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Brewer KM, Brewer KK, Richardson NC, Berbari NF. Neuronal cilia in energy homeostasis. Front Cell Dev Biol 2022; 10:1082141. [PMID: 36568981 PMCID: PMC9773564 DOI: 10.3389/fcell.2022.1082141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
A subset of genetic disorders termed ciliopathies are associated with obesity. The mechanisms behind cilia dysfunction and altered energy homeostasis in these syndromes are complex and likely involve deficits in both development and adult homeostasis. Interestingly, several cilia-associated gene mutations also lead to morbid obesity. While cilia have critical and diverse functions in energy homeostasis, including their roles in centrally mediated food intake and peripheral tissues, many questions remain. Here, we briefly discuss syndromic ciliopathies and monogenic cilia signaling mutations associated with obesity. We then focus on potential ways neuronal cilia regulate energy homeostasis. We discuss the literature around cilia and leptin-melanocortin signaling and changes in ciliary G protein-coupled receptor (GPCR) signaling. We also discuss the different brain regions where cilia are implicated in energy homeostasis and the potential for cilia dysfunction in neural development to contribute to obesity. We close with a short discussion on the challenges and opportunities associated with studies looking at neuronal cilia and energy homeostasis. This review highlights how neuronal cilia-mediated signaling is critical for proper energy homeostasis.
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Affiliation(s)
- Kathryn M. Brewer
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Katlyn K. Brewer
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Nicholas C. Richardson
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Nicolas F. Berbari
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States,Stark Neurosciences Research Institute, Indiana University, Indianapolis, IN, United States,Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, United States,*Correspondence: Nicolas F. Berbari,
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2
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Deng J, Lin X, Li Q, Cai XY, Wu LW, Wang W, Zhang B, Li YL, Hu J, Lin NM. Decreased INPP5B expression predicts poor prognosis in lung adenocarcinoma. Cancer Cell Int 2022; 22:189. [PMID: 35568951 PMCID: PMC9107680 DOI: 10.1186/s12935-022-02609-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Inositol Polyphosphate-5-Phosphatase B (INPP5B), a inositol 5-phosphatase, plays an important role in many biological processes through phosphorylating PI(4,5)P2 and/or PI(3,4,5)P3 at the 5-position. Nevertheless, little is known about its function and cellular pathways in tumors. This study aims to investigate the potential role of INPP5B as a diagnostic and prognostic biomarker for lung adenocarcinoma (LUAD), as well as its biological functions and molecular mechanisms in LUAD. Methods TCGA, GEO, CTPAC, and HPA datasets were used for differential expression analysis and pathological stratification comparison. The prognostic and diagnostic role of INPP5B was determined by Kaplan–Meier curves, univariate and multivariate Cox regression analysis, and receiver operating characteristics (ROC) curve analyses. The potential mechanism of INPP5B was explored through GO, KEGG, and GSEA enrichment analysis, as well as GeneMANIA and STRING protein–protein interaction (PPI) network. PicTar, PITA, and miRmap databases were used for exploring miRNA targeting INPP5B. In molecular biology experiments, immunohistochemical analyses and Western blot analyses were used to determine protein expression. Co-immunoprecipitation assay was used to detect protein–protein interactions. CCK8 assays and colony formation assays were used for the measurement of cell proliferation. Cell cycle was assessed by PI staining with flow cytometry. Cell migration was performed by Transwell assays and wound healing assays. Result INPP5B was decreased in LUAD tissues compared with normal adjacent tissues. And the low expression of INPP5B was associated with late-stage pathological features. In addition, INPP5B was found to be a significant independent prognostic and diagnostic factor for LUAD patients. Hsa-miR-582-5p was predicted as a negative regulator of INPP5B mRNA expression. INPP5B was significantly correlated with the expression of PTEN and the activity of PI3K/AKT signaling pathways, as determined by enrichment analysis and PPI network. In vitro experiments partially confirmed the aforementioned findings. INPP5B could interact directly with PTEN. INPP5B overexpression inhibited LUAD cell proliferation and migration while downregulating the AKT pathway. Conclusion Our results demonstrated that INPP5B could inhibit the proliferation and metastasis of LUAD cells. It could serve as a novel diagnostic and prognostic biomarker for LUAD patients. Trial registration LUAD tissues and corresponding para-cancerous tissues were collected from 10 different LUAD patients at Hangzhou First People’s Hospital. The Ethics Committee of Hangzhou First People’s Hospital has approved this study. (registration number: IIT-20210907-0031-01; registration date: 2021.09.13) Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02609-8.
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Affiliation(s)
- Jun Deng
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Xu Lin
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qi Li
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Xiao-Yu Cai
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.,Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Lin-Wen Wu
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.,Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Wei Wang
- Department of Pathology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Bo Zhang
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.,Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Yang-Ling Li
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.,Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Jian Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Neng-Ming Lin
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China. .,Department of Clinical Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China. .,Westlake Laboratory of Life Sciences and Biomedicine of Zhejiang Province, Hangzhou, 310024, China. .,Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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3
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Walpole GFW, Pacheco J, Chauhan N, Clark J, Anderson KE, Abbas YM, Brabant-Kirwan D, Montaño-Rendón F, Liu Z, Zhu H, Brumell JH, Deiters A, Stephens LR, Hawkins PT, Hammond GRV, Grinstein S, Fairn GD. Kinase-independent synthesis of 3-phosphorylated phosphoinositides by a phosphotransferase. Nat Cell Biol 2022; 24:708-722. [PMID: 35484249 PMCID: PMC9107517 DOI: 10.1038/s41556-022-00895-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 03/08/2022] [Indexed: 01/10/2023]
Abstract
Despite their low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and their survival in host organisms. We demonstrate that PtdIns(3,4)P2 is a major product generated in host cells by the effectors of the enteropathogenic bacteria Salmonella and Shigella. Pharmacological, gene silencing and heterologous expression experiments revealed that, remarkably, the biosynthesis of PtdIns(3,4)P2 occurs independently of phosphoinositide 3-kinases. Instead, we found that the Salmonella effector SopB, heretofore believed to be a phosphatase, generates PtdIns(3,4)P2 de novo via a phosphotransferase/phosphoisomerase mechanism. Recombinant SopB is capable of generating PtdIns(3,4,5)P3 and PtdIns(3,4)P2 from PtdIns(4,5)P2 in a cell-free system. Through a remarkable instance of convergent evolution, bacterial effectors acquired the ability to synthesize 3-phosphorylated phosphoinositides by an ATP- and kinase-independent mechanism, thereby subverting host signalling to gain entry and even provoke oncogenic transformation.
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Affiliation(s)
- Glenn F W Walpole
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Neha Chauhan
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | | | | | - Yazan M Abbas
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Fernando Montaño-Rendón
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Zetao Liu
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hongxian Zhu
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sergio Grinstein
- Division of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.
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4
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Moiso E, Provero P. Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. Cancers (Basel) 2022; 14:cancers14092145. [PMID: 35565274 PMCID: PMC9104370 DOI: 10.3390/cancers14092145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary The metabolic alterations characteristic of cancer cells play a significant role in tumors’ natural history and response to therapy. Recent technological advances have allowed the production of unprecedented amounts of data on many types of cancers. We exploited the most comprehensive collection of such data, The Cancer Genome Atlas (TCGA), to systematically investigate the associations between metabolic alterations and other tumor features. We used sets of genes known to be associated with specific metabolic pathways to classify patients into “metabolic subtypes”. Then, we systematically looked for associations between the metabolic subtypes and other tumor features, including histological classification, patient survival, and genome alterations. Our results, while correlative in nature, can provide a guide to the formulation of specific mechanistic hypotheses to be tested experimentally so as to improve our understanding of the biology of cancer and our ability to tailor therapeutic interventions to the specific features of each patient. Abstract The alterations of metabolic pathways in cancer have been investigated for many years, beginning long before the discovery of the role of oncogenes and tumor suppressors, and the last few years have witnessed renewed interest in this topic. Large-scale molecular and clinical data on tens of thousands of samples allow us to tackle the problem from a general point of view. Here, we show that transcriptomic profiles of tumors can be exploited to define metabolic cancer subtypes, which can be systematically investigated for associations with other molecular and clinical data. We find thousands of significant associations between metabolic subtypes and molecular features such as somatic mutations, structural variants, epigenetic modifications, protein abundance and activation, and with clinical/phenotypic data, including survival probability, tumor grade, and histological types, which we make available to the community in a dedicated web resource. Our work provides a methodological framework and a rich database of statistical associations, which will contribute to the understanding of the role of metabolic alterations in cancer and to the development of precision therapeutic strategies.
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Affiliation(s)
- Enrico Moiso
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Correspondence: (E.M.); (P.P.)
| | - Paolo Provero
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
- Center for Omics Sciences, San Raffaele Scientific Institute IRCSS, 20132 Milan, Italy
- Correspondence: (E.M.); (P.P.)
