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Seffernick AE, Archer KJ. Penalized Bayesian forward continuation ratio model with application to high-dimensional data with discrete survival outcomes. PLoS One 2024; 19:e0300638. [PMID: 38547174 PMCID: PMC10977717 DOI: 10.1371/journal.pone.0300638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/03/2024] [Indexed: 04/02/2024] Open
Abstract
While time-to-event data are often continuous, there are several instances where discrete survival data, which are inherently ordinal, may be available or are more appropriate or useful. Several discrete survival models exist, but the forward continuation ratio model with a complementary log-log link has a survival interpretation and is closely related to the Cox proportional hazards model, despite being an ordinal model. This model has previously been implemented in the high-dimensional setting using the ordinal generalized monotone incremental forward stagewise algorithm. Here, we propose a Bayesian penalized forward continuation ratio model with a complementary log-log link and explore different priors to perform variable selection and regularization. Through simulations, we show that our Bayesian model outperformed the existing frequentist method in terms of variable selection performance, and that a 10% prior inclusion probability performed better than 1% or 50%. We also illustrate our model on a publicly available acute myeloid leukemia dataset to identify genomic features associated with discrete survival. We identified nine features that map to ten unique genes, five of which have been previously associated with leukemia in the literature. In conclusion, our proposed Bayesian model is flexible, allows simultaneous variable selection and uncertainty quantification, and performed well in simulation studies and application to real data.
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Affiliation(s)
- Anna Eames Seffernick
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
- Division of Biostatistics, College of Public Health, Ohio State University, Columbus, OH, United States of America
| | - Kellie J. Archer
- Division of Biostatistics, College of Public Health, Ohio State University, Columbus, OH, United States of America
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2
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Hayes B, van der Geer P. STS-1 and STS-2, Multi-Enzyme Proteins Equipped to Mediate Protein-Protein Interactions. Int J Mol Sci 2023; 24:ijms24119214. [PMID: 37298164 DOI: 10.3390/ijms24119214] [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: 04/22/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
STS-1 and STS-2 form a small family of proteins that are involved in the regulation of signal transduction by protein-tyrosine kinases. Both proteins are composed of a UBA domain, an esterase domain, an SH3 domain, and a PGM domain. They use their UBA and SH3 domains to modify or rearrange protein-protein interactions and their PGM domain to catalyze protein-tyrosine dephosphorylation. In this manuscript, we discuss the various proteins that have been found to interact with STS-1 or STS-2 and describe the experiments used to uncover their interactions.
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Affiliation(s)
- Barbara Hayes
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr., San Diego, CA 92105, USA
| | - Peter van der Geer
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr., San Diego, CA 92105, USA
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3
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Mian AA, Zafar U, Ahmed SMA, Ottmann OG, Lalani ENMA. Oncogene-independent resistance in Philadelphia chromosome - positive (Ph +) acute lymphoblastic leukemia (ALL) is mediated by activation of AKT/mTOR pathway. Neoplasia 2021; 23:1016-1027. [PMID: 34403880 PMCID: PMC8368770 DOI: 10.1016/j.neo.2021.07.009] [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: 05/20/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) such as imatinib, nilotinib, dasatinib, and ponatinib have significantly improved the life expectancy of Philadelphia chromosome-positive (Ph+) acute lymphocytic leukemia (ALL) patients; however, resistance to TKIs remains a major clinical challenge. Point mutations in the tyrosine kinase domain (TKD) of BCR-ABL1 have emerged as the predominant cause of acquired resistance. In approximately 30% of patients, the mechanism of resistance to TKIs remains elusive. This study aimed to investigate mechanisms of nonmutational resistance in Ph+ ALL. Here we report the development of a nonmutational resistance cell line SupB15-RT; conferring resistance to approved ABL kinase inhibitors (AKIs) and allosteric inhibitors GNF-2, ABL001, and crizotinib, except for dasatinib (IC90 50nM), a multitarget kinase inhibitor. We found that the AKT/mTOR pathway is activated in these cells and their proliferation inhibited by Torin-1 with an IC50 of 24.7 nM. These observations were confirmed using 3 different ALL patient-derived long term cultures (PDLTCs): (1) HP (BCR-ABL1 negative), (2) PH (BCR-ABL1 positive and responsive to TKIs) and (3) BV (BCR-ABL1 positive and nonmutational resistant to TKIs). Furthermore, Torin-1 and NVP-BEZ235 induced apoptosis in PH and BV cells but not in HP cells. Our experiments provide evidence of the involvement of AKT/mTOR pathway in the evolution of nonmutational resistance in Ph+ ALL which will assist in developing novel targeted therapy for Ph+ ALL patients with BCR-ABL1 independent nonmutational resistance.
