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Petersen M, Chorzalska A, Pardo M, Rodriguez A, Morgan J, Ahsan N, Zhao TC, Liang O, Kotula L, Bertone P, Gruppuso PA, Dubielecka PM. Proximity proteomics reveals role of Abelson interactor 1 in the regulation of TAK1/RIPK1 signaling. Mol Oncol 2023; 17:2356-2379. [PMID: 36635880 PMCID: PMC10620119 DOI: 10.1002/1878-0261.13374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
Dysregulation of the adaptor protein Abelson interactor 1 (ABI1) is linked to malignant transformation. To interrogate the role of ABI1 in cancer development, we mapped the ABI1 interactome using proximity-dependent labeling (PDL) with biotin followed by mass spectrometry. Using a novel PDL data filtering strategy, considering both peptide spectral matches and peak areas of detected peptides, we identified 212 ABI1 proximal interactors. These included WAVE2 complex components such as CYFIP1, NCKAP1, or WASF1, confirming the known role of ABI1 in the regulation of actin-polymerization-dependent processes. We also identified proteins associated with the TAK1-IKK pathway, including TAK1, TAB2, and RIPK1, denoting a newly identified function of ABI1 in TAK1-NF-κB inflammatory signaling. Functional assays using TNFα-stimulated, ABI1-overexpressing or ABI1-deficient cells showed effects on the TAK1-NF-kB pathway-dependent signaling to RIPK1, with ABI1-knockout cells being less susceptible to TNFα-induced, RIPK1-mediated, TAK1-dependent apoptosis. In sum, our PDL-based strategy enabled mapping of the ABI1 proximal interactome, thus revealing a previously unknown role of this adaptor protein in TAK1/RIPK1-based regulation of cell death and survival.
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Affiliation(s)
- Max Petersen
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Division of Biology and Medicine, Department of Pathology and Laboratory MedicineBrown UniversityProvidenceRIUSA
| | - Anna Chorzalska
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
| | - Makayla Pardo
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
| | - Anaelena Rodriguez
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
| | - John Morgan
- Flow Cytometry and Cell Sorting Core FacilityRoger Williams Medical CenterProvidenceRIUSA
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core FacilityRhode Island HospitalProvidenceRIUSA
- Department of Chemistry and BiochemistryThe University of OklahomaNormanOKUSA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research CenterThe University of OklahomaNormanOKUSA
| | - Ting C. Zhao
- Department of SurgeryRhode Island Hospital and Warren Alpert Medical School of Brown UniversityProvidenceRIUSA
| | - Olin Liang
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Legorreta Cancer Center, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
| | - Leszek Kotula
- Department of UrologySUNY Upstate Medical UniversitySyracuseNYUSA
- Department of Biochemistry and Molecular BiologySUNY Upstate Medical UniversitySyracuseNYUSA
- Upstate Cancer CenterSUNY Upstate Medical UniversitySyracuseNYUSA
| | - Paul Bertone
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Legorreta Cancer Center, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
| | - Philip A. Gruppuso
- Division of Pediatric EndocrinologyRhode Island Hospital and Warren Alpert Medical School of Brown UniversityProvidenceRIUSA
| | - Patrycja M. Dubielecka
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Division of Biology and Medicine, Department of Pathology and Laboratory MedicineBrown UniversityProvidenceRIUSA
- Legorreta Cancer Center, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
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2
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Ahsan N, Fornelli L, Najar FZ, Gamagedara S, Hossan MR, Rao RSP, Punyamurtula U, Bauer A, Yang Z, Foster SB, Kane MA. Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum. Proteomics 2023; 23:e2300150. [PMID: 37199141 PMCID: PMC11166006 DOI: 10.1002/pmic.202300150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%-19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.
