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Haykir B, Moser SO, Pastor-Arroyo EM, Schnitzbauer U, Radvanyi Z, Prucker I, Qiu D, Fiedler D, Saiardi A, Jessen HJ, Hernando N, Wagner CA. The Ip6k1 and Ip6k2 Kinases Are Critical for Normal Renal Tubular Function. J Am Soc Nephrol 2024; 35:441-455. [PMID: 38317282 PMCID: PMC11000740 DOI: 10.1681/asn.0000000000000303] [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: 10/05/2023] [Accepted: 12/24/2023] [Indexed: 02/07/2024] Open
Abstract
SIGNIFICANCE STATEMENT Kidneys are gatekeepers of systemic inorganic phosphate balance because they control urinary phosphate excretion. In yeast and plants, inositol hexakisphosphate kinases (IP6Ks) are central to regulate phosphate metabolism, whereas their role in mammalian phosphate homeostasis is mostly unknown. We demonstrate in a renal cell line and in mice that Ip6k1 and Ip6k2 are critical for normal expression and function of the major renal Na + /Pi transporters NaPi-IIa and NaPi-IIc. Moreover, Ip6k1/2-/- mice also show symptoms of more generalized kidney dysfunction. Thus, our results suggest that IP6Ks are essential for phosphate metabolism and proper kidney function in mammals. BACKGROUND Inorganic phosphate is an essential mineral, and its plasma levels are tightly regulated. In mammals, kidneys are critical for maintaining phosphate homeostasis through mechanisms that ultimately regulate the expression of the Na + /Pi cotransporters NaPi-IIa and NaPi-IIc in proximal tubules. Inositol pyrophosphate 5-IP 7 , generated by IP6Ks, is a main regulator of phosphate metabolism in yeast and plants. IP6Ks are conserved in mammals, but their role in phosphate metabolism in vivo remains unexplored. METHODS We used in vitro (opossum kidney cells) and in vivo (renal tubular-specific Ip6k1/2-/- mice) models to analyze the role of IP6K1/2 in phosphate homeostasis in mammals. RESULTS In both systems, Ip6k1 and Ip6k2 are responsible for synthesis of 5-IP 7 . Depletion of Ip6k1/2 in vitro reduced phosphate transport and mRNA expression of Na + /Pi cotransporters, and it blunts phosphate transport adaptation to changes in ambient phosphate. Renal ablation of both kinases in mice also downregulates the expression of NaPi-IIa and NaPi-IIc and lowered the uptake of phosphate into proximal renal brush border membranes. In addition, the absence of Ip6k1 and Ip6k2 reduced the plasma concentration of fibroblast growth factor 23 and increased bone resorption, despite of which homozygous males develop hypophosphatemia. Ip6k1/2-/- mice also show increased diuresis, albuminuria, and hypercalciuria, although the morphology of glomeruli and proximal brush border membrane seemed unaffected. CONCLUSIONS Depletion of renal Ip6k1/2 in mice not only altered phosphate homeostasis but also dysregulated other kidney functions.
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Affiliation(s)
- Betül Haykir
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
| | - Seraina Olivia Moser
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
| | - Eva Maria Pastor-Arroyo
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
| | - Udo Schnitzbauer
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
| | - Zsuzsa Radvanyi
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
| | - Isabel Prucker
- The Center for Integrative Biological Signalling Studies, Institute of Organic Chemistry and CIBSS, University of Freiburg, Freiburg, Germany
| | - Danye Qiu
- The Center for Integrative Biological Signalling Studies, Institute of Organic Chemistry and CIBSS, University of Freiburg, Freiburg, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Henning J. Jessen
- The Center for Integrative Biological Signalling Studies, Institute of Organic Chemistry and CIBSS, University of Freiburg, Freiburg, Germany
| | - Nati Hernando
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
| | - Carsten A. Wagner
- Switzerland and National Center of Competence in Research NCCR Kidney.CH, Institute of Physiology, University of Zurich, Zürich, Switzerland
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Chakkour M, Greenberg ML. Insights into the roles of inositol hexakisphosphate kinase 1 (IP6K1) in mammalian cellular processes. J Biol Chem 2024; 300:107116. [PMID: 38403246 PMCID: PMC11065760 DOI: 10.1016/j.jbc.2024.107116] [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: 12/29/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/27/2024] Open
Abstract
Inositol phosphates and their metabolites play a significant role in several biochemical pathways, gene expression regulation, and phosphate homeostasis. Among the different inositol phosphates, inositol hexakisphosphate (IP6) is a substrate of inositol hexakisphosphate kinases (IP6Ks), which phosphorylate one or more of the IP6 phosphate groups. Pyrophosphorylation of IP6 leads to the formation of inositol pyrophosphates, high-energy signaling molecules that mediate physiological processes through their ability to modify target protein activities, either by directly binding to their target protein or by pyrophosphorylating protein serine residues. 5-diphosphoinositol pentakisphosphate, the most abundant inositol pyrophosphate in mammals, has been extensively studied and found to be significantly involved in a wide range of physiological processes. Three IP6K (IP6K1, IP6K2, and IP6K3) isoforms regulate IP7 synthesis in mammals. Here, we summarize our current understanding of IP6K1's roles in cytoskeletal remodeling, trafficking, cellular migration, metabolism, gene expression, DNA repair, and immunity. We also briefly discuss current gaps in knowledge, highlighting the need for further investigation.
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Affiliation(s)
- Mohamed Chakkour
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
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3
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Qi J, Shi L, Zhu L, Chen Y, Zhu H, Cheng W, Chen AF, Fu C. Functions, Mechanisms, and therapeutic applications of the inositol pyrophosphates 5PP-InsP 5 and InsP 8 in mammalian cells. J Cardiovasc Transl Res 2024; 17:197-215. [PMID: 37615888 DOI: 10.1007/s12265-023-10427-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]
Abstract
Water-soluble myo-inositol phosphates have long been characterized as second messengers. The signaling properties of these compounds are determined by the number and arrangement of phosphate groups on the myo-inositol backbone. Recently, higher inositol phosphates with pyrophosphate groups were recognized as signaling molecules. 5-Diphosphoinositol 1,2,3,4,6-pentakisphosphate (5PP-InsP5) is the most abundant isoform, constituting more than 90% of intracellular inositol pyrophosphates. 5PP-InsP5 can be further phosphorylated to 1,5-bisdiphosphoinositol 2,3,4,6-tetrakisphosphate (InsP8). These two molecules, 5PP-InsP5 and InsP8, are present in various subcellular compartments, where they participate in regulating diverse cellular processes such as cell death, energy homeostasis, and cytoskeletal dynamics. The synthesis and metabolism of inositol pyrophosphates are subjected to tight regulation, allowing for their highly specific functions. Blocking the 5PP-InsP5/InsP8 signaling pathway by inhibiting the biosynthesis of 5PP-InsP5 demonstrates therapeutic benefits in preclinical studies, and thus holds promise as a therapeutic approach for certain diseases treatment, such as metabolic disorders.
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Affiliation(s)
- Ji Qi
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Linhui Shi
- Department of Critical Care Unit, Ningbo Medical Center Li Huili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Limei Zhu
- Department of Trauma Orthopedics, Ningbo No.6 Hospital, Ningbo, 315040, China
| | - Yuanyuan Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Hong Zhu
- Department of Obstetrics and Gynecology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Weiwei Cheng
- Department of Nuclear Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Alex F Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Chenglai Fu
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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4
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Sunder S, Bauman JS, Decker SJ, Lifton AR, Kumar A. The yeast AMP-activated protein kinase Snf1 phosphorylates the inositol polyphosphate kinase Kcs1. J Biol Chem 2024; 300:105657. [PMID: 38224949 PMCID: PMC10851228 DOI: 10.1016/j.jbc.2024.105657] [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: 11/03/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
The yeast Snf1/AMP-activated kinase (AMPK) maintains energy homeostasis, controlling metabolic processes and glucose derepression in response to nutrient levels and environmental cues. Under conditions of nitrogen or glucose limitation, Snf1 regulates pseudohyphal growth, a morphological transition characterized by the formation of extended multicellular filaments. During pseudohyphal growth, Snf1 is required for wild-type levels of inositol polyphosphate (InsP), soluble phosphorylated species of the six-carbon cyclitol inositol that function as conserved metabolic second messengers. InsP levels are established through the activity of a family of inositol kinases, including the yeast inositol polyphosphate kinase Kcs1, which principally generates pyrophosphorylated InsP7. Here, we report that Snf1 regulates Kcs1, affecting Kcs1 phosphorylation and inositol kinase activity. A snf1 kinase-defective mutant exhibits decreased Kcs1 phosphorylation, and Kcs1 is phosphorylated in vivo at Ser residues 537 and 646 during pseudohyphal growth. By in vitro analysis, Snf1 directly phosphorylates Kcs1, predominantly at amino acids 537 and 646. A yeast strain carrying kcs1 encoding Ser-to-Ala point mutations at these residues (kcs1-S537A,S646A) shows elevated levels of pyrophosphorylated InsP7, comparable to InsP7 levels observed upon deletion of SNF1. The kcs1-S537A,S646A mutant exhibits decreased pseudohyphal growth, invasive growth, and cell elongation. Transcriptional profiling indicates extensive perturbation of metabolic pathways in kcs1-S537A,S646A. Growth of kcs1-S537A,S646A is affected on medium containing sucrose and antimycin A, consistent with decreased Snf1p signaling. This work identifies Snf1 phosphorylation of Kcs1, collectively highlighting the interconnectedness of AMPK activity and InsP signaling in coordinating nutrient availability, energy homoeostasis, and cell growth.
