1
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Yan T, Boatner LM, Cui L, Tontonoz PJ, Backus KM. Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics. JACS AU 2023; 3:3506-3523. [PMID: 38155636 PMCID: PMC10751780 DOI: 10.1021/jacsau.3c00707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
The plasma membrane proteome is a rich resource of functionally important and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here, we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of low-density lipoprotein (LDL) particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Lisa M. Boatner
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Liujuan Cui
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Peter J. Tontonoz
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Keriann M. Backus
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- DOE
Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli
and Edythe
Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
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2
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Yan T, Boatner LM, Cui L, Tontonoz P, Backus KM. Defining the Cell Surface Cysteinome using Two-step Enrichment Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562832. [PMID: 37904933 PMCID: PMC10614875 DOI: 10.1101/2023.10.17.562832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
The plasma membrane proteome is a rich resource of functional and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of LDL particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Lisa M. Boatner
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Liujuan Cui
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Peter Tontonoz
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Keriann M. Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 (USA)
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 (USA)
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095 (USA)
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3
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Xu Y, Wang Y, Höti N, Clark DJ, Chen SY, Zhang H. The next "sweet" spot for pancreatic ductal adenocarcinoma: Glycoprotein for early detection. MASS SPECTROMETRY REVIEWS 2023; 42:822-843. [PMID: 34766650 PMCID: PMC9095761 DOI: 10.1002/mas.21748] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/07/2021] [Accepted: 10/24/2021] [Indexed: 05/02/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common neoplastic disease of the pancreas, accounting for more than 90% of all pancreatic malignancies. As a highly lethal malignancy, PDAC is the fourth leading cause of cancer-related deaths worldwide with a 5-year overall survival of less than 8%. The efficacy and outcome of PDAC treatment largely depend on the stage of disease at the time of diagnosis. Surgical resection followed by adjuvant chemotherapy remains the only possibly curative therapy, yet 80%-90% of PDAC patients present with nonresectable PDAC stages at the time of clinical presentation. Despite our advancing knowledge of PDAC, the prognosis remains strikingly poor, which is primarily due to the difficulty of diagnosing PDAC at the early stages. Recent advances in glycoproteomics and glycomics based on mass spectrometry have shown that aberrations in protein glycosylation plays a critical role in carcinogenesis, tumor progression, metastasis, chemoresistance, and immuno-response of PDAC and other types of cancers. A growing interest has thus been placed upon protein glycosylation as a potential early detection biomarker for PDAC. We herein take stock of the advancements in the early detection of PDAC that were carried out with mass spectrometry, with special focus on protein glycosylation.
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Affiliation(s)
- Yuanwei Xu
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yuefan Wang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Naseruddin Höti
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - David J Clark
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shao-Yung Chen
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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4
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Li W, Lückstädt W, Wöhner B, Bub S, Schulz A, Socher E, Arnold P. Structural and functional properties of meprin β metalloproteinase with regard to cell signaling. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119136. [PMID: 34626678 DOI: 10.1016/j.bbamcr.2021.119136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/05/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
The metalloproteinase meprin β plays an important role during collagen I deposition in the skin, mucus detachment in the small intestine and also regulates the abundance of different cell surface proteins such as the interleukin-6 receptor (IL-6R), the triggering receptor expressed on myeloid cells 2 (TREM2), the cluster of differentiation 99 (CD99), the amyloid precursor protein (APP) and the cluster of differentiation 109 (CD109). With that, regulatory mechanisms that control meprin β activity and regulate its release from the cell surface to enable access to distant substrates are increasingly important. Here, we will summarize factors that alternate meprin β activity and thereby regulate its proteolytic activity on the cell surface or in the supernatant. We will also discuss cleavage of the IL-6R and TREM2 on the cell surface and compare it to CD109. CD109, as a substrate of meprin β, is cleaved within the protein core, thereby releasing defined fragments from the cell surface. At last, we will also summarize the role of proteases in general and meprin β in particular in substrate release on extracellular vesicles.
