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Ji X, Cheng J, Su J, Wen R, Zhang Q, Liu G, Peng Y, Mao J. PTPN7 mediates macrophage-polarization and determines immunotherapy in gliomas: A single-cell sequencing analysis. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38581214 DOI: 10.1002/tox.24259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/09/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Protein tyrosine phosphatase non-receptor type 7 (PTPN7) is a signaling molecule that regulates a multitude of cellular processes, spanning cell proliferation, cellular differentiation, the mitotic cycle, and oncogenic metamorphosis. However, the characteristic of PTPN7 in the glioma microenvironment has yet to be elucidated. METHODS The prognostic value, genomic features, immune characteristics, chemotherapy prediction, and immunotherapy prediction of PTPN7 were systematically explored at the bulk sequencing level. The cell evolution trajectory, cell communication pattern, and cell metabolic activity related to PTPN7 were systematically explored at the single-cell sequencing level. HMC3 and M0 cells were cocultured with U251 and T98G cells, and flow cytometry was carried out to investigate the polarization of HMC3 and M0. Transwell assay and CCK-8 assay were performed to explore the migration and proliferation activity of U251 and T98G. RESULTS The expression level of PTPN7 is significantly elevated in glioma and indicates malignant features. PTPN7 expression predicts worse prognosis of glioma patients. PTPN7 is associated with genome alteration and immune infiltration. Besides, PTPN7 plays a crucial role in modulating metabolic and immunogenic processes, particularly by influencing the activity of microglia and macrophages through multiple signaling pathways involved in cellular communication. Specifically, PTPN7 actively mediates inflammation-resolving-polarization of macrophages and microglia and protects glioma from immune attack. PTPN7 could also predict the response of immunotherapy. CONCLUSIONS PTPN7 is critically involved in inflammation-resolving-polarization mediated by macrophage and microglia and promotes the immune escape of glioma cells.
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Affiliation(s)
- Xiang Ji
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jingsong Cheng
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jing Su
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Rong Wen
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Qi Zhang
- Department of Neurosurgery, Tongnan Hospital of TCM, Chongqing, China
| | - Guodong Liu
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yun Peng
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jinning Mao
- Health Management Center, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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2
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Bashore F, Annor-Gyamfi J, Du Y, Katis V, Nwogbo F, Flax RG, Frye SV, Pearce KH, Fu H, Willson TM, Drewry DH, Axtman AD. Fused Tetrahydroquinolines Are Interfering with Your Assay. J Med Chem 2023; 66:14434-14446. [PMID: 37874947 PMCID: PMC10641811 DOI: 10.1021/acs.jmedchem.3c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Tricyclic tetrahydroquinolines (THQs) have been repeatedly reported as hits across a diverse range of high-throughput screening (HTS) campaigns. The activities of these compounds, however, are likely due to reactive byproducts that interfere with the assay. As a lesser studied class of pan-assay interference compounds, the mechanism by which fused THQs react with protein targets remains largely unknown. During HTS follow-up, we characterized the behavior and stability of several fused tricyclic THQs. We synthesized key analogues to pinpoint the cyclopentene ring double bond as a source of reactivity of fused THQs. We found that these compounds degrade in solution under standard laboratory conditions in days. Importantly, these observations make it likely that fused THQs, which are ubiquitously found within small molecule screening libraries, are unlikely the intact parent compounds. We urge deprioritization of tricylic THQ hits in HTS follow-up and caution against the investment of resources to follow-up on these problematic compounds.
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Affiliation(s)
- Frances
M. Bashore
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joel Annor-Gyamfi
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yuhong Du
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Vittorio Katis
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Centre for Medicines
Discovery, Nuffield Department of Medicine Research Building, Old
Road Campus, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Felix Nwogbo
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Raymond G. Flax
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Haian Fu
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Timothy M. Willson
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David H. Drewry
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger
Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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3
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Innocenti M. Investigating Mammalian Formins with SMIFH2 Fifteen Years in: Novel Targets and Unexpected Biology. Int J Mol Sci 2023; 24:ijms24109058. [PMID: 37240404 DOI: 10.3390/ijms24109058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The mammalian formin family comprises fifteen multi-domain proteins that regulate actin dynamics and microtubules in vitro and in cells. Evolutionarily conserved formin homology (FH) 1 and 2 domains allow formins to locally modulate the cell cytoskeleton. Formins are involved in several developmental and homeostatic processes, as well as human diseases. However, functional redundancy has long hampered studies of individual formins with genetic loss-of-function approaches and prevents the rapid inhibition of formin activities in cells. The discovery of small molecule inhibitor of formin homology 2 domains (SMIFH2) in 2009 was a disruptive change that provided a powerful chemical tool to explore formins' functions across biological scales. Here, I critically discuss the characterization of SMIFH2 as a pan-formin inhibitor, as well as growing evidence of unexpected off-target effects. By collating the literature and information hidden in public repositories, outstanding controversies and fundamental open questions about the substrates and mechanism of action of SMIFH2 emerge. Whenever possible, I propose explanations for these discrepancies and roadmaps to address the paramount open questions. Furthermore, I suggest that SMIFH2 be reclassified as a multi-target inhibitor for its appealing activities on proteins involved in pathological formin-dependent processes. Notwithstanding all drawbacks and limitations, SMIFH2 will continue to prove useful in studying formins in health and disease in the years to come.
