth T Yu
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anastasia Kralli
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ronald M Evans
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Katja A Lamia
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
36
|
Takeuchi K, Senda M, Lo YH, Kofuji S, Ikeda Y, Sasaki AT, Senda T. Structural reverse genetics study of the PI5P4Kβ-nucleotide complexes reveals the presence of the GTP bioenergetic system in mammalian cells. FEBS J 2017; 283:3556-3562. [PMID: 27090388 DOI: 10.1111/febs.13739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 12/13/2022]
Abstract
Reverse genetic analysis can connect a gene and its protein counterpart to a biological function(s) by knockout or knockdown of the specific gene. However, when a protein has multiple biochemical activities, the conventional genetics strategy is incapable of distinguishing which biochemical activity of the protein is critical for the particular biological function(s). Here, we propose a structural reverse genetics strategy to overcome this problem. In a structural reverse genetics study, multiple biochemical activities of a protein are segregated by mapping those activities to a structural element(s) in the atomic resolution tertiary structure. Based on the structural mapping, a mutant lacking one biochemical activity of interest can be produced with the other activities kept intact. Expression of the mutant by knockin or ectopic expression in the knockout strain along with the following analysis can connect the single biochemical activity of interest to a biological function. Using the structural reverse genetics strategy, we have dissected the newly identified GTP-dependent activity of a lipid kinase PI5P4Kβ from its ATP-dependent activity. The GTP-insensitive mutant has demonstrated the existence of the GTP bioenergetic sensor system in mammalian cells and its critical role in tumorigenesis. As structural reverse genetics can identify in vivo significance of individual biochemical activity, it is a powerful approach to reveal hidden biological functions, which could be a novel pharmacological target for therapeutic intervention. Given the recent expansion of choices in structural biological methods and advances in genome editing technologies, the time is ripe for structural reverse genetics strategies.
Collapse
Affiliation(s)
- Koh Takeuchi
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo, Japan.,JST, PRESTO, Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Yu-Hua Lo
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Satoshi Kofuji
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA. .,Department of Cancer Biology, Brain Tumor Center, Neuroscience Institute, University of Cincinnati College of Medicine, OH, USA. .,Department of Neurosurgery, Brain Tumor Center, Neuroscience Institute, University of Cincinnati College of Medicine, OH, USA.
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan. .,Department of Materials Structure Science, School of High Energy Accelerator Science, The graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki, Japan.
| |
Collapse
|
37
|
Lien CY, Tixier-Boichard M, Wu SW, Wang WF, Ng CS, Chen CF. Detection of QTL for traits related to adaptation to sub-optimal climatic conditions in chickens. Genet Sel Evol 2017; 49:39. [PMID: 28427323 PMCID: PMC5399330 DOI: 10.1186/s12711-017-0314-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/31/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption). A total of 844 animals were genotyped with the 60 K Illumina single nucleotide polymorphism (SNP) chip. Whole-genome interval linkage mapping and a genome-wide association study (GWAS) were performed for body weight at 0, 4, 8, 12, and 16 weeks of age, shank length at 8 weeks of age, size of comb area at 16 weeks of age, and antibody response to sheep red blood cells at 11 weeks of age (7 and 14 days after primary immunization). Relevant genes were identified based on functional annotation of candidate genes and potentially relevant SNPs were detected by comparing whole-genome sequences of several birds between the parental lines. RESULTS Whole-genome QTL analysis revealed 47 QTL and 714 effects associated with 178 SNPs were identified by GWAS with 5% Bonferroni genome-wide significance. Little overlap was observed between the QTL and GWAS results, with only two chromosomal regions detected by both approaches, i.e. one on GGA24 (GGA for Gallus gallus chromosome) for BW04 and one on GGAZ for six growth-related traits. Based on whole-genome sequence, differences between the parental lines based on several birds were screened in the genome-wide QTL regions and in a region detected by both methods, resulting in the identification of 106 putative candidate genes with a total of 15,443 SNPs, of which 41 were missense and 1698 were not described in the dbSNP archive. CONCLUSIONS The QTL detected in this study for growth and morphological traits likely influence adaptation of chickens to sub-tropical climate. Using whole-genome sequence data, we identified candidate SNPs for further confirmation of QTL in the F2 design. A strong QTL effect found on GGAZ underlines the importance of sex-linked inheritance for growth traits in chickens.