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Affiliation(s)
- Wenjia Li
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Wiebke Lückstädt
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Birte Wöhner
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Simon Bub
- Department of Molecular-Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Antonia Schulz
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Eileen Socher
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Philipp Arnold
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany.
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5
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Lückstädt W, Bub S, Koudelka T, Pavlenko E, Peters F, Somasundaram P, Becker-Pauly C, Lucius R, Zunke F, Arnold P. Cell Surface Processing of CD109 by Meprin β Leads to the Release of Soluble Fragments and Reduced Expression on Extracellular Vesicles. Front Cell Dev Biol 2021; 9:622390. [PMID: 33738281 PMCID: PMC7960916 DOI: 10.3389/fcell.2021.622390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/29/2021] [Indexed: 12/21/2022] Open
Abstract
Cluster of differentiation 109 (CD109) is a glycosylphosphatidylinositol (GPI)-anchored protein expressed on primitive hematopoietic stem cells, activated platelets, CD4+ and CD8+ T cells, and keratinocytes. In recent years, CD109 was also associated with different tumor entities and identified as a possible future diagnostic marker linked to reduced patient survival. Also, different cell signaling pathways were proposed as targets for CD109 interference including the TGFβ, JAK-STAT3, YAP/TAZ, and EGFR/AKT/mTOR pathways. Here, we identify the metalloproteinase meprin β to cleave CD109 at the cell surface and thereby induce the release of cleavage fragments of different size. Major cleavage was identified within the bait region of CD109 residing in the middle of the protein. To identify the structural localization of the bait region, homology modeling and single-particle analysis were applied, resulting in a molecular model of membrane-associated CD109, which allows for the localization of the newly identified cleavage sites for meprin β and the previously published cleavage sites for the metalloproteinase bone morphogenetic protein-1 (BMP-1). Full-length CD109 localized on extracellular vesicles (EVs) was also identified as a release mechanism, and we can show that proteolytic cleavage of CD109 at the cell surface reduces the amount of CD109 sorted to EVs. In summary, we identified meprin β as the first membrane-bound protease to cleave CD109 within the bait region, provide a first structural model for CD109, and show that cell surface proteolysis correlates negatively with CD109 released on EVs.
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Affiliation(s)
- Wiebke Lückstädt
- Anatomical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Simon Bub
- Anatomical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
- Department of Molecular Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Tomas Koudelka
- Systematic Proteomics and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Egor Pavlenko
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Florian Peters
- Lab for Retinal Cell Biology, Department of Ophthalmology, University of Zurich, Schlieren, Switzerland
| | - Prasath Somasundaram
- Systematic Proteomics and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | | | - Ralph Lucius
- Anatomical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Friederike Zunke
- Department of Molecular Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Philipp Arnold
- Anatomical Institute, Christian-Albrechts-University Kiel, Kiel, Germany
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6
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Lee KY, Shueng PW, Chou CM, Lin BX, Lin MH, Kuo DY, Tsai IL, Wu SM, Lin CW. Elevation of CD109 promotes metastasis and drug resistance in lung cancer via activation of EGFR-AKT-mTOR signaling. Cancer Sci 2020; 111:1652-1662. [PMID: 32133706 PMCID: PMC7226182 DOI: 10.1111/cas.14373] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 02/19/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the most commonly diagnosed cancer worldwide, and metastasis in lung cancer is the leading cause of cancer‐related deaths. Thus, understanding the mechanism of lung cancer metastasis will improve the diagnosis and treatment of lung cancer patients. Herein, we found that expression of cluster of differentiation 109 (CD109) was correlated with the invasive and metastatic capacities of lung adenocarcinoma cells. CD109 is upregulated in tumorous tissues, and CD109 overexpression was associated with tumor progression, distant metastasis, and a poor prognosis in patient with lung adenocarcinoma. Mechanistically, expression of CD109 regulates protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling via its association with the epidermal growth factor receptor (EGFR). Inhibition of CD109 decreases EGFR phosphorylation, diminishes EGF‐elicited activation of AKT/mTOR, and sensitizes tumor cells to an EGFR inhibitor. Taken together, our results show that CD109 is a potential diagnostic and therapeutic target in lung cancer patients.