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Affiliation(s)
- Metello Innocenti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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4
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Vedhapriya K, Balaji G, Dhiyaneshwari B, Irfan A, Thirunavukkarasu M, Kaleeswaran S, Obairdur Rab S, Muthu S. Effect of green solvents, molecular structure and topological studies on 4-amino-1-β-d-ribofuranosyl-1,3,5 triazin-2(1H)-one - anti-blood cancer agent. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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5
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Raveendra-Panickar D, Finlay D, Layng FI, Lambert LJ, Celeridad M, Zhao M, Barbosa K, De Backer LJS, Kwong E, Gosalia P, Rodiles S, Holleran J, Ardecky R, Grotegut S, Olson S, Hutchinson JH, Pasquale EB, Vuori K, Deshpande AJ, Cosford NDP, Tautz L. Discovery of novel furanylbenzamide inhibitors that target oncogenic tyrosine phosphatase SHP2 in leukemia cells. J Biol Chem 2022; 298:101477. [PMID: 34896393 PMCID: PMC8760490 DOI: 10.1016/j.jbc.2021.101477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/11/2022] Open
Abstract
Disturbance of the dynamic balance between tyrosine phosphorylation and dephosphorylation of signaling molecules, controlled by protein tyrosine kinases and protein tyrosine phosphatases (PTPs), is known to lead to the development of cancer. While most approved targeted cancer therapies are tyrosine kinase inhibitors, PTPs have long been stigmatized as undruggable and have only recently gained renewed attention in drug discovery. One PTP target is the Src-homology 2 domain-containing phosphatase 2 (SHP2). SHP2 is implicated in tumor initiation, progression, metastasis, and treatment resistance, primarily because of its role as a signaling nexus of the extracellular signal-regulated kinase pathway, acting upstream of the small GTPase Ras. Efforts to develop small molecules that target SHP2 are ongoing, and several SHP2 allosteric inhibitors are currently in clinical trials for the treatment of solid tumors. However, while the reported allosteric inhibitors are highly effective against cells expressing WT SHP2, none have significant activity against the most frequent oncogenic SHP2 variants that drive leukemogenesis in several juvenile and acute leukemias. Here, we report the discovery of novel furanylbenzamide molecules as inhibitors of both WT and oncogenic SHP2. Importantly, these inhibitors readily cross cell membranes, bind and inhibit SHP2 under physiological conditions, and effectively decrease the growth of cancer cells, including triple-negative breast cancer cells, acute myeloid leukemia cells expressing either WT or oncogenic SHP2, and patient-derived acute myeloid leukemia cells. These novel compounds are effective chemical probes of active SHP2 and may serve as starting points for therapeutics targeting WT or mutant SHP2 in cancer.
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Affiliation(s)
- Dhanya Raveendra-Panickar
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Fabiana Izidro Layng
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lester J Lambert
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Maria Celeridad
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Ming Zhao
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Karina Barbosa
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Laurent J S De Backer
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Elizabeth Kwong
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Palak Gosalia
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Socorro Rodiles
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John Holleran
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Robert Ardecky
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Stefan Grotegut
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Steven Olson
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John H Hutchinson
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Elena B Pasquale
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Kristiina Vuori
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Aniruddha J Deshpande
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Nicholas D P Cosford
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
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6
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Prado DS, Cattley RT, Shipman CW, Happe C, Lee M, Boggess WC, MacDonald ML, Hawse WF. Synergistic and additive interactions between receptor signaling networks drive the regulatory T cell versus T helper 17 cell fate choice. J Biol Chem 2021; 297:101330. [PMID: 34688667 PMCID: PMC8645459 DOI: 10.1016/j.jbc.2021.101330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 12/04/2022] Open
Abstract
CD4+ T cells differentiate into subsets that promote immunity or minimize damage to the host. T helper 17 cells (Th17) are effector cells that function in inflammatory responses. T regulatory cells (Tregs) maintain tolerance and prevent autoimmunity by secreting immunosuppressive cytokines and expressing check point receptors. While the functions of Th17 and Treg cells are different, both cell fate trajectories require T cell receptor (TCR) and TGF-β receptor (TGF-βR) signals, and Th17 polarization requires an additional IL-6 receptor (IL-6R) signal. Utilizing high-resolution phosphoproteomics, we identified that both synergistic and additive interactions between TCR, TGF-βR, and IL-6R shape kinase signaling networks to differentially regulate key pathways during the early phase of Treg versus Th17 induction. Quantitative biochemical analysis revealed that CD4+ T cells integrate receptor signals via SMAD3, which is a mediator of TGF-βR signaling. Treg induction potentiates the formation of the canonical SMAD3/4 trimer to activate a negative feedback loop through kinases PKA and CSK to suppress TCR signaling, phosphatidylinositol metabolism, and mTOR signaling. IL-6R signaling activates STAT3 to bind SMAD3 and block formation of the SMAD3/4 trimer during the early phase of Th17 induction, which leads to elevated TCR and PI3K signaling. These data provide a biochemical mechanism by which CD4+ T cells integrate TCR, TGF-β, and IL-6 signals via generation of alternate SMAD3 complexes that control the development of early signaling networks to potentiate the choice of Treg versus Th17 cell fate.