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Affiliation(s)
- Afsar Ali Mian
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan.
| | - Usva Zafar
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
| | | | | | - El-Nasir M A Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
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4
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Mian AA, Haberbosch I, Khamaisie H, Agbarya A, Pietsch L, Eshel E, Najib D, Chiriches C, Ottmann OG, Hantschel O, Biondi RM, Ruthardt M, Mahajna J. Crizotinib acts as ABL1 inhibitor combining ATP-binding with allosteric inhibition and is active against native BCR-ABL1 and its resistance and compound mutants BCR-ABL1 T315I and BCR-ABL1 T315I-E255K. Ann Hematol 2021; 100:2023-2029. [PMID: 34110462 PMCID: PMC8285356 DOI: 10.1007/s00277-020-04357-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022]
Abstract
Resistance remains the major clinical challenge for the therapy of Philadelphia chromosome-positive (Ph+) leukemia. With the exception of ponatinib, all approved tyrosine kinase inhibitors (TKIs) are unable to inhibit the common "gatekeeper" mutation T315I. Here we investigated the therapeutic potential of crizotinib, a TKI approved for targeting ALK and ROS1 in non-small cell lung cancer patients, which inhibited also the ABL1 kinase in cell-free systems, for the treatment of advanced and therapy-resistant Ph+ leukemia. By inhibiting the BCR-ABL1 kinase, crizotinib efficiently suppressed growth of Ph+ cells without affecting growth of Ph- cells. It was also active in Ph+ patient-derived long-term cultures (PD-LTCs) independently of the responsiveness/resistance to other TKIs. The efficacy of crizotinib was confirmed in vivo in syngeneic mouse models of BCR-ABL1- or BCR-ABL1T315I-driven chronic myeloid leukemia-like disease and in BCR-ABL1-driven acute lymphoblastic leukemia (ALL). Although crizotinib binds to the ATP-binding site, it also allosterically affected the myristol binding pocket, the binding site of GNF2 and asciminib (former ABL001). Therefore, crizotinib has a seemingly unique double mechanism of action, on the ATP-binding site and on the myristoylation binding pocket. These findings strongly suggest the clinical evaluation of crizotinib for the treatment of advanced and therapy-resistant Ph+ leukemia.
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Affiliation(s)
- Afsar Ali Mian
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.,Center for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
| | | | - Hazem Khamaisie
- Department of Nutrition and Natural Products, Migal-Galilee Technology Center, PO Box 831, 11016, Kiryat Shmona, Israel
| | - Abed Agbarya
- Oncology Department, Bnai Zion MC, Haifa, Israel
| | - Larissa Pietsch
- Department of Internal Medicine I, Clinic of Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Frankfurt, Germany
| | - Elizabeh Eshel
- Hematology Institute, Ziv Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Zfat, Israel
| | - Dally Najib
- Hematology Institute, Ziv Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Zfat, Israel
| | - Claudia Chiriches
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Oliver Gerhard Ottmann
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland.,Medical Biochemistry and Pharmacology Center, Institute for Physiological Chemistry, Philipps-University, Marburg, Germany
| | - Ricardo M Biondi
- Department of Internal Medicine I, Clinic of Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Frankfurt, Germany.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Martin Ruthardt
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Jamal Mahajna
- Department of Nutrition and Natural Products, Migal-Galilee Technology Center, PO Box 831, 11016, Kiryat Shmona, Israel. .,The Department of Nutritional Sciences, Tel Hai Academic College, Kiryat Shmona, Israel.
