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Sikirzhytskaya A, Tyagin I, Sutton SS, Wyatt MD, Safro I, Shtutman M. AI-based mining of biomedical literature: Applications for drug repurposing for the treatment of dementia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597745. [PMID: 38895485 PMCID: PMC11185689 DOI: 10.1101/2024.06.06.597745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Neurodegenerative pathologies such as Alzheimer's disease, Parkinson's disease, Huntington's disease, Amyotrophic lateral sclerosis, Multiple sclerosis, HIV-associated neurocognitive disorder, and others significantly affect individuals, their families, caregivers, and healthcare systems. While there are no cures yet, researchers worldwide are actively working on the development of novel treatments that have the potential to slow disease progression, alleviate symptoms, and ultimately improve the overall health of patients. Huge volumes of new scientific information necessitate new analytical approaches for meaningful hypothesis generation. To enable the automatic analysis of biomedical data we introduced AGATHA, an effective AI-based literature mining tool that can navigate massive scientific literature databases, such as PubMed. The overarching goal of this effort is to adapt AGATHA for drug repurposing by revealing hidden connections between FDA-approved medications and a health condition of interest. Our tool converts the abstracts of peer-reviewed papers from PubMed into multidimensional space where each gene and health condition are represented by specific metrics. We implemented advanced statistical analysis to reveal distinct clusters of scientific terms within the virtual space created using AGATHA-calculated parameters for selected health conditions and genes. Partial Least Squares Discriminant Analysis was employed for categorizing and predicting samples (122 diseases and 20889 genes) fitted to specific classes. Advanced statistics were employed to build a discrimination model and extract lists of genes specific to each disease class. Here we focus on drugs that can be repurposed for dementia treatment as an outcome of neurodegenerative diseases. Therefore, we determined dementia-associated genes statistically highly ranked in other disease classes. Additionally, we report a mechanism for detecting genes common to multiple health conditions. These sets of genes were classified based on their presence in biological pathways, aiding in selecting candidates and biological processes that are exploitable with drug repurposing. Author Summary This manuscript outlines our project involving the application of AGATHA, an AI-based literature mining tool, to discover drugs with the potential for repurposing in the context of neurocognitive disorders. The primary objective is to identify connections between approved medications and specific health conditions through advanced statistical analysis, including techniques like Partial Least Squares Discriminant Analysis (PLSDA) and unsupervised clustering. The methodology involves grouping scientific terms related to different health conditions and genes, followed by building discrimination models to extract lists of disease-specific genes. These genes are then analyzed through pathway analysis to select candidates for drug repurposing.
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Langhammer M, Schöpf J, Jaquet T, Horn K, Angel M, Spohr C, Christen D, Uhl FM, Maié T, Jacobi H, Feyerabend TB, Huber J, Panning M, Sitaru C, Costa I, Zeiser R, Aumann K, Becker H, Braunschweig T, Koschmieder S, Shoumariyeh K, Huber M, Schemionek-Reinders M, Brummer T, Halbach S. Mast cell deficiency prevents BCR::ABL1 induced splenomegaly and cytokine elevation in a CML mouse model. Leukemia 2023:10.1038/s41375-023-01916-x. [PMID: 37161070 DOI: 10.1038/s41375-023-01916-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Abstract
The persistence of leukemic stem cells (LSCs) represents a problem in the therapy of chronic myeloid leukemia (CML). Hence, it is of utmost importance to explore the underlying mechanisms to develop new therapeutic approaches to cure CML. Using the genetically engineered ScltTA/TRE-BCR::ABL1 mouse model for chronic phase CML, we previously demonstrated that the loss of the docking protein GAB2 counteracts the infiltration of mast cells (MCs) in the bone marrow (BM) of BCR::ABL1 positive mice. Here, we show for the first time that BCR::ABL1 drives the cytokine independent expansion of BM derived MCs and sensitizes them for FcεRI triggered degranulation. Importantly, we demonstrate that genetic mast cell deficiency conferred by the Cpa3Cre allele prevents BCR::ABL1 induced splenomegaly and impairs the production of pro-inflammatory cytokines. Furthermore, we show in CML patients that splenomegaly is associated with high BM MC counts and that upregulation of pro-inflammatory cytokines in patient serum samples correlates with tryptase levels. Finally, MC-associated transcripts were elevated in human CML BM samples. Thus, our study identifies MCs as essential contributors to disease progression and suggests considering them as an additional target in CML therapy. Mast cells play a key role in the pro-inflammatory tumor microenvironment of the bone marrow. Shown is a cartoon summarizing our results from the mouse model. BCR::ABL1 transformed MCs, as part of the malignant clone, are essential for the elevation of pro-inflammatory cytokines, known to be important in disease initiation and progression.