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Affiliation(s)
- Douglas S Prado
- Department of Immunology and Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Richard T Cattley
- Department of Immunology and Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Corey W Shipman
- Department of Immunology and Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Cassandra Happe
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - William C Boggess
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew L MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William F Hawse
- Department of Immunology and Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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7
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A New Paradigm for KIM-PTP Drug Discovery: Identification of Allosteric Sites with Potential for Selective Inhibition Using Virtual Screening and LEI Analysis. Int J Mol Sci 2021; 22:ijms222212206. [PMID: 34830087 PMCID: PMC8624330 DOI: 10.3390/ijms222212206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 02/04/2023] Open
Abstract
The kinase interaction motif protein tyrosine phosphatases (KIM-PTPs), HePTP, PTPSL and STEP, are involved in the negative regulation of mitogen-activated protein kinase (MAPK) signalling pathways and are important therapeutic targets for a number of diseases. We have used VSpipe, a virtual screening pipeline, to identify a ligand cluster distribution that is unique to this subfamily of PTPs. Several clusters map onto KIM-PTP specific sequence motifs in contrast to the cluster distribution obtained for PTP1B, a classic PTP that mapped to general PTP motifs. Importantly, the ligand clusters coincide with previously reported functional and substrate binding sites in KIM-PTPs. Assessment of the KIM-PTP specific clusters, using ligand efficiency index (LEI) plots generated by the VSpipe, ascertained that the binders in these clusters reside in a more drug-like chemical-biological space than those at the active site. LEI analysis showed differences between clusters across all KIM-PTPs, highlighting a distinct and specific profile for each phosphatase. The most druggable cluster sites are unexplored allosteric functional sites unique to each target. Exploiting these sites may facilitate the delivery of inhibitors with improved drug-like properties, with selectivity amongst the KIM-PTPs and over other classical PTPs.
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8
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Targeting SHP2 as a therapeutic strategy for inflammatory diseases. Eur J Med Chem 2021; 214:113264. [PMID: 33582386 DOI: 10.1016/j.ejmech.2021.113264] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022]
Abstract
With the change of lifestyle and the acceleration of aging process, inflammatory diseases have increasingly become one of the most vital threats to global human health. SHP2 protein is a non-receptor tyrosine phosphatase encoded by PTPN11 gene, and it is widely expressed in various tissues and cells. Numerous studies have shown that SHP2 plays important roles in the regulation of inflammatory diseases, including cancer-related inflammation, neurodegenerative diseases and metabolic diseases. In this paper, the roles of SHP2 in inflammatory diseases of various physiological systems were reviewed. At the same time, the latest SHP2 inhibitors were summarized, which will hold a promise for the therapeutic potential in future.
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9
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Priebe V, Sartori G, Napoli S, Chung EYL, Cascione L, Kwee I, Arribas AJ, Mensah AA, Rinaldi A, Ponzoni M, Zucca E, Rossi D, Efremov D, Lenz G, Thome M, Bertoni F. Role of ETS1 in the Transcriptional Network of Diffuse Large B Cell Lymphoma of the Activated B Cell-Like Type. Cancers (Basel) 2020; 12:cancers12071912. [PMID: 32679859 PMCID: PMC7409072 DOI: 10.3390/cancers12071912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 01/08/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is a heterogenous disease that has been distinguished into at least two major molecular entities, the germinal center-like B cell (GCB) DLBCL and activated-like B cell (ABC) DLBCL, based on transcriptome expression profiling. A recurrent ch11q24.3 gain is observed in roughly a fourth of DLBCL cases resulting in the overexpression of two ETS transcription factor family members, ETS1 and FLI1. Here, we knocked down ETS1 expression by siRNA and analyzed expression changes integrating them with ChIP-seq data to identify genes directly regulated by ETS1. ETS1 silencing affected expression of genes involved in B cell signaling activation, B cell differentiation, cell cycle, and immune processes. Integration of RNA-Seq (RNA sequencing) data and ChIP-Seq (chromatin immunoprecipitation sequencing) identified 97 genes as bona fide, positively regulated direct targets of ETS1 in ABC-DLBCL. Among these was the Fc receptor for IgM, FCMR (also known as FAIM3 or Toso), which showed higher expression in ABC- than GCB-DLBCL clinical specimens. These findings show that ETS1 is contributing to the lymphomagenesis in a subset of DLBCL and identifies FCMR as a novel target of ETS1, predominantly expressed in ABC-DLBCL.