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5
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Wang Y, Chen L, Li Q, Gao S, Liu S, Ma J, Xie Y, Wang J, Cao Z, Liu Z. Inositol Polyphosphate 4-Phosphatase Type II Is a Tumor Suppressor in Multiple Myeloma. Front Oncol 2022; 11:785297. [PMID: 35070988 PMCID: PMC8767114 DOI: 10.3389/fonc.2021.785297] [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: 09/30/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022] Open
Abstract
Inositol polyphosphate-4-phosphatase type II (INPP4B) has been identified as a tumor suppressor, while little is known about its expression and function in multiple myeloma (MM). In this study, we evaluated the expression of INPP4B in 28 cases of newly diagnosed MM patients and 42 cases of extramedullary plasmacytoma (EMP) patients compared with normal plasma cells and found that low INPP4B expression was correlated with poor outcomes in MM patients. Moreover, expression of INPP4B in seven MM cell lines was all lower than that in normal plasma cells. In addition, loss of function of INPP4B promoted cell proliferation in MM cells; however, gain of function suppressed MM cells proliferation and arrested the cell cycle at G0/G1 phage. Meanwhile, knockdown of INPP4B enhanced resistance, but overexpression promoted sensitivity to bortezomib treatment in MM cells. Mechanistically, we found that INPP4B exerted its role via inhibiting the phosphorylation of Akt at lysine 473 but not threonine 308, which attenuated the activation of the PI3K/Akt/mammalian target of rapamycin (mTOR) signaling pathway. Therefore, we identified an inhibitory effect of INPP4B in MM, and our findings suggested that loss of INPP4B expression is a risk factor of aggressive MM.
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Affiliation(s)
- Yafei Wang
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Lin Chen
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Hematology, Tianjin Cancer Hospital Airport Branch, Tianjin, China
| | - Qian Li
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Shuang Gao
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Hematology, Tianjin Cancer Hospital Airport Branch, Tianjin, China
| | - Su Liu
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Hematology, Tianjin Cancer Hospital Airport Branch, Tianjin, China
| | - Jing Ma
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Hematology, Tianjin Cancer Hospital Airport Branch, Tianjin, China
| | - Ying Xie
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Jingya Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Zeng Cao
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Zhiqiang Liu
- Department of Hematology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
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6
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Inositol monophosphatase 1 (IMPA1) mutation in intellectual disability patients impairs neurogenesis but not gliogenesis. Mol Psychiatry 2021; 26:3558-3571. [PMID: 32839513 DOI: 10.1038/s41380-020-00862-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022]
Abstract
A homozygous mutation in the inositol monophosphatase 1 (IMPA1) gene was recently identified in nine individuals with severe intellectual disability (ID) and disruptive behavior. These individuals belong to the same family from Northeastern Brazil, which has 28 consanguineous marriages and 59 genotyped family members. IMPA1 is responsible for the generation of free inositol from de novo biosynthesis and recycling from inositol polyphosphates and participates in the phosphatidylinositol signaling pathway. To understand the role of IMPA1 deficiency in ID, we generated induced pluripotent stem cells (iPSCs) from patients and neurotypical controls and differentiated these into hippocampal dentate gyrus-like neurons and astrocytes. IMPA1-deficient neuronal progenitor cells (NPCs) revealed substantial deficits in proliferation and neurogenic potential. At low passage NPCs (P1 to P3), we observed cell cycle arrest, apoptosis, progressive change to a glial morphology and reduction in neuronal differentiation. These observations were validated by rescuing the phenotype with myo-inositol supplemented media during differentiation of patient-derived iPSCs into neurons and by the reduction of neurogenic potential in control NPCs-expressing shIMPA1. Transcriptome analysis showed that NPCs and neurons derived from ID patients have extensive deregulation of gene expression affecting pathways necessary for neurogenesis and upregulation of gliogenic genes. IMPA1 deficiency did not affect cell cycle progression or survival in iPSCs and glial progenitor cells or astrocyte differentiation. Therefore, this study shows that the IMPA1 mutation specifically affects NPC survival and neuronal differentiation.
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7
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Lei C, Chen W, Wang Y, Zhao B, Liu P, Kong Z, Liu D, Dai C, Wang Y, Wang Y, Ma W. Prognostic Prediction Model for Glioblastoma: A Metabolic Gene Signature and Independent External Validation. J Cancer 2021; 12:3796-3808. [PMID: 34093788 PMCID: PMC8176239 DOI: 10.7150/jca.53827] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Glioblastoma (GBM) is the most common primary malignant intracranial tumor and closely related to metabolic alteration. However, few accepted prognostic models are currently available, especially models based on metabolic genes. Methods: The transcriptome data were obtained for all of the patients diagnosed with GBM from the Gene Expression Omnibus (GEO) (training cohort, n=369) and The Cancer Genome Atlas (TCGA) (validation cohort, n=152) with the following variables: age at diagnosis, sex, follow-up and overall survival (OS). Metabolic genes according to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were contracted, and a Lasso regression model was constructed. Survival was assessed by univariate or multivariate Cox proportional hazards regression and Kaplan-Meier analysis, and an independent external validation was also conducted to examine the model. Results: There were 341 metabolic genes showed significant differences between normal brain and GBM tissues in both the training and validation cohorts, among which 56 genes were dramatically correlated to the OS of patients. Lasso regression revealed that the metabolic prognostic model was composed of 18 genes, including COX10, COMT, and GPX2 with protective effects, as well as OCRL and RRM2 with unfavorable effects. Patients classified as high-risk by the risk score from this model had markedly shorter OS than low-risk patients (P<0.0001), and this significant result was also observed in independent external validation (P<0.001). Conclusions: The prognosis of GBM was dramatically related to metabolic pathways, and our metabolic prognostic model had high accuracy and application value in predicting the OS of GBM patients.
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Affiliation(s)
- Chuxiang Lei
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Wenlin Chen
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Yuekun Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Binghao Zhao
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Penghao Liu
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Ziren Kong
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Delin Liu
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Congxin Dai
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Yaning Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Yu Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
| | - Wenbin Ma
- Department of Neurosurgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing, China
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8
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Conduit SE, Vanhaesebroeck B. Phosphoinositide lipids in primary cilia biology. Biochem J 2020; 477:3541-3565. [PMID: 32970140 PMCID: PMC7518857 DOI: 10.1042/bcj20200277] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/30/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022]
Abstract
Primary cilia are solitary signalling organelles projecting from the surface of most cell types. Although the ciliary membrane is continuous with the plasma membrane it exhibits a unique phospholipid composition, a feature essential for normal cilia formation and function. Recent studies have illustrated that distinct phosphoinositide lipid species localise to specific cilia subdomains, and have begun to build a 'phosphoinositide map' of the cilium. The abundance and localisation of phosphoinositides are tightly regulated by the opposing actions of lipid kinases and lipid phosphatases that have also been recently discovered at cilia. The critical role of phosphoinositides in cilia biology is highlighted by the devastating consequences of genetic defects in cilia-associated phosphoinositide regulatory enzymes leading to ciliopathy phenotypes in humans and experimental mouse and zebrafish models. Here we provide a general introduction to primary cilia and the roles phosphoinositides play in cilia biology. In addition to increasing our understanding of fundamental cilia biology, this rapidly expanding field may inform novel approaches to treat ciliopathy syndromes caused by deregulated phosphoinositide metabolism.
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Affiliation(s)
- Sarah E. Conduit
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, U.K
| | - Bart Vanhaesebroeck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, U.K
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9
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Primary Cilia Signaling Promotes Axonal Tract Development and Is Disrupted in Joubert Syndrome-Related Disorders Models. Dev Cell 2020; 51:759-774.e5. [PMID: 31846650 DOI: 10.1016/j.devcel.2019.11.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/08/2019] [Accepted: 11/10/2019] [Indexed: 12/18/2022]
Abstract
Appropriate axonal growth and connectivity are essential for functional wiring of the brain. Joubert syndrome-related disorders (JSRD), a group of ciliopathies in which mutations disrupt primary cilia function, are characterized by axonal tract malformations. However, little is known about how cilia-driven signaling regulates axonal growth and connectivity. We demonstrate that the deletion of related JSRD genes, Arl13b and Inpp5e, in projection neurons leads to de-fasciculated and misoriented axonal tracts. Arl13b deletion disrupts the function of its downstream effector, Inpp5e, and deregulates ciliary-PI3K/AKT signaling. Chemogenetic activation of ciliary GPCR signaling and cilia-specific optogenetic modulation of downstream second messenger cascades (PI3K, AKT, and AC3) commonly regulated by ciliary signaling receptors induce rapid changes in axonal dynamics. Further, Arl13b deletion leads to changes in transcriptional landscape associated with dysregulated PI3K/AKT signaling. These data suggest that ciliary signaling acts to modulate axonal connectivity and that impaired primary cilia signaling underlies axonal tract defects in JSRD.