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Affiliation(s)
- Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Pei-Wei Shueng
- Division of Radiation Oncology, Far Eastern Memorial Hospital, New Taipei City, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Ming Chou
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Bo-Xing Lin
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mei-Hsiang Lin
- Graduate Institute of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Deng-Yu Kuo
- Division of Radiation Oncology, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - I-Lin Tsai
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Center for Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Wei Lin
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Center for Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, Taiwan.,Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
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7
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Arias-Pinilla GA, Dalgleish AG, Mudan S, Bagwan I, Walker AJ, Modjtahedi H. Development of novel monoclonal antibodies against CD109 overexpressed in human pancreatic cancer. Oncotarget 2018; 9:19994-20007. [PMID: 29731998 PMCID: PMC5929441 DOI: 10.18632/oncotarget.25017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Pancreatic cancer is one of the most aggressive and lethal types of cancer, and more effective therapeutic agents are urgently needed. Overexpressed cell surface antigens are ideal targets for therapy with monoclonal antibody (mAb)-based drugs, but none have been approved for the treatment of pancreatic cancer. Here, we report development of two novel mouse mAbs, KU42.33C and KU43.13A, against the human pancreatic cancer cell line BxPC-3. Using ELISA, flow cytometry, competitive assay and immunoprecipitation followed by mass spectrometry, we discovered that these two mAbs target two distinct epitopes on the external domain of CD109 that are overexpressed by varying amounts in human pancreatic cancer cell lines. Treatment with these two naked antibodies alone did not affect tumour cell growth or migration in vitro. Of the two mAbs, only KU42.33C was useful in determining the expression of CD109 in tumour cells by Western blot and immunohistochemistry. Interestingly, immunohistochemistry of human pancreatic carcinoma tissue arrays with mAb KU42.33C showed that 94% of the 65 human pancreatic adenocarcinoma cases were CD109 positive, with no expression in normal pancreatic tissues. Our results suggest that these two novel mAbs are excellent tools for determining the expression level of CD109 in the tumour specimens and sera of patients with a wide range of cancers, in particular pancreatic cancer, and for investigating its diagnostic, prognostic and predictive value. Further research is warranted and should aim to unravel the therapeutic potential of the humanised forms or conjugated versions of such antibodies in patients whose tumours overexpress CD109 antigen.
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Affiliation(s)
- Gustavo A Arias-Pinilla
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Kingston-upon-Thames, Surrey, UK
| | - Angus G Dalgleish
- Department of Cellular and Molecular Medicine, St George's University of London, London, UK
| | - Satvinder Mudan
- Department of Surgery of Hammersmith Campus, Imperial College, London, UK
| | - Izhar Bagwan
- Department of Histopathology, Royal Surrey County Hospital, Guildford, UK
| | - Anthony J Walker
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Kingston-upon-Thames, Surrey, UK
| | - Helmout Modjtahedi
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Kingston-upon-Thames, Surrey, UK
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8
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Kanhaiya K, Czeizler E, Gratie C, Petre I. Controlling Directed Protein Interaction Networks in Cancer. Sci Rep 2017; 7:10327. [PMID: 28871116 PMCID: PMC5583175 DOI: 10.1038/s41598-017-10491-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023] Open
Abstract
Control theory is a well-established approach in network science, with applications in bio-medicine and cancer research. We build on recent results for structural controllability of directed networks, which identifies a set of driver nodes able to control an a-priori defined part of the network. We develop a novel and efficient approach for the (targeted) structural controllability of cancer networks and demonstrate it for the analysis of breast, pancreatic, and ovarian cancer. We build in each case a protein-protein interaction network and focus on the survivability-essential proteins specific to each cancer type. We show that these essential proteins are efficiently controllable from a relatively small computable set of driver nodes. Moreover, we adjust the method to find the driver nodes among FDA-approved drug-target nodes. We find that, while many of the drugs acting on the driver nodes are part of known cancer therapies, some of them are not used for the cancer types analyzed here; some drug-target driver nodes identified by our algorithms are not known to be used in any cancer therapy. Overall we show that a better understanding of the control dynamics of cancer through computational modelling can pave the way for new efficient therapeutic approaches and personalized medicine.