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Affiliation(s)
- Melanie Langhammer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Julia Schöpf
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Timo Jaquet
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Katharina Horn
- Institute of Biochemistry and Molecular Immunology, RWTH Aachen University, Aachen, Germany
| | - Moritz Angel
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Franziska Maria Uhl
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tiago Maié
- Institute for Computational Genomics, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Henrike Jacobi
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Huber
- Department of Pathology, Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cassian Sitaru
- Department of Dermatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ivan Costa
- Institute for Computational Genomics, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Robert Zeiser
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konrad Aumann
- Department of Pathology, Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heiko Becker
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Till Braunschweig
- Department of Pathology, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Khalid Shoumariyeh
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Huber
- Institute of Biochemistry and Molecular Immunology, RWTH Aachen University, Aachen, Germany
| | - Mirle Schemionek-Reinders
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Herr R, Halbach S, Heizmann M, Busch H, Boerries M, Brummer T. BRAF inhibition upregulates a variety of receptor tyrosine kinases and their downstream effector Gab2 in colorectal cancer cell lines. Oncogene 2018; 37:1576-1593. [PMID: 29326440 DOI: 10.1038/s41388-017-0063-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 10/30/2017] [Accepted: 11/19/2017] [Indexed: 12/28/2022]
Abstract
BRAF mutations occur in ~10% of colorectal cancer (CRC) and are associated with poor prognosis. Inhibitors selective for the BRAFV600E oncoprotein, the most common BRAF mutant, elicit only poor response rates in BRAF-mutant CRC as single agents. This unresponsiveness was mechanistically attributed to the loss of negative feedbacks on the epidermal growth factor receptor (EGFR) and initiated clinical trials that combine BRAF (and MEK) inhibitors, either singly or in combination, with the anti-EGFR antibodies cetuximab or panitumumab. First results of these combinatorial studies demonstrated improved efficacy, however, the response rates still were heterogeneous. Here, we show that BRAF inhibition leads to the upregulation of a variety of receptor tyrosine kinases (RTKs) in CRC cell lines, including not only the EGFR, but also human epidermal growth factor receptor (HER) 2 and HER3. Importantly, combination of the BRAF inhibitors (BRAFi) vemurafenib (PLX4032), dabrafenib, or encorafenib with inhibitors dually targeting the EGFR and HER2 (such as lapatinib, canertinib, and afatinib) significantly reduced the metabolic activity and proliferative potential of CRC cells. This re-sensitization was also observed after genetic depletion of HER2 or HER3. Interestingly, BRAF inhibitors did not only upregulate RTKs, but also increased the abundance of the GRB2-associated binders (Gab) 1 and Gab2, two important amplifiers of RTK signaling. An allele-specific shRNA-mediated knockdown of BRAFV600E revealed that Gab2 upregulation was directly dependent on the loss of the oncoprotein and was not caused by an "off-target" effect of these kinase inhibitors. Furthermore, Gab2 and Gab2-mediated Shp2 signaling were shown to be functionally important in BRAFi resistance. These findings highlight potential new escape mechanisms to these targeted therapies and indicate that a broad suppression of RTK signaling might be beneficial and should be taken into account in future research addressing targeted therapy in BRAF-mutant CRC.