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10
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Ratzan W, Rayaprolu V, Killian SE, Bradley R, Kohout SC. The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells. PLoS One 2019; 14:e0209056. [PMID: 30964862 PMCID: PMC6456211 DOI: 10.1371/journal.pone.0209056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/21/2019] [Indexed: 12/29/2022] Open
Abstract
Voltage-sensing phosphatases (VSPs) are transmembrane proteins that couple changes in membrane potential to hydrolysis of inositol signaling lipids. VSPs catalyze the dephosphorylation of phosphatidylinositol phosphates (PIPs) that regulate diverse aspects of cell membrane physiology including cell division, growth and migration. VSPs are highly conserved among chordates, and their RNA transcripts have been detected in the adult and embryonic stages of frogs, fish, chickens, mice and humans. However, the subcellular localization and biological function of VSP remains unknown. Using reverse transcriptase-PCR (RT-PCR), we show that both Xenopus laevis VSPs (Xl-VSP1 and Xl-VSP2) mRNAs are expressed in early embryos, suggesting that both Xl-VSPs are involved in early tadpole development. To understand which embryonic tissues express Xl-VSP mRNA, we used in situ hybridization (ISH) and found Xl-VSP mRNA in both the brain and kidney of NF stage 32-36 embryos. By Western blot analysis with a VSP antibody, we show increasing levels of Xl-VSP protein in the developing embryo, and by immunohistochemistry (IHC), we demonstrate that Xl-VSP protein is specifically localized to the apical membrane of both embryonic and adult kidney tubules. We further characterized the catalytic activity of both Xl-VSP homologs and found that while Xl-VSP1 catalyzes 3- and 5-phosphate removal, Xl-VSP2 is a less efficient 3-phosphatase with different substrate specificity. Our results suggest that Xl-VSP1 and Xl-VSP2 serve different functional roles and that VSPs are an integral component of voltage-dependent PIP signaling pathways during vertebrate kidney tubule development and function.
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Affiliation(s)
- Wil Ratzan
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
| | - Vamseedhar Rayaprolu
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
| | - Scott E. Killian
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
| | - Roger Bradley
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
| | - Susy C. Kohout
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
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11
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Abstract
Phosphoinositides (PIs) play pivotal roles in the regulation of many biological processes. The quality and quantity of PIs is regulated in time and space by the activity of PI kinases and PI phosphatases. The number of PI-metabolizing enzymes exceeds the number of PIs with, in many cases, more than one enzyme controlling the same biochemical step. This would suggest that the PI system has an intrinsic ability to buffer and compensate for the absence of a specific enzymatic activity. However, there are several examples of severe inherited human diseases caused by mutations in one of the PI enzymes, although other enzymes with the same activity are fully functional. The kidney depends strictly on PIs for physiological processes, such as cell polarization, filtration, solute reabsorption, and signal transduction. Indeed, alteration of the PI system in the kidney very often results in pathological conditions, both inherited and acquired. Most of the knowledge of the roles that PIs play in the kidney comes from the study of KO animal models for genes encoding PI enzymes and from the study of human genetic diseases, such as Lowe syndrome/Dent disease 2 and Joubert syndrome, caused by mutations in the genes encoding the PI phosphatases, OCRL and INPP5E, respectively.
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Affiliation(s)
- Leopoldo Staiano
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy .,University of Naples Federico II, 80131 Naples, Italy
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12
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Gawden-Bone CM, Frazer GL, Richard AC, Ma CY, Strege K, Griffiths GM. PIP5 Kinases Regulate Membrane Phosphoinositide and Actin Composition for Targeted Granule Secretion by Cytotoxic Lymphocytes. Immunity 2018; 49:427-437.e4. [PMID: 30217409 PMCID: PMC6162341 DOI: 10.1016/j.immuni.2018.08.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 06/22/2018] [Accepted: 08/21/2018] [Indexed: 01/19/2023]
Abstract
How cytotoxic T lymphocytes (CTLs) sense T cell receptor (TCR) signaling in order to specialize an area of plasma membrane for granule secretion is not understood. Here, we demonstrate that immune synapse formation led to rapid localized changes in the phosphoinositide composition of the plasma membrane, both reducing phosphoinositide-4-phosphate (PI(4)P), PI(4,5)P2, and PI(3,4,5)P3 and increasing diacylglycerol (DAG) and PI(3,4)P2 within the first 2 min of synapse formation. These changes reduced negative charge across the synapse, triggering the release of electrostatically bound PIP5 kinases that are required to replenish PI(4,5)P2. As PI(4,5)P2 decreased, actin was depleted from the membrane, allowing secretion. Forced localization of PIP5Kβ across the synapse prevented actin depletion, blocking both centrosome docking and secretion. Thus, PIP5Ks act as molecular sensors of TCR activation, controlling actin recruitment across the synapse, ensuring exquisite co-ordination between TCR signaling and CTL secretion. Immune synapse formation triggers rapid changes in the membrane composition and charge PIP5K is a molecular sensor of TCR activation and is rapidly depleted at the synapse PIP5K distribution controls actin recruitment across the immune synapse Membrane specialization controls accessibility for centrosome docking and secretion
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Affiliation(s)
- Christian M Gawden-Bone
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Gordon L Frazer
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Arianne C Richard
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Cancer Research UK Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0RE, UK
| | - Claire Y Ma
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Katharina Strege
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Gillian M Griffiths
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
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13
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Dong R, Zhu T, Benedetti L, Gowrishankar S, Deng H, Cai Y, Wang X, Shen K, De Camilli P. The inositol 5-phosphatase INPP5K participates in the fine control of ER organization. J Cell Biol 2018; 217:3577-3592. [PMID: 30087126 PMCID: PMC6168264 DOI: 10.1083/jcb.201802125] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022] Open
Abstract
Endoplasmic reticulum (ER) morphology is dynamic and key to its function during different cellular processes. Dong et al. now show in convergent studies in human cells and Caenorhabditis elegans neurons that a phosphoinositide phosphatase (INPP5K) is localized on the surface of the ER network and helps control the shape of the ER. INPP5K (SKIP) is an inositol 5-phosphatase that localizes in part to the endoplasmic reticulum (ER). We show that recruitment of INPP5K to the ER is mediated by ARL6IP1, which shares features of ER-shaping proteins. Like ARL6IP1, INPP5K is preferentially localized in ER tubules and enriched, relative to other ER resident proteins (Sec61β, VAPB, and Sac1), in newly formed tubules that grow along microtubule tracks. Depletion of either INPP5K or ARL6IP1 results in the increase of ER sheets. In a convergent but independent study, a screen for mutations affecting the distribution of the ER network in dendrites of the PVD neurons of Caenorhabditis elegans led to the isolation of mutants in CIL-1, which encodes the INPP5K worm orthologue. The mutant phenotype was rescued by expression of wild type, but not of catalytically inactive CIL-1. Our results reveal an unexpected role of an ER localized polyphosphoinositide phosphatase in the fine control of ER network organization.
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Affiliation(s)
- Rui Dong
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Ting Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lorena Benedetti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Swetha Gowrishankar
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Huichao Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yiying Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Xiangming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kang Shen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China.,Department of Biology, Stanford University School of Medicine, Stanford, CA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT.,Kavli Institute for Neurosciences, Yale University School of Medicine, New Haven, CT
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14
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Yue H, Zhu X, Li S, Wang F, Wang X, Guan Z, Zhu Z, Niu B, Zhang T, Guo J, Wang J. Relationship Between INPP5E Gene Expression and Embryonic Neural Development in a Mouse Model of Neural Tube Defect. Med Sci Monit 2018; 24:2053-2059. [PMID: 29626185 PMCID: PMC5903545 DOI: 10.12659/msm.906095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The INPP5E gene encodes for the inositol polyphosphate-5-phosphatase (INPP5E) 72 kDa protein that regulates the phosphoinositide signaling pathway and other cellular activities, but the functional role of this gene in embryonic neurodevelopment and neural tube defect (NTD) remains unclear. The aim of this study was to use a mouse model of NTD to investigate the expression levels of the INPP5E gene during neural development and the occurrence of NTD. Material/Methods In an established NTD mouse model, stereoscopy was used to look for morphological defects. Transcription and expression levels of the INPP5E gene in neural tissues were detected using real-time fluorescence quantitative polymerase chain reaction (PCR) and Western blotting in the NTD mouse embryos and compared with control mouse embryos. Results The expression levels of the INPP5E gene decreased as embryonic development progressed in the neural tissue of control mice embryos, but showed no obvious trend in the neural tissues of the NTD mouse embryos. The expression levels of the INPP5E gene in NTD mouse embryos were significantly lower compared with control embryos, at the time of neural tube closure (gestational day 11.5). Conclusions The INPP5E gene regulates the process of embryonic neural development. Abnormal levels of expression of the INPP5E gene may contribute to NTDs. Increased knowledge of the expression pattern of the INPP5E gene may lead to an advanced understanding of the molecular mechanism of embryonic neurodevelopment and identify more specific directions to explore potential treatments for NTDs associated with abnormalities in INPP5E gene expression levels.
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Affiliation(s)
- Huixuan Yue
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Xiting Zhu
- Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Shen Li
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Fang Wang
- Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Xiuwei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Zhen Guan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Zhiqiang Zhu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Bo Niu
- Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Jin Guo
- Capital Institute of Pediatrics, Beijing, China (mainland)
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (mainland)
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15
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Abstract
Selective enrichment of the polyphosphoinositides (PPIn), such as PtdIns(4,5)P2 and PtdIns4P, helps to determine the identity of the plasma membrane (PM) and regulates many aspects of cell biology through a vast number of protein effectors. Polarity proteins had long been assumed to be non-PPIn-binding proteins that mainly associate with PM/cell cortex through their extensive protein-protein interaction network. However, recent studies began to reveal that several key polarity proteins electrostatically bind to PPIn through their positively charged protein domains or structures and such PPIn-binding property is essential for their direct and specific attachment to PM. Although the physical nature of the charge-based PPIn binding appears to be simple and nonspecific, it serves as an elegant mechanism that can be efficiently and specifically regulated for achieving polarized PM targeting of polarity proteins. As an unexpected consequence, subcellular localization of PPIn-binding polarity proteins are also subject to regulations by physiological conditions such as hypoxia and ischemia that acutely and reversibly depletes PPIn from PM.