Collapse
Affiliation(s)
- Ching-Yi Lien
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Department of Animal Science, National Chung Hsing University, 145 Xingda Rd., South District, Taichung, 40227, Taiwan.,Livestock Research Institute, Council of Agriculture, Executive Yuan, 112 Muchang, Xinhua District, Tainan, 71246, Taiwan
| | | | - Shih-Wen Wu
- Fonghuanggu Bird and Ecology Park, National Museum of Natural Science, 1-9 Renyi Rd., Lugu Township, Nantou County, 55841, Taiwan
| | - Woei-Fuh Wang
- Biodiversity Research Center, Academia Sinica, 128 Academia Rd., Section 2, Nankang, Taipei, 11529, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, 145 Xingda Rd., South District, Taichung, 40227, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, No. 250, Guoguang Rd., South District, Taichung, 40227, Taiwan.
| |
Collapse
|
38
|
Phosphoinositides in the nucleus and myogenic differentiation: how a nuclear turtle with a PHD builds muscle. Biochem Soc Trans 2016; 44:299-306. [PMID: 26862219 DOI: 10.1042/bst20150238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Phosphoinositides are a family of phospholipid messenger molecules that control various aspects of cell biology in part by interacting with and regulating downstream protein partners. Importantly, phosphoinositides are present in the nucleus. They form part of the nuclear envelope and are present within the nucleus in nuclear speckles, intra nuclear chromatin domains, the nuclear matrix and in chromatin. What their exact role is within these compartments is not completely clear, but the identification of nuclear specific proteins that contain phosphoinositide interaction domains suggest that they are important regulators of DNA topology, chromatin conformation and RNA maturation and export. The plant homeo domain (PHD) finger is a phosphoinositide binding motif that is largely present in nuclear proteins that regulate chromatin conformation. In the present study I outline how changes in the levels of the nuclear phosphoinositide PtdIns5P impact on muscle cell differentiation through the PHD finger of TAF3 (TAF, TATA box binding protein (TBP)-associated factor), which is a core component of a number of different basal transcription complexes.
Collapse
|
39
|
In B cells, phosphatidylinositol 5-phosphate 4-kinase-α synthesizes PI(4,5)P2 to impact mTORC2 and Akt signaling. Proc Natl Acad Sci U S A 2016; 113:10571-6. [PMID: 27601656 DOI: 10.1073/pnas.1522478113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are enigmatic lipid kinases with physiological functions that are incompletely understood, not the least because genetic deletion and cell transfection have led to contradictory data. Here, we used the genetic tractability of DT40 cells to create cell lines in which endogenous PI5P4Kα was removed, either stably by genetic deletion or transiently (within 1 h) by tagging the endogenous protein genomically with the auxin degron. In both cases, removal impacted Akt phosphorylation, and by leaving one PI5P4Kα allele present but mutating it to be kinase-dead or have PI4P 5-kinase activity, we show that all of the effects on Akt phosphorylation were dependent on the ability of PI5P4Kα to synthesize phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] rather than to remove PI5P. Although stable removal of PI5P4Kα resulted in a pronounced decrease in Akt phosphorylation at Thr308 and Ser473, in part because of reduced plasma membrane PIP3, its acute removal led to an increase in Akt phosphorylation only at Ser473. This process invokes activation primarily of mammalian target of rapamycin complex 2 (mTORC2), which was confirmed by increased phosphorylation of other mTORC2 substrates. These findings establish PI5P4Kα as a kinase that synthesizes a physiologically relevant pool of PI(4,5)P2 and as a regulator of mTORC2, and show a phenomenon similar to the "butterfly effect" described for phosphatidylinositol 3-kinase Iα [Hart JR, et al. (2015) Proc Natl Acad Sci USA 112(4):1131-1136], whereby through apparently the same underlying mechanism, the removal of a protein's activity from a cell can have widely divergent effects depending on the time course of that removal.