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Affiliation(s)
- Ricarda Herr
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Sebastian Halbach
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Heizmann
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment, IMMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment, IMMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Centre Freiburg (CCCF), University of Freiburg, Freiburg, Germany
| | - Tilman Brummer
- Signal Transduction in Tumour Development and Drug Resistance Group, Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Comprehensive Cancer Centre Freiburg (CCCF), University of Freiburg, Freiburg, Germany. .,Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany.
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Eisenhardt AE, Sprenger A, Röring M, Herr R, Weinberg F, Köhler M, Braun S, Orth J, Diedrich B, Lanner U, Tscherwinski N, Schuster S, Dumaz N, Schmidt E, Baumeister R, Schlosser A, Dengjel J, Brummer T. Phospho-proteomic analyses of B-Raf protein complexes reveal new regulatory principles. Oncotarget 2018; 7:26628-52. [PMID: 27034005 PMCID: PMC5042004 DOI: 10.18632/oncotarget.8427] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 03/07/2016] [Indexed: 12/19/2022] Open
Abstract
B-Raf represents a critical physiological regulator of the Ras/RAF/MEK/ERK-pathway and a pharmacological target of growing clinical relevance, in particular in oncology. To understand how B-Raf itself is regulated, we combined mass spectrometry with genetic approaches to map its interactome in MCF-10A cells as well as in B-Raf deficient murine embryonic fibroblasts (MEFs) and B-Raf/Raf-1 double deficient DT40 lymphoma cells complemented with wildtype or mutant B-Raf expression vectors. Using a multi-protease digestion approach, we identified a novel ubiquitination site and provide a detailed B-Raf phospho-map. Importantly, we identify two evolutionary conserved phosphorylation clusters around T401 and S419 in the B-Raf hinge region. SILAC labelling and genetic/biochemical follow-up revealed that these clusters are phosphorylated in the contexts of oncogenic Ras, sorafenib induced Raf dimerization and in the background of the V600E mutation. We further show that the vemurafenib sensitive phosphorylation of the T401 cluster occurs in trans within a Raf dimer. Substitution of the Ser/Thr-residues of this cluster by alanine residues enhances the transforming potential of B-Raf, indicating that these phosphorylation sites suppress its signaling output. Moreover, several B-Raf phosphorylation sites, including T401 and S419, are somatically mutated in tumors, further illustrating the importance of phosphorylation for the regulation of this kinase.
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Affiliation(s)
- Anja E Eisenhardt
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Adrian Sprenger
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Institute for Experimental and Clinical Pharmacology and Toxicology, ALU, Freiburg, Germany.,INSERM U976 and Universitéi Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Michael Röring
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Ricarda Herr
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Florian Weinberg
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Martin Köhler
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Joachim Orth
- Institute for Experimental and Clinical Pharmacology and Toxicology, ALU, Freiburg, Germany
| | - Britta Diedrich
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, University Medical Centre, ALU, Freiburg, Germany
| | - Ulrike Lanner
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Natalja Tscherwinski
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Simon Schuster
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Nicolas Dumaz
- INSERM U976 and Universitéi Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Enrico Schmidt
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Ralf Baumeister
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, ALU, Freiburg, Germany
| | - Andreas Schlosser
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Jörn Dengjel
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, University Medical Centre, ALU, Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, ALU, Freiburg, Germany.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
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Gab2 is essential for Bcr-Abl-mediated leukemic transformation and hydronephrosis in a chronic myeloid leukemia mouse model. Leukemia 2016; 30:1942-5. [PMID: 27125306 DOI: 10.1038/leu.2016.92] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes. Sci Rep 2016; 6:23530. [PMID: 27025927 PMCID: PMC4812247 DOI: 10.1038/srep23530] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/08/2016] [Indexed: 02/07/2023] Open
Abstract
Interleukin-2 (IL-2) stimulation results in T-cell growth as a consequence of activation of highly sophisticated and fine-tuned signaling pathways. Despite lacking intrinsic enzymatic activity, scaffold proteins such as Gab2, play a pivotal role in IL-2-triggered signal transduction integrating, diversifying and amplifying the signal by serving as a platform for the assembly of effectors proteins. Traditionally, Gab2-mediated protein recruitment was believed to solely depend on cytokine-induced phosphotyrosine moieties. At present, phosphorylation on serine/threonine residues is also emerging as a key mediator of Gab2-dependent signal regulation. Despite its relevance, IL-2-triggered regulation on Gab2 phosphorylation is yet poorly understood. Combining antibody- and TiO2-based enrichment of the scaffold protein with SILAC quantitative mass spectrometry we disclose the prominent regulation IL-2 exerts on Gab2 serine/threonine phosphorylation by showing that at least 18 serines and 1 threonine, including previously non-reported ones, become phosphorylated in response to cytokine stimulation. Additionally, we decipher the interactome of the docking protein in resting and cytokine-treated T-lymphocytes and besides well-known Gab2 interactors we discover three novel cytokine-inducible Gab2-binding proteins. Thus, our data provide novel insights and a wealth of candidates for future studies that will shed light into the role of Gab2 in IL-2-initiated signal transduction.