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Affiliation(s)
- Krishna Kanhaiya
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
| | - Eugen Czeizler
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
- National Institute for Research and Development for Biological Sciences, Bucharest, Romania
| | - Cristian Gratie
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
| | - Ion Petre
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland.
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9
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Shukla S, Evans JR, Malik R, Feng FY, Dhanasekaran SM, Cao X, Chen G, Beer DG, Jiang H, Chinnaiyan AM. Development of a RNA-Seq Based Prognostic Signature in Lung Adenocarcinoma. J Natl Cancer Inst 2016; 109:2905970. [PMID: 27707839 DOI: 10.1093/jnci/djw200] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/02/2016] [Indexed: 01/08/2023] Open
Abstract
Background Precision therapy for lung cancer will require comprehensive genomic testing to identify actionable targets as well as ascertain disease prognosis. RNA-seq is a robust platform that meets these requirements, but microarray-derived prognostic signatures are not optimal for RNA-seq data. Thus, we undertook the first prognostic analysis of lung adenocarcinoma RNA-seq data and generated a prognostic signature. Methods Lung adenocarcinoma RNA-seq and clinical data from The Cancer Genome Atlas (TCGA) were divided chronologically into training (n = 255) and validation (n = 157) cohorts. In the training cohort, prognostic association was assessed by univariate Cox analysis. A prognostic signature was built with stepwise multivariable Cox analysis. Outcomes by risk group, stage, and mutation status were analyzed with Kaplan-Meier and multivariable Cox analyses. All the statistical tests were two-sided. Results In the training cohort, 96 genes had prognostic association with P values of less than or equal to 1.00x10-4, including five long noncoding RNAs (lncRNAs). Stepwise regression generated a four-gene signature, including one lncRNA. Signature high-risk cases had worse overall survival (OS) in the TCGA validation cohort (hazard ratio [HR] = 3.07, 95% confidence interval [CI] = 2.00 to 14.62) and a University of Michigan institutional cohort (n = 67; HR = 2.05, 95% CI = 1.18 to 4.55), and worse metastasis-free survival in the TCGA validation cohort (HR = 3.05, 95% CI = 2.31 to 13.37). The four-gene prognostic signature also statistically significantly stratified overall survival in important clinical subsets, including stage I (HR = 2.78, 95% CI = 1.91 to 11.13), EGFR wild-type (HR = 3.01, 95% CI = 1.73 to 14.98), and EGFR mutant (HR = 8.99, 95% CI = 62.23 to 141.44). The four-gene prognostic signature also stood out on top when compared with other prognostic signatures. Conclusions Here, we present the first RNA-seq prognostic signature for lung adenocarcinoma that can provide a powerful prognostic tool for precision oncology as part of an integrated RNA-seq clinical sequencing program.
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Affiliation(s)
- Sudhanshu Shukla
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Joseph R Evans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Rohit Malik
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI.,Department of Radiation Oncology, University of Michigan, Ann Arbor, MI.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Guoan Chen
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI
| | - David G Beer
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI.,Department of Biostatistics, University of Michigan, Ann Arbor, MI.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
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10
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Karandish F, Mallik S. Biomarkers and Targeted Therapy in Pancreatic Cancer. BIOMARKERS IN CANCER 2016; 8:27-35. [PMID: 27147897 PMCID: PMC4847554 DOI: 10.4137/bic.s34414] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/06/2016] [Accepted: 03/11/2016] [Indexed: 12/18/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) constitutes 90% of pancreatic cancers. PDAC is a complex and devastating disease with only 1%-3% survival rate in five years after the second stage. Treatment of PDAC is complicated due to the tumor microenvironment, changing cell behaviors to the mesenchymal type, altered drug delivery, and drug resistance. Considering that pancreatic cancer shows early invasion and metastasis, critical research is needed to explore different aspects of the disease, such as elaboration of biomarkers, specific signaling pathways, and gene aberration. In this review, we highlight the biomarkers, the fundamental signaling pathways, and their importance in targeted drug delivery for pancreatic cancers.