Collapse
|
40
|
Deletion of the gene Pip4k2c, a novel phosphatidylinositol kinase, results in hyperactivation of the immune system. Proc Natl Acad Sci U S A 2016; 113:7596-601. [PMID: 27313209 DOI: 10.1073/pnas.1600934113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Type 2 phosphatidylinositol-5-phosphate 4-kinase (PI5P4K) converts phosphatidylinositol-5-phosphate to phosphatidylinositol-4,5-bisphosphate. Mammals have three enzymes PI5P4Kα, PI5P4Kβ, and PI5P4Kγ, and these enzymes have been implicated in metabolic control, growth control, and a variety of stress responses. Here, we show that mice with germline deletion of type 2 phosphatidylinositol-5-phosphate 4-kinase gamma (Pip4k2c), the gene encoding PI5P4Kγ, appear normal in regard to growth and viability but have increased inflammation and T-cell activation as they age. Immune cell infiltrates increased in Pip4k2c(-/-) mouse tissues. Also, there was an increase in proinflammatory cytokines, including IFNγ, interleukin 12, and interleukin 2 in plasma of Pip4k2c(-/-) mice. Pip4k2c(-/-) mice had an increase in T-helper-cell populations and a decrease in regulatory T-cell populations with increased proliferation of T cells. Interestingly, mammalian target of rapamycin complex 1 (mTORC1) signaling was hyperactivated in several tissues from Pip4k2c(-/-) mice and treating Pip4k2c(-/-) mice with rapamycin reduced the inflammatory phenotype, resulting in a decrease in mTORC1 signaling in tissues and a decrease in proinflammatory cytokines in plasma. These results indicate that PI5P4Kγ plays a role in the regulation of the immune system via mTORC1 signaling.
Collapse
|
41
|
Kolay S, Basu U, Raghu P. Control of diverse subcellular processes by a single multi-functional lipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Biochem J 2016; 473:1681-92. [PMID: 27288030 PMCID: PMC6609453 DOI: 10.1042/bcj20160069] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 12/16/2022]
Abstract
Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a multi-functional lipid that regulates several essential subcellular processes in eukaryotic cells. In addition to its well-established function as a substrate for receptor-activated signalling at the plasma membrane (PM), it is now recognized that distinct PI(4,5)P2 pools are present at other organelle membranes. However, a long-standing question that remains unresolved is the mechanism by which a single lipid species, with an invariant functional head group, delivers numerous functions without loss of fidelity. In the present review, we summarize studies that have examined the molecular processes that shape the repertoire of PI(4,5)P2 pools in diverse eukaryotes. Collectively, these studies indicate a conserved role for lipid kinase isoforms in generating functionally distinct pools of PI(4,5)P2 in diverse metazoan species. The sophistication underlying the regulation of multiple functions by PI(4,5)P2 is also shaped by mechanisms that regulate its availability to enzymes involved in its metabolism as well as molecular processes that control its diffusion at nanoscales in the PM. Collectively, these mechanisms ensure the specificity of PI(4,5)P2 mediated signalling at eukaryotic membranes.