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Affiliation(s)
- Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
| | - Luca Fornelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Fares Z. Najar
- High-Performance Computing Center (HPCC), Oklahoma State University, Stillwater, OK, USA
| | | | | | | | - Ujwal Punyamurtula
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Bauer
- Department of Neurosurgery, University of Oklahoma-Health Science Center, Oklahoma City, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Steven B. Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
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3
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Teape D, Peterson A, Ahsan N, Ellis K, Correia N, Luo R, Hegarty K, Yao H, Dennery P. Hyperoxia impairs intraflagellar transport and causes dysregulated metabolism with resultant decreased cilia length. Am J Physiol Lung Cell Mol Physiol 2023; 324:L325-L334. [PMID: 36719084 PMCID: PMC9988522 DOI: 10.1152/ajplung.00522.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Supplemental oxygen is a lifesaving measure in infants born premature to facilitate oxygenation. Unfortunately, it may lead to alveolar simplification and loss of proximal airway epithelial cilia. Little is known about the mechanism by which hyperoxia causes ciliary dysfunction in the proximal respiratory tract. We hypothesized that hyperoxia causes intraflagellar transport (IFT) dysfunction with resultant decreased cilia length. Differentiated basal human airway epithelial cells (HAEC) were exposed to hyperoxia or air for up to 48 h. Neonatal mice (<12 h old) were exposed to hyperoxia for 72 h and recovered in room air until postnatal day (PND) 60. Cilia length was measured from scanning electron microscopy images using a MATLAB-derived program. Proteomics and metabolomics were carried out in cells after hyperoxia. After hyperoxia, there was a significant time-dependent reduction in cilia length after hyperoxia in HAEC. Proteomic analysis showed decreased abundance of multiple proteins related to IFT including dynein motor proteins. In neonatal mice exposed to hyperoxia, there was a significant decrease in acetylated α tubulin at PND10 followed by recovery to normal levels at PND60. In HAEC, hyperoxia decreased the abundance of multiple proteins associated with complex I of the electron transport chain. In HAEC, hyperoxia increased levels of malate, fumarate, and citrate, and reduced the ATP/ADP ratio at 24 h with a subsequent increase at 36 h. Exposure to hyperoxia reduced cilia length, and this was associated with aberrant IFT protein expression and dysregulated metabolism. This suggests that hyperoxic exposure leads to aberrant IFT protein expression in the respiratory epithelium resulting in shortened cilia.
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Affiliation(s)
- Daniella Teape
- Department of Pediatrics, Alpert Medical School, Brown University, Providence, Rhode Island, United States
| | - Abigail Peterson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development at Rhode Island Hospital, Proteomics Core Facility, Division of Surgical Research, Brown University, Providence, Rhode Island, United States
| | - Kimberlyn Ellis
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Nicholas Correia
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
| | - Ryan Luo
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
| | - Katy Hegarty
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
| | - Hongwei Yao
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
| | - Phyllis Dennery
- Department of Pediatrics, Alpert Medical School, Brown University, Providence, Rhode Island, United States
- Department of Molecular Biology, Cell Biology, and Biochemistry, Alpert Medical School, Brown University, Providence, Rhode Island, United States
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4
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Noyes C, Kitajima S, Li F, Suita Y, Miriyala S, Isaac S, Ahsan N, Knelson E, Vajdi A, Tani T, Thai TC, Xu D, Murai J, Tapinos N, Takahashi C, Barbie DA, Yajima M. The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells. Commun Biol 2023; 6:65. [PMID: 36653474 PMCID: PMC9849207 DOI: 10.1038/s42003-023-04444-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Human cancers often re-express germline factors, yet their mechanistic role in oncogenesis and cancer progression remains unknown. Here we demonstrate that DEAD-box helicase 4 (DDX4), a germline factor and RNA helicase conserved in all multicellular organisms, contributes to increased cell motility and cisplatin-mediated drug resistance in small cell lung cancer (SCLC) cells. Proteomic analysis suggests that DDX4 expression upregulates proteins related to DNA repair and immune/inflammatory response. Consistent with these trends in cell lines, DDX4 depletion compromised in vivo tumor development while its overexpression enhanced tumor growth even after cisplatin treatment in nude mice. Further, the relatively higher DDX4 expression in SCLC patients correlates with decreased survival and shows increased expression of immune/inflammatory response markers. Taken together, we propose that DDX4 increases SCLC cell survival, by increasing the DNA damage and immune response pathways, especially under challenging conditions such as cisplatin treatment.
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Affiliation(s)
- Christopher Noyes
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Fengkai Li
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - Yusuke Suita
- Laboratory of Cancer Epigenetics and Plasticity, Department of Neurosurgery, Brown University, Providence, RI, 02903, USA
| | - Saradha Miriyala
- Laboratory of Cancer Epigenetics and Plasticity, Department of Neurosurgery, Brown University, Providence, RI, 02903, USA
| | - Shakson Isaac
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, OK, 73019, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, 73019, USA
| | - Erik Knelson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Amir Vajdi
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tetsuo Tani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Derek Xu
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Nikos Tapinos
- Laboratory of Cancer Epigenetics and Plasticity, Department of Neurosurgery, Brown University, Providence, RI, 02903, USA
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Mamiko Yajima
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA.