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Halbach S, Hu Z, Gretzmeier C, Ellermann J, Wöhrle FU, Dengjel J, Brummer T. Axitinib and sorafenib are potent in tyrosine kinase inhibitor resistant chronic myeloid leukemia cells. Cell Commun Signal 2016; 14:6. [PMID: 26912052 PMCID: PMC4765141 DOI: 10.1186/s12964-016-0129-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/16/2016] [Indexed: 02/08/2023] Open
Abstract
Background Chronic myeloid leukemia (CML) is driven by the fusion kinase Bcr-Abl. Bcr-Abl tyrosine kinase inhibitors (TKIs), such as imatinib mesylate (IM), revolutionized CML therapy. Nevertheless, about 20 % of CMLs display primary or acquired TKI resistance. TKI resistance can be either caused by mutations within the Bcr-Abl kinase domain or by aberrant signaling by its effectors, e.g. Lyn or Gab2. Bcr-Abl mutations are frequently observed in TKI resistance and can only in some cases be overcome by second line TKIs. In addition, we have previously shown that the formation of Gab2 complexes can be regulated by Bcr-Abl and that Gab2 signaling counteracts the efficacy of four distinct Bcr-Abl inhibitors. Therefore, TKI resistance still represents a challenge for disease management and alternative therapies are urgently needed. Findings Using different CML cell lines and models, we identified the clinically approved TKIs sorafenib (SF) and axitinib (AX) as drugs overcoming the resistance mediated by the Bcr AblT315I mutant as well as the one mediated by Gab2 and LynY508F. In addition, we demonstrated that AX mainly affects the Bcr-Abl/Grb2/Gab2 axis, whereas SF seems to act independently of the fusion kinase and most likely by blocking signaling pathways up- and downstream of Gab2. Conclusion We demonstrate that SF and AX show potency in various and mechanistically distinct scenarios of TKI resistance, including Bcr-AblT315I as well as Lyn- and Gab2-mediated resistances. Our data invites for further evaluation und consideration of these inhibitors in the treatment of TKI resistant CML. Electronic supplementary material The online version of this article (doi:10.1186/s12964-016-0129-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Faculty of Biology, University of Freiburg, Freiburg, Germany. .,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.
| | - Zehan Hu
- Freiburg Institute for Advanced Studies (FRIAS), and Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany. .,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany.
| | - Christine Gretzmeier
- Freiburg Institute for Advanced Studies (FRIAS), and Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany. .,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany.
| | - Julia Ellermann
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Faculty of Biology, University of Freiburg, Freiburg, Germany.
| | - Franziska U Wöhrle
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Faculty of Biology, University of Freiburg, Freiburg, Germany. .,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Jörn Dengjel
- Freiburg Institute for Advanced Studies (FRIAS), and Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany.
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Deutsches Konsortium für Translationale Krebsforschung (DKTK) and Comprehensive Cancer Center Freiburg, University Medical Center, Freiburg, Germany.