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Affiliation(s)
- Valdemar Priebe
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
| | - Elaine Yee Lin Chung
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Ivo Kwee
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
- Dalle Molle Institute for Artificial Intelligence (IDSIA), 6928 Manno, Switzerland
| | - Alberto Jesus Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Afua Adjeiwaa Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
| | - Maurilio Ponzoni
- San Raffaele Scientific Institute, Vita Salute University, 20132 Milan, Italy;
| | - Emanuele Zucca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
- Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - Davide Rossi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
- Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - Dimitar Efremov
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy;
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, 48149 Münster, Germany;
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland;
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland; (V.P.); (G.S.); (S.N.); (E.Y.L.C.); (L.C.); (I.K.); (A.J.A.); (A.A.M.); (A.R.); (E.Z.); (D.R.)
- Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
- Correspondence: ; Tel.: +41-91-8200-367; Fax: +41-91-8200-397
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10
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Romero C, Lambert LJ, Sheffler DJ, De Backer LJS, Raveendra-Panickar D, Celeridad M, Grotegut S, Rodiles S, Holleran J, Sergienko E, Pasquale EB, Cosford NDP, Tautz L. A cellular target engagement assay for the characterization of SHP2 (PTPN11) phosphatase inhibitors. J Biol Chem 2020; 295:2601-2613. [PMID: 31953320 DOI: 10.1074/jbc.ra119.010838] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/14/2020] [Indexed: 12/21/2022] Open
Abstract
The nonreceptor protein-tyrosine phosphatase (PTP) SHP2 is encoded by the proto-oncogene PTPN11 and is a ubiquitously expressed key regulator of cell signaling, acting on a number of cellular processes and components, including the Ras/Raf/Erk, PI3K/Akt, and JAK/STAT pathways and immune checkpoint receptors. Aberrant SHP2 activity has been implicated in all phases of tumor initiation, progression, and metastasis. Gain-of-function PTPN11 mutations drive oncogenesis in several leukemias and cause developmental disorders with increased risk of malignancy such as Noonan syndrome. Until recently, small molecule-based targeting of SHP2 was hampered by the failure of orthosteric active-site inhibitors to achieve selectivity and potency within a useful therapeutic window. However, new SHP2 allosteric inhibitors with excellent potency and selectivity have sparked renewed interest in the selective targeting of SHP2 and other PTP family members. Crucially, drug discovery campaigns focusing on SHP2 would greatly benefit from the ability to validate the cellular target engagement of candidate inhibitors. Here, we report a cellular thermal shift assay that reliably detects target engagement of SHP2 inhibitors. Using this assay, based on the DiscoverX InCell Pulse enzyme complementation technology, we characterized the binding of several SHP2 allosteric inhibitors in intact cells. Moreover, we demonstrate the robustness and reliability of a 384-well miniaturized version of the assay for the screening of SHP2 inhibitors targeting either WT SHP2 or its oncogenic E76K variant. Finally, we provide an example of the assay's ability to identify and characterize novel compounds with specific cellular potency for either WT or mutant SHP2.
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Affiliation(s)
- Celeste Romero
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Lester J Lambert
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Douglas J Sheffler
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Laurent J S De Backer
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Dhanya Raveendra-Panickar
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Maria Celeridad
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Stefan Grotegut
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Socorro Rodiles
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - John Holleran
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Eduard Sergienko
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Elena B Pasquale
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Nicholas D P Cosford
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Lutz Tautz
- Cancer Metabolism & Signaling Networks Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037.
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11
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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12
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Sommers JA, Kulikowicz T, Croteau DL, Dexheimer T, Dorjsuren D, Jadhav A, Maloney DJ, Simeonov A, Bohr VA, Brosh RM. A high-throughput screen to identify novel small molecule inhibitors of the Werner Syndrome Helicase-Nuclease (WRN). PLoS One 2019; 14:e0210525. [PMID: 30625228 PMCID: PMC6326523 DOI: 10.1371/journal.pone.0210525] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/26/2018] [Indexed: 01/26/2023] Open
Abstract
Werner syndrome (WS), an autosomal recessive genetic disorder, displays accelerated clinical symptoms of aging leading to a mean lifespan less than 50 years. The WS helicase-nuclease (WRN) is involved in many important pathways including DNA replication, recombination and repair. Replicating cells are dependent on helicase activity, leading to the pursuit of human helicases as potential therapeutic targets for cancer treatment. Small molecule inhibitors of DNA helicases can be used to induce synthetic lethality, which attempts to target helicase-dependent compensatory DNA repair pathways in tumor cells that are already genetically deficient in a specific pathway of DNA repair. Alternatively, helicase inhibitors may be useful as tools to study the specialized roles of helicases in replication and DNA repair. In this study, approximately 350,000 small molecules were screened based on their ability to inhibit duplex DNA unwinding by a catalytically active WRN helicase domain fragment in a high-throughput fluorometric assay to discover new non-covalent small molecule inhibitors of the WRN helicase. Select compounds were screened to exclude ones that inhibited DNA unwinding by other helicases in the screen, bound non-specifically to DNA, acted as irreversible inhibitors, or possessed unfavorable chemical properties. Several compounds were tested for their ability to impair proliferation of cultured tumor cells. We observed that two of the newly identified WRN helicase inhibitors inhibited proliferation of cancer cells in a lineage-dependent manner. These studies represent the first high-throughput screen for WRN helicase inhibitors and the results have implications for anti-cancer strategies targeting WRN in different cancer cells and genetic backgrounds.