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Affiliation(s)
- Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Joshua S Bauman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stuart J Decker
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandra R Lifton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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5
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Bhat AA, Afzal O, Afzal M, Gupta G, Thapa R, Ali H, Hassan Almalki W, Kazmi I, Alzarea SI, Saleem S, Samuel VP, Gubbiyappa SK, Subramaniyan V. MALAT1: A key regulator in lung cancer pathogenesis and therapeutic targeting. Pathol Res Pract 2024; 253:154991. [PMID: 38070223 DOI: 10.1016/j.prp.2023.154991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024]
Abstract
Lung cancer remains a formidable global health burden, necessitating a comprehensive understanding of the underlying molecular mechanisms driving its progression. Recently, lncRNAs have become necessary controllers of various biological functions, including cancer development. MALAT1 has garnered significant attention due to its multifaceted role in lung cancer progression. Lung cancer, among other malignancies, upregulates MALAT1. Its overexpression has been associated with aggressive tumor behavior and poor patient prognosis. MALAT1 promotes cellular proliferation, epithelial-mesenchymal transition (EMT), and angiogenesis in lung cancer, collectively facilitating tumor growth and metastasis. Additionally, MALAT1 enhances cancer cell invasion by interacting with numerous signaling pathways. Furthermore, MALAT1 has been implicated in mediating drug resistance in lung cancer, contributing to the limited efficacy of conventional therapies. Recent advancements in molecular biology and high-throughput sequencing technologies have offered fresh perspectives into the regulatory networks of MALAT1 in lung cancer. It exerts its oncogenic effects by acting as a ceRNA to sponge microRNAs, thereby relieving their inhibitory effects on target genes. Moreover, MALAT1 also influences chromatin remodeling and post-translational modifications to modulate gene expression, further expanding its regulatory capabilities. This review sheds light on the multifaceted roles of MALAT1 in lung cancer progression, underscoring its potential as an innovative therapeutic target and diagnostic biomarker. Targeting MALAT1 alone or combined with existing therapies holds promise to mitigate lung cancer progression and improve patient outcomes.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health. College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Vijaya Paul Samuel
- Department of Anatomy, RAK College of Medicine, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE
| | | | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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6
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Bhat SA, Malla AB, Oddi V, Sen J, Bhandari R. Inositol hexakisphosphate kinase 1 is essential for cell junction integrity in the mouse seminiferous epithelium. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119596. [PMID: 37742721 DOI: 10.1016/j.bbamcr.2023.119596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
Inositol hexakisphosphate kinases (IP6Ks) are enzymes that catalyse the synthesis of the inositol pyrophosphate 5-IP7 which is involved in the regulation of many physiological processes in mammals. The IP6K paralog IP6K1 is expressed at high levels in the mammalian testis, and its deletion leads to sterility in male mice. Here, we show that the loss of IP6K1 in mice causes a delay in the first wave of spermatogenesis. Testes from juvenile Ip6k1 knockout mice show downregulation of transcripts that are involved in cell adhesion and formation of the testis-specific inter-Sertoli cell impermeable junction complex known as the blood-testis barrier (BTB). We demonstrate that loss of IP6K1 in the mouse testis causes BTB disruption associated with transcriptional misregulation of the tight junction protein claudin 3, and subcellular mislocalization of the gap junction protein connexin 43. In addition to BTB disruption, we also observe a loss of germ cell adhesion in the seminiferous epithelium of Ip6k1 knockout mice, ultimately resulting in premature sloughing of round spermatids into the epididymis. Mechanistically, we show that loss of IP6K1 in the testis enhances cofilin dephosphorylation in conjunction with increased AKT/ERK and integrin signalling, resulting in destabilization of the actin-based cytoskeleton in Sertoli cells and germ cell loss.
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Affiliation(s)
- Sameer Ahmed Bhat
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India
| | - Aushaq Bashir Malla
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India; Manipal Academy of Higher Education, Manipal 576104, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India
| | - Jayraj Sen
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India; Graduate Studies, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India.
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7
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Chen Y, Xu J, Liu X, Guo L, Yi P, Cheng C. Potential therapies targeting nuclear metabolic regulation in cancer. MedComm (Beijing) 2023; 4:e421. [PMID: 38034101 PMCID: PMC10685089 DOI: 10.1002/mco2.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023] Open
Abstract
The interplay between genetic alterations and metabolic dysregulation is increasingly recognized as a pivotal axis in cancer pathogenesis. Both elements are mutually reinforcing, thereby expediting the ontogeny and progression of malignant neoplasms. Intriguingly, recent findings have highlighted the translocation of metabolites and metabolic enzymes from the cytoplasm into the nuclear compartment, where they appear to be intimately associated with tumor cell proliferation. Despite these advancements, significant gaps persist in our understanding of their specific roles within the nuclear milieu, their modulatory effects on gene transcription and cellular proliferation, and the intricacies of their coordination with the genomic landscape. In this comprehensive review, we endeavor to elucidate the regulatory landscape of metabolic signaling within the nuclear domain, namely nuclear metabolic signaling involving metabolites and metabolic enzymes. We explore the roles and molecular mechanisms through which metabolic flux and enzymatic activity impact critical nuclear processes, including epigenetic modulation, DNA damage repair, and gene expression regulation. In conclusion, we underscore the paramount significance of nuclear metabolic signaling in cancer biology and enumerate potential therapeutic targets, associated pharmacological interventions, and implications for clinical applications. Importantly, these emergent findings not only augment our conceptual understanding of tumoral metabolism but also herald the potential for innovative therapeutic paradigms targeting the metabolism-genome transcriptional axis.
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Affiliation(s)
- Yanjie Chen
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Jie Xu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Xiaoyi Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Linlin Guo
- Department of Microbiology and ImmunologyThe Indiana University School of MedicineIndianapolisIndianaUSA
| | - Ping Yi
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Chunming Cheng
- Department of Radiation OncologyJames Comprehensive Cancer Center and College of Medicine at The Ohio State UniversityColumbusOhioUSA
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8
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Pullagurla NJ, Shome S, Yadav R, Laha D. ITPK1 Regulates Jasmonate-Controlled Root Development in Arabidopsis thaliana. Biomolecules 2023; 13:1368. [PMID: 37759768 PMCID: PMC10526342 DOI: 10.3390/biom13091368] [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: 07/01/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Jasmonic acid (JA) is a plant hormone that regulates a plethora of physiological processes including immunity and development and is perceived by the F-Box protein, Coronatine-insensitive protein 1 (COI1). The discovery of inositol phosphates (InsPs) in the COI1 receptor complex highlights their role in JAperception. InsPs are phosphate-rich signaling molecules that control many aspects of plant physiology. Inositol pyrophosphates (PP-InsPs) are diphosphate containing InsP species, of which InsP7 and InsP8 are the best characterized ones. Different InsP and PP-InsP species are linked with JA-related plant immunity. However, role of PP-InsP species in regulating JA-dependent developmental processes are poorly understood. Recent identification of ITPK1 kinase, responsible for the production of 5-InsP7 from InsP6in planta, provides a platform to investigate the possible involvement of ITPK-derived InsP species in JA-related plant development. Here, in this study, we report that ITPK1-defective plants exhibit increased root growth inhibition to bioactive JA treatment. The itpk1 plants also show increased lateral root density when treated with JA. Notably, JA treatment does not increase ITPK1 protein levels. Gene expression analyses revealed that JA-biosynthetic genes are not differentially expressed in ITPK1-deficient plants. We further demonstrate that genes encoding different JAZ repressor proteins are severely down-regulated in ITPK1-defective plants. Taken together, our study highlights the role of ITPK1 in regulating JA-dependent root architecture development through controlling the expression of different JAZ repressor proteins.
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Affiliation(s)
| | | | | | - Debabrata Laha
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science (IISc), Bengaluru 560012, India; (N.J.P.); (S.S.); (R.Y.)
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9
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Lin H, Leman LJ, Krishnamurthy R. One-pot chemical pyro- and tri-phosphorylation of peptides by using diamidophosphate in water. Chem Sci 2022; 13:13741-13747. [PMID: 36544739 PMCID: PMC9713773 DOI: 10.1039/d2sc04160j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
Protein (pyro)phosphorylation is emerging as a post-translational modification (PTM) in signalling pathways involved in many cellular processes. However, access to synthetic pyrophosphopeptides that can serve as tools for understanding protein pyrophosphorylation is quite limited. Herein, we report a chemical phosphorylation method that enables the synthesis of pyrophosphopeptides in aqueous medium without the need for protecting groups. The strategy employs diamidophosphate (DAP) in a one-pot sequential phosphorylation-hydrolysis of mono-phosphorylated peptide precursors. This operationally simple method exploits the intrinsic nucleophilicity of a phosphate moiety installed on serine, threonine or tyrosine residues in complex peptides with excellent chemoselectivity and good yields under mild conditions. We demonstrate the installation of the pyrophosphate group within a wide range of model peptides and showcase the potential of this methodology by selectively pyrophosphorylating the highly functionalized Nopp140 peptide fragment. The potential to produce higher (poly)phosphorylated peptides was demonstrated as a proof-of-principle experiment where we synthesized the triphosphorylated peptides using this one-pot strategy.
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Affiliation(s)
- Huacan Lin
- Department of Chemistry, The Scripps Research InstituteLa JollaCalifornia 92037USA
| | - Luke J. Leman
- Department of Chemistry, The Scripps Research InstituteLa JollaCalifornia 92037USA
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10
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Lazcano P, Schmidtke MW, Onu C, Greenberg ML. Phosphatidic acid inhibits inositol synthesis by inducing nuclear translocation of kinase IP6K1 and repression of myo-inositol-3-P synthase. J Biol Chem 2022; 298:102363. [PMID: 35963434 PMCID: PMC9478396 DOI: 10.1016/j.jbc.2022.102363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Inositol is an essential metabolite that serves as a precursor for structural and signaling molecules. Although perturbation of inositol homeostasis has been implicated in numerous human disorders, surprisingly little is known about how inositol levels are regulated in mammalian cells. A recent study in mouse embryonic fibroblasts demonstrated that nuclear translocation of inositol hexakisphosphate kinase 1 (IP6K1) mediates repression of myo-inositol-3-P synthase (MIPS), the rate-limiting inositol biosynthetic enzyme. Binding of IP6K1 to phosphatidic acid (PA) is required for this repression. Here, we elucidate the role of PA in IP6K1 repression. Our results indicate that increasing PA levels through pharmacological stimulation of phospholipase D (PLD) or direct supplementation of 18:1 PA induces nuclear translocation of IP6K1 and represses expression of the MIPS protein. We found that this effect was specific to PA synthesized in the plasma membrane, as endoplasmic reticulum–derived PA did not induce IP6K1 translocation. Furthermore, we determined that PLD-mediated PA synthesis can be stimulated by the master metabolic regulator 5′ AMP-activated protein kinase (AMPK). We show that activation of AMPK by glucose deprivation or by treatment with the mood-stabilizing drugs valproate or lithium recapitulated IP6K1 nuclear translocation and decreased MIPS expression. This study demonstrates for the first time that modulation of PA levels through the AMPK-PLD pathway regulates IP6K1-mediated repression of MIPS.