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Halbach S, Dengjel J, Brummer T. Quantitative Proteomics Analysis of Leukemia Cells. Methods Mol Biol 2016; 1465:139-48. [PMID: 27581145 DOI: 10.1007/978-1-4939-4011-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Chronic myeloid leukemia (CML) is driven by the oncogenic fusion kinase Bcr-Abl, which organizes its own signaling network with various proteins. These proteins, their interactions, and their role in relevant signaling pathways can be analyzed by quantitative mass spectrometry (MS) approaches in various models systems, e.g., in cell culture models. In this chapter, we describe in detail immunoprecipitations and quantitative proteomics analysis using stable isotope labeling by amino acids in cell culture (SILAC) of components of the Bcr-Abl signaling pathway in the human CML cell line K562.
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Affiliation(s)
- Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104, Freiburg im Breisgau, Germany.,Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jörn Dengjel
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany. .,FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany. .,Department of Dermatology, University Medical Center, University of Freiburg, Freiburg im Breisgau, Germany. .,ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104, Freiburg im Breisgau, Germany. .,Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany. .,Deutsches Konsortium für Translationale Krebsforschung (DKTK) and Comprehensive Cancer Center Freiburg, University Medical Center, Freiburg im Breisgau, Germany.
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9
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Litchfield K, Holroyd A, Lloyd A, Broderick P, Nsengimana J, Eeles R, Easton DF, Dudakia D, Bishop DT, Reid A, Huddart RA, Grotmol T, Wiklund F, Shipley J, Houlston RS, Turnbull C. Identification of four new susceptibility loci for testicular germ cell tumour. Nat Commun 2015; 6:8690. [PMID: 26503584 PMCID: PMC4846317 DOI: 10.1038/ncomms9690] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple risk loci for testicular germ cell tumour (TGCT), revealing a polygenic model of disease susceptibility strongly influenced by common variation. To identify additional single-nucleotide polymorphisms (SNPs) associated with TGCT, we conducted a multistage GWAS with a combined data set of >25,000 individuals (6,059 cases and 19,094 controls). We identified new risk loci for TGCT at 3q23 (rs11705932, TFDP2, P=1.5 × 10(-9)), 11q14.1 (rs7107174, GAB2, P=9.7 × 10(-11)), 16p13.13 (rs4561483, GSPT1, P=1.6 × 10(-8)) and 16q24.2 (rs55637647, ZFPM1, P=3.4 × 10(-9)). We additionally present detailed functional analysis of these loci, identifying a statistically significant relationship between rs4561483 risk genotype and increased GSPT1 expression in TGCT patient samples. These findings provide additional support for a polygenic model of TGCT risk and further insight into the biological basis of disease development.
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Affiliation(s)
- Kevin Litchfield
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Amy Lloyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Leeds LS9 7TF, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Douglas F Easton
- Cancer Research UK, Genetic Epidemiology Unit, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Darshna Dudakia
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Leeds LS9 7TF, UK
| | - Alison Reid
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Robert A. Huddart
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Tom Grotmol
- Department of Research, Cancer Registry of Norway, 0369 Oslo, Norway
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
- William Harvey Research Institute, Queen Mary University, London EC1M 6BQ, UK
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10
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Ding CB, Yu WN, Feng JH, Luo JM. Structure and function of Gab2 and its role in cancer (Review). Mol Med Rep 2015; 12:4007-4014. [PMID: 26095858 PMCID: PMC4526075 DOI: 10.3892/mmr.2015.3951] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 05/19/2015] [Indexed: 12/30/2022] Open
Abstract
The docking proteins of the Grb-associated binder (Gab) family transduce cellular signals between receptors and intracellular downstream effectors, and provide a platform for protein-protein interactions. Gab2, a key member of the Gab family of proteins, is involved in the amplification and integration of signal transduction, evoked by a variety of extracellular stimuli, including growth factors, cytokines and antigen receptors. Gab2 protein lacks intrinsic catalytic activity; however, when phosphorylated by protein-tyrosine kinases (PTKs), Gab2 recruits several Src homology-2 (SH2) domain-containing proteins, including the SH2-containing protein tyrosine phosphatase 2 (SHP2), the p85 subunit of phosphoinositide-3 kinase (PI3K), phospholipase C-γ (PLCγ)1, Crk, and GC-GAP. Through these interactions, the Gab2 protein triggers various downstream signal effectors, including SHP2/rat sarcoma viral oncogene/RAF/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase and PI3K/AKT, involved in cell growth, differentiation, migration and apoptosis. It has been previously reported that aberrant Gab2 and/or Gab2 signaling is closely associated with human tumorigenesis, particularly in breast cancer, leukemia and melanoma. The present review aimed to focus on the structure and effector function of Gab2, its role in cancer and its potential for use as an effective therapeutic target.