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5
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Xu CM, Karbasiafshar C, Brinck Teixeira R, Ahsan N, Blume Corssac G, Sellke FW, Abid MR. Proteomic Assessment of Hypoxia-Pre-Conditioned Human Bone Marrow Mesenchymal Stem Cell-Derived Extracellular Vesicles Demonstrates Promise in the Treatment of Cardiovascular Disease. Int J Mol Sci 2023; 24:1674. [PMID: 36675188 PMCID: PMC9866304 DOI: 10.3390/ijms24021674] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
Human bone marrow mesenchymal stem cell derived-extracellular vesicles (HBMSC-EV) are known for their regenerative and anti-inflammatory effects in animal models of myocardial ischemia. However, it is not known whether the efficacy of the EVs can be modulated by pre-conditioning of HBMSC by exposing them to either starvation or hypoxia prior to EV collection. HBMSC-EVs were isolated following normoxia starvation (NS), normoxia non-starvation (NNS), hypoxia starvation (HS), or hypoxia non-starvation (HNS) pre-conditioning. The HBMSC-EVs were characterized by nanoparticle tracking analysis, electron microscopy, Western blot, and proteomic analysis. Comparative proteomic profiling revealed that starvation pre-conditioning led to a smaller variety of proteins expressed, with the associated lesser effect of normoxia versus hypoxia pre-conditioning. In the absence of starvation, normoxia and hypoxia pre-conditioning led to disparate HBMSC-EV proteomic profiles. HNS HBMSC-EV was found to have the greatest variety of proteins overall, with 74 unique proteins, the greatest number of redox proteins, and pathway analysis suggestive of improved angiogenic properties. Future HBMSC-EV studies in the treatment of cardiovascular disease may achieve the most therapeutic benefits from hypoxia non-starved pre-conditioned HBMSC. This study was limited by the lack of functional and animal models of cardiovascular disease and transcriptomic studies.
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Affiliation(s)
- Cynthia M. Xu
- Cardiovascular Research Center, Rhode Island Hospital, Providence, RI 02903, USA
- Division of Cardiothoracic Surgery, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02903, USA
| | | | - Rayane Brinck Teixeira
- Cardiovascular Research Center, Rhode Island Hospital, Providence, RI 02903, USA
- Division of Cardiothoracic Surgery, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02903, USA
| | - Nagib Ahsan
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Giana Blume Corssac
- Cardiovascular Physiology Laboratory, Basic Health Sciences Institute, UFRGS, Porto Alegre, RS, Brazil
| | - Frank W. Sellke
- Cardiovascular Research Center, Rhode Island Hospital, Providence, RI 02903, USA
- Division of Cardiothoracic Surgery, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02903, USA
| | - M. Ruhul Abid
- Cardiovascular Research Center, Rhode Island Hospital, Providence, RI 02903, USA
- Division of Cardiothoracic Surgery, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02903, USA
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6
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Teixeira RB, Pfeiffer M, Zhang P, Shafique E, Rayta B, Karbasiafshar C, Ahsan N, Sellke FW, Abid MR. Reduction in mitochondrial ROS improves oxidative phosphorylation and provides resilience to coronary endothelium in non-reperfused myocardial infarction. Basic Res Cardiol 2023; 118:3. [PMID: 36639609 PMCID: PMC9839395 DOI: 10.1007/s00395-022-00976-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023]
Abstract
Recent studies demonstrated that mitochondrial antioxidant MnSOD that reduces mitochondrial (mito) reactive oxygen species (ROS) helps maintain an optimal balance between sub-cellular ROS levels in coronary vascular endothelial cells (ECs). However, it is not known whether EC-specific mito-ROS modulation provides resilience to coronary ECs after a non-reperfused acute myocardial infarction (MI). This study examined whether a reduction in endothelium-specific mito-ROS improves the survival and proliferation of coronary ECs in vivo. We generated a novel conditional binary transgenic animal model that overexpresses (OE) mitochondrial antioxidant MnSOD in an EC-specific manner (MnSOD-OE). EC-specific MnSOD-OE was validated in heart sections and mouse heart ECs (MHECs). Mitosox and mito-roGFP assays demonstrated that MnSOD-OE resulted in a 50% reduction in mito-ROS in MHEC. Control and MnSOD-OE mice were subject to non-reperfusion MI surgery, echocardiography, and heart harvest. In post-MI hearts, MnSOD-OE promoted EC proliferation (by 2.4 ± 0.9 fold) and coronary angiogenesis (by 3.4 ± 0.9 fold), reduced myocardial infarct size (by 27%), and improved left ventricle ejection fraction (by 16%) and fractional shortening (by 20%). Interestingly, proteomic and Western blot analyses demonstrated upregulation in mitochondrial complex I and oxidative phosphorylation (OXPHOS) proteins in MnSOD-OE MHECs. These MHECs also showed increased mitochondrial oxygen consumption rate (OCR) and membrane potential. These findings suggest that mito-ROS reduction in EC improves coronary angiogenesis and cardiac function in non-reperfused MI, which are associated with increased activation of OXPHOS in EC-mitochondria. Activation of an energy-efficient mechanism in EC may be a novel mechanism to confer resilience to coronary EC during MI.
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Affiliation(s)
- Rayane Brinck Teixeira
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA
| | - Melissa Pfeiffer
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA
| | - Peng Zhang
- Vascular Research Laboratory/Providence VA Medical Center and Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Ehtesham Shafique
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA
| | - Bonnie Rayta
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA
| | - Catherine Karbasiafshar
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA
| | - Nagib Ahsan
- Division of Biology and Medicine, Alpert Medical School, Brown University, Providence, RI, 02903, USA
- Proteomics Core Facility, Center for Cancer Research and Development, Rhode Island Hospital, Providence, RI, 02903, USA
- Department of Chemistry and Biochemistry, Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA
| | - Frank W Sellke
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA
| | - M Ruhul Abid
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Brown University Warren Alpert Medical School, 1 Hoppin Street, Providence, RI, 02903, USA.