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Current Views on the Interplay between Tyrosine Kinases and Phosphatases in Chronic Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13102311. [PMID: 34065882 PMCID: PMC8151247 DOI: 10.3390/cancers13102311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The chromosomal alteration t(9;22) generating the BCR-ABL1 fusion protein represents the principal feature that distinguishes some types of leukemia. An increasing number of articles have focused the attention on the relevance of protein phosphatases and their potential role in the control of BCR-ABL1-dependent or -independent signaling in different areas related to the biology of chronic myeloid leukemia. Herein, we discuss how tyrosine and serine/threonine protein phosphatases may interact with protein kinases, in order to regulate proliferative signal cascades, quiescence and self-renewals on leukemic stem cells, and drug-resistance, indicating how BCR-ABL1 can (directly or indirectly) affect these critical cells behaviors. We provide an updated review of the literature on the function of protein phosphatases and their regulation mechanism in chronic myeloid leukemia. Abstract Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by BCR-ABL1 oncogene expression. This dysregulated protein-tyrosine kinase (PTK) is known as the principal driver of the disease and is targeted by tyrosine kinase inhibitors (TKIs). Extensive documentation has elucidated how the transformation of malignant cells is characterized by multiple genetic/epigenetic changes leading to the loss of tumor-suppressor genes function or proto-oncogenes expression. The impairment of adequate levels of substrates phosphorylation, thus affecting the balance PTKs and protein phosphatases (PPs), represents a well-established cellular mechanism to escape from self-limiting signals. In this review, we focus our attention on the characterization of and interactions between PTKs and PPs, emphasizing their biological roles in disease expansion, the regulation of LSCs and TKI resistance. We decided to separate those PPs that have been validated in primary cell models or leukemia mouse models from those whose studies have been performed only in cell lines (and, thus, require validation), as there may be differences in the manner that the associated pathways are modified under these two conditions. This review summarizes the roles of diverse PPs, with hope that better knowledge of the interplay among phosphatases and kinases will eventually result in a better understanding of this disease and contribute to its eradication.
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Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics. Nat Commun 2021; 12:71. [PMID: 33397984 PMCID: PMC7782698 DOI: 10.1038/s41467-020-20367-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/27/2020] [Indexed: 02/02/2023] Open
Abstract
Signaling complexes are often organized in a spatiotemporal manner and on a minute timescale. Proximity labeling based on engineered ascorbate peroxidase APEX2 pioneered in situ capture of spatiotemporal membrane protein complexes in living cells, but its application to cytosolic proteins remains limited due to the high labeling background. Here, we develop proximity labeling probes with increased labeling selectivity. These probes, in combination with label-free quantitative proteomics, allow exploring cytosolic protein assemblies such as phosphotyrosine-mediated protein complexes formed in response to minute-scale EGF stimulation. As proof-of-concept, we systematically profile the spatiotemporal interactome of the EGFR signaling component STS1. For STS1 core complexes, our proximity proteomics approach shows comparable performance to affinity purification-mass spectrometry-based temporal interactome profiling, while also capturing additional—especially endosomally-located—protein complexes. In summary, we provide a generic approach for exploring the interactome of mobile cytosolic proteins in living cells at a temporal resolution of minutes. APEX-based proximity labeling allows capturing protein interaction dynamics but its high labeling background limits its utility for cytosolic proteins. Here, the authors develop more selective proximity labeling probes, enabling the APEX-based characterization of time-resolved cytosolic protein interactomes.
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7
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Gregor T, Bosakova MK, Nita A, Abraham SP, Fafilek B, Cernohorsky NH, Rynes J, Foldynova-Trantirkova S, Zackova D, Mayer J, Trantirek L, Krejci P. Elucidation of protein interactions necessary for the maintenance of the BCR-ABL signaling complex. Cell Mol Life Sci 2020; 77:3885-3903. [PMID: 31820037 PMCID: PMC11104816 DOI: 10.1007/s00018-019-03397-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/05/2019] [Accepted: 11/26/2019] [Indexed: 10/25/2022]
Abstract
Many patients with chronic myeloid leukemia in deep remission experience return of clinical disease after withdrawal of tyrosine kinase inhibitors (TKIs). This suggests signaling of inactive BCR-ABL, which allows the survival of cancer cells, and relapse. We show that TKI treatment inhibits catalytic activity of BCR-ABL, but does not dissolve BCR-ABL core signaling complex, consisting of CRKL, SHC1, GRB2, SOS1, cCBL, p85a-PI3K, STS1 and SHIP2. Peptide microarray and co-immunoprecipitation results demonstrate that CRKL binds to proline-rich regions located in C-terminal, intrinsically disordered region of BCR-ABL, that SHC1 requires pleckstrin homology, src homology and tyrosine kinase domains of BCR-ABL for binding, and that BCR-ABL sequence motif located in disordered region around phosphorylated tyrosine 177 mediates binding of three core complex members, i.e., GRB2, SOS1, and cCBL. Further, SHIP2 binds to the src homology and tyrosine kinase domains of BCR-ABL and its inositol phosphatase activity contributes to BCR-ABL-mediated phosphorylation of SHC1. Together, this study characterizes protein-protein interactions within the BCR-ABL core complex and determines the contribution of particular BCR-ABL domains to downstream signaling. Understanding the structure and dynamics of BCR-ABL interactome is critical for the development of drugs targeting integrity of the BCR-ABL core complex.