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Affiliation(s)
- Gerald R Hammond
- Department of Cell Biology, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania 15261
| | - Yang Hong
- Department of Cell Biology, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania 15261
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16
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Li KP, Fang YP, Liao JQ, Duan JD, Feng LG, Luo XZ, Liang ZJ. Upregulation of miR‑598 promotes cell proliferation and cell cycle progression in human colorectal carcinoma by suppressing INPP5E expression. Mol Med Rep 2017; 17:2991-2997. [PMID: 29257251 PMCID: PMC5783518 DOI: 10.3892/mmr.2017.8207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/18/2017] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer worldwide. Recently, microRNAs (miRs) have been considered as novel therapeutic targets for the treatment of cancer. miR‑598 is a poorly investigated miR. The underlying mechanism of miR‑598 in CRC cells remains to be elucidated. In the present study, miR‑598 was demonstrated to be significantly upregulated in CRC tissue by analyzing data from The Cancer Genome Atlas and the Gene Expression Omnibus. The results of a polymerase chain reaction demonstrated that miR‑598 expression was significantly upregulated in CRC tissues and cells. Gain of function and loss of function assays demonstrated that miR‑598 significantly promoted cell proliferation and cell cycle progression. miR‑598 was demonstrated to modulate cell functions by regulating 72 kDa inositol polyphosphate‑5‑phosphatase (INPP5E). In addition, knockdown of INPP5E counteracted the growth arrest caused by an miR‑598‑inhibitor. In conclusion, the present study demonstrated that miR‑598 contributed to cell proliferation and cell cycle progression in CRC by targeting INPP5E.
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Affiliation(s)
- Kun-Ping Li
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Yong-Ping Fang
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Jin-Qi Liao
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Jin-Dong Duan
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Li-Guang Feng
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Xiao-Zai Luo
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
| | - Zhi-Jian Liang
- Department of General Surgery, Huizhou First Hospital, Huizhou, Guangdong 516000, P.R. China
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17
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Andrés-Benito P, Moreno J, Domínguez R, Aso E, Povedano M, Ferrer I. Inflammatory Gene Expression in Whole Peripheral Blood at Early Stages of Sporadic Amyotrophic Lateral Sclerosis. Front Neurol 2017; 8:546. [PMID: 29081763 PMCID: PMC5645505 DOI: 10.3389/fneur.2017.00546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/27/2017] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Characterization of altered expression of selected transcripts linked to inflammation in the peripheral blood of sporadic amyotrophic lateral sclerosis (sALS) patients at early stage of disease to increase knowledge about peripheral inflammatory response in sALS. METHODS RNA expression levels of 45 genes were assessed by RT-qPCR in 22 sALS cases in parallel with 13 age-matched controls. Clinical and serum parameters were assessed at the same time. RESULTS Upregulation of genes coding for factors involved in leukocyte extravasation (ITGB2, INPP5D, SELL, and ICAM1) and extracellular matrix remodeling (MMP9 and TIMP2), as well as downregulation of certain chemokines (CCL5 and CXC5R), anti-inflammatory cytokines (IL10, TGFB2, and IL10RA), pro-inflammatory cytokines (IL-6), and T-cell regulators (CD2 and TRBC1) was found in sALS cases independently of gender, clinical symptoms at onset (spinal, respiratory, or bulbar), progression, peripheral leukocyte number, and integrity of RNA. MMP9 levels positively correlated with age, whereas CCR5, CCL5, and TRBC1 negatively correlated with age in sALS but not in controls. Relatively higher TNFA expression levels correlate with higher creatinine kinase protein levels in plasma. CONCLUSION Present findings show early inflammatory responses characterized by upregulation of factors enabling extravasation of leukocytes and extracellular matrix remodeling in blood in sALS cases, in addition to increased TNFA levels paralleling skeletal muscle damage.
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Affiliation(s)
- Pol Andrés-Benito
- Neuropathology, Pathologic Anatomy Service, Bellvitge University Hospital, IDIBELL, Hospitalet de Llobregat, Spain.,Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute Carlos III, Hospitalet de Llobregat, Spain
| | - Jesús Moreno
- Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute Carlos III, Hospitalet de Llobregat, Spain
| | - Raúl Domínguez
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, Hospitalet de Llobregat, Spain
| | - Ester Aso
- Neuropathology, Pathologic Anatomy Service, Bellvitge University Hospital, IDIBELL, Hospitalet de Llobregat, Spain.,Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute Carlos III, Hospitalet de Llobregat, Spain
| | - Mónica Povedano
- Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute Carlos III, Hospitalet de Llobregat, Spain.,Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, Hospitalet de Llobregat, Spain
| | - Isidro Ferrer
- Neuropathology, Pathologic Anatomy Service, Bellvitge University Hospital, IDIBELL, Hospitalet de Llobregat, Spain.,Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute Carlos III, Hospitalet de Llobregat, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,Institute of Neurosciences, University of Barcelona, Hospitalet de Llobregat, Spain
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18
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Kim SO, Jackman JA, Elazar M, Cho SJ, Glenn JS, Cho NJ. Quantitative Evaluation of Viral Protein Binding to Phosphoinositide Receptors and Pharmacological Inhibition. Anal Chem 2017; 89:9742-9750. [PMID: 28809547 PMCID: PMC5724528 DOI: 10.1021/acs.analchem.7b01568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is significant interest in developing analytical methods to characterize molecular recognition events between proteins and phosphoinositides, which are a medically important class of carbohydrate-functionalized lipids. Within this scope, one area of high priority involves quantitatively evaluating drug candidates that pharmacologically inhibit protein-phosphoinositide interactions. As full-length proteins are often difficult to produce, establishing methods to study these interactions with shorter, bioactive peptides would be advantageous. Herein, we report an atomic force microscopy (AFM)-based force spectroscopic approach to detect the specific interaction between an amphipathic, α-helical (AH) peptide derived from the hepatitis C virus NS5A protein and its biological target, the phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] phosphoinositide receptor. After optimization of the peptide tethering strategy and measurement parameters, the binding specificity of AH peptide for PI(4,5)P2 receptors was comparatively evaluated across a panel of phosphoinositides and the influence of ionic strength on AH-PI(4,5)P2 binding strength was tested. Importantly, these capabilities were translated into the development of a novel experimental methodology to determine the inhibitory activity of a small-molecule drug candidate acting against the AH-PI(4,5)P2 interaction, and extracted kinetic parameters agree well with literature values obtained by conventional biochemical methods. Taken together, our findings provide a nanomechanical basis for explaining the high binding specificity of the NS5A AH to PI(4,5)P2 receptors, in turn establishing an analytical framework to study phosphoinositide-binding viral peptides and proteins as well as a broadly applicable approach to evaluate candidate inhibitors of protein-phosphoinositide interactions.
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Affiliation(s)
- Seong-Oh Kim
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Drive, 637553 Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Drive, 637553 Singapore.,Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Menashe Elazar
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Sang-Joon Cho
- Advanced Institute of Convergence Technology, Seoul National University , Suwon 443-270, South Korea
| | - Jeffrey S Glenn
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine , Stanford, California 94305, United States.,Veterans Administration Medical Center , Palo Alto, California 94304, United States
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Drive, 637553 Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University , 62 Nanyang Drive, 637459 Singapore
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19
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Mäki-Nevala S, Sarhadi VK, Knuuttila A, Scheinin I, Ellonen P, Lagström S, Rönty M, Kettunen E, Husgafvel-Pursiainen K, Wolff H, Knuutila S. Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing. Lung 2016; 194:125-35. [PMID: 26463840 DOI: 10.1007/s00408-015-9814-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/27/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Asbestos is a carcinogen linked to malignant mesothelioma (MM) and lung cancer. Some gene aberrations related to asbestos exposure are recognized, but many associated mutations remain obscure. We performed exome sequencing to determine the association of previously known mutations (driver gene mutations) with asbestos and to identify novel mutations related to asbestos exposure in lung adenocarcinoma (LAC) and MM. METHODS Exome sequencing was performed on DNA from 47 tumor tissues of MM (21) and LAC (26) patients, 27 of whom had been asbestos-exposed (18 MM, 9 LAC). In addition, 9 normal lung/blood samples of LAC were sequenced. Novel mutations identified from exome data were validated by amplicon-based deep sequencing. Driver gene mutations in BRAF, EGFR, ERBB2, HRAS, KRAS, MET, NRAS, PIK3CA, STK11, and ephrin receptor genes (EPHA1-8, 10 and EPHB1-4, 6) were studied for both LAC and MM, and in BAP1, CUL1, CDKN2A, and NF2 for MM. RESULTS In asbestos-exposed MM patients, previously non-described NF2 frameshift mutation (one) and BAP1 mutations (four) were detected. Exome data mining revealed some genes potentially associated with asbestos exposure, such as MRPL1 and SDK1. BAP1 and COPG1 mutations were seen exclusively in MM. Pathogenic KRAS mutations were common in LAC patients (42 %), both in non-exposed (n = 5) and exposed patients (n = 6). Pathogenic BRAF mutations were found in two LACs. CONCLUSION BAP1 mutations occurred in asbestos-exposed MM. MRPL1, SDK1, SEMA5B, and INPP4A could possibly serve as candidate genes for alterations associated with asbestos exposure. KRAS mutations in LAC were not associated with asbestos exposure.