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Affiliation(s)
- Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Michael W Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
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11
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Beon J, Han S, Yang H, Park SE, Hyun K, Lee SY, Rhee HW, Seo JK, Kim J, Kim S, Lee D. Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells. eLife 2022; 11:73523. [PMID: 35551737 PMCID: PMC9098221 DOI: 10.7554/elife.73523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Inositol polyphosphate multikinase (IPMK), a key enzyme in inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events, including transcriptional control. In the yeast, IPMK and its IP products promote the activity of the chromatin remodeling complex SWI/SNF, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct link between IPMK and chromatin remodelers remains unclear, raising the question of how IPMK contributes to transcriptional regulation in mammals. By employing unbiased screening approaches and in vivo/in vitro immunoprecipitation, here we demonstrate that mammalian IPMK physically interacts with the SWI/SNF complex by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for IPMK-SMARCB1 binding. Notably, using CUT&RUN and ATAC-seq assays, we discovered that IPMK co-localizes with BRG1 and regulates BRG1 localization as well as BRG1-mediated chromatin accessibility in a genome-wide manner in mouse embryonic stem cells. Together, these findings show that IPMK regulates the promoter targeting of the SWI/SNF complex, thereby contributing to SWI/SNF-meditated chromatin accessibility, transcription, and differentiation in mouse embryonic stem cells.
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Affiliation(s)
- Jiyoon Beon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sungwook Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hyeokjun Yang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seung Eun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,KAIST Stem Cell Center, KAIST, Daejeon, Republic of Korea.,KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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12
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Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
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13
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Declerck K, Novo CP, Grielens L, Van Camp G, Suter A, Vanden Berghe W. Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences. BMC Complement Med Ther 2021; 21:141. [PMID: 33980308 PMCID: PMC8114977 DOI: 10.1186/s12906-021-03310-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Herbal remedies of Echinacea purpurea tinctures are widely used today to reduce common cold respiratory tract infections. Methods Transcriptome, epigenome and kinome profiling allowed a systems biology level characterisation of genomewide immunomodulatory effects of a standardized Echinacea purpurea (L.) Moench extract in THP1 monocytes. Results Gene expression and DNA methylation analysis revealed that Echinaforce® treatment triggers antiviral innate immunity pathways, involving tonic IFN signaling, activation of pattern recognition receptors, chemotaxis and immunometabolism. Furthermore, phosphopeptide based kinome activity profiling and pharmacological inhibitor experiments with filgotinib confirm a key role for Janus Kinase (JAK)-1 dependent gene expression changes in innate immune signaling. Finally, Echinaforce® treatment induces DNA hypermethylation at intergenic CpG, long/short interspersed nuclear DNA repeat elements (LINE, SINE) or long termininal DNA repeats (LTR). This changes transcription of flanking endogenous retroviral sequences (HERVs), involved in an evolutionary conserved (epi) genomic protective response against viral infections. Conclusions Altogether, our results suggest that Echinaforce® phytochemicals strengthen antiviral innate immunity through tonic IFN regulation of pattern recognition and chemokine gene expression and DNA repeat hypermethylated silencing of HERVs in monocytes. These results suggest that immunomodulation by Echinaforce® treatment holds promise to reduce symptoms and duration of infection episodes of common cold corona viruses (CoV), Severe Acute Respiratory Syndrome (SARS)-CoV, and new occurring strains such as SARS-CoV-2, with strongly impaired interferon (IFN) response and weak innate antiviral defense. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03310-5.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Claudina Perez Novo
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Lisa Grielens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, Department of Biomedical Sciences, University of Antwerp (UA) and University Hospital Antwerp (UZA), Antwerp, Belgium
| | | | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium.
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14
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Laha D, Portela-Torres P, Desfougères Y, Saiardi A. Inositol phosphate kinases in the eukaryote landscape. Adv Biol Regul 2020; 79:100782. [PMID: 33422459 PMCID: PMC8024741 DOI: 10.1016/j.jbior.2020.100782] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023]
Abstract
Inositol phosphate encompasses a large multifaceted family of signalling molecules that originate from the combinatorial attachment of phosphate groups to the inositol ring. To date, four distinct inositol kinases have been identified, namely, IPK, ITPK, IPPK (IP5-2K), and PPIP5K. Although, ITPKs have recently been identified in archaea, eukaryotes have taken advantage of these enzymes to create a sophisticated signalling network based on inositol phosphates. However, it remains largely elusive what fundamental biochemical principles control the signalling cascade. Here, we present an evolutionary approach to understand the development of the 'inositol phosphate code' in eukaryotes. Distribution analyses of these four inositol kinase groups throughout the eukaryotic landscape reveal the loss of either ITPK, or of PPIP5K proteins in several species. Surprisingly, the loss of IPPK, an enzyme thought to catalyse the rate limiting step of IP6 (phytic acid) synthesis, was also recorded. Furthermore, this study highlights a noteworthy difference between animal (metazoan) and plant (archaeplastida) lineages. While metazoan appears to have a substantial amplification of IPK enzymes, archaeplastida genomes show a considerable increase in ITPK members. Differential evolution of IPK and ITPK between plant and animal lineage is likely reflective of converging functional adaptation of these two types of inositol kinases. Since, the IPK family comprises three sub-types IPMK, IP6K, and IP3-3K each with dedicated enzymatic specificity in metazoan, we propose that the amplified ITPK group in plant could be classified in sub-types with distinct enzymology.
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Affiliation(s)
- Debabrata Laha
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Paloma Portela-Torres
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Yann Desfougères
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK.
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15
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Minini M, Senni A, Unfer V, Bizzarri M. The Key Role of IP 6K: A Novel Target for Anticancer Treatments? Molecules 2020; 25:molecules25194401. [PMID: 32992691 PMCID: PMC7583815 DOI: 10.3390/molecules25194401] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Inositol and its phosphate metabolites play a pivotal role in several biochemical pathways and gene expression regulation: inositol pyrophosphates (PP-IPs) have been increasingly appreciated as key signaling modulators. Fluctuations in their intracellular levels hugely impact the transfer of phosphates and the phosphorylation status of several target proteins. Pharmacological modulation of the proteins associated with PP-IP activities has proved to be beneficial in various pathological settings. IP7 has been extensively studied and found to play a key role in pathways associated with PP-IP activities. Three inositol hexakisphosphate kinase (IP6K) isoforms regulate IP7 synthesis in mammals. Genomic deletion or enzymic inhibition of IP6K1 has been shown to reduce cell invasiveness and migration capacity, protecting against chemical-induced carcinogenesis. IP6K1 could therefore be a useful target in anticancer treatment. Here, we summarize the current understanding that established IP6K1 and the other IP6K isoforms as possible targets for cancer therapy. However, it will be necessary to determine whether pharmacological inhibition of IP6K is safe enough to begin clinical study. The development of safe and selective inhibitors of IP6K isoforms is required to minimize undesirable effects.
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Affiliation(s)
- Mirko Minini
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy;
- Department of Surgery ‘P. Valdoni’, Sapienza University of Rome, 00161 Rome, Italy
- Systems Biology Group Lab, Sapienza University of Rome, 00185 Rome, Italy;
- Correspondence: (M.M.); (M.B.)
| | - Alice Senni
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy;
- Department of Surgery ‘P. Valdoni’, Sapienza University of Rome, 00161 Rome, Italy
| | - Vittorio Unfer
- Systems Biology Group Lab, Sapienza University of Rome, 00185 Rome, Italy;
| | - Mariano Bizzarri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy;
- Systems Biology Group Lab, Sapienza University of Rome, 00185 Rome, Italy;
- Correspondence: (M.M.); (M.B.)
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16
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Izzotti A, Ceccaroli C, Geretto M, Ruggieri FG, Schenone S, Di Maria E. Predicting Response to Neoadjuvant Therapy in Colorectal Cancer Patients the Role of Messenger-and Micro-RNA Profiling. Cancers (Basel) 2020; 12:cancers12061652. [PMID: 32580435 PMCID: PMC7352797 DOI: 10.3390/cancers12061652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer patients' responses to neoadjuvant therapy undergo broad inter-individual variations. The aim of this systematic review is to identify a molecular signature that is predictive of colon cancer downstaging and/or downgrading after neoadjuvant therapy. Among the hundreds analysed in the available studies, only 19 messenger-RNAs (mRNAs) and six micro-RNAs (miRNAs) were differentially expressed in responders versus non-responders in two or more independent studies. Therefore, a mRNA/miRNA signature can be designed accordingly, with limitations caused by the retrospective nature of these studies, the heterogeneity in study designs and the downgrading/downstaging assessment criteria. This signature can be proposed to tailor neoadjuvant therapy regimens on an individual basis.
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Affiliation(s)
- Alberto Izzotti
- Department of Experimental Medicine, University of Genova, 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy;
- Correspondence: ; Tel.: +39-010-353-8522
| | | | - Marta Geretto
- Department of Experimental Medicine, University of Genova, 16132 Genova, Italy;
| | | | - Sara Schenone
- Department of Health Sciences, University of Genova, 16132 Genova, Italy; (S.S.); (E.D.M.)
| | - Emilio Di Maria
- Department of Health Sciences, University of Genova, 16132 Genova, Italy; (S.S.); (E.D.M.)