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Affiliation(s)
- Joshua A. Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Deborah L. Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Thomas Dexheimer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Dorjbal Dorjsuren
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Robert M. Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
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13
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Wu L, Tai Y, Hu S, Zhang M, Wang R, Zhou W, Tao J, Han Y, Wang Q, Wei W. Bidirectional Role of β2-Adrenergic Receptor in Autoimmune Diseases. Front Pharmacol 2018; 9:1313. [PMID: 30538630 PMCID: PMC6277539 DOI: 10.3389/fphar.2018.01313] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022] Open
Abstract
Disorder of the sympathetic nervous system (SNS) is closely related to the pathogenesis of various autoimmune diseases (ADs). Catecholamine triggered beta2-adrenergic receptor (β2-AR) signaling is important in creating a bidirectional response in the progression of ADs due to factors including diverse expression patterns, single nucleotide polymorphisms (SNPs), biased signals, and desensitization of β2-AR, as well as different subtypes of Gα binding to β2-AR. In this review, we summarize the actions of β2-AR signaling in regulating the functions of immunocytes and in the pathogenesis of ADs, and the application of β2-AR agonists or antagonists in treating major types of ADs is also discussed. We suggest that restoring the immune balance via a soft regulation of the expression or activation of β2-AR is one of the promising therapeutic strategies for systematic ADs.
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Affiliation(s)
- Li Wu
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Yu Tai
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Shanshan Hu
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Mei Zhang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Rui Wang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Weijie Zhou
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Juan Tao
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Yongsheng Han
- Department of Emergency Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Qingtong Wang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Wei Wei
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
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14
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Machado LESF, Page R, Peti W. 1H, 15N and 13C sequence specific backbone assignment of the vanadate inhibited hematopoietic tyrosine phosphatase. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:5-9. [PMID: 28856606 PMCID: PMC5832517 DOI: 10.1007/s12104-017-9770-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
The sequence-specific backbone assignment of hematopoietic protein tyrosine phosphatase (HePTP; PTPN7) in presence of vanadate has been determined, based on triple-resonance experiments using uniformly [13C,15N]-labeled protein. These assignments facilitate further studies of HePTP in the presence of inhibitors to target leukemia and provide further insights into the function of protein tyrosine phosphatases.
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Affiliation(s)
- Luciana E S F Machado
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA.
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.
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15
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Transcriptional signature associated with early rheumatoid arthritis and healthy individuals at high risk to develop the disease. PLoS One 2018; 13:e0194205. [PMID: 29584756 PMCID: PMC5870959 DOI: 10.1371/journal.pone.0194205] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/27/2018] [Indexed: 12/17/2022] Open
Abstract
Background Little is known regarding the mechanisms underlying the loss of tolerance in the early and preclinical stages of autoimmune diseases. The aim of this work was to identify the transcriptional profile and signaling pathways associated to non-treated early rheumatoid arthritis (RA) and subjects at high risk. Several biomarker candidates for early RA are proposed. Methods Whole blood total RNA was obtained from non-treated early RA patients with <1 year of evolution as well as from healthy first-degree relatives of patients with RA (FDR) classified as ACCP+ and ACCP- according to their antibodies serum levels against cyclic citrullinated peptides. Complementary RNA (cRNA) was synthetized and hybridized to high-density microarrays. Data was analyzed in Genespring Software and functional categories were assigned to a specific transcriptome identified in subjects with RA and FDR ACCP positive. Specific signaling pathways for genes associated to RA were identified. Gene expression was evaluated by qPCR. Receiver operating characteristic (ROC) analysis was used to evaluate these genes as biomarkers. Results A characteristic transcriptome of 551 induced genes and 4,402 repressed genes were identified in early RA patients. Bioinformatics analysis of the data identified a specific transcriptome in RA patients. Moreover, some overlapped transcriptional profiles between patients with RA and ACCP+ were identified, suggesting an up-regulated distinctive transcriptome from the preclinical stages up to progression to an early RA state. A total of 203 pathways have up-regulated genes that are shared between RA and ACCP+. Some of these genes show potential to be used as progression biomarkers for early RA with area under the curve of ROC > 0.92. These genes come from several functional categories associated to inflammation, Wnt signaling and type I interferon pathways. Conclusion The presence of a specific transcriptome in whole blood of RA patients suggests the activation of a specific inflammatory transcriptional signature in early RA development. The set of overexpressed genes in early RA patients that are shared with ACCP+ subjects but not with ACCP- subjects, can represent a transcriptional signature involved with the transition of a preclinical to a clinical RA stage. Some of these particular up-regulated and down-regulated genes are related to inflammatory processes and could be considered as biomarker candidates for disease progression in subjects at risk to develop RA.