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MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Motifs
- Binding Sites
- Cell Line, Tumor
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- HEK293 Cells
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism
- Phosphorylation
- Protein Array Analysis
- Protein Binding/drug effects
- Protein Kinase Inhibitors/pharmacology
- Pyrimidines/pharmacology
- Signal Transduction/drug effects
- Src Homology 2 Domain-Containing, Transforming Protein 1/metabolism
- src Homology Domains
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Affiliation(s)
- Tomas Gregor
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
| | - Michaela Kunova Bosakova
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Institute of Animal Physiology and Genetics of the CAS, 60200, Brno, Czech Republic
| | - Alexandru Nita
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the CAS, 16610, Prague, Czech Republic
| | - Sara P Abraham
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Bohumil Fafilek
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Institute of Animal Physiology and Genetics of the CAS, 60200, Brno, Czech Republic
| | - Nicole H Cernohorsky
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Jan Rynes
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | - Daniela Zackova
- Department of Internal Medicine, Hematology and Oncology, Masaryk University Hospital, 62500, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology, Masaryk University Hospital, 62500, Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic.
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic.
- Institute of Animal Physiology and Genetics of the CAS, 60200, Brno, Czech Republic.
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8
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Komorowski L, Fidyt K, Patkowska E, Firczuk M. Philadelphia Chromosome-Positive Leukemia in the Lymphoid Lineage-Similarities and Differences with the Myeloid Lineage and Specific Vulnerabilities. Int J Mol Sci 2020; 21:E5776. [PMID: 32806528 PMCID: PMC7460962 DOI: 10.3390/ijms21165776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Philadelphia chromosome (Ph) results from a translocation between the breakpoint cluster region (BCR) gene on chromosome 9 and ABL proto-oncogene 1 (ABL1) gene on chromosome 22. The fusion gene, BCR-ABL1, is a constitutively active tyrosine kinase which promotes development of leukemia. Depending on the breakpoint site within the BCR gene, different isoforms of BCR-ABL1 exist, with p210 and p190 being the most prevalent. P210 isoform is the hallmark of chronic myeloid leukemia (CML), while p190 isoform is expressed in majority of Ph-positive B cell acute lymphoblastic leukemia (Ph+ B-ALL) cases. The crucial component of treatment protocols of CML and Ph+ B-ALL patients are tyrosine kinase inhibitors (TKIs), drugs which target both BCR-ABL1 isoforms. While TKIs therapy is successful in great majority of CML patients, Ph+ B-ALL often relapses as a drug-resistant disease. Recently, the high-throughput genomic and proteomic analyses revealed significant differences between CML and Ph+ B-ALL. In this review we summarize recent discoveries related to differential signaling pathways mediated by different BCR-ABL1 isoforms, lineage-specific genetic lesions, and metabolic reprogramming. In particular, we emphasize the features distinguishing Ph+ B-ALL from CML and focus on potential therapeutic approaches exploiting those characteristics, which could improve the treatment of Ph+ B-ALL.