- Unit of Medical Genetics, Galliera Hospital, 16128 Genoa, Italy
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17
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Inositol Pyrophosphates: Signaling Molecules with Pleiotropic Actions in Mammals. Molecules 2020; 25:molecules25092208. [PMID: 32397291 PMCID: PMC7249018 DOI: 10.3390/molecules25092208] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
Inositol pyrophosphates (PP-IPs) such as 5-diphosphoinositol pentakisphosphate (5-IP7) are inositol metabolites containing high-energy phosphoanhydride bonds. Biosynthesis of PP-IPs is mediated by IP6 kinases (IP6Ks) and PPIP5 kinases (PPIP5Ks), which transfer phosphate to inositol hexakisphosphate (IP6). Pleiotropic actions of PP-IPs are involved in many key biological processes, including growth, vesicular remodeling, and energy homeostasis. PP-IPs function to regulate their target proteins through allosteric interactions or protein pyrophosphorylation. This review summarizes the current understanding of how PP-IPs control mammalian cellular signaling networks in physiology and disease.
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18
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Case KC, Salsaa M, Yu W, Greenberg ML. Regulation of Inositol Biosynthesis: Balancing Health and Pathophysiology. Handb Exp Pharmacol 2020; 259:221-260. [PMID: 30591968 DOI: 10.1007/164_2018_181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Inositol is the precursor for all inositol compounds and is essential for viability of eukaryotic cells. Numerous cellular processes and signaling functions are dependent on inositol compounds, and perturbation of their synthesis leads to a wide range of human diseases. Although considerable research has been directed at understanding the function of inositol compounds, especially phosphoinositides and inositol phosphates, a focus on regulatory and homeostatic mechanisms controlling inositol biosynthesis has been largely neglected. Consequently, little is known about how synthesis of inositol is regulated in human cells. Identifying physiological regulators of inositol synthesis and elucidating the molecular mechanisms that regulate inositol synthesis will contribute fundamental insight into cellular processes that are mediated by inositol compounds and will provide a foundation to understand numerous disease processes that result from perturbation of inositol homeostasis. In addition, elucidating the mechanisms of action of inositol-depleting drugs may suggest new strategies for the design of second-generation pharmaceuticals to treat psychiatric disorders and other illnesses.
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Affiliation(s)
- Kendall C Case
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Michael Salsaa
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Wenxi Yu
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
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19
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Wu X, Li R, Song Q, Zhang C, Jia R, Han Z, Zhou L, Sui H, Liu X, Zhu H, Yang L, Wang Y, Ji Q, Li Q. JMJD2C promotes colorectal cancer metastasis via regulating histone methylation of MALAT1 promoter and enhancing β-catenin signaling pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:435. [PMID: 31665047 PMCID: PMC6819649 DOI: 10.1186/s13046-019-1439-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/06/2019] [Indexed: 12/26/2022]
Abstract
Background Our previous work demonstrated that lncRNA-MALAT1 was overexpressed in recurrent colorectal cancer (CRC) and metastatic sites in post-surgical patients. However, the upstream regulatory mechanism of MALAT1 is not well-defined. Histone demethylase JMJD2C holds great potential of epigenetic regulating mechanism in tumor diseases, especially the moderating effect on the promoter activity of targeted genes associated closely with tumor development. Therefore, we herein investigated whether JMJD2C could epigeneticly regulate the promoter activity of MALAT1 and the downstream β-catenin signaling pathway, thereby affecting the metastatic abilities of CRC cells. Methods JMJD2C expressions in human CRC samples were detected by real-time PCR and immunohistochemistry staining. Gene silencing and overexpressing efficiencies of JMJD2C were confirmed by real-time PCR and western blot. The migration of CRC cells in vitro were tested by transwell and wound healing assays. The protein expression and cellular localization of JMJD2C and β-catenin were characterized by immunofluorescence staining and western blot. The histone methylation level of MALAT1 promoter region (H3K9me3 and H3K36me3) was tested by ChIP-PCR assays. The promoter activity of MALAT1 was detected by luciferase reporter assay. The expressions of MALAT1 and the downstream β-catenin signaling pathway related genes in CRC cells were detected by real-time PCR and western blot, respectively. The nude mice tail vein metastasis model was established to observe the effect of JMJD2C on the lung metastasis of CRC cells in vivo. Results Our present results indicated that histone demethylase JMJD2C was overexpressed in matched CRC tumor tissues of primary and metastatic foci, and CRC patients with lower JMJD2C expression in primary tumors had better prognosis with longer OS (Overall Survival). The following biological function observation suggested that JMJD2C promoted CRC metastasis in vitro and in vivo. Further molecular mechanism investigation demonstrated that JMJD2C protein translocated into the nuclear, lowered the histone methylation level of MALAT1 promoter in the sites of H3K9me3 and H3K36me3, up-regulated the expression of MALAT1, and enhanced the β-catenin signaling pathway in CRC cells. Conclusion Our data demonstrated that JMJD2C could enhance the metastatic abilities of CRC cells in vitro and in vivo by regulating the histone methylation level of MALAT1 promoter, thereby up-regulating the expression of MALAT1 and enhancing the activity of β-catenin signaling pathway, providing that JMJD2C might be a novel therapeutic target for CRC metastasis.
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Affiliation(s)
- Xinnan Wu
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ruixiao Li
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Song
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Medical Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Chengcheng Zhang
- Department of Medical Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ru Jia
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhifen Han
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lihong Zhou
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hua Sui
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xuan Liu
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huirong Zhu
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liu Yang
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yan Wang
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Ji
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Qi Li
- Department of Medical Oncology and Cancer Institute of Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China. .,Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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20
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Hung KH, Woo YH, Lin IY, Liu CH, Wang LC, Chen HY, Chiang BL, Lin KI. The KDM4A/KDM4C/NF-κB and WDR5 epigenetic cascade regulates the activation of B cells. Nucleic Acids Res 2019; 46:5547-5560. [PMID: 29718303 PMCID: PMC6009645 DOI: 10.1093/nar/gky281] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
T follicular helper (Tfh) cell-derived signals promote activation and proliferation of antigen-primed B cells. It remains unclear whether epigenetic regulation is involved in the B cell responses to Tfh cell-derived signals. Here, we demonstrate that Tfh cell-mimicking signals induce the expression of histone demethylases KDM4A and KDM4C, and the concomitant global down-regulation of their substrates, H3K9me3/me2, in B cells. Depletion of KDM4A and KDM4C potentiates B cell activation and proliferation in response to Tfh cell-derived signals. ChIP-seq and de novo motif analysis reveals NF-κB p65 as a binding partner of KDM4A and KDM4C. Their co-targeting to Wdr5, a MLL complex member promoting H3K4 methylation, up-regulates cell cycle inhibitors Cdkn2c and Cdkn3. Thus, Tfh cell-derived signals trigger KDM4A/KDM4C - WDR5 - Cdkn2c/Cdkn3 cascade in vitro, an epigenetic mechanism regulating proper proliferation of activated B cells. This pathway is dysregulated in B cells from systemic lupus erythematosus patients and may represent a pathological link.
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Affiliation(s)
- Kuo-Hsuan Hung
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yong H Woo
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - I-Ying Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Hsiu Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.,PhD Program in Translational Medicine, Kaohsiung Medical University and Academia Sinica, Division of Allergy, Immunology and Rheumatology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan
| | - Li-Chieh Wang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hsin-Yu Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Bor-Luen Chiang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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21
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Inositol hexakisphosphate kinase 3 promotes focal adhesion turnover via interactions with dynein intermediate chain 2. Proc Natl Acad Sci U S A 2019; 116:3278-3287. [PMID: 30718399 DOI: 10.1073/pnas.1817001116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cells express a family of three inositol hexakisphosphate kinases (IP6Ks). Although sharing the same enzymatic activity, individual IP6Ks mediate different cellular processes. Here we report that IP6K3 is enriched at the leading edge of migrating cells where it associates with dynein intermediate chain 2 (DIC2). Using immunofluorescence microscopy and total internal reflection fluorescence microscopy, we found that DIC2 and IP6K3 are recruited interdependently to the leading edge of migrating cells, where they function coordinately to enhance the turnover of focal adhesions. Deletion of IP6K3 causes defects in cell motility and neuronal dendritic growth, eventually leading to brain malformations. Our results reveal a mechanism whereby IP6K3 functions in coordination with DIC2 in a confined intracellular microenvironment to promote focal adhesion turnover.
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22
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FDHE-IW: A Fast Approach for Detecting High-Order Epistasis in Genome-Wide Case-Control Studies. Genes (Basel) 2018; 9:genes9090435. [PMID: 30158504 PMCID: PMC6162554 DOI: 10.3390/genes9090435] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022] Open
Abstract
Detecting high-order epistasis in genome-wide association studies (GWASs) is of importance when characterizing complex human diseases. However, the enormous numbers of possible single-nucleotide polymorphism (SNP) combinations and the diversity among diseases presents a significant computational challenge. Herein, a fast method for detecting high-order epistasis based on an interaction weight (FDHE-IW) method is evaluated in the detection of SNP combinations associated with disease. First, the symmetrical uncertainty (SU) value for each SNP is calculated. Then, the top-k SNPs are isolated as guiders to identify 2-way SNP combinations with significant interaction weight values. Next, a forward search is employed to detect high-order SNP combinations with significant interaction weight values as candidates. Finally, the findings were statistically evaluated using a G-test to isolate true positives. The developed algorithm was used to evaluate 12 simulated datasets and an age-related macular degeneration (AMD) dataset and was shown to perform robustly in the detection of some high-order disease-causing models.