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20
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Ikonomov OC, Sbrissa D, Delvecchio K, Rillema JA, Shisheva A. Unexpected severe consequences of Pikfyve deletion by aP2- or Aq-promoter-driven Cre expression for glucose homeostasis and mammary gland development. Physiol Rep 2016; 4:4/11/e12812. [PMID: 27273882 PMCID: PMC4908490 DOI: 10.14814/phy2.12812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/04/2016] [Indexed: 01/03/2023] Open
Abstract
Systemic deficiency of PIKfyve, the evolutionarily conserved phosphoinositide kinase synthesizing cellular PtdIns5P and PtdIns(3,5)P2 and implicated in insulin signaling, causes early embryonic death in mice. In contrast, mice with muscle‐specific Pikfyve disruption have normal lifespan but exhibit early‐age whole‐body glucose intolerance and muscle insulin resistance, thus establishing the key role of muscle PIKfyve in glucose homeostasis. Fat and muscle tissues control postprandial glucose clearance through different mechanisms, raising questions as to whether adipose Pikfyve disruption will also trigger whole‐body metabolic abnormalities, and if so, what the mechanism might be. To clarify these issues, here we have characterized two new mouse models with adipose tissue disruption of Pikfyve through Cre recombinase expression driven by adipose‐specific aP2‐ or adiponectin (Aq) promoters. Whereas both mouse lines were ostensibly normal until adulthood, their glucose homeostasis and systemic insulin sensitivity were severely dysregulated. These abnormalities stemmed in part from accelerated fat‐cell lipolysis and elevated serum FFA. Intriguingly, aP2‐Cre‐PIKfyvefl/fl but not Aq‐Cre‐PIKfyvefl/fl females had severely impaired pregnancy‐induced mammary gland differentiation and lactogenesis, consistent with aP2‐Cre‐mediated Pikfyve excision in nonadipogenic tissues underlying this defect. Intriguingly, whereas mammary glands from postpartum control and Aq‐Cre‐PIKfyvefl/fl mice or ex vivo mammary gland explants showed profound upregulation of PIKfyve protein levels subsequent to prolactin receptor activation, such increases were not apparent in aP2‐Cre‐PIKfyvefl/fl females. Collectively, our data identify for the first time that adipose tissue Pikfyve plays a key role in the mechanisms regulating glucose homeostasis and that the PIKfyve pathway is critical in mammary epithelial differentiation during pregnancy and lactogenesis downstream of prolactin receptor signaling.
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Affiliation(s)
- Ognian C Ikonomov
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan
| | - Diego Sbrissa
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan
| | - Khortnal Delvecchio
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan
| | - James A Rillema
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan
| | - Assia Shisheva
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan
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21
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Figueiredo T, Melo US, Pessoa ALS, Nobrega PR, Kitajima JP, Rusch H, Vaz F, Lucato LT, Zatz M, Kok F, Santos S. A homozygous loss-of-function mutation in inositol monophosphatase 1 (IMPA1) causes severe intellectual disability. Mol Psychiatry 2016; 21:1125-9. [PMID: 26416544 DOI: 10.1038/mp.2015.150] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 11/09/2022]
Abstract
The genetic basis of intellectual disability (ID) is extremely heterogeneous and relatively little is known about the role of autosomal recessive traits. In a field study performed in a highly inbred area of Northeastern Brazil, we identified and investigated a large consanguineous family with nine adult members affected by severe ID associated with disruptive behavior. The Genome-Wide Human SNP Array 6.0 microarray was used to determine regions of homozygosity by descent from three affected and one normal family member. Whole-exome sequencing (WES) was performed in one affected patient using the Nextera Rapid-Capture Exome kit and Illumina HiSeq2500 system to identify the causative mutation. Potentially deleterious variants detected in regions of homozygosity by descent and not present in either 59 723 unrelated individuals from the Exome Aggregation Consortium (Browser) or 1484 Brazilians were subject to further scrutiny and segregation analysis by Sanger sequencing. Homozygosity-by-descent analysis disclosed a 20.7-Mb candidate region at 8q12.3-q21.2 (lod score: 3.11). WES identified a homozygous deleterious variant in inositol monophosphatase 1 (IMPA1) (NM_005536), consisting of a 5-bp duplication (c.489_493dupGGGCT; chr8: 82,583,247; GRCh37/hg19) leading to a frameshift and a premature stop codon (p.Ser165Trpfs*10) that cosegregated with the disease in 26 genotyped family members. The IMPA1 gene product is responsible for the final step of biotransformation of inositol triphosphate and diacylglycerol, two second messengers. Despite its many physiological functions, no clinical phenotype has been assigned to this gene dysfunction to date. Additionally, IMPA1 is the main target of lithium, a drug that is at the forefront of treatment for bipolar disorder.
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Affiliation(s)
- T Figueiredo
- Northeast Biotechnology Network (RENORBIO), Federal University of Paraiba (UFPB), Joao Pessoa, Brazil.,Department of Biology, Paraiba State University (UEPB), Campina Grande, Brazil.,Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - U S Melo
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - A L S Pessoa
- Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil.,School of Medicine, Fortaleza University (UNIFOR), Fortaleza, Brazil
| | - P R Nobrega
- Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil
| | | | - H Rusch
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry, University of Amsterdam, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - F Vaz
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry, University of Amsterdam, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - L T Lucato
- Institute of Radiology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - M Zatz
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - F Kok
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil.,Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil.,Mendelics Genomic Analysis, Sao Paulo, Brazil
| | - S Santos
- Northeast Biotechnology Network (RENORBIO), Federal University of Paraiba (UFPB), Joao Pessoa, Brazil.,Department of Biology, Paraiba State University (UEPB), Campina Grande, Brazil
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22
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Hu QL, Wang HB, Yang M. Significance of expression of INPP4B in gastric cancer. Shijie Huaren Xiaohua Zazhi 2016; 24:2478-2484. [DOI: 10.11569/wcjd.v24.i16.2478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression of inositol polyphosphate-4-phosphatase, type II (INPP4B) in gastric cancer, and to analyze its relationship with clinical and pathological characteristics.
METHODS: The expression of INPP4B mRNA and protein in 50 gastric cancer tissues and matched tumor-adjacent normal tissues was detected by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC), respectively. The relationship between INPP4B expression and clinical and pathological characteristics was then analyzed.
RESULTS: INPP4B mRNA expression was significantly lower in gastric cancer tissue than in adjacent normal tissues (P < 0.01). The expression of INPP4B protein in gastric cancer tissues was also significantly lower compared with adjacent normal tissues (28.0% vs 82.0%, P < 0.01). The expression of INPP4B mRNA and protein was significantly related to tumor differentiation, lymph node metastasis and TNM stage in GC (P < 0.05), but not to gender, age or tumor size (P > 0.05).
CONCLUSION: Both INPP4B protein and mRNA are down-regulated in gastric cancer, and its expression significantly correlates with tumor differentiation, lymph node metastasis and TNM stage. INPP4B may be a tumor suppressor gene for gastric cancer.
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23
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Hakim S, Dyson JM, Feeney SJ, Davies EM, Sriratana A, Koenig MN, Plotnikova OV, Smyth IM, Ricardo SD, Hobbs RM, Mitchell CA. Inpp5e suppresses polycystic kidney disease via inhibition of PI3K/Akt-dependent mTORC1 signaling. Hum Mol Genet 2016; 25:2295-2313. [PMID: 27056978 DOI: 10.1093/hmg/ddw097] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/17/2016] [Indexed: 12/20/2022] Open
Abstract
Polycystic kidney disease (PKD) is a common cause of renal failure with few effective treatments. INPP5E is an inositol polyphosphate 5-phosphatase that dephosphorylates phosphoinositide 3-kinase (PI3K)-generated PI(3,4,5)P3 and is mutated in ciliopathy syndromes. Germline Inpp5e deletion is embryonically lethal, attributed to cilia stability defects, and is associated with polycystic kidneys. However, the molecular mechanisms responsible for PKD development upon Inpp5e loss remain unknown. Here, we show conditional inactivation of Inpp5e in mouse kidney epithelium results in severe PKD and renal failure, associated with a partial reduction in cilia number and hyperactivation of PI3K/Akt and downstream mammalian target of rapamycin complex 1 (mTORC1) signaling. Treatment with an mTORC1 inhibitor improved kidney morphology and function, but did not affect cilia number or length. Therefore, we identify Inpp5e as an essential inhibitor of the PI3K/Akt/mTORC1 signaling axis in renal epithelial cells, and demonstrate a critical role for Inpp5e-dependent mTORC1 regulation in PKD suppression.