Collapse
Affiliation(s)
- Sourav Kolay
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India Manipal University, Madhav Nagar, Manipal 576104, Karnataka, India
| | - Urbashi Basu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bangalore 560065, India
| |
Collapse
|
42
|
Sumita K, Lo YH, Takeuchi K, Senda M, Kofuji S, Ikeda Y, Terakawa J, Sasaki M, Yoshino H, Majd N, Zheng Y, Kahoud ER, Yokota T, Emerling BM, Asara JM, Ishida T, Locasale JW, Daikoku T, Anastasiou D, Senda T, Sasaki AT. The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis. Mol Cell 2016; 61:187-98. [PMID: 26774281 DOI: 10.1016/j.molcel.2015.12.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/21/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022]
Abstract
While cellular GTP concentration dramatically changes in response to an organism's cellular status, whether it serves as a metabolic cue for biological signaling remains elusive due to the lack of molecular identification of GTP sensors. Here we report that PI5P4Kβ, a phosphoinositide kinase that regulates PI(5)P levels, detects GTP concentration and converts them into lipid second messenger signaling. Biochemical analyses show that PI5P4Kβ preferentially utilizes GTP, rather than ATP, for PI(5)P phosphorylation, and its activity reflects changes in direct proportion to the physiological GTP concentration. Structural and biological analyses reveal that the GTP-sensing activity of PI5P4Kβ is critical for metabolic adaptation and tumorigenesis. These results demonstrate that PI5P4Kβ is the missing GTP sensor and that GTP concentration functions as a metabolic cue via PI5P4Kβ. The critical role of the GTP-sensing activity of PI5P4Kβ in cancer signifies this lipid kinase as a cancer therapeutic target.
Collapse
Affiliation(s)
- Kazutaka Sumita
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu-Hua Lo
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Koh Takeuchi
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Satoshi Kofuji
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jumpei Terakawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Hirofumi Yoshino
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Nazanin Majd
- Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Yuxiang Zheng
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Emily Rose Kahoud
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Takehiro Yokota
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Brooke M Emerling
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - John M Asara
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tetsuo Ishida
- Department of Chemistry, Biology & Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute and Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Takiko Daikoku
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki 305-0801, Japan.
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Cancer Biology and Department of Neurosurgery, University of Cincinnati College of Medicine, Brain Tumor Center at University of Cincinnati Neuroscience Institute, Cincinnati, OH 45267, USA.
| |
Collapse
|
43
|
Giudici ML, Clarke JH, Irvine RF. Phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ), a lipid signalling enigma. Adv Biol Regul 2015; 61:47-50. [PMID: 26710750 DOI: 10.1016/j.jbior.2015.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 11/26/2022]
Abstract
The phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are an important family of enzymes, whose physiological roles are being teased out by a variety of means. Phosphatidylinositol-5-phosphate 4-kinase γ (PI5P4Kγ) is especially intriguing as its in vitro activity is very low. Here we review what is known about this enzyme and discuss some recent advances towards an understanding of its physiology. Additionally, the effects of the ATP-competitive inhibitor I-OMe Tyrphostin AG-538 on all three mammalian PI5P4Ks was explored, including two PI5P4Kγ mutants with altered ATP- or PI5P-binding sites. The results suggest a strategy for targeting non-ATP binding sites on inositol lipid kinases.
Collapse
Affiliation(s)
| | - Jonathan H Clarke
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Robin F Irvine
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK.
| |
Collapse
|
44
|
Wang H, Chen Y, Lu XA, Liu G, Fu Y, Luo Y. Endostatin Prevents Dietary-Induced Obesity by Inhibiting Adipogenesis and Angiogenesis. Diabetes 2015; 64:2442-56. [PMID: 25605807 DOI: 10.2337/db14-0528] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 01/13/2015] [Indexed: 11/13/2022]
Abstract
Endostatin is a well-known angiogenesis inhibitor. Although angiogenesis has been considered as a potential therapeutic target of obesity, the inhibitory effect of endostatin on adipogenesis and dietary-induced obesity has never been demonstrated. Adipogenesis plays a critical role in controlling adipocyte cell number, body weight, and metabolic profile in a homeostatic state. Here we reveal that endostatin inhibits adipogenesis and dietary-induced obesity. The antiadipogenic mechanism of endostatin lies in its interaction with Sam68 RNA-binding protein in the nuclei of preadipocytes. This interaction competitively impairs the binding of Sam68 to intron 5 of mammalian target of rapamycin (mTOR), causing an error in mTOR transcript. This consequently decreases the expression of mTOR, results in decreased activities of the mTOR complex 1 pathway, and leads to defects in adipogenesis. Moreover, our findings demonstrate that the antiangiogenic function of endostatin also contributes to its obesity-inhibitory activity. Through the combined functions on adipogenesis and angiogenesis, endostatin prevents dietary-induced obesity and its related metabolic disorders, including insulin resistance, glucose intolerance, and hepatic steatosis. Thus, our findings reveal that endostatin has a potential application for antiobesity therapy and the prevention of obesity-related metabolic syndromes.