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23
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Garcia J, Lizcano F. Kdm4c is Recruited to Mitotic Chromosomes and Is Relevant for Chromosomal Stability, Cell Migration and Invasion of Triple Negative Breast Cancer Cells. BREAST CANCER-BASIC AND CLINICAL RESEARCH 2018; 12:1178223418773075. [PMID: 30083054 PMCID: PMC6073829 DOI: 10.1177/1178223418773075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/04/2018] [Indexed: 01/23/2023]
Abstract
Members of the jumonji-containing lysine demethylase protein family have been associated with cancer development, although their specific roles in the evolution of tumor cells remain unknown. This work examines the effects of lysine demethylase 4C (KDM4C) knockdown on the behavior of a triple-negative breast cancer cell line. KDM4C expression was knocked-down by siRNA and analyzed by Western blot and immunofluorescence. HCC38 cell proliferation was examined by MTT assay, while breast cancer cells’ migration and invasion were tested in Transwell format by chemotaxis. Immunofluorescence assays showed that KDM4C, which is a key protein for modulating histone demethylation and chromosome stability through the distribution of genetic information, is located at the chromosomes during mitosis. Proliferation assays demonstrated that KDM4C is important for cell survival, while Transwell migration and invasion assays indicated that this protein is relevant for cancer progression. These data indicate that KDM4C is relevant for breast cancer progression and highlight its importance as a potential therapeutic target.
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Affiliation(s)
- Jeison Garcia
- Doctorate in Biociences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
| | - Fernando Lizcano
- Doctorate in Biociences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
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24
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Phospholipids and inositol phosphates linked to the epigenome. Histochem Cell Biol 2018; 150:245-253. [DOI: 10.1007/s00418-018-1690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2018] [Indexed: 12/17/2022]
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25
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Norman KL, Shively CA, De La Rocha AJ, Mutlu N, Basu S, Cullen PJ, Kumar A. Inositol polyphosphates regulate and predict yeast pseudohyphal growth phenotypes. PLoS Genet 2018; 14:e1007493. [PMID: 29939992 PMCID: PMC6034902 DOI: 10.1371/journal.pgen.1007493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/06/2018] [Accepted: 06/14/2018] [Indexed: 11/18/2022] Open
Abstract
Pseudohyphal growth is a nutrient-regulated program in which budding yeast form multicellular filaments of elongated and connected cells. Filamentous growth is required for virulence in pathogenic fungi and provides an informative model of stress-responsive signaling. The genetics and regulatory networks modulating pseudohyphal growth have been studied extensively, but little is known regarding the changes in metabolites that enable pseudohyphal filament formation. Inositol signaling molecules are an important class of metabolite messengers encompassing highly phosphorylated and diffusible inositol polyphosphates (InsPs). We report here that the InsP biosynthesis pathway is required for wild-type pseudohyphal growth. Under nitrogen-limiting conditions that can induce filamentation, InsPs exhibit characteristic profiles, distinguishing the InsP7 pyrophosphate isoforms 1PP-InsP5 and 5PP-InsP5. Deletion and overexpression analyses of InsP kinases identify elevated levels of 5PP-InsP5 relative to 1PP-InsP5 in mutants exhibiting hyper-filamentous growth. Overexpression of KCS1, which promotes formation of inositol pyrophosphates, is sufficient to drive pseudohyphal filamentation on medium with normal nitrogen levels. We find that the kinases Snf1p (AMPK), Kss1p, and Fus3p (MAPKs), required for wild-type pseudohyphal growth, are also required for wild-type InsP levels. Deletion analyses of the corresponding kinase genes indicate elevated InsP3 levels and an absence of exaggerated 5PP-InsP5 peaks in trace profiles from snf1Δ/Δ and kss1Δ/Δ mutants exhibiting decreased pseudohyphal filamentation. Elevated 5PP-InsP5:1PP-InsP5 ratios are present in the hyperfilamentous fus3 deletion mutant. Collectively, the data identify the presence of elevated 5PP-InsP5 levels relative to other inositol pyrophosphates as an in vivo marker of hyper-filamentous growth, while providing initial evidence for the regulation of InsP signaling by pseudohyphal growth kinases. Changes in metabolite levels underlie important biological processes, including cellular responses to nutrient stress. One such response encompasses the nitrogen stress-induced transition of budding yeast cells into multicellular filaments, relevant as a model of directional growth and fungal pathogenesis. We report here that a conserved family of charged lipid-derived metabolites, inositol polyphosphates, exhibits characteristic changes as yeast cell form filaments in response to conditions of nitrogen limitation. The ratios of doubly charged inositol pyrophosphates consistently match with the degree of filament formation. Enzymes of the inositol polyphosphate synthesis pathway are required for filament formation, and inositol polyphosphate levels are dependent on kinases that enable wild-type filamentation. Our data indicate that inositol polyphosphates mark filamentous growth states, highlighting a new regulatory role for these ubiquitous eukaryotic second messengers.
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Affiliation(s)
- Kaitlyn L. Norman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christian A. Shively
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amberlene J. De La Rocha
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nebibe Mutlu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sukanya Basu
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Paul J. Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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26
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Fu P, Ebenezer DL, Ha AW, Suryadevara V, Harijith A, Natarajan V. Nuclear lipid mediators: Role of nuclear sphingolipids and sphingosine-1-phosphate signaling in epigenetic regulation of inflammation and gene expression. J Cell Biochem 2018; 119:6337-6353. [PMID: 29377310 DOI: 10.1002/jcb.26707] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/23/2018] [Indexed: 12/18/2022]
Abstract
Phospholipids, sphingolipids, and cholesterol are integral components of eukaryotic cell organelles, including the nucleus. Recent evidence shows characteristic features of nuclear lipid composition and signaling, which are distinct from that of the cytoplasm and plasma membrane. While the nuclear phosphoinositol lipid signaling in cell cycle regulation and differentiation has been well described, there is a paucity on the role of nuclear sphingolipids and sphingolipid signaling in different physiological and pathophysiological human conditions. In this prospective, we describe the role of sphingolipids and specifically focus on the sphingoid bases, such as sphingosine, ceramide, and sphingosine-1-phosphate (S1P) generation and catabolism in nuclear signaling and function. Particularly, S1P generated in the nucleus by phosphorylation of SPHK2 modulates HDAC activity either by direct binding or through activation of nuclear reactive oxygen species and regulates cell cycle and pro-inflammatory gene expression. Potential implication of association of SPHK2 with the co-repressor complexes and generation of S1P in the nucleus on chromatin remodeling under normal and pathological conditions is discussed. A better understanding of sphingolipid signaling in the nucleus will facilitate the design and development of new and novel therapeutic approaches to modulate expression of pro-inflammatory and cell cycle dependent genes in human pathologies such as cancer, bacterial lung infection, neurodegeneration, and cystic fibrosis.
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Affiliation(s)
- Panfeng Fu
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - David L Ebenezer
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois
| | - Alison W Ha
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois
| | | | - Anantha Harijith
- Department of Pediatrics, University of Illinois, Chicago, Illinois
| | - Viswanathan Natarajan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois.,Department of Medicine, University of Illinois, Chicago, Illinois
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27
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Elich M, Sauer K. Regulation of Hematopoietic Cell Development and Function Through Phosphoinositides. Front Immunol 2018; 9:931. [PMID: 29780388 PMCID: PMC5945867 DOI: 10.3389/fimmu.2018.00931] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/16/2018] [Indexed: 01/01/2023] Open
Abstract
One of the most paramount receptor-induced signal transduction mechanisms in hematopoietic cells is production of the lipid second messenger phosphatidylinositol(3,4,5)trisphosphate (PIP3) by class I phosphoinositide 3 kinases (PI3K). Defective PIP3 signaling impairs almost every aspect of hematopoiesis, including T cell development and function. Limiting PIP3 signaling is particularly important, because excessive PIP3 function in lymphocytes can transform them and cause blood cancers. Here, we review the key functions of PIP3 and related phosphoinositides in hematopoietic cells, with a special focus on those mechanisms dampening PIP3 production, turnover, or function. Recent studies have shown that beyond “canonical” turnover by the PIP3 phosphatases and tumor suppressors phosphatase and tensin homolog (PTEN) and SH2 domain-containing inositol-5-phosphatase-1 (SHIP-1/2), PIP3 function in hematopoietic cells can also be dampened through antagonism with the soluble PIP3 analogs inositol(1,3,4,5)tetrakisphosphate (IP4) and inositol-heptakisphosphate (IP7). Other evidence suggests that IP4 can promote PIP3 function in thymocytes. Moreover, IP4 or the kinases producing it limit store-operated Ca2+ entry through Orai channels in B cells, T cells, and neutrophils to control cell survival and function. We discuss current models for how soluble inositol phosphates can have such diverse functions and can govern as distinct processes as hematopoietic stem cell homeostasis, neutrophil macrophage and NK cell function, and development and function of B cells and T cells. Finally, we will review the pathological consequences of dysregulated IP4 activity in immune cells and highlight contributions of impaired inositol phosphate functions in disorders such as Kawasaki disease, common variable immunodeficiency, or blood cancer.
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Affiliation(s)
- Mila Elich
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Karsten Sauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,Oncology R&D, Pfizer Worldwide R&D, San Diego, CA, United States
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28
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Fu C, Rojas T, Chin AC, Cheng W, Bernstein IA, Albacarys LK, Wright WW, Snyder SH. Multiple aspects of male germ cell development and interactions with Sertoli cells require inositol hexakisphosphate kinase-1. Sci Rep 2018; 8:7039. [PMID: 29728588 PMCID: PMC5935691 DOI: 10.1038/s41598-018-25468-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/19/2018] [Indexed: 12/30/2022] Open
Abstract
Inositol hexakisphosphate kinase-1 (IP6K1) is required for male fertility, but the underlying mechanisms have been elusive. Here, we report that IP6K1 is required for multiple aspects of male germ cell development. This development requires selective interactions between germ cells and Sertoli cells, namely apical ectoplasmic specialization. Spermiation (sperm release) requires tubulobulbar complexes. We found that the apical ectoplasmic specialization and tubulobulbar complexes were poorly formed or disrupted in IP6K1 KOs. Deletion of IP6K1 elicited several aberrations, including: 1, sloughing off of round germ cells; 2, disorientation and malformation of elongating/elongated spermatids; 3, degeneration of acrosomes; 4, defects in germ-Sertoli cell interactions and 5, failure of spermiation. Eventually the sperm cells were not released but phagocytosed by Sertoli cells leading to an absence of sperm in the epididymis.