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Affiliation(s)
- Lukasz Komorowski
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Trojdena 2a St, 02-091 Warsaw, Poland
| | - Klaudyna Fidyt
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Trojdena 2a St, 02-091 Warsaw, Poland
| | - Elżbieta Patkowska
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Indiry Gandhi 14, 02-776 Warsaw, Poland;
| | - Malgorzata Firczuk
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
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Held MA, Greenfest-Allen E, Su S, Stoeckert CJ, Stokes MP, Wojchowski DM. Phospho-PTM proteomic discovery of novel EPO- modulated kinases and phosphatases, including PTPN18 as a positive regulator of EPOR/JAK2 Signaling. Cell Signal 2020; 69:109554. [PMID: 32027948 DOI: 10.1016/j.cellsig.2020.109554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023]
Abstract
The formation of erythroid progenitor cells depends sharply upon erythropoietin (EPO), its cell surface receptor (erythropoietin receptor, EPOR), and Janus kinase 2 (JAK2). Clinically, recombinant human EPO (rhEPO) additionally is an important anti-anemia agent for chronic kidney disease (CKD), myelodysplastic syndrome (MDS) and chemotherapy, but induces hypertension, and can exert certain pro-tumorigenic effects. Cellular signals transduced by EPOR/JAK2 complexes, and the nature of EPO-modulated signal transduction factors, therefore are of significant interest. By employing phospho-tyrosine post-translational modification (p-Y PTM) proteomics and human EPO- dependent UT7epo cells, we have identified 22 novel kinases and phosphatases as novel EPO targets, together with their specific sites of p-Y modification. New kinases modified due to EPO include membrane palmitoylated protein 1 (MPP1) and guanylate kinase 1 (GUK1) guanylate kinases, together with the cytoskeleton remodeling kinases, pseudopodium enriched atypical kinase 1 (PEAK1) and AP2 associated kinase 1 (AAK1). Novel EPO- modified phosphatases include protein tyrosine phosphatase receptor type A (PTPRA), phosphohistidine phosphatase 1 (PHPT1), tensin 2 (TENC1), ubiquitin associated and SH3 domain containing B (UBASH3B) and protein tyrosine phosphatase non-receptor type 18 (PTPN18). Based on PTPN18's high expression in hematopoietic progenitors, its novel connection to JAK kinase signaling, and a unique EPO- regulated PTPN18-pY389 motif which is modulated by JAK2 inhibitors, PTPN18's actions in UT7epo cells were investigated. Upon ectopic expression, wt-PTPN18 promoted EPO dose-dependent cell proliferation, and survival. Mechanistically, PTPN18 sustained the EPO- induced activation of not only mitogen-activated protein kinases 1 and 3 (ERK1/2), AKT serine/threonine kinase 1-3 (AKT), and signal transducer and activator of transcription 5A and 5B (STAT5), but also JAK2. Each effect further proved to depend upon PTPN18's EPO- modulated (p)Y389 site. In analyses of the EPOR and the associated adaptor protein RHEX (regulator of hemoglobinization and erythroid cell expansion), wt-PTPN18 increased high molecular weight EPOR forms, while sharply inhibiting the EPO-induced phosphorylation of RHEX-pY141. Each effect likewise depended upon PTPN18-Y389. PTPN18 thus promotes signals for EPO-dependent hematopoietic cell growth, and may represent a new druggable target for myeloproliferative neoplasms.
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Affiliation(s)
- Matthew A Held
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, United States of America
| | - Emily Greenfest-Allen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Su Su
- Molecular Medicine Department, Maine Medical Center Research Institute, Scarborough, ME, 04074, United States of America
| | - Christian J Stoeckert
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Matthew P Stokes
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923., United States of America
| | - Don M Wojchowski
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, United States of America.
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10
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Tsygankov AY. TULA proteins as signaling regulators. Cell Signal 2019; 65:109424. [PMID: 31639493 DOI: 10.1016/j.cellsig.2019.109424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
Two members of the UBASH3/STS/TULA family exhibit a unique protein domain structure, which includes a histidine phosphatase domain, and play a key role in regulating cellular signaling. UBASH3A/STS-2/TULA is mostly a lymphoid protein, while UBASH3B/STS-1/TULA-2 is expressed ubiquitously. Dephosphorylation of tyrosine-phosphorylated proteins by TULA-2 and, probably to a lesser extent, by TULA critically contribute to the molecular basis of their regulatory effect. The notable differences between the effects of the two family members on cellular signaling and activation are likely to be linked to the difference between their specific enzymatic activities. However, these differences might also be related to the functions of their domains other than the phosphatase domain and independent of their phosphatase activity. The down-regulation of the Syk/Zap-70-mediated signaling, which to-date appears to be the best-studied regulatory effect of TULA family, is discussed in detail in this publication.
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Fels Institute for Cancer Research and Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, 3400 N. Broad Street, Philadelphia, PA, 19140, United States.
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