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Affiliation(s)
- Sandra Hakim
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jennifer M Dyson
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sandra J Feeney
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Elizabeth M Davies
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Absorn Sriratana
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Monica N Koenig
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Olga V Plotnikova
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ian M Smyth
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia Development and Stem Cell program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Development and Stem Cell program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Robin M Hobbs
- Development and Stem Cell program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Christina A Mitchell
- Cancer Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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24
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Qualitative and Quantitative In Vitro Analysis of Phosphatidylinositol Phosphatase Substrate Specificity. Methods Mol Biol 2016; 1376:55-75. [PMID: 26552675 DOI: 10.1007/978-1-4939-3170-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phosphoinositides compromise a family of eight membrane lipids which play important roles in many cellular signaling pathways. Signaling through phosphoinositides has been shown in a variety of cellular functions such cell proliferation, cell growth, apoptosis, and vesicle trafficking. Phospholipid phosphatases regulate cell signaling by modifying the concentration of phosphoinositides and their dephosphorylated products. To understand the role of individual lipid phosphatases in phosphoinositide turnover and functional signaling, it is crucial to determine the substrate specificity of the lipid phosphatase of interest. In this chapter we describe how the substrate specificity of an individual lipid phosphatase can be qualitatively and quantitatively measured in an in vitro radiometric assay. In addition, we specify the different expression systems and purification methods required to produce the necessary yield and functionality in order to further characterize these enzymes. The outstanding versatility and sensitivity of this assay system are yet unmatched and are therefore currently considered the standard of the field.
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25
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Bales KL, Gross AK. Aberrant protein trafficking in retinal degenerations: The initial phase of retinal remodeling. Exp Eye Res 2015; 150:71-80. [PMID: 26632497 DOI: 10.1016/j.exer.2015.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 12/18/2022]
Abstract
Retinal trafficking proteins are involved in molecular assemblies that govern protein transport, orchestrate cellular events involved in cilia formation, regulate signal transduction, autophagy and endocytic trafficking, all of which if not properly controlled initiate retinal degeneration. Improper function and or trafficking of these proteins and molecular networks they are involved in cause a detrimental cascade of neural retinal remodeling due to cell death, resulting as devastating blinding diseases. A universal finding in retinal degenerative diseases is the profound detection of retinal remodeling, occurring as a phased modification of neural retinal function and structure, which begins at the molecular level. Retinal remodeling instigated by aberrant trafficking of proteins encompasses many forms of retinal degenerations, such as the diverse forms of retinitis pigmentosa (RP) and disorders that resemble RP through mutations in the rhodopsin gene, retinal ciliopathies, and some forms of glaucoma and age-related macular degeneration (AMD). As a large majority of genes associated with these different retinopathies are overlapping, it is imperative to understand their underlying molecular mechanisms. This review will discuss some of the most recent discoveries in vertebrate retinal remodeling and retinal degenerations caused by protein mistrafficking.
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Affiliation(s)
- Katie L Bales
- University of Alabama at Birmingham, Birmingham, AL, United States
| | - Alecia K Gross
- University of Alabama at Birmingham, Birmingham, AL, United States.
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26
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Russo CM, Adhikari AA, Wallach DR, Fernandes S, Balch AN, Kerr WG, Chisholm JD. Synthesis and initial evaluation of quinoline-based inhibitors of the SH2-containing inositol 5'-phosphatase (SHIP). Bioorg Med Chem Lett 2015; 25:5344-8. [PMID: 26453006 PMCID: PMC4628863 DOI: 10.1016/j.bmcl.2015.09.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/30/2022]
Abstract
Recently, inhibition of the SH2-containing inositol 5'-phosphatase 1 (SHIP1) has become an attractive strategy for facilitating engraftment of MHC-I mismatched bone marrow grafts, increasing the number of adult stem cells in vivo, and inducing mobilization of hematopoietic stem cells. Utilizing high-throughput screening, two quinoline small molecules (NSC13480 and NSC305787) that inhibit SHIP1 enzymatic activity were discovered. New syntheses of these inhibitors have been developed which verified the relative stereochemistry of these structures. Utilizing this synthetic route, some analogs of these quinolines have been prepared and tested for their ability to inhibit SHIP. These structure activity studies determined that an amine tethered to the quinoline core is required for SHIP inhibition. SHIP inhibition may explain the antitumor effects of similar quinoline amino alcohols and provides an impetus for further synthetic studies in this class of compounds.
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Affiliation(s)
- Christopher M Russo
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, NY 13244-4100, USA
| | - Arijit A Adhikari
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, NY 13244-4100, USA
| | - Daniel R Wallach
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, NY 13244-4100, USA
| | - Sandra Fernandes
- Department of Microbiology & Immunology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Amanda N Balch
- Department of Microbiology & Immunology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - William G Kerr
- Department of Microbiology & Immunology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - John D Chisholm
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, NY 13244-4100, USA
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27
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Kohout SC, Villalba-Galea CA. Editorial: Phosphoinositides and their phosphatases: Linking electrical and chemical signals in biological processes. Front Pharmacol 2015. [PMID: 26217228 PMCID: PMC4495603 DOI: 10.3389/fphar.2015.00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Susy C Kohout
- Department of Cell Biology and Neuroscience, Montana State University Bozeman, MT, USA
| | - Carlos A Villalba-Galea
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine Richmond, VA, USA
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28
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Zhang X, Zhang Y, Yu Y, Liu J, Yuan Y, Zhao Y, Li H, Wang J, Wang Z. Convergence and divergence of genetic and modular networks between diabetes and breast cancer. J Cell Mol Med 2015; 19:1094-102. [PMID: 25752479 PMCID: PMC4420611 DOI: 10.1111/jcmm.12504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/22/2014] [Indexed: 12/03/2022] Open
Abstract
Diabetes mellitus (DM) and breast cancer (BC) can simultaneously occur in the same patient populations, but the molecular relationship between them remains unknown. In this study, we constructed genetic networks and used modularized analysis approaches to investigate the multi-dimensional characteristics of two diseases and one disease subtype. A text search engine (Agilent Literature Search 2.71) and MCODE software were applied to validate potential subnetworks and to divide the modules, respectively. A total of 793 DM-related genes, 386 type 2 diabetes (T2DM) genes and 873 BC-related genes were identified from the Online Mendelian Inheritance in Man database. For DM and BC, a total of 99 overlapping genes, 9 modules, 29 biological processes and 7 pathways were identified. Meanwhile, for T2DM and BC, 56 overlapping genes, 5 modules, 20 biological processes and 12 pathways were identified. Based on the Gene Ontology functional enrichment analysis of the top 10 non-overlapping modules of the two diseases, 10 biological functions and 5 pathways overlapped between them. The glycosphingolipid and lysosome pathways verified molecular mechanisms of cell death related to both DM and BC. We also identified new biological functions of dopamine receptors and four signalling pathways (Parkinson's disease, Alzheimer's disease, Huntington's disease and long-term depression) related to both diseases; these warrant further investigation. Our results illustrate the landscape of the novel molecular substructures between DM and BC, which may support a new model for complex disease classification and rational therapies for multiple diseases.
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Affiliation(s)
- Xiaoxu Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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29
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Tan J, Yu CY, Wang ZH, Chen HY, Guan J, Chen YX, Fang JY. Genetic variants in the inositol phosphate metabolism pathway and risk of different types of cancer. Sci Rep 2015; 5:8473. [PMID: 25683757 PMCID: PMC4329558 DOI: 10.1038/srep08473] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/21/2015] [Indexed: 12/23/2022] Open
Abstract
Members of the inositol phosphate metabolism pathway regulate cell proliferation, migration and phosphatidylinositol-3-kinase (PI3K)/Akt signaling, and are frequently dysregulated in cancer. Whether germline genetic variants in inositol phosphate metabolism pathway are associated with cancer risk remains to be clarified. We examined the association between inositol phosphate metabolism pathway genes and risk of eight types of cancer using data from genome-wide association studies. Logistic regression models were applied to evaluate SNP-level associations. Gene- and pathway-based associations were tested using the permutation-based adaptive rank-truncated product method. The overall inositol phosphate metabolism pathway was significantly associated with risk of lung cancer (P = 2.00 × 10−4), esophageal squamous cell carcinoma (P = 5.70 × 10−3), gastric cancer (P = 3.03 × 10−2) and renal cell carcinoma (P = 1.26 × 10−2), but not with pancreatic cancer (P = 1.40 × 10−1), breast cancer (P = 3.03 × 10−1), prostate cancer (P = 4.51 × 10−1), and bladder cancer (P = 6.30 × 10−1). Our results provide a link between inherited variation in the overall inositol phosphate metabolism pathway and several individual genes and cancer. Further studies will be needed to validate these positive findings, and to explore its mechanisms.