Collapse
Affiliation(s)
- Hui Wang
- National Engineering Laboratory of Anti-tumor Protein Therapeutics, Beijing Key Laboratory of Protein Therapeutics, and Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Chen
- National Engineering Laboratory of Anti-tumor Protein Therapeutics, Beijing Key Laboratory of Protein Therapeutics, and Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin-an Lu
- National Engineering Laboratory of Anti-tumor Protein Therapeutics, Beijing Key Laboratory of Protein Therapeutics, and Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Guanghua Liu
- National Engineering Laboratory of Anti-tumor Protein Therapeutics, Beijing Key Laboratory of Protein Therapeutics, and Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Fu
- National Engineering Laboratory of Anti-tumor Protein Therapeutics, Beijing Key Laboratory of Protein Therapeutics, and Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongzhang Luo
- National Engineering Laboratory of Anti-tumor Protein Therapeutics, Beijing Key Laboratory of Protein Therapeutics, and Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
45
|
The function of phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ) explored using a specific inhibitor that targets the PI5P-binding site. Biochem J 2015; 466:359-67. [PMID: 25495341 PMCID: PMC4687057 DOI: 10.1042/bj20141333] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NIH-12848 (NCGC00012848-02), a putative phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ) inhibitor, was explored as a tool for investigating this enigmatic, low activity, lipid kinase. PI5P4K assays in vitro showed that NIH-12848 inhibited PI5P4Kγ with an IC50 of approximately 1 μM but did not inhibit the α and β PI5P4K isoforms at concentrations up to 100 μM. A lack of inhibition of PI5P4Kγ ATPase activity suggested that NIH-12848 does not interact with the enzyme's ATP-binding site and direct exploration of binding using hydrogen–deuterium exchange (HDX)-MS (HDX-MS) revealed the putative PI5P-binding site of PI5P4Kγ to be the likely region of interaction. This was confirmed by a series of mutation experiments which led to the identification of a single PI5P4Kγ amino acid residue that can be mutated to its PI5P4Ks α and β homologue to render PI5P4Kγ resistant NIH-12848 inhibition. NIH-12848 (10 μM) was applied to cultured mouse principal kidney cortical collecting duct (mpkCCD) cells which, we show, express PI5P4Kγ that increases when the cells grow to confluence and polarize. NIH-12848 inhibited the translocation of Na+/K+-ATPase to the plasma membrane that occurs when mpkCCD cells grow to confluence and also prevented reversibly their forming of ‘domes’ on the culture dish. Both these NIH-12848-induced effects were mimicked by specific RNAi knockdown of PI5P4Kγ, but not that of PI5P4Ks α or β. Overall, the data reveal a probable contribution of PI5P4Kγ to the development and maintenance of epithelial cell functional polarity and show that NIH-12848 is a potentially powerful tool for exploring the cell physiology of PI5P4Ks. We have characterised a specific inhibitor of the enzyme Phosphatidylinositol 5-phosphate 4-kinase γ, including establishing where on the enzyme the inhibitor binds, and then applied this inhibitor to a kidney cell line to elucidate the intracellular functions of the enzyme.