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16
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Machado LESF, Shen TL, Page R, Peti W. The KIM-family protein-tyrosine phosphatases use distinct reversible oxidation intermediates: Intramolecular or intermolecular disulfide bond formation. J Biol Chem 2017; 292:8786-8796. [PMID: 28389559 DOI: 10.1074/jbc.m116.774174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 04/07/2017] [Indexed: 11/06/2022] Open
Abstract
The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes hematopoietic protein-tyrosine phosphatase (HePTP), striatal-enriched protein-tyrosine phosphatase (STEP), and protein-tyrosine phosphatase receptor type R (PTPRR). KIM-PTPs bind and dephosphorylate mitogen-activated protein kinases (MAPKs) and thereby critically modulate cell proliferation and differentiation. PTP activity can readily be diminished by reactive oxygen species (ROS), e.g. H2O2, which oxidize the catalytically indispensable active-site cysteine. This initial oxidation generates an unstable sulfenic acid intermediate that is quickly converted into either a sulfinic/sulfonic acid (catalytically dead and irreversible inactivation) or a stable sulfenamide or disulfide bond intermediate (reversible inactivation). Critically, our understanding of ROS-mediated PTP oxidation is not yet sufficient to predict the molecular responses of PTPs to oxidative stress. However, identifying distinct responses will enable novel routes for PTP-selective drug design, important for managing diseases such as cancer and Alzheimer's disease. Therefore, we performed a detailed biochemical and molecular study of all KIM-PTP family members to determine their H2O2 oxidation profiles and identify their reversible inactivation mechanism(s). We show that despite having nearly identical 3D structures and sequences, each KIM-PTP family member has a unique oxidation profile. Furthermore, we also show that whereas STEP and PTPRR stabilize their reversibly oxidized state by forming an intramolecular disulfide bond, HePTP uses an unexpected mechanism, namely, formation of a reversible intermolecular disulfide bond. In summary, despite being closely related, KIM-PTPs significantly differ in oxidation profiles. These findings highlight that oxidation protection is critical when analyzing PTPs, for example, in drug screening.
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Affiliation(s)
| | | | - Rebecca Page
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912
| | - Wolfgang Peti
- From the Departments of Molecular Pharmacology, Physiology and Biotechnology, .,Chemistry, and
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17
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Baldeón R L, Weigelt K, de Wit H, Ozcan B, van Oudenaren A, Sempértegui F, Sijbrands E, Grosse L, van Zonneveld AJ, Drexhage HA, Leenen PJM. Type 2 Diabetes Monocyte MicroRNA and mRNA Expression: Dyslipidemia Associates with Increased Differentiation-Related Genes but Not Inflammatory Activation. PLoS One 2015; 10:e0129421. [PMID: 26083362 PMCID: PMC4471054 DOI: 10.1371/journal.pone.0129421] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 05/10/2015] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE To study the expression pattern of microRNAs and mRNAs related to inflammation in T2D monocytes. DESIGN A microRNA finding study on monocytes of T2D patients and controls using array profiling was followed by a quantitative Real Time PCR (qPCR) study on monocytes of an Ecuadorian validation cohort testing the top over/under-expressed microRNAs. In addition, monocytes of the validation cohort were tested for 24 inflammation-related mRNAs and 2 microRNAs previously found deregulated in (auto)-inflammatory monocytes. RESULTS In the finding study, 142 significantly differentially expressed microRNAs were identified, 15 having the strongest power to discriminate T2D patients from controls (sensitivity 66%, specificity 90%). However, differences in expression of these microRNAs between patients and controls were small. On the basis of >1.4 or <0.6-fold change expression 5 microRNAs were selected for further validation. One microRNA (miR-34c-5p) was validated as significantly over-expressed in T2D monocytes. In addition, we found over expression of 3 mRNAs (CD9, DHRS3 and PTPN7) in the validation cohort. These mRNAs are important for cell morphology, adhesion, shape change, and cell differentiation. Classical inflammatory genes (e.g. TNFAIP3) were only over-expressed in monocytes of patients with normal serum lipids. Remarkably, in dyslipidemia, there was a reduction in the expression of inflammatory genes (e.g. ATF3, DUSP2 and PTGS2). CONCLUSIONS The expression profile of microRNAs/mRNAs in monocytes of T2D patients indicates an altered adhesion, differentiation, and shape change potential. Monocyte inflammatory activation was only found in patients with normal serum lipids. Abnormal lipid values coincided with a reduced monocyte inflammatory state.