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7
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Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
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8
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Neil CR, Jeschonek SP, Cabral SE, O'Connell LC, Powrie EA, Otis JP, Wood TR, Mowry KL. L-bodies are RNA-protein condensates driving RNA localization in Xenopus oocytes. Mol Biol Cell 2021; 32:ar37. [PMID: 34613784 PMCID: PMC8694076 DOI: 10.1091/mbc.e21-03-0146-t] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membraneless compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule structure and function in vivo remain unclear. In Xenopus laevis oocytes, maternal mRNAs are localized as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here we demonstrate that RNPs containing vegetally localized RNAs represent a new class of cytoplasmic RNP granule, termed localization-bodies (L-bodies). We show that L-bodies contain a dynamic protein-containing phase surrounding a nondynamic RNA-containing phase. Our results support a role for RNA as a critical component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.
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Affiliation(s)
- Christopher R Neil
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Samantha P Jeschonek
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Sarah E Cabral
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Liam C O'Connell
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Erin A Powrie
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jessica P Otis
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Timothy R Wood
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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9
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Nadolny C, Zhang X, Chen Q, Hashmi SF, Ali W, Hemme C, Ahsan N, Chen Y, Deng R. Dysregulation and activities of ubiquitin specific peptidase 2b in the pathogenesis of hepatocellular carcinoma. Am J Cancer Res 2021; 11:4746-4767. [PMID: 34765291 PMCID: PMC8569343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023] Open
Abstract
Ubiquitin specific peptidase-2 (USP2) plays important roles in a myriad of cellular activities through deubiquitinating target proteins and its implications in various diseases, especially cancers, are starting to emerge. Our current understanding on USP2 expression in subjects with hepatocellular carcinoma (HCC) and its roles in the pathogenesis of HCC is limited. In this study, we found that USP2 protein and mRNA levels were significantly dysregulated in HCC tumor (HCC-T) when compared to adjacent non-tumor (HCC-NT) or normal liver tissues from both human and mouse HCC model. Among the USP2 isoforms, USP2b was the predominant isoform in the normal liver and markedly down-regulated in HCC-T tissues in both human and mice. Data from overexpression, chemical inhibition and knockout studies consistently demonstrated that USP2b promoted cell proliferation, colony formation and wound healing in HepG2 and Huh 7 cells. On the other hand, USP2b exhibited proapoptotic and pronecrtotic activities through enhancing bile acid-induced apoptosis and necrosis in both HepG2 and Huh 7 cells. Unbiased proteomic analysis of USP2-knockout (KO) and parental HepG2 cells resulted in identification of USP2-regulated downstream target proteins involved in cell proliferation, apoptosis, and tumorigenesis, including serine/threonine kinase 4 (STK4), epidermal growth factor receptor (EGFR), dipeptidyl peptidase 4 (DPP4) and fatty acid binding protein 1 (FABP1). In conclusion, USP2b expression was dysregulated in subjects with HCC and contributed to the pathogenesis of HCC by promoting cell proliferation and exerting proapoptotic and pronecrotic activities. The findings provide the molecular basis for developing therapies for HCC through modulating USP2b expression or activities.
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Affiliation(s)
- Christina Nadolny
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Xinmu Zhang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Qiwen Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Syed F Hashmi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Winifer Ali
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Christopher Hemme
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island HospitalProvidence, RI 02903, USA
- Division of Biology and Medicine, Brown UniversityProvidence, RI 02903, USA
- Department of Chemistry and Biochemistry, University of Oklahoma101 Stephenson Parkway, Norman, OK 73019, USA
| | - Yuan Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
| | - Ruitang Deng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island7 Greenhouse Road, Kingston, RI 02881, USA
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10
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Najrana T, Ahsan N, Abu-Eid R, Uzun A, Noble L, Tollefson G, Sanchez-Esteban J. Proteomic analysis of a murine model of lung hypoplasia induced by oligohydramnios. Pediatr Pulmonol 2021; 56:2740-2750. [PMID: 34102042 PMCID: PMC8631439 DOI: 10.1002/ppul.25525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 02/02/2023]
Abstract
Severe oligohydramnios (OH) due to prolonged loss of amniotic fluid can cause pulmonary hypoplasia. Animal model of pulmonary hypoplasia induced by amniotic fluid drainage is partly attributed to changes in mechanical compression of the lung. Although numerous studies on OH-model have demonstrated changes in several individual proteins, however, the underlying mechanisms for interrupting normal lung development in response to a decrease of amniotic fluid volume are not fully understood. In this study, we used a proteomic approach to explore differences in the expression of a wide range of proteins after induction of OH in a mouse model of pulmonary hypoplasia to find out the signaling/molecular pathways involved in fetal lung development. Liquid chromatography-massspectromery/mass spectrometry analysis found 474 proteins that were differentially expressed in OH-induced hypoplastic lungs in comparison to untouched (UnT) control. Among these proteins, we confirmed the downregulation of AKT1, SP-D, and CD200, and provided proof-of-concept for the first time about the potential role that these proteins could play in fetal lung development.