Collapse
|
46
|
Papp SJ, Huber AL, Jordan SD, Kriebs A, Nguyen M, Moresco JJ, Yates JR, Lamia KA. DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization. eLife 2015; 4. [PMID: 25756610 PMCID: PMC4352707 DOI: 10.7554/elife.04883] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/10/2015] [Indexed: 11/13/2022] Open
Abstract
The circadian transcriptional repressors cryptochrome 1 (Cry1) and 2 (Cry2) evolved from photolyases, bacterial light-activated DNA repair enzymes. In this study, we report that while they have lost DNA repair activity, Cry1/2 adapted to protect genomic integrity by responding to DNA damage through posttranslational modification and coordinating the downstream transcriptional response. We demonstrate that genotoxic stress stimulates Cry1 phosphorylation and its deubiquitination by Herpes virus associated ubiquitin-specific protease (Hausp, a.k.a Usp7), stabilizing Cry1 and shifting circadian clock time. DNA damage also increases Cry2 interaction with Fbxl3, destabilizing Cry2. Thus, genotoxic stress increases the Cry1/Cry2 ratio, suggesting distinct functions for Cry1 and Cry2 following DNA damage. Indeed, the transcriptional response to genotoxic stress is enhanced in Cry1-/- and blunted in Cry2-/- cells. Furthermore, Cry2-/- cells accumulate damaged DNA. These results suggest that Cry1 and Cry2, which evolved from DNA repair enzymes, protect genomic integrity via coordinated transcriptional regulation.
Collapse
Affiliation(s)
- Stephanie J Papp
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Anne-Laure Huber
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Sabine D Jordan
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Anna Kriebs
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Madelena Nguyen
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Katja A Lamia
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| |
Collapse
|
47
|
Fiume R, Stijf-Bultsma Y, Shah ZH, Keune WJ, Jones DR, Jude JG, Divecha N. PIP4K and the role of nuclear phosphoinositides in tumour suppression. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:898-910. [PMID: 25728392 DOI: 10.1016/j.bbalip.2015.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/03/2015] [Accepted: 02/17/2015] [Indexed: 12/27/2022]
Abstract
Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated lipid kinases that phosphorylate PtdIns5P to generate PtdIns(4,5)P₂. There are three isoforms of PIP4Ks: PIP4K2A, 2B and 2C, which localise to different subcellular compartments with the PIP4K2B isoform being localised predominantly in the nucleus. Suppression of PIP4K expression selectively prevents tumour cell growth in vitro and prevents tumour development in mice that have lost the tumour suppressor p53. p53 is lost or mutated in over 70% of all human tumours. These studies suggest that inhibition of PIP4K signalling constitutes a novel anti-cancer therapeutic target. In this review we will discuss the role of PIP4K in tumour suppression and speculate on how PIP4K modulates nuclear phosphoinositides (PPIns) and how this might impact on nuclear functions to regulate cell growth. This article is part of a Special Issue entitled Phosphoinositides.
Collapse
Affiliation(s)
- Roberta Fiume
- Cellular Signalling Laboratory, DIBINEM, University of Bologna, Bologna, Italy.
| | - Yvette Stijf-Bultsma
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Zahid H Shah
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Willem Jan Keune
- The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - David R Jones
- Oncology iMED, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, UK
| | - Julian Georg Jude
- IMP - Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Nullin Divecha
- Inositide Laboratory, Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Life Sciences Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
| |
Collapse
|
48
|
Wright BD, Simpson C, Stashko M, Kireev D, Hull-Ryde EA, Zylka MJ, Janzen WP. Development of a High-Throughput Screening Assay to Identify Inhibitors of the Lipid Kinase PIP5K1C. ACTA ACUST UNITED AC 2014; 20:655-62. [PMID: 25534829 DOI: 10.1177/1087057114564057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/23/2014] [Indexed: 11/16/2022]
Abstract
Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) regulate a variety of cellular processes, including signaling through G protein-coupled receptors (GPCRs), endocytosis, exocytosis, and cell migration. These lipid kinases synthesize phosphatidylinositol 4,5-bisphosphate (PIP2) from phosphatidylinositol 4-phosphate [PI(4)P]. Because small-molecule inhibitors of these lipid kinases did not exist, molecular and genetic approaches were predominantly used to study PIP5K1 regulation of these cellular processes. Moreover, standard radioisotope-based lipid kinase assays cannot be easily adapted for high-throughput screening. Here, we report a novel, high-throughput, microfluidic mobility shift assay to identify inhibitors of PIP5K1C. This assay uses fluorescently labeled phosphatidylinositol 4-phosphate as the substrate and recombinant human PIP5K1C. Our assay exhibited high reproducibility, had a calculated adenosine triphosphate Michaelis constant (Km) of 15 µM, performed with z' values >0.7, and was used to screen a kinase-focused library of ~4700 compounds. From this screen, we identified several potent inhibitors of PIP5K1C, including UNC3230, a compound that we recently found can reduce nociceptive sensitization in animal models of chronic pain. This novel assay will allow continued drug discovery efforts for PIP5K1C and can be adapted easily to screen additional lipid kinases.