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Affiliation(s)
- Juan Tan
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Chen-Yang Yu
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Zhen-Hua Wang
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Hao-Yan Chen
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jian Guan
- Department of Otolaryngology, The Affiliated Sixth People's Hospital, Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China
| | - Ying-Xuan Chen
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jing-Yuan Fang
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
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30
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Shisheva A, Sbrissa D, Ikonomov O. Plentiful PtdIns5P from scanty PtdIns(3,5)P2 or from ample PtdIns? PIKfyve-dependent models: Evidence and speculation (response to: DOI 10.1002/bies.201300012). Bioessays 2014; 37:267-77. [PMID: 25404370 DOI: 10.1002/bies.201400129] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recently, we have presented data supporting the notion that PIKfyve not only produces the majority of constitutive phosphatidylinositol 5-phosphate (PtdIns5P) in mammalian cells but that it does so through direct synthesis from PtdIns. Another group, albeit obtaining similar data, suggests an alternative pathway whereby the low-abundance PtdIns(3,5)P2 undergoes hydrolysis by unidentified 3-phosphatases, thereby serving as a precursor for most of PtdIns5P. Here, we review the experimental evidence supporting constitutive synthesis of PtdIns5P from PtdIns by PIKfyve. We further emphasize that the experiments presented in support of the alternative pathway are also compatible with a direct mechanism for PIKfyve-catalyzed synthesis of PtdIns5P. While agreeing with the authors that constitutive PtdIns5P could theoretically be produced from PtdIns(3,5)P2 by 3-dephosphorylation, we argue that until direct evidence for such an alternative pathway is obtained, we should adhere to the existing experimental evidence and quantitative considerations, which favor direct PIKfyve-catalyzed synthesis for most constitutive PtdIns5P.
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Affiliation(s)
- Assia Shisheva
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
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31
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Shang D, Li C, Yao Q, Yang H, Xu Y, Han J, Li J, Su F, Zhang Y, Zhang C, Li D, Li X. Prioritizing candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways. PLoS One 2014; 9:e104934. [PMID: 25153931 PMCID: PMC4143229 DOI: 10.1371/journal.pone.0104934] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022] Open
Abstract
Identification of key metabolites for complex diseases is a challenging task in today's medicine and biology. A special disease is usually caused by the alteration of a series of functional related metabolites having a global influence on the metabolic network. Moreover, the metabolites in the same metabolic pathway are often associated with the same or similar disease. Based on these functional relationships between metabolites in the context of metabolic pathways, we here presented a pathway-based random walk method called PROFANCY for prioritization of candidate disease metabolites. Our strategy not only takes advantage of the global functional relationships between metabolites but also sufficiently exploits the functionally modular nature of metabolic networks. Our approach proved successful in prioritizing known metabolites for 71 diseases with an AUC value of 0.895. We also assessed the performance of PROFANCY on 16 disease classes and found that 4 classes achieved an AUC value over 0.95. To investigate the robustness of the PROFANCY, we repeated all the analyses in two metabolic networks and obtained similar results. Then we applied our approach to Alzheimer's disease (AD) and found that a top ranked candidate was potentially related to AD but had not been reported previously. Furthermore, our method was applicable to prioritize the metabolites from metabolomic profiles of prostate cancer. The PROFANCY could identify prostate cancer related-metabolites that are supported by literatures but not considered to be significantly differential by traditional differential analysis. We also developed a freely accessible web-based and R-based tool at http://bioinfo.hrbmu.edu.cn/PROFANCY.
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Affiliation(s)
- Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Chunquan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, P. R. China
| | - Qianlan Yao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Jing Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Fei Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
| | - Dongguo Li
- School of Biomedical Engineering, Capital Medical University, No. 10 You An Men Wai Xi Tou Tiao, Beijing, P.R. China
- * E-mail: (DL); (XL)
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P. R. China
- * E-mail: (DL); (XL)
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32
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Pirruccello M, Nandez R, Idevall-Hagren O, Alcazar-Roman A, Abriola L, Berwick SA, Lucast L, Morel D, De Camilli P. Identification of inhibitors of inositol 5-phosphatases through multiple screening strategies. ACS Chem Biol 2014; 9:1359-68. [PMID: 24742366 PMCID: PMC4076014 DOI: 10.1021/cb500161z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Phosphoinositides are low abundance
membrane phospholipids that
have key roles in signaling, membrane trafficking, and cytoskeletal
dynamics in all cells. Until recently, strategies for robust and quantitative
development of pharmacological tools for manipulating phosphoinositide
levels have focused selectively on PI(3,4,5)P3 due to the
importance of this lipid in growth factor signaling and cell proliferation.
However, drugs that affect levels of other phosphoinositides have
potential therapeutic applications and will be powerful research tools.
Here, we describe methodology for the high-throughput screening of
small molecule modulators of the inositol 5-phosphatases, which dephosphorylate
PI(4,5)P2 (the precursor for PI(3,4,5)P3) and
PI(3,4,5)P3). We developed three complementary in vitro activity assays, tested hit compounds on a panel
of 5-phosphatases, and monitored efficacy toward various substrates.
Two prominent chemical scaffolds were identified with high nanomolar/low
micromolar activity, with one class showing inhibitory activity toward
all 5-phosphatases tested and the other selective activity toward
OCRL and INPP5B, which are closely related to each other. One highly
soluble OCRL/INPP5B-specific inhibitor shows a direct interaction
with the catalytic domain of INPP5B. The efficacy of this compound
in living cells was validated through its property to enhance actin
nucleation at the cell cortex, a PI(4,5)P2 dependent process,
and to inhibit PI(4,5)P2 dephosphorylation by OCRL (both
overexpressed and endogenous enzyme). The assays and screening strategies
described here are applicable to other phosphoinositide-metabolizing
enzymes, at least several of which have major clinical relevance.
Most importantly, this study identifies the first OCRL/INPP5B specific
inhibitor and provides a platform for the design of more potent inhibitors
of this family of enzymes.
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Affiliation(s)
- Michelle Pirruccello
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Ramiro Nandez
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Olof Idevall-Hagren
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Abel Alcazar-Roman
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Laura Abriola
- Yale
Center for Molecular Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Shana Alexandra Berwick
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Louise Lucast
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Dayna Morel
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
| | - Pietro De Camilli
- Department
of Cell Biology, Howard Hughes Medical Institute and Program in Cellular
Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven Connecticut 06510, United States
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Viernes DR, Choi LB, Kerr WG, Chisholm JD. Discovery and development of small molecule SHIP phosphatase modulators. Med Res Rev 2013; 34:795-824. [PMID: 24302498 DOI: 10.1002/med.21305] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Inositol phospholipids play an important role in the transfer of signaling information across the cell membrane in eukaryotes. These signals are often governed by the phosphorylation patterns on the inositols, which are mediated by a number of inositol kinases and phosphatases. The src homology 2 (SH2) containing inositol 5-phosphatase (SHIP) plays a central role in these processes, influencing signals delivered through the PI3K/Akt/mTOR pathway. SHIP modulation by small molecules has been implicated as a treatment in a number of human disease states, including cancer, inflammatory diseases, diabetes, atherosclerosis, and Alzheimer's disease. In addition, alteration of SHIP phosphatase activity may provide a means to facilitate bone marrow transplantation and increase blood cell production. This review discusses the cellular signaling pathways and protein-protein interactions that provide the molecular basis for targeting the SHIP enzyme in these disease states. In addition, a comprehensive survey of small molecule modulators of SHIP1 and SHIP2 is provided, with a focus on the structure, potency, selectivity, and solubility properties of these compounds.
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Affiliation(s)
- Dennis R Viernes
- Department of Chemistry, Syracuse University, Syracuse, NY, USA 13244
| | - Lydia B Choi
- Department of Chemistry, Syracuse University, Syracuse, NY, USA 13244
| | - William G Kerr
- Department of Chemistry, Syracuse University, Syracuse, NY, USA 13244.,Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY, USA 13210.,Department of Pediatrics, SUNY Upstate Medical University, Syracuse, NY, USA 13210
| | - John D Chisholm
- Department of Chemistry, Syracuse University, Syracuse, NY, USA 13244
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Regulation of OSR1 and the sodium, potassium, two chloride cotransporter by convergent signals. Proc Natl Acad Sci U S A 2013; 110:18826-31. [PMID: 24191005 DOI: 10.1073/pnas.1318676110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Ste20 family protein kinases oxidative stress-responsive 1 (OSR1) and the STE20/SPS1-related proline-, alanine-rich kinase directly regulate the solute carrier 12 family of cation-chloride cotransporters and thereby modulate a range of processes including cell volume homeostasis, blood pressure, hearing, and kidney function. OSR1 and STE20/SPS1-related proline-, alanine-rich kinase are activated by with no lysine [K] protein kinases that phosphorylate the essential activation loop regulatory site on these kinases. We found that inhibition of phosphoinositide 3-kinase (PI3K) reduced OSR1 activation by osmotic stress. Inhibition of the PI3K target pathway, the mammalian target of rapamycin complex 2 (mTORC2), by depletion of Sin1, one of its components, decreased activation of OSR1 by sorbitol and reduced activity of the OSR1 substrate, the sodium, potassium, two chloride cotransporter, in HeLa cells. OSR1 activity was also reduced with a pharmacological inhibitor of mTOR. mTORC2 phosphorylated OSR1 on S339 in vitro, and mutation of this residue eliminated OSR1 phosphorylation by mTORC2. Thus, we identify a previously unrecognized connection of the PI3K pathway through mTORC2 to a Ste20 protein kinase and ion homeostasis.