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Affiliation(s)
- Chenglai Fu
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, 300070, China. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Tomas Rojas
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alfred C Chin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Weiwei Cheng
- Division of Neuropathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Isaac A Bernstein
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Lauren K Albacarys
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - William W Wright
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Solomon H Snyder
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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29
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Chakraborty A. The inositol pyrophosphate pathway in health and diseases. Biol Rev Camb Philos Soc 2018; 93:1203-1227. [PMID: 29282838 PMCID: PMC6383672 DOI: 10.1111/brv.12392] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Inositol pyrophosphates (IPPs) are present in organisms ranging from plants, slime moulds and fungi to mammals. Distinct classes of kinases generate different forms of energetic diphosphate-containing IPPs from inositol phosphates (IPs). Conversely, polyphosphate phosphohydrolase enzymes dephosphorylate IPPs to regenerate the respective IPs. IPPs and/or their metabolizing enzymes regulate various cell biological processes by modulating many proteins via diverse mechanisms. In the last decade, extensive research has been conducted in mammalian systems, particularly in knockout mouse models of relevant enzymes. Results obtained from these studies suggest impacts of the IPP pathway on organ development, especially of brain and testis. Conversely, deletion of specific enzymes in the pathway protects mice from various diseases such as diet-induced obesity (DIO), type-2 diabetes (T2D), fatty liver, bacterial infection, thromboembolism, cancer metastasis and aging. Furthermore, pharmacological inhibition of the same class of enzymes in mice validates the therapeutic importance of this pathway in cardio-metabolic diseases. This review critically analyses these findings and summarizes the significance of the IPP pathway in mammalian health and diseases. It also evaluates benefits and risks of targeting this pathway in disease therapies. Finally, future directions of mammalian IPP research are discussed.
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Affiliation(s)
- Anutosh Chakraborty
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, MO 63104, U.S.A
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30
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Cordeiro CD, Saiardi A, Docampo R. The inositol pyrophosphate synthesis pathway in Trypanosoma brucei is linked to polyphosphate synthesis in acidocalcisomes. Mol Microbiol 2017; 106:319-333. [PMID: 28792096 DOI: 10.1111/mmi.13766] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
Abstract
Inositol pyrophosphates are novel signaling molecules possessing high-energy pyrophosphate bonds and involved in a number of biological functions. Here, we report the correct identification and characterization of the kinases involved in the inositol pyrophosphate biosynthetic pathway in Trypanosoma brucei: inositol polyphosphate multikinase (TbIPMK), inositol pentakisphosphate 2-kinase (TbIP5K) and inositol hexakisphosphate kinase (TbIP6K). TbIP5K and TbIP6K were not identifiable by sequence alone and their activities were validated by enzymatic assays with the recombinant proteins or by their complementation of yeast mutants. We also analyzed T. brucei extracts for the presence of inositol phosphates using polyacrylamide gel electrophoresis and high-performance liquid chromatography. Interestingly, we could detect inositol phosphate (IP), inositol 4,5-bisphosphate (IP2 ), inositol 1,4,5-trisphosphate (IP3 ), and inositol hexakisphosphate (IP6 ) in T. brucei different stages. Bloodstream forms unable to produce inositol pyrophosphates, due to downregulation of TbIPMK expression by conditional knockout, have reduced levels of polyphosphate and altered acidocalcisomes. Our study links the inositol pyrophosphate pathway to the synthesis of polyphosphate in acidocalcisomes, and may lead to better understanding of these organisms and provide new targets for drug discovery.
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Affiliation(s)
- Ciro D Cordeiro
- Department of Cellular Biology, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E 6BT, Gower Street, London, UK
| | - Roberto Docampo
- Department of Cellular Biology, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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31
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Histone demethylase JMJD2C: epigenetic regulators in tumors. Oncotarget 2017; 8:91723-91733. [PMID: 29207681 PMCID: PMC5710961 DOI: 10.18632/oncotarget.19176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022] Open
Abstract
Histone methylation is one of the major epigenetic modifications, and various histone methylases and demethylases participate in the epigenetic regulating. JMJD2C has been recently identified as one of the histone lysine demethylases. As one member of the Jumonji-C histone demethylase family, JMJD2C has the ability to demethylate tri- or di-methylated histone 3 and 2 in either K9 (lysine residue 9) or K36 (lysine residue 36) sites by an oxidative reaction, thereby affecting heterochromatin formation, genomic imprinting, X-chromosome inactivation, and transcriptional regulation of genes. JMJD2C was firstly found to involve in embryonic development and stem cell regulation. Afterwards, aberrant status of JMJD2C histone methylation was observed during the formation and development of various tumors, and it has been reported to play crucial roles in the progression of breast cancer, prostate carcinomas, osteosarcoma, blood neoplasms and so on, indicating that JMJD2C represents a promising anti-cancer target. In this review, we will focus on the research progress and prospect of JMJD2C in tumors, and provide abundant evidence for the functional application and therapeutic potential of targeting JMJD2C in tumors.
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32
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Hamann BL, Blind RD. Nuclear phosphoinositide regulation of chromatin. J Cell Physiol 2017; 233:107-123. [PMID: 28256711 DOI: 10.1002/jcp.25886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022]
Abstract
Phospholipid signaling has clear connections to a wide array of cellular processes, particularly in gene expression and in controlling the chromatin biology of cells. However, most of the work elucidating how phospholipid signaling pathways contribute to cellular physiology have studied cytoplasmic membranes, while relatively little attention has been paid to the role of phospholipid signaling in the nucleus. Recent work from several labs has shown that nuclear phospholipid signaling can have important roles that are specific to this cellular compartment. This review focuses on the nuclear phospholipid functions and the activities of phospholipid signaling enzymes that regulate metazoan chromatin and gene expression. In particular, we highlight the roles that nuclear phosphoinositides play in several nuclear-driven physiological processes, such as differentiation, proliferation, and gene expression. Taken together, the recent discovery of several specifically nuclear phospholipid functions could have dramatic impact on our understanding of the fundamental mechanisms that enable tight control of cellular physiology.
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Affiliation(s)
- Bree L Hamann
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Raymond D Blind
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Departments of Medicine, Biochemistry and Pharmacology, Division of Diabetes Endocrinology and Metabolism, The Vanderbilt Diabetes Research and Training Center and the Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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33
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Shah A, Ganguli S, Sen J, Bhandari R. Inositol Pyrophosphates: Energetic, Omnipresent and Versatile Signalling Molecules. J Indian Inst Sci 2017; 97:23-40. [PMID: 32214696 PMCID: PMC7081659 DOI: 10.1007/s41745-016-0011-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy-rich signalling molecules found in all eukaryotic cells. These are derivatives of inositol that contain one or more diphosphate (or pyrophosphate) groups in addition to monophosphates. The more abundant and best studied PP-IPs are diphosphoinositol pentakisphosphate (IP7) and bis-diphosphoinositol tetrakisphosphate (IP8). These molecules can influence protein function by two mechanisms: binding and pyrophosphorylation. The former involves the specific interaction of a particular inositol pyrophosphate with a binding site on a protein, while the latter is a unique attribute of inositol pyrophosphates, wherein the β-phosphate moiety is transferred from a PP-IP to a pre-phosphorylated serine residue in a protein to generate pyrophosphoserine. Both these events can result in changes in the target protein’s activity, localisation or its interaction with other partners. As a consequence of their ubiquitous presence in all eukaryotic organisms and all cell types examined till date, and their ability to modify protein function, PP-IPs have been found to participate in a wide range of metabolic, developmental, and signalling pathways. This review highlights
many of the known functions of PP-IPs in the context of their temporal and spatial distribution in eukaryotic cells.
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Affiliation(s)
- Akruti Shah
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Jayraj Sen
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
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Abstract
To help define the molecular basis of cellular signalling cascades, and their biological functions, there is considerable value in utilizing a high-quality chemical 'probe' that has a well-defined interaction with a specific cellular protein. Such reagents include inhibitors of protein kinases and small molecule kinases, as well as mimics or antagonists of intracellular signals. The purpose of this review is to consider recent progress and promising future directions for the development of novel molecules that can interrogate and manipulate the cellular actions of inositol pyrophosphates (PP-IPs)--a specialized, 'energetic' group of cell-signalling molecules in which multiple phosphate and diphosphate groups are crammed around a cyclohexane polyol scaffold.
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35
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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.
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36
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Shears SB, Baughman BM, Gu C, Nair VS, Wang H. The significance of the 1-kinase/1-phosphatase activities of the PPIP5K family. Adv Biol Regul 2016; 63:98-106. [PMID: 27776974 DOI: 10.1016/j.jbior.2016.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/29/2023]
Abstract
The inositol pyrophosphates (diphosphoinositol polyphosphates), which include 1-InsP7, 5-InsP7, and InsP8, are highly 'energetic' signaling molecules that play important roles in many cellular processes, particularly with regards to phosphate and bioenergetic homeostasis. Two classes of kinases synthesize the PP-InsPs: IP6Ks and PPIP5Ks. The significance of the IP6Ks - and their 5-InsP7 product - has been widely reported. However, relatively little is known about the biological significance of the PPIP5Ks. The purpose of this review is to provide an update on developments in our understanding of key features of the PPIP5Ks, which we believe strengthens the hypothesis that their catalytic activities serve important cellular functions. Central to this discussion is the recent discovery that the PPIP5K is a rare example of a single protein that catalyzes a kinase/phosphatase futile cycle.