Collapse
Affiliation(s)
- Brittany D Wright
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA National Center for Advancing Translational Science, Rockville, MD 20850
| | - Catherine Simpson
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Stashko
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dmitri Kireev
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily A Hull-Ryde
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark J Zylka
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
49
|
Mackey AM, Sarkes DA, Bettencourt I, Asara JM, Rameh LE. PIP4kγ is a substrate for mTORC1 that maintains basal mTORC1 signaling during starvation. Sci Signal 2014; 7:ra104. [PMID: 25372051 DOI: 10.1126/scisignal.2005191] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphatidylinositol-5-phosphate 4-kinases (PIP4ks) are a family of lipid kinases that specifically use phosphatidylinositol 5-monophosphate (PI-5-P) as a substrate to synthesize phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Suppression of PIP4k function in Drosophila results in smaller cells and reduced target of rapamycin complex 1 (TORC1) signaling. We showed that the γ isoform of PIP4k stimulated signaling through mammalian TORC1 (mTORC1). Knockdown of PIP4kγ reduced cell mass in cells in which mTORC1 is constitutively activated by Tsc2 deficiency. In Tsc2 null cells, mTORC1 activation was partially independent of amino acids or glucose and glutamine. PIP4kγ knockdown inhibited the nutrient-independent activation of mTORC1 in Tsc2 knockdown cells and reduced basal mTORC1 signaling in wild-type cells. PIP4kγ was phosphorylated by mTORC1 and associated with the complex. Phosphorylated PIP4kγ was enriched in light microsomal vesicles, whereas the unphosphorylated form was enriched in heavy microsomal vesicles associated with the Golgi. Furthermore, basal mTORC1 signaling was enhanced by overexpression of unphosphorylated wild-type PIP4kγ or a phosphorylation-defective mutant and decreased by overexpression of a phosphorylation-mimetic mutant. Together, these results demonstrate that PIP4kγ and mTORC1 interact in a self-regulated feedback loop to maintain low and tightly regulated mTORC1 activation during starvation.
Collapse
Affiliation(s)
- Ashley M Mackey
- Boston Biomedical Research Institute, Watertown, MA 02472, USA. Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Ian Bettencourt
- Boston Biomedical Research Institute, Watertown, MA 02472, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Lucia E Rameh
- Boston Biomedical Research Institute, Watertown, MA 02472, USA. Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| |
Collapse
|
50
|
Bulley SJ, Clarke JH, Droubi A, Giudici ML, Irvine RF. Exploring phosphatidylinositol 5-phosphate 4-kinase function. Adv Biol Regul 2014; 57:193-202. [PMID: 25311266 PMCID: PMC4359101 DOI: 10.1016/j.jbior.2014.09.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
The family of phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) is emerging from a comparative backwater in inositide signalling into the mainstream, as is their substrate, phosphatidylinositol 5-phosphate (PI5P). Here we review some of the key questions about the PI5P4Ks, their localisation, interaction, and regulation and also we summarise our current understanding of how PI5P is synthesised and what its cellular functions might be. Finally, some of the evidence for the involvement of PI5P4Ks in pathology is discussed.
Collapse
Affiliation(s)
- Simon J Bulley
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Jonathan H Clarke
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Alaa Droubi
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Robin F Irvine
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK.
| |
Collapse
|