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Devereaux K, Dall’Armi C, Alcazar-Roman A, Ogasawara Y, Zhou X, Wang F, Yamamoto A, De Camilli P, Di Paolo G. Regulation of mammalian autophagy by class II and III PI 3-kinases through PI3P synthesis. PLoS One 2013; 8:e76405. [PMID: 24098492 PMCID: PMC3789715 DOI: 10.1371/journal.pone.0076405] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/30/2013] [Indexed: 11/19/2022] Open
Abstract
Synthesis of phosphatidylinositol-3-phosphate (PI3P) by Vps34, a class III phosphatidylinositol 3-kinase (PI3K), is critical for the initial steps of autophagosome (AP) biogenesis. Although Vps34 is the sole source of PI3P in budding yeast, mammalian cells can produce PI3P through alternate pathways, including direct synthesis by the class II PI3Ks; however, the physiological relevance of these alternate pathways in the context of autophagy is unknown. Here we generated Vps34 knockout mouse embryonic fibroblasts (MEFs) and using a higher affinity 4x-FYVE finger PI3P-binding probe found a Vps34-independent pool of PI3P accounting for (~)35% of the total amount of this lipid species by biochemical analysis. Importantly, WIPI-1, an autophagy-relevant PI3P probe, still formed some puncta upon starvation-induced autophagy in Vps34 knockout MEFs. Additional characterization of autophagy by electron microscopy as well as protein degradation assays showed that while Vps34 is important for starvation-induced autophagy there is a significant component of functional autophagy occurring in the absence of Vps34. Given these findings, class II PI3Ks (α and β isoforms) were examined as potential positive regulators of autophagy. Depletion of class II PI3Ks reduced recruitment of WIPI-1 and LC3 to AP nucleation sites and caused an accumulation of the autophagy substrate, p62, which was exacerbated upon the concomitant ablation of Vps34. Our studies indicate that while Vps34 is the main PI3P source during autophagy, class II PI3Ks also significantly contribute to PI3P generation and regulate AP biogenesis.
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Affiliation(s)
- Kelly Devereaux
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, New York, United States of America
| | - Claudia Dall’Armi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, New York, United States of America
| | - Abel Alcazar-Roman
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yuta Ogasawara
- Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Xiang Zhou
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Fan Wang
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Akitsugu Yamamoto
- Department of Animal Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Gilbert Di Paolo
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, New York, United States of America
- * E-mail:
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Srivastava N, Sudan R, Kerr WG. Role of inositol poly-phosphatases and their targets in T cell biology. Front Immunol 2013; 4:288. [PMID: 24069021 PMCID: PMC3779868 DOI: 10.3389/fimmu.2013.00288] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 09/03/2013] [Indexed: 11/13/2022] Open
Abstract
T lymphocytes play a critical role in host defense in all anatomical sites including mucosal surfaces. This not only includes the effector arm of the immune system, but also regulation of immune responses in order to prevent autoimmunity. Genetic targeting of PI3K isoforms suggests that generation of PI(3,4,5)P3 by PI3K plays a critical role in promoting effector T cell responses. Consequently, the 5'- and 3'-inositol poly-phosphatases SHIP1, SHIP2, and phosphatase and tensin homolog capable of targeting PI(3,4,5)P3 are potential genetic determinants of T cell effector functions in vivo. In addition, the 5'-inositol poly-phosphatases SHIP1 and 2 can shunt PI(3,4,5)P3 to the rare but potent signaling phosphoinositide species PI(3,4)P2 and thus these SHIP1/2, and the INPP4A/B enzymes that deplete PI(3,4)P2 may have precise roles in T cell biology to amplify or inhibit effectors of PI3K signaling that are selectively recruited to and activated by PI(3,4)P2. Here we summarize recent genetic and chemical evidence that indicates the inositol poly-phosphatases have important roles in both the effector and regulatory functions of the T cell compartment. In addition, we will discuss future genetic studies that might be undertaken to further elaborate the role of these enzymes in T cell biology as well as potential pharmaceutical manipulation of these enzymes for therapeutic purposes in disease settings where T cell function is a key in vivo target.
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Affiliation(s)
- Neetu Srivastava
- Department of Microbiology and Immunology, SUNY Upstate Medical University , Syracuse, NY , USA
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Reifler A, Lenk GM, Li X, Groom L, Brooks SV, Wilson D, Bowerson M, Dirksen RT, Meisler MH, Dowling JJ. Murine Fig4 is dispensable for muscle development but required for muscle function. Skelet Muscle 2013; 3:21. [PMID: 24004519 PMCID: PMC3844516 DOI: 10.1186/2044-5040-3-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Phosphatidylinositol phosphates (PIPs) are low-abundance phospholipids that participate in a range of cellular processes, including cell migration and membrane traffic. PIP levels and subcellular distribution are regulated by a series of lipid kinases and phosphatases. In skeletal muscle, PIPs and their enzymatic regulators serve critically important functions exemplified by mutations of the PIP phosphatase MTM1 in myotubular myopathy (MTM), a severe muscle disease characterized by impaired muscle structure and abnormal excitation-contraction coupling. FIG4 functions as a PIP phosphatase that participates in both the synthesis and breakdown of phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). Mutation of FIG4 results in a severe neurodegenerative disorder in mice and a progressive peripheral polyneuropathy in humans. The effect of FIG4 mutation on skeletal muscle has yet to be examined. METHODS Herein we characterize the impact of FIG4 on skeletal muscle development and function using the spontaneously occurring mouse mutant pale tremor (plt), a mouse line with a loss of function mutation in Fig4. RESULTS In plt mice, we characterized abnormalities in skeletal muscle, including reduced muscle size and specific force generation. We also uncovered ultrastructural abnormalities and increased programmed cell death. Conversely, we detected no structural or functional abnormalities to suggest impairment of excitation-contraction coupling, a process previously shown to be influenced by PI(3,5)P2 levels. Conditional rescue of Fig4 mutation in neurons prevented overt muscle weakness and the development of obvious muscle abnormalities, suggesting that the changes observed in the plt mice were primarily related to denervation of skeletal muscle. On the basis of the ability of reduced FIG4 levels to rescue aspects of Mtmr2-dependent neuropathy, we evaluated the effect of Fig4 haploinsufficiency on the myopathy of Mtm1-knockout mice. Male mice with a compound Fig4+/-/Mtm1-/Y genotype displayed no improvements in muscle histology, muscle size or overall survival, indicating that FIG4 reduction does not ameliorate the Mtm1-knockout phenotype. CONCLUSIONS Overall, these data indicate that loss of Fig4 impairs skeletal muscle function but does not significantly affect its structural development.
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Affiliation(s)
- Aaron Reifler
- Department of Pediatrics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Guy M Lenk
- Department of Human Genetics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
| | - Xingli Li
- Department of Pediatrics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
| | - Linda Groom
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Susan V Brooks
- Molecular and Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
| | - Desmond Wilson
- Department of Pediatrics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
| | - Michyla Bowerson
- Department of Pediatrics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
| | - Robert T Dirksen
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
| | - James J Dowling
- Department of Pediatrics, University of Michigan Medical Center, Ann Arbor, MI 48109-2200, USA
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Shisheva A. PtdIns5P: news and views of its appearance, disappearance and deeds. Arch Biochem Biophys 2013; 538:171-80. [PMID: 23916588 DOI: 10.1016/j.abb.2013.07.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/22/2013] [Indexed: 12/24/2022]
Abstract
Accumulated evidence indicates that PtdIns5P, one of the seven phosphoinositides, found now to be constitutively present in yeast, plants and metazoa, serves as a signaling molecule to modulate pleiotropic cellular functions in both the nucleus and the cytoplasm. The enzymatic routes in biogenesis of basal PtdIns5P have remained incompletely understood. The role for candidate kinase PIKfyve that is principally involved in PtdIns(3,5)P2 production, has been questioned. In this review article we scrutinize the past obstacles that prevented the definitive implication of PIKfyve in PtdIns5P biosynthesis from PtdIns and focus on the recent pharmacological and genetic advancements that now make this conclusion well supported. We further summarize our current knowledge of the diverse stimuli modulating PtdIns5P levels, binding partners and regulated cellular process, with particular reference to the available mechanistic insights for the relevant signaling pathways.
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Affiliation(s)
- Assia Shisheva
- Department of Physiology, Wayne State University School of Medicine, 540 E. Canfield, Detroit, MI 48201, United States.
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Pulido R, Stoker AW, Hendriks WJAJ. PTPs emerge as PIPs: protein tyrosine phosphatases with lipid-phosphatase activities in human disease. Hum Mol Genet 2013; 22:R66-76. [PMID: 23900072 DOI: 10.1093/hmg/ddt347] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) constitute a family of key homeostatic regulators, with wide implications on physiology and disease. Recent findings have unveiled that the biological activity of PTPs goes beyond the dephosphorylation of phospho-proteins to shut down protein tyrosine kinase-driven signaling cascades. Substrates dephosphorylated by clinically relevant PTPs extend to phospholipids and phosphorylated carbohydrates as well. In addition, non-catalytic functions are also used by PTPs to regulate essential cellular functions. Consequently, PTPs have emerged as novel potential therapeutic targets for human diseases, including cancer predispositions, myopathies and neuropathies. In this review, we highlight recent advances on the multifaceted role of lipid-phosphatase PTPs in human pathology, with an emphasis on hereditary diseases. The involved PTP regulatory networks and PTP modulatory strategies with potential therapeutic application are discussed.
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