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Affiliation(s)
- Lucy Baldeón R
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands; Department of Immunology, Central University of Ecuador, Quito, Ecuador
| | - Karin Weigelt
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Harm de Wit
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Behiye Ozcan
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Eric Sijbrands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Grosse
- Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Hemmo A Drexhage
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands; Prometeo Program SENESCYT, Central University of Ecuador and Universidad de las Fuerzas Armadas, Quito, Ecuador
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18
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Spinelli L, Lindsay YE, Leslie NR. PTEN inhibitors: an evaluation of current compounds. Adv Biol Regul 2014; 57:102-11. [PMID: 25446882 DOI: 10.1016/j.jbior.2014.09.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/06/2014] [Indexed: 12/22/2022]
Abstract
Small molecule inhibitors of many classes of enzymes, including phosphatases, have widespread use as experimental tools and as therapeutics. Efforts to develop inhibitors against the lipid phosphatase and tumour suppressor, PTEN, was for some time limited by concerns that their use as therapy could result in increased risk of cancer. However, the accumulation of evidence that short term PTEN inhibition may be valuable in conditions such as nerve injury has raised interest. Here we investigate the inhibition of PTEN by four available PTEN inhibitors, bpV(phen), bpV(pic), VO-OHpic and SF1670 and compared this inhibition with that of only 3 other related enzymes, the tyrosine phosphatase SHP1 and the phosphoinositide phosphatases INPP4A and INPP4B. Even with this very small number of comparators, for all compounds, inhibition of multiple enzymes was observed and with all three vanadate compounds, this was similar or more potent than the inhibition of PTEN. In particular, the bisperoxovanadate compounds were found to inhibit PTEN poorly in the presence of reducing agents including the cellular redox buffer glutathione.
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Affiliation(s)
- Laura Spinelli
- Institute of Biological Chemistry, Biophysics and Bioengineering, Nasmyth Building, Heriot Watt University, Edinburgh, EH14 4AS, UK; Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Yvonne E Lindsay
- Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Nicholas R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, Nasmyth Building, Heriot Watt University, Edinburgh, EH14 4AS, UK; Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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19
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Inhibitor of the tyrosine phosphatase STEP reverses cognitive deficits in a mouse model of Alzheimer's disease. PLoS Biol 2014; 12:e1001923. [PMID: 25093460 PMCID: PMC4122355 DOI: 10.1371/journal.pbio.1001923] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
STEP (STriatal-Enriched protein tyrosine Phosphatase) is a neuron-specific phosphatase that regulates N-methyl-D-aspartate receptor (NMDAR) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) trafficking, as well as ERK1/2, p38, Fyn, and Pyk2 activity. STEP is overactive in several neuropsychiatric and neurodegenerative disorders, including Alzheimer's disease (AD). The increase in STEP activity likely disrupts synaptic function and contributes to the cognitive deficits in AD. AD mice lacking STEP have restored levels of glutamate receptors on synaptosomal membranes and improved cognitive function, results that suggest STEP as a novel therapeutic target for AD. Here we describe the first large-scale effort to identify and characterize small-molecule STEP inhibitors. We identified the benzopentathiepin 8-(trifluoromethyl)-1,2,3,4,5-benzopentathiepin-6-amine hydrochloride (known as TC-2153) as an inhibitor of STEP with an IC50 of 24.6 nM. TC-2153 represents a novel class of PTP inhibitors based upon a cyclic polysulfide pharmacophore that forms a reversible covalent bond with the catalytic cysteine in STEP. In cell-based secondary assays, TC-2153 increased tyrosine phosphorylation of STEP substrates ERK1/2, Pyk2, and GluN2B, and exhibited no toxicity in cortical cultures. Validation and specificity experiments performed in wild-type (WT) and STEP knockout (KO) cortical cells and in vivo in WT and STEP KO mice suggest specificity of inhibitors towards STEP compared to highly homologous tyrosine phosphatases. Furthermore, TC-2153 improved cognitive function in several cognitive tasks in 6- and 12-mo-old triple transgenic AD (3xTg-AD) mice, with no change in beta amyloid and phospho-tau levels.
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Abstract
Phosphatases are a heterogeneous group of enzymes catalyzing dephosphorylation of diverse substrates ranging from small organic molecules to large phosphorylated multiprotein complexes. A wide variety of biochemical approaches for measuring phosphatase activity exists. Spectrophotometric methods utilizing artificial chromogenic, fluorogenic, and luminogenic substrates and taking advantage of the optical properties of dephosphorylated products are broadly used by research community. Another major assay type is based on quantitation of the second product of any phosphatase reactions, inorganic phosphate, using a variety of phosphate detection methods. Although, in theory, compatible with any phosphatase substrate, these assays often are unable to provide acceptable high-throughput screening adaptations of native phosphatase reactions. Conversely, phosphatase assays with artificial substrates frequently are incapable to mirror the intricacies of substrate binding and catalysis of the native reaction and, as a result, unable to deliver biologically relevant phosphatase modulators. Utilization of comprehensive phosphatase assay panels, employing honed biochemical assays and cell-based model systems, in conjunction with novel approaches for screening phosphatases may aid in identification of potent, selective, and biologically active phosphatase modulators.