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Affiliation(s)
- Tanbir Najrana
- Department of Pediatrics, Women and Infants Hospital/Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development at Rhode Island Hospital, Proteomics Core Facility, Division of Surgical Research, Brown University, Providence, Rhode Island, USA.,Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.,Mass Spectrometry, Proteomics and Metabolomic Core Facility, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rasha Abu-Eid
- Institute of Dentistry, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, UK
| | - Alper Uzun
- Department of Pediatrics, Women and Infants Hospital/Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA.,Center of Computational Molecular Biology, Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
| | - Lelia Noble
- COBRE Center for Cancer Research Development at Rhode Island Hospital, Proteomics Core Facility, Division of Surgical Research, Brown University, Providence, Rhode Island, USA
| | - George Tollefson
- Department of Pediatrics, Women and Infants Hospital/Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Juan Sanchez-Esteban
- Department of Pediatrics, Women and Infants Hospital/Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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11
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Hernandez Borrero L, Dicker DT, Santiago J, Sanders J, Tian X, Ahsan N, Lev A, Zhou L, El-Deiry WS. A subset of CB002 xanthine analogs bypass p53-signaling to restore a p53 transcriptome and target an S-phase cell cycle checkpoint in tumors with mutated-p53. eLife 2021; 10:70429. [PMID: 34324416 PMCID: PMC8321552 DOI: 10.7554/elife.70429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations in TP53 occur commonly in the majority of human tumors and confer aggressive tumor phenotypes, including metastasis and therapy resistance. CB002 and structural-analogs restore p53 signaling in tumors with mutant-p53 but we find that unlike other xanthines such as caffeine, pentoxifylline, and theophylline, they do not deregulate the G2 checkpoint. Novel CB002-analogs induce pro-apoptotic Noxa protein in an ATF3/4-dependent manner, whereas caffeine, pentoxifylline, and theophylline do not. By contrast to caffeine, CB002-analogs target an S-phase checkpoint associated with increased p-RPA/RPA2, p-ATR, decreased Cyclin A, p-histone H3 expression, and downregulation of essential proteins in DNA-synthesis and DNA-repair. CB002-analog #4 enhances cell death, and decreases Ki-67 in patient-derived tumor-organoids without toxicity to normal human cells. Preliminary in vivo studies demonstrate anti-tumor efficacy in mice. Thus, a novel class of anti-cancer drugs shows the activation of p53 pathway signaling in tumors with mutated p53, and targets an S-phase checkpoint.
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Affiliation(s)
- Liz Hernandez Borrero
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - David T Dicker
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - John Santiago
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Jennifer Sanders
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Department of Pediatrics, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Xiaobing Tian
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, United States
| | - Avital Lev
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States
| | - Lanlan Zhou
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Hematology-Oncology Division, Department of Medicine, Rhode Island Hospital and Brown University, Providence, United States
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12
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Hernandez Borrero L, Dicker DT, Santiago J, Sanders J, Tian X, Ahsan N, Lev A, Zhou L, El-Deiry WS. A subset of CB002 xanthine analogs bypass p53-signaling to restore a p53 transcriptome and target an S-phase cell cycle checkpoint in tumors with mutated-p53. eLife 2021. [PMID: 34324416 DOI: 10.10.7554/elife.70429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutations in TP53 occur commonly in the majority of human tumors and confer aggressive tumor phenotypes, including metastasis and therapy resistance. CB002 and structural-analogs restore p53 signaling in tumors with mutant-p53 but we find that unlike other xanthines such as caffeine, pentoxifylline, and theophylline, they do not deregulate the G2 checkpoint. Novel CB002-analogs induce pro-apoptotic Noxa protein in an ATF3/4-dependent manner, whereas caffeine, pentoxifylline, and theophylline do not. By contrast to caffeine, CB002-analogs target an S-phase checkpoint associated with increased p-RPA/RPA2, p-ATR, decreased Cyclin A, p-histone H3 expression, and downregulation of essential proteins in DNA-synthesis and DNA-repair. CB002-analog #4 enhances cell death, and decreases Ki-67 in patient-derived tumor-organoids without toxicity to normal human cells. Preliminary in vivo studies demonstrate anti-tumor efficacy in mice. Thus, a novel class of anti-cancer drugs shows the activation of p53 pathway signaling in tumors with mutated p53, and targets an S-phase checkpoint.