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Affiliation(s)
- Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Brandi M Baughman
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Chunfang Gu
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Vasudha S Nair
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Huanchen Wang
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 101 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
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37
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Zhu Q, Ghoshal S, Rodrigues A, Gao S, Asterian A, Kamenecka TM, Barrow JC, Chakraborty A. Adipocyte-specific deletion of Ip6k1 reduces diet-induced obesity by enhancing AMPK-mediated thermogenesis. J Clin Invest 2016; 126:4273-4288. [PMID: 27701146 DOI: 10.1172/jci85510] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/29/2016] [Indexed: 12/15/2022] Open
Abstract
Enhancing energy expenditure (EE) is an attractive strategy to combat obesity and diabetes. Global deletion of Ip6k1 protects mice from diet-induced obesity (DIO) and insulin resistance, but the tissue-specific mechanism by which IP6K1 regulates body weight is unknown. Here, we have demonstrated that IP6K1 regulates fat accumulation by modulating AMPK-mediated adipocyte energy metabolism. Cold exposure led to downregulation of Ip6k1 in murine inguinal and retroperitoneal white adipose tissue (IWAT and RWAT) depots. Adipocyte-specific deletion of Ip6k1 (AdKO) enhanced thermogenic EE, which protected mice from high-fat diet-induced weight gain at ambient temperature (23°C), but not at thermoneutral temperature (30°C). AdKO-induced increases in thermogenesis also protected mice from cold-induced decreases in body temperature. UCP1, PGC1α, and other markers of browning and thermogenesis were elevated in IWAT and RWAT of AdKO mice. Cold-induced activation of sympathetic signaling was unaltered, whereas AMPK was enhanced, in AdKO IWAT. Moreover, beige adipocytes from AdKO IWAT displayed enhanced browning, which was diminished by AMPK depletion. Furthermore, we determined that IP6 and IP6K1 differentially regulate upstream kinase-mediated AMPK stimulatory phosphorylation in vitro. Finally, treating mildly obese mice with the IP6K inhibitor TNP enhanced thermogenesis and inhibited progression of DIO. Thus, IP6K1 regulates energy metabolism via a mechanism that could potentially be targeted in obesity.
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Contribution of polymorphic variation of inositol hexakisphosphate kinase 3 ( IP6K3 ) gene promoter to the susceptibility to late onset Alzheimer's disease. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1766-73. [DOI: 10.1016/j.bbadis.2016.06.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/19/2016] [Accepted: 06/14/2016] [Indexed: 01/16/2023]
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Thota SG, Bhandari R. The emerging roles of inositol pyrophosphates in eukaryotic cell physiology. J Biosci 2016; 40:593-605. [PMID: 26333405 DOI: 10.1007/s12038-015-9549-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inositol pyrophosphates are water soluble derivatives of inositol that contain pyrophosphate or diphosphate moieties in addition to monophosphates. The best characterised inositol pyrophosphates, are IP7 (diphosphoinositol pentakisphosphate or PP-IP5), and IP8 (bisdiphosphoinositol tetrakisphosphate or (PP)2-IP4). These energy-rich small molecules are present in all eukaryotic cells, from yeast to mammals, and are involved in a wide range of cellular functions including apoptosis, vesicle trafficking, DNA repair, osmoregulation, phosphate homeostasis, insulin sensitivity, immune signalling, cell cycle regulation, and ribosome synthesis. Identified more than 20 years ago, there is still only a rudimentary understanding of the mechanisms by which inositol pyrophosphates participate in these myriad pathways governing cell physiology and homeostasis. The unique stereochemical and bioenergetic properties these molecules possess as a consequence of the presence of one or two pyrophosphate moieties in the vicinity of densely packed monophosphates are likely to form the molecular basis for their participation in multiple signalling and metabolic pathways. The aim of this review is to provide first time researchers in this area with an introduction to inositol pyrophosphates and a comprehensive overview on their cellular functions.
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Affiliation(s)
- Swarna Gowri Thota
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
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40
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Deletion of inositol hexakisphosphate kinase 1 (IP6K1) reduces cell migration and invasion, conferring protection from aerodigestive tract carcinoma in mice. Cell Signal 2016; 28:1124-36. [PMID: 27140681 PMCID: PMC4913618 DOI: 10.1016/j.cellsig.2016.04.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/20/2016] [Accepted: 04/28/2016] [Indexed: 11/21/2022]
Abstract
Inositol hexakisphosphate kinases (IP6Ks), a family of enzymes found in all eukaryotes, are responsible for the synthesis of 5-diphosphoinositol pentakisphosphate (5-IP7) from inositol hexakisphosphate (IP6). Three isoforms of IP6Ks are found in mammals, and gene deletions of each isoform lead to diverse, non-overlapping phenotypes in mice. Previous studies show a facilitatory role for IP6K2 in cell migration and invasion, properties that are essential for the early stages of tumorigenesis. However, IP6K2 also has an essential role in cancer cell apoptosis, and mice lacking this protein are more susceptible to the development of aerodigestive tract carcinoma upon treatment with the oral carcinogen 4-nitroquinoline-1-oxide (4NQO). Not much is known about the functions of the equally abundant and ubiquitously expressed IP6K1 isoform in cell migration, invasion and cancer progression. We conducted a gene expression analysis on mouse embryonic fibroblasts (MEFs) lacking IP6K1, revealing a role for this protein in cell receptor-extracellular matrix interactions that regulate actin cytoskeleton dynamics. Consequently, cells lacking IP6K1 manifest defects in adhesion-dependent signaling, evident by lower FAK and Paxillin activation, leading to reduced cell spreading and migration. Expression of active, but not inactive IP6K1 reverses migration defects in IP6K1 knockout MEFs, suggesting that 5-IP7 synthesis by IP6K1 promotes cell locomotion. Actin cytoskeleton remodeling and cell migration support the ability of cancer cells to achieve their complete oncogenic potential. Cancer cells with lower IP6K1 levels display reduced migration, invasion, and anchorage-independent growth. When fed an oral carcinogen, mice lacking IP6K1 show reduced progression from epithelial dysplasia to invasive carcinoma. Thus, our data reveal that like IP6K2, IP6K1 is also involved in early cytoskeleton remodeling events during cancer progression. However, unlike IP6K2, IP6K1 is essential for 4NQO-induced invasive carcinoma. Our study therefore uncovers similarities and differences in the roles of IP6K1 and IP6K2 in cancer progression, and we propose that an isoform-specific IP6K1 inhibitor may provide a novel route to suppress carcinogenesis. Gene-expression analysis of Ip6k1 knockout MEFs reveals down-regulation of cell surface-extracellular matrix signaling. Ip6k1 knockout MEFs show reduced adhesion-dependent signaling, cell spreading and migration. Cancer cells deficient in IP6K1 display reduced migration, invasion and anchorage independent growth. Mice lacking IP6K1 are resistant to progression from epithelial dysplasia to invasive carcinoma.
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41
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Yu W, Greenberg ML. Inositol depletion, GSK3 inhibition and bipolar disorder. FUTURE NEUROLOGY 2016; 11:135-148. [PMID: 29339929 DOI: 10.2217/fnl-2016-0003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/04/2016] [Indexed: 12/31/2022]
Abstract
Valproic acid and lithium are widely used to treat bipolar disorder, a severe illness characterized by cycles of mania and depression. However, their efficacy is limited, and treatment is often accompanied by serious side effects. The therapeutic mechanisms of these drugs are not understood, hampering the development of more effective treatments. Among the plethora of biochemical effects of the drugs, those that are common to both may be more related to therapeutic efficacy. Two common outcomes include inositol depletion and GSK3 inhibition, which have been proposed to explain the efficacy of both valproic acid and lithium. Here, we discuss the inositol depletion and GSK3 inhibition hypotheses, and introduce a unified model suggesting that inositol depletion and GSK3 inhibition are inter-related.
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Affiliation(s)
- Wenxi Yu
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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42
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Yu W, Ye C, Greenberg ML. Inositol Hexakisphosphate Kinase 1 (IP6K1) Regulates Inositol Synthesis in Mammalian Cells. J Biol Chem 2016; 291:10437-44. [PMID: 26953345 DOI: 10.1074/jbc.m116.714816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Indexed: 01/12/2023] Open
Abstract
myo-Inositol, the precursor of all inositol compounds, has pivotal roles in cell metabolism and signaling pathways. Although physiological studies indicate a strong correlation between abnormal intracellular inositol levels and neurological disorders, very little is known about the regulation of inositol synthesis in mammalian cells. In this study, we report that IP6K1, an inositol hexakisphosphate kinase that catalyzes the synthesis of inositol pyrophosphate, regulates inositol synthesis in mammalian cells. Ip6k1 ablation led to profound changes in DNA methylation and expression of Isyna1 (designated mIno1), which encodes the rate-limiting enzyme inositol-3-phosphate synthase. Interestingly, IP6K1 preferentially bound to the phospholipid phosphatidic acid, and this binding was required for IP6K1 nuclear localization and the regulation of mIno1 transcription. This is the first demonstration of IP6K1 as a novel negative regulator of inositol synthesis in mammalian cells.
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Affiliation(s)
- Wenxi Yu
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Cunqi Ye
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Miriam L Greenberg
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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43
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Abstract
Eukaryotic cells have ubiquitously utilized the myo-inositol backbone to generate a diverse array of signalling molecules. This is achieved by arranging phosphate groups around the six-carbon inositol ring. There is virtually no biological process that does not take advantage of the uniquely variable architecture of phosphorylated inositol. In inositol biology, phosphates are able to form three distinct covalent bonds: phosphoester, phosphodiester and phosphoanhydride bonds, with each providing different properties. The phosphoester bond links phosphate groups to the inositol ring, the variable arrangement of which forms the basis of the signalling capacity of the inositol phosphates. Phosphate groups can also form the structural bridge between myo-inositol and diacylglycerol through the phosphodiester bond. The resulting lipid-bound inositol phosphates, or phosphoinositides, further expand the signalling potential of this family of molecules. Finally, inositol is also notable for its ability to host more phosphates than it has carbons. These unusual organic molecules are commonly referred to as the inositol pyrophosphates (PP-IPs), due to the presence of high-energy phosphoanhydride bonds (pyro- or diphospho-). PP-IPs themselves constitute a varied family of molecules with one or more pyrophosphate moiety/ies located around the inositol. Considering the relationship between phosphate and inositol, it is no surprise that members of the inositol phosphate family also regulate cellular phosphate homoeostasis. Notably, the PP-IPs play a fundamental role in controlling the metabolism of the ancient polymeric form of phosphate, inorganic polyphosphate (polyP). Here we explore the intimate links between phosphate, inositol phosphates and polyP, speculating on the evolution of these relationships.