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Abstract
The importance of tyrosine phosphorylation in normal cell physiology is well established, highlighted by the many human diseases that stem from abnormalities in protein tyrosine kinase (PTK) and protein tyrosine phosphatase (PTP) function. Contrary to earlier assumptions, it is now clear that both PTKs and PTPs are highly specific, non-redundant, and tightly regulated enzymes. Hematopoietic cells express particularly high numbers of PTKs and PTPs, and aberrant function of these proteins have been linked to many hematopoietic disorders. While PTK inhibitors are among FDA approved drugs for the treatment of leukemia and other cancers, efforts to develop therapeutics that target specific PTPs are still in its infancy. Here, we describe methods on how to evaluate effects of PTP inhibitors on T cell receptor signaling. Moreover, we provide a comprehensive strategy for compound prioritization, applicable to any drug discovery project involving T cells. We present a testing funnel that starts with relatively high-throughput luciferase reporter assays, followed by immunoblot, calcium flux, flow cytometry, and proliferation assays, continues with cytokine bead arrays, and finishes with specificity assays that involve RNA interference. We provide protocols for experiments in the Jurkat T cell line, but more importantly give detailed instructions, paired with numerous tips, on how to prepare and work with primary human T cells.
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Tautz L, Sergienko EA. High-throughput screening for protein tyrosine phosphatase activity modulators. Methods Mol Biol 2013; 1053:223-40. [PMID: 23860657 DOI: 10.1007/978-1-62703-562-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Reversible phosphorylation of proteins, principally on serine, threonine, or tyrosine residues, is central to the regulation of most aspects of eukaryotic cell function. Dysregulation of protein kinases and protein phosphatases is linked to numerous human diseases. Consequently, many efforts have been made to target these enzymes with small molecules in order to develop new therapeutic agents. While protein kinase inhibitors have been successfully brought to the market, the development of specific protein phosphatase inhibitors is still in its infancy. The largest and most diverse protein phosphatase superfamily in humans is comprised by the protein tyrosine phosphatases, a group of over 100 enzymes. Here, we describe high-throughput screening methods to search for protein tyrosine phosphatase activity modulators. We illustrate the implementation of relatively simple phosphatase assays, using generic absorbance- or fluorescence-based substrates, in 384- or 1536-well microtiter plates. We discuss steps to optimize HTS assay quality and performance, and describe several PTP screening methods on the basis of previously performed successful HTS campaigns. Finally, we discuss how to confirm, follow up, and prioritize hit compounds, and point out a number of common pitfalls that are encountered in this process.
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Affiliation(s)
- Lutz Tautz
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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23
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Tautz L, Critton DA, Grotegut S. Protein tyrosine phosphatases: structure, function, and implication in human disease. Methods Mol Biol 2013; 1053:179-221. [PMID: 23860656 DOI: 10.1007/978-1-62703-562-0_13] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein tyrosine phosphorylation is a key regulatory mechanism in eukaryotic cell physiology. Aberrant expression or function of protein tyrosine kinases and protein tyrosine phosphatases can lead to serious human diseases, including cancer, diabetes, as well as cardiovascular, infectious, autoimmune, and neuropsychiatric disorders. Here, we give an overview of the protein tyrosine phosphatase superfamily with its over 100 members in humans. We review their structure, function, and implications in human diseases, and discuss their potential as novel drug targets, as well as current challenges and possible solutions to developing therapeutics based on these enzymes.
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Affiliation(s)
- Lutz Tautz
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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He R, Zeng LF, He Y, Zhang S, Zhang ZY. Small molecule tools for functional interrogation of protein tyrosine phosphatases. FEBS J 2012; 280:731-50. [PMID: 22816879 DOI: 10.1111/j.1742-4658.2012.08718.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The importance of protein tyrosine phosphatases (PTPs) in the regulation of cellular signalling is well established. Malfunction of PTP activity is also known to be associated with cancer, metabolic syndromes and autoimmune disorders, as well as neurodegenerative and infectious diseases. However, a detailed understanding of the roles played by the PTPs in normal physiology and in pathogenic conditions has been hampered by the absence of PTP-specific small molecule agents. In addition, the therapeutic benefits of modulating this target class are underexplored as a result of a lack of suitable chemical probes. Potent and specific PTP inhibitors could significantly facilitate functional analysis of the PTPs in complex cellular signal transduction pathways and may constitute valuable therapeutics in the treatment of several human diseases. We highlight the current challenges to and opportunities for developing PTP-specific small molecule agents. We also review available selective small molecule inhibitors developed for a number of PTPs, including PTP1B, TC-PTP, SHP2, lymphoid-specific tyrosine phosphatase, haematopoietic protein tyrosine phosphatase, CD45, PTPβ, PTPγ, PTPRO, Vaccinia H1-related phosphatase, mitogen-activated protein kinase phosphatase-1, mitogen-activated protein kinase phosphatase-3, Cdc25, YopH, mPTPA and mPTPB.
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Affiliation(s)
- Rongjun He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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25
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Pike KA, Tremblay ML. Regulating naïve and memory CD8 T cell homeostasis - a role for protein tyrosine phosphatases. FEBS J 2012; 280:432-44. [DOI: 10.1111/j.1742-4658.2012.08587.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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