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Affiliation(s)
- Liz Hernandez Borrero
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - David T Dicker
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - John Santiago
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Jennifer Sanders
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Department of Pediatrics, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Xiaobing Tian
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, United States
| | - Avital Lev
- The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States
| | - Lanlan Zhou
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, United States.,The Joint Program in Cancer Biology, Brown University and the Lifespan Health System, Providence, United States.,Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, United States.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, United States.,Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, United States.,Hematology-Oncology Division, Department of Medicine, Rhode Island Hospital and Brown University, Providence, United States
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13
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Cyclin-Dependent Kinase-Mediated Phosphorylation of FANCD2 Promotes Mitotic Fidelity. Mol Cell Biol 2021; 41:e0023421. [PMID: 34096775 DOI: 10.1128/mcb.00234-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease characterized by increased risk for bone marrow failure and cancer. The FA proteins function together to repair damaged DNA. A central step in the activation of the FA pathway is the monoubiquitination of the FANCD2 and FANCI proteins, which occurs upon exposure to DNA-damaging agents and during the S phase of the cell cycle. The regulatory mechanisms governing S-phase monoubiquitination, in particular, are poorly understood. In this study, we have identified a cyclin-dependent kinase (CDK) regulatory phosphosite (S592) proximal to the site of FANCD2 monoubiquitination. FANCD2 S592 phosphorylation was detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and by immunoblotting with an S592 phospho-specific antibody. Mutation of S592 leads to abrogated monoubiquitination of FANCD2 during the S phase. Furthermore, FA-D2 (FANCD2-/-) patient cells expressing S592 mutants display reduced proliferation under conditions of replication stress and increased mitotic aberrations, including micronuclei and multinucleated cells. Our findings describe a novel cell cycle-specific regulatory mechanism for the FANCD2 protein that promotes mitotic fidelity.
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14
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Ahsan N, Rao RSP, Wilson RS, Punyamurtula U, Salvato F, Petersen M, Ahmed MK, Abid MR, Verburgt JC, Kihara D, Yang Z, Fornelli L, Foster SB, Ramratnam B. Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches. Proteomics 2021; 21:e2000279. [PMID: 33860983 PMCID: PMC8250252 DOI: 10.1002/pmic.202000279] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022]
Abstract
While protein–protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and rationalize the results obtained by various mass spectrometry (MS)‐based proteomic approaches applied to the functional characterization of proteins and pathways associated with SARS‐CoV‐2‐mediated infections in humans. Comparative analysis of cell‐lines versus tissue samples indicates that our knowledge in proteome profile alternation in response to SARS‐CoV‐2 infection is still incomplete and the tissue‐specific response to SARS‐CoV‐2 infection can probably not be recapitulated efficiently by in vitro experiments. However, regardless of the viral infection period, sample types, and experimental strategies, a thorough cross‐comparison of the recently published proteome, phosphoproteome, and interactome datasets led to the identification of a common set of proteins and kinases associated with PI3K‐Akt, EGFR, MAPK, Rap1, and AMPK signaling pathways. Ephrin receptor A2 (EPHA2) was identified by 11 studies including all proteomic platforms, suggesting it as a potential future target for SARS‐CoV‐2 infection mechanisms and the development of new therapeutic strategies. We further discuss the potentials of future proteomics strategies for identifying prognostic SARS‐CoV‐2 responsive age‐, gender‐dependent, tissue‐specific protein targets.
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Affiliation(s)
- Nagib Ahsan
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - R. Shyama Prasad Rao
- Biostatistics and Bioinformatics DivisionYenepoya Research CenterYenepoya UniversityMangaluruIndia
| | - Rashaun S. Wilson
- Keck Mass Spectrometry and Proteomics ResourceYale UniversityNew HavenConnecticutUSA
| | - Ujwal Punyamurtula
- COBRE Center for Cancer Research DevelopmentProteomics Core FacilityRhode Island HospitalProvidenceRhode IslandUSA
| | - Fernanda Salvato
- Department of Plant and Microbial BiologyCollege of Agriculture and Life SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Max Petersen
- Signal Transduction Lab, Division of Hematology/OncologyRhode Island Hospital, Warren Alpert Medical School, Brown UniversityProvidenceRhode IslandUSA
| | - Mohammad Kabir Ahmed
- Department of BiochemistryFaculty of MedicineUniversiti Kuala Lumpur Royal College of Medicine PerakIpohPerakMalaysia
| | - M. Ruhul Abid
- Department of SurgeryCardiovascular Research CenterRhode Island HospitalWarren Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
| | - Jacob C. Verburgt
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Daisuke Kihara
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Zhibo Yang
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - Luca Fornelli
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
- Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Steven B. Foster
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - Bharat Ramratnam
- COBRE Center for Cancer Research DevelopmentProteomics Core FacilityRhode Island HospitalProvidenceRhode IslandUSA
- Division of Infectious DiseasesDepartment of MedicineWarren Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
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15
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Jalali S, Shi J, Ahsan N, Wellik L, Serres M, Buko A, Paludo J, Kim H, Tang X, Yang ZZ, Novak A, Kyle R, Ansell S. Progression from Monoclonal gammopathy of undetermined significance of the immunoglobulin M class (IgM-MGUS) to Waldenstrom Macroglobulinemia is associated with an alteration in lipid metabolism. Redox Biol 2021; 41:101927. [PMID: 33690107 PMCID: PMC7941163 DOI: 10.1016/j.redox.2021.101927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 01/18/2023] Open
Abstract
The molecular events that modulate the progression of monoclonal gammopathy of undetermined significance of the immunoglobulin M class (IgM-MGUS) to Waldenstrom Macroglobulinemia (WM) are mostly unknown. We implemented comparative proteomics and metabolomics analyses on patient serum samples to identify differentially expressed molecules crucial to the progression from IgM-MGUS to WM. Our data identified altered lipid metabolism as a discriminating factor between MGUS, WM, and matched normal controls. Levels of many fatty acids, including polyunsaturated fatty acids and dicarboxylic acids, were significantly downregulated in WM sera when compared to MGUS. These reductions were associated with diminished 15-LOX and PPAR protein expression and increased 5-LOX and GPX4 expression in WM versus MGUS patients’ samples. Furthermore, WM serum samples showed increased lipid peroxidation compared to MGUS. Treatment with IL-6 or TNFα, upstream regulators of differentially expressed proteins between MGUS and WM, increased lipid absorption and lipid peroxidation in WM cell lines. Knock-down of 15-LOX expression increased WM cell survival, an effect accompanied by increased 5-LOX and GPX4 expression. In summary, our data show that reduced fatty acid and lipid metabolite levels in the serum of the WM patients are associated with increased lipid peroxidation and that downregulation of 15-LOX increases the survival of WM cells. These data are highly significant in identifying the biomarkers of disease progression and designing targeted therapeutic intervention.
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Affiliation(s)
- Shahrzad Jalali
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Jie Shi
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA; Department of Hematology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI, USA; Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - LindaE Wellik
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - MaKayla Serres
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alex Buko
- Human Metabolome Technologies (HMT) America, Boston, MA, USA
| | - Jonas Paludo
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - HyoJin Kim
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - XinYi Tang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zhi-Zhang Yang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - AnneJ Novak
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - RobertA Kyle
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - StephenM Ansell
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA.
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16
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Tian X, Ahsan N, Lulla A, Lev A, Abbosh P, Dicker DT, Zhang S, El-Deiry WS. P53-independent partial restoration of the p53 pathway in tumors with mutated p53 through ATF4 transcriptional modulation by ERK1/2 and CDK9. Neoplasia 2021; 23:304-325. [PMID: 33582407 PMCID: PMC7890376 DOI: 10.1016/j.neo.2021.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/17/2022] Open
Abstract
A long-term goal in the cancer-field has been to develop strategies for treating p53-mutated tumors. A novel small-molecule, PG3-Oc, restores p53 pathway-signaling in tumor cells with mutant-p53, independently of p53/p73. PG3-Oc partially upregulates the p53-transcriptome (13.7% of public p53 target-gene dataset; 15.2% of in-house dataset) and p53-proteome (18%, HT29; 16%, HCT116-p53−/−). Bioinformatic analysis indicates critical p53-effectors of growth-arrest (p21), apoptosis (PUMA, DR5, Noxa), autophagy (DRAM1), and metastasis-suppression (NDRG1) are induced by PG3-Oc. ERK1/2- and CDK9-kinases are required to upregulate ATF4 by PG3-Oc which restores p53 transcriptomic-targets in cells without functional-p53. PG3-Oc represses MYC (ATF4-independent), and upregulates PUMA (ATF4-dependent) in mediating cell death. With largely nonoverlapping transcriptomes, induced-ATF4 restores p53 transcriptomic targets in drug-treated cells including functionally important mediators such as PUMA and DR5. Our results demonstrate novel p53-independent drug-induced molecular reprogramming involving ERK1/2, CDK9, and ATF4 to restore upregulation of p53 effector genes required for cell death and tumor suppression.
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Affiliation(s)
- Xiaobing Tian
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, USA; The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI, USA; Division of Biology and Medicine, Brown University, Providence, RI, USA; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Nagib Ahsan
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, USA; COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI, USA; Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Amriti Lulla
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Avital Lev
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Philip Abbosh
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - David T Dicker
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, USA; The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI, USA; Division of Biology and Medicine, Brown University, Providence, RI, USA; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Shengliang Zhang
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, USA; The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI, USA; Division of Biology and Medicine, Brown University, Providence, RI, USA; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, USA; The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI, USA; Division of Biology and Medicine, Brown University, Providence, RI, USA; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA; Hematology-Oncology Division, Department of Medicine, Rhode Island Hospital and Brown University, Providence, RI, USA.
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17
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Baltanás FC, Zarich N, Rojas-Cabañeros JM, Santos E. SOS GEFs in health and disease. Biochim Biophys Acta Rev Cancer 2020; 1874:188445. [PMID: 33035641 DOI: 10.1016/j.bbcan.2020.188445] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
SOS1 and SOS2 are the most universal and widely expressed family of guanine exchange factors (GEFs) capable or activating RAS or RAC1 proteins in metazoan cells. SOS proteins contain a sequence of modular domains that are responsible for different intramolecular and intermolecular interactions modulating mechanisms of self-inhibition, allosteric activation and intracellular homeostasis. Despite their homology, analyses of SOS1/2-KO mice demonstrate functional prevalence of SOS1 over SOS2 in cellular processes including proliferation, migration, inflammation or maintenance of intracellular redox homeostasis, although some functional redundancy cannot be excluded, particularly at the organismal level. Specific SOS1 gain-of-function mutations have been identified in inherited RASopathies and various sporadic human cancers. SOS1 depletion reduces tumorigenesis mediated by RAS or RAC1 in mouse models and is associated with increased intracellular oxidative stress and mitochondrial dysfunction. Since WT RAS is essential for development of RAS-mutant tumors, the SOS GEFs may be considered as relevant biomarkers or therapy targets in RAS-dependent cancers. Inhibitors blocking SOS expression, intrinsic GEF activity, or productive SOS protein-protein interactions with cellular regulators and/or RAS/RAC targets have been recently developed and shown preclinical and clinical effectiveness blocking aberrant RAS signaling in RAS-driven and RTK-driven tumors.
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Affiliation(s)
- Fernando C Baltanás
- Centro de Investigación del Cáncer - IBMCC (CSIC-USAL) and CIBERONC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Natasha Zarich
- Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC) and CIBERONC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Jose M Rojas-Cabañeros
- Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC) and CIBERONC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Eugenio Santos
- Centro de Investigación del Cáncer - IBMCC (CSIC-USAL) and CIBERONC, Universidad de Salamanca, 37007 Salamanca, Spain.
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18
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Al-Mohanna T, Bokros NT, Ahsan N, Popescu GV, Popescu SC. Methods for Optimization of Protein Extraction and Proteogenomic Mapping in Sweet Potato. Methods Mol Biol 2020; 2139:309-324. [PMID: 32462596 DOI: 10.1007/978-1-0716-0528-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The complexity in chemical composition alongside the genomic complexity of crop plants poses significant challenges for the characterization of their proteomes. This chapter provides specific methods that can be used for the extraction and identification of proteins from sweet potato, and a proteogenomic method for the subsequent peptide mapping on the haplotype-derived sweet potato genome assembly. We outline two basic methods for extracting proteins expressed in root and leaf tissues for the label-free quantitative proteomics-one phenol-based procedure and one polyethylene glycol (PEG) 4000-based fractionation method-and discuss strategies for the organ-specific protein extraction and increased recovery of low-abundance proteins. Next, we describe computational methods for improved proteome annotation of sweet potato based on aggregated genomics and transcriptomics resources available in our and public databases. Lastly, we describe an easily customizable proteogenomics approach for mapping sweet potato peptides back to their genome location and exemplify its use in improving genome annotations using a mass spectrometry data set.
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Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Norbert T Bokros
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island, USA Hospital, Providence, Division of Biology and Medicine, Brown University, Providence, RI, USA
- Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA.
- The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania.
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA.
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Shaheen N, Halima O, Akhter KT, Nuzhat N, Rao RSP, Wilson RS, Ahsan N. Proteomic characterization of low molecular weight allergens and putative allergen proteins in lentil (Lens culinaris) cultivars of Bangladesh. Food Chem 2019; 297:124936. [DOI: 10.1016/j.foodchem.2019.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/31/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
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Lu H, Tang X, Sibley M, Coburn J, Rao RSP, Ahsan N, Ramratnam B. Impact of exosomal HIV-1 Tat expression on the human cellular proteome. Oncotarget 2019; 10:5632-5644. [PMID: 31608139 PMCID: PMC6771461 DOI: 10.18632/oncotarget.27207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/27/2019] [Indexed: 11/25/2022] Open
Abstract
HIV-1 exists in a latent form in all infected patients. When antiretroviral therapy is stopped, viral replication resumes. The HIV-1 Tat protein is a potent activator of viral transcription. Our previous work has demonstrated that exosomal formulations of Tat can reverse HIV-1 latency in primary CD4+ T lymphocytes isolated from long term antiretroviral treated individuals suggesting a potential role for Tat as a therapeutic HIV-1 Latency Reversal Agent (LRA). Here, we employed the label-free