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Affiliation(s)
- Chen-Bo Ding
- Department of Immunology and Immunology Innovation Base for Postgraduate Education in Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
| | - Wei-Na Yu
- Department of Immunology and Immunology Innovation Base for Postgraduate Education in Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
| | - Ji-Hong Feng
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
| | - Jun-Min Luo
- Department of Immunology and Immunology Innovation Base for Postgraduate Education in Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
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11
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Chereda B, Melo JV. Natural course and biology of CML. Ann Hematol 2015; 94 Suppl 2:S107-21. [PMID: 25814077 DOI: 10.1007/s00277-015-2325-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/07/2014] [Indexed: 12/14/2022]
Abstract
Chronic myeloid leukaemia (CML) is a myeloproliferative disorder arising in the haemopoietic stem cell (HSC) compartment. This disease is characterised by a reciprocal t(9;22) chromosomal translocation, resulting in the formation of the Philadelphia (Ph) chromosome containing the BCR-ABL1 gene. As such, diagnosis and monitoring of disease involves detection of BCR-ABL1. It is the BCR-ABL1 protein, in particular its constitutively active tyrosine kinase activity, that forges the pathogenesis of CML. This aberrant kinase signalling activates downstream targets that reprogram the cell to cause uncontrolled proliferation and results in myeloid hyperplasia and 'indolent' symptoms of chronic phase (CP) CML. Without successful intervention, the disease will progress into blast crisis (BC), resembling an acute leukaemia. This advanced disease stage takes on an aggressive phenotype and is almost always fatal. The cell biology of CML is also centred on BCR-ABL1. The presence of BCR-ABL1 can explain virtually all the cellular features of the leukaemia (enhanced cell growth, inhibition of apoptosis, altered cell adhesion, growth factor independence, impaired genomic surveillance and differentiation). This article provides an overview of the clinical and cell biology of CML, and highlights key findings and unanswered questions essential for understanding this disease.
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MESH Headings
- Animals
- Disease Progression
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/physiopathology
- Mutation
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Prognosis
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Affiliation(s)
- Bradley Chereda
- Departments of Genetics and Molecular Pathology, and Haematology, Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, 5000, Australia,
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12
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Zarei M, Sprenger A, Gretzmeier C, Dengjel J. Rapid Combinatorial ERLIC–SCX Solid-Phase Extraction for In-Depth Phosphoproteome Analysis. J Proteome Res 2013; 12:5989-95. [DOI: 10.1021/pr4007969] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mostafa Zarei
- Freiburg
Institute for Advanced Studies (FRIAS), School of Life Sciences-LifeNet, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
- ZBSA
Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Adrian Sprenger
- Freiburg
Institute for Advanced Studies (FRIAS), School of Life Sciences-LifeNet, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
- ZBSA
Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
- Department
of Dermatology, University Freiburg Medical Center, Hauptstr. 7, 79104 Freiburg, Germany
| | - Christine Gretzmeier
- Freiburg
Institute for Advanced Studies (FRIAS), School of Life Sciences-LifeNet, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
- ZBSA
Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Joern Dengjel
- Freiburg
Institute for Advanced Studies (FRIAS), School of Life Sciences-LifeNet, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
- ZBSA
Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
- Department
of Dermatology, University Freiburg Medical Center, Hauptstr. 7, 79104 Freiburg, Germany
- BIOSS
Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
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