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Williams FJ, Fiedler D. A Fluorescent Sensor and Gel Stain for Detection of Pyrophosphorylated Proteins. ACS Chem Biol 2015; 10:1958-63. [PMID: 26061479 DOI: 10.1021/acschembio.5b00256] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The design and synthesis of a fluorescent sensor of diphosphate esters along with its application for in-gel detection is described. Dinuclear zinc complex 1 selectively binds diphosphate esters in the presence of various other functional groups, including monophosphate esters. Complex 1 also constitutes a competent stain for visualization of pyrophosphorylated proteins in polyacrylamide gels. This reagent will facilitate the validation and exploration of protein pyrophosphorylation.
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Affiliation(s)
- Florence J. Williams
- Department
of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Department
of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
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Jung ES, Sim YJ, Jeong HS, Kim SJ, Yun YJ, Song JH, Jeon SH, Choe C, Park KT, Kim CH, Kim KS. Jmjd2C increases MyoD transcriptional activity through inhibiting G9a-dependent MyoD degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1081-94. [PMID: 26149774 DOI: 10.1016/j.bbagrm.2015.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/17/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023]
Abstract
Skeletal muscle cell differentiation requires a family of proteins called myogenic regulatory factors (MRFs) to which MyoD belongs. The activity of MyoD is under epigenetic regulation, however, the molecular mechanism by which histone KMTs and KDMs regulate MyoD transcriptional activity through methylation remains to be determined. Here we provide evidence for a unique regulatory mechanism of MyoD transcriptional activity through demethylation by Jmjd2C demethylase whose level increases during muscle differentiation. G9a decreases MyoD stability via methylation-dependent MyoD ubiquitination. Jmjd2C directly associates with MyoD in vitro and in vivo to demethylate and stabilize MyoD. The hypo-methylated MyoD due to Jmjd2C is significantly more stable than hyper-methylated MyoD by G9a. Cul4/Ddb1/Dcaf1 pathway is essential for the G9a-mediated MyoD degradation in myoblasts. By the stabilization of MyoD, Jmjd2C increases myogenic conversion of mouse embryonic fibroblasts and MyoD transcriptional activity with erasing repressive H3K9me3 level at the promoter of MyoD target genes. Collectively, Jmjd2C increases MyoD transcriptional activity to facilitate skeletal muscle differentiation by increasing MyoD stability through inhibiting G9a-dependent MyoD degradation.
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Affiliation(s)
- Eun-Shil Jung
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Ye-Ji Sim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Hoe-Su Jeong
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Su-Jin Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Ye-Jin Yun
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Joo-Hoon Song
- Bio Focus Co., Ltd., Gyeonggi-do 437-753, Republic of Korea
| | - Su-Hee Jeon
- Department of Biological & Environmental Science, Dongguk University, Seoul 100-175, Republic of Korea
| | - Chungyoul Choe
- Samsung Biomedical Research Institute, School of Medicine, Sungkyunkwan University, Seoul 135-710, Republic of Korea
| | - Kyung-Tae Park
- Center for Cancer Research, Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Chang-Hoon Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea.
| | - Kye-Seong Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea.
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Ye Q, Holowatyj A, Wu J, Liu H, Zhang L, Suzuki T, Yang ZQ. Genetic alterations of KDM4 subfamily and therapeutic effect of novel demethylase inhibitor in breast cancer. Am J Cancer Res 2015; 5:1519-1530. [PMID: 26101715 PMCID: PMC4473328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023] Open
Abstract
The histone lysine demethylase KDM4 subfamily, comprised of four members (A, B, C, and D), play critical roles in controlling transcription, chromatin architecture and cellular differentiation. We previously demonstrated that KDM4C is significantly amplified and overexpressed in aggressive basal-like breast cancers and functions as a transforming oncogene. However, information regarding the genomic and transcriptomic alterations of the KDM4 subfamily in different subtypes of breast cancer remains largely incomplete. Here, we conducted a meta-analysis of KDM4A, B, C and D in breast cancer and identified associations among recurrent copy number alterations, gene expression and breast cancer subtypes. We demonstrated that KDM4A and D are also significantly overexpressed in basal-like breast cancer, whereas KDM4B overexpression is more dominant in estrogen-receptor-positive, luminal breast cancer. Next, we investigated the therapeutic potential of a novel histone demethylase inhibitor, NCDM-32B, in breast cancer. The treatment of basal breast cancer cell lines with NCDM-32B resulted in the decrease of cell viability and anchorage independent growth in soft agar. Furthermore, we found that NCDM-32B impaired several critical pathways that drive cellular proliferation and transformation in breast cancer. Our findings demonstrate genetic amplification and overexpression of the KDM4 demethylases in different subtypes of breast cancer. Furthermore, histone methylation is reversible and KDM4 demethylases are druggable targets. Thus, KDM4 inhibitors may serve as a novel therapeutic approach for a subset of aggressive breast cancer.
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Affiliation(s)
- Qin Ye
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
- School of Life Science, Jiangsu Normal UniversityJiangsu 221116, China
| | - Andreana Holowatyj
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
| | - Jack Wu
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
| | - Hui Liu
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
| | - Lihong Zhang
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
- Shandong Provincial Research Institute for Family PlanningJinan, Shandong 250002, China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of MedicineKyoto, 606-0823, Japan
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer InstituteDetroit, MI 48201, USA
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47
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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.
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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.
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48
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Yates LM, Fiedler D. Establishing the Stability and Reversibility of Protein Pyrophosphorylation with Synthetic Peptides. Chembiochem 2015; 16:415-23. [DOI: 10.1002/cbic.201402589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 12/24/2022]
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49
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Rao F, Xu J, Khan AB, Gadalla MM, Cha JY, Xu R, Tyagi R, Dang Y, Chakraborty A, Snyder SH. Inositol hexakisphosphate kinase-1 mediates assembly/disassembly of the CRL4-signalosome complex to regulate DNA repair and cell death. Proc Natl Acad Sci U S A 2014; 111:16005-10. [PMID: 25349427 PMCID: PMC4234592 DOI: 10.1073/pnas.1417900111] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inositol polyphosphates containing an energetic pyrophosphate bond are formed primarily by a family of three inositol hexakisphosphate (IP6) kinases (IP6K1-3). The Cullin-RING ubiquitin ligases (CRLs) regulate diverse biological processes through substrate ubiquitylation. CRL4, comprising the scaffold Cullin 4A/B, the E2-interacting Roc1/2, and the adaptor protein damage-specific DNA-binding protein 1, is activated by DNA damage. Basal CRL4 activity is inhibited by binding to the COP9 signalosome (CSN). UV radiation and other stressors dissociate the complex, leading to E3 ligase activation, but signaling events that trigger signalosome dissociation from CRL4 have been unclear. In the present study, we show that, under basal conditions, IP6K1 forms a ternary complex with CSN and CRL4 in which IP6K1 and CRL4 are inactive. UV dissociates IP6K1 to generate IP7, which then dissociates CSN-CRL4 to activate CRL4. Thus, IP6K1 is a novel CRL4 subunit that transduces UV signals to mediate disassembly of the CRL4-CSN complex, thereby regulating nucleotide excision repair and cell death.
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Affiliation(s)
- Feng Rao
- The Solomon H. Snyder Department of Neuroscience
| | - Jing Xu
- The Solomon H. Snyder Department of Neuroscience
| | - A Basit Khan
- The Solomon H. Snyder Department of Neuroscience
| | - Moataz M Gadalla
- The Solomon H. Snyder Department of Neuroscience, Department of Pharmacology and Molecular Sciences, and
| | | | - Risheng Xu
- The Solomon H. Snyder Department of Neuroscience, Department of Pharmacology and Molecular Sciences, and
| | - Richa Tyagi
- The Solomon H. Snyder Department of Neuroscience
| | - Yongjun Dang
- Department of Pharmacology and Molecular Sciences, and
| | | | - Solomon H Snyder
- The Solomon H. Snyder Department of Neuroscience, Department of Pharmacology and Molecular Sciences, and Department of Psychiatry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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50
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Desai M, Rangarajan P, Donahue JL, Williams SP, Land ES, Mandal MK, Phillippy BQ, Perera IY, Raboy V, Gillaspy GE. Two inositol hexakisphosphate kinases drive inositol pyrophosphate synthesis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:642-53. [PMID: 25231822 DOI: 10.1111/tpj.12669] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 05/24/2023]
Abstract
Inositol pyrophosphates are unique cellular signaling molecules with recently discovered roles in energy sensing and metabolism. Studies in eukaryotes have revealed that these compounds have a rapid turnover, and thus only small amounts accumulate. Inositol pyrophosphates have not been the subject of investigation in plants even though seeds produce large amounts of their precursor, myo-inositol hexakisphosphate (InsP6 ). Here, we report that Arabidopsis and maize InsP6 transporter mutants have elevated levels of inositol pyrophosphates in their seed, providing unequivocal identification of their presence in plant tissues. We also show that plant seeds store a little over 1% of their inositol phosphate pool as InsP7 and InsP8 . Many tissues, including, seed, seedlings, roots and leaves accumulate InsP7 and InsP8 , thus synthesis is not confined to tissues with high InsP6 . We have identified two highly similar Arabidopsis genes, AtVip1 and AtVip2, which are orthologous to the yeast and mammalian VIP kinases. Both AtVip1 and AtVip2 encode proteins capable of restoring InsP7 synthesis in yeast mutants, thus AtVip1 and AtVip2 can function as bonafide InsP6 kinases. AtVip1 and AtVip2 are differentially expressed in plant tissues, suggesting non-redundant or non-overlapping functions in plants. These results contribute to our knowledge of inositol phosphate metabolism and will lay a foundation for understanding the role of InsP7 and InsP8 in plants.
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Affiliation(s)
- Mintu Desai
- Department of Plant and Microbial Biology, North Carolina State University, Room 4209, Gardner Hall, Raleigh, NC 27695, USA
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