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Affiliation(s)
- Fataneh Karandish
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
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Shields B, Shalin SC, Tackett AJ. Microscopes and Mass Spectrometers. ACTA ACUST UNITED AC 2016; 9. [PMID: 29910559 PMCID: PMC5998814 DOI: 10.4172/jpb.s10-e001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteomics is a relatively young discipline while pathology is one of the oldest forms of scientific inquiry. These two fields have different methods and aims, but have many areas of overlap and shared interests. Cultivation of synergistic projects between physicians who study static images of disease and biologists who study the dynamic environment that produces disease states will help further biomedical research providing new diagnostic, prognostic, and therapeutic approaches. Here, a pathologist and a proteomic scientist share their views on recent collaborations among the fields.
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Affiliation(s)
- Bradley Shields
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Sara C Shalin
- Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA.,Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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Haun RS, Quick CM, Siegel ER, Raju I, Mackintosh SG, Tackett AJ. Bioorthogonal labeling cell-surface proteins expressed in pancreatic cancer cells to identify potential diagnostic/therapeutic biomarkers. Cancer Biol Ther 2015; 16:1557-65. [PMID: 26176765 DOI: 10.1080/15384047.2015.1071740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To develop new diagnostic and therapeutic tools to specifically target pancreatic tumors, it is necessary to identify cell-surface proteins that may serve as potential tumor-specific targets. In this study we used an azido-labeled bioorthogonal chemical reporter to metabolically label N-linked glycoproteins on the surface of pancreatic cancer cell lines to identify potential targets that may be exploited for detection and/or treatment of pancreatic cancer. Labeled glycoproteins were tagged with biotin using click chemistry, purified by streptavidin-coupled magnetic beads, separated by gel electrophoresis, and identified by liquid chromatography-tandem mass spectrometry (MS). MS/MS analysis of peptides from 3 cell lines revealed 954 unique proteins enriched in the azido sugar samples relative to control sugar samples. A comparison of the proteins identified in each sample indicated 20% of these proteins were present in 2 cell lines (193 of 954) and 17 of the proteins were found in all 3 cell lines. Five of the 17 proteins identified in all 3 cell lines have not been previously reported to be expressed in pancreatic cancer; thus indicating that novel cell-surface proteins can be revealed through glycoprotein profiling. Western analysis of one of these glycoproteins, ecto-5'-nucleotidase (NT5E), revealed it is expressed in 8 out of 8 pancreatic cancer cell lines examined. Further, immunohistochemical analysis of human pancreatic tissues indicates NT5E is significantly overexpressed in pancreatic tumors compared to normal pancreas. Thus, we have demonstrated that metabolic labeling with bioorthogonal chemical reporters can be used to selectively enrich and identify novel cell-surface glycoproteins expressed in pancreatic ductal adenocarcinomas.
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Affiliation(s)
- Randy S Haun
- a Central Arkansas Veterans Healthcare System; Little Rock , AR USA.,b Department of Pharmaceutical Sciences ; University of Arkansas for Medical Sciences; Little Rock , AR USA
| | - Charles M Quick
- c Department of Pathology; University of Arkansas for Medical Sciences; Little Rock , AR USA
| | - Eric R Siegel
- d Department of Biostatistics; University of Arkansas for Medical Sciences; Little Rock , AR USA
| | - Ilangovan Raju
- b Department of Pharmaceutical Sciences ; University of Arkansas for Medical Sciences; Little Rock , AR USA
| | - Samuel G Mackintosh
- e Department of Biochemistry & Molecular Biology; University of Arkansas for Medical Sciences; Little Rock , AR USA
| | - Alan J Tackett
- e Department of Biochemistry & Molecular Biology; University of Arkansas for Medical Sciences; Little Rock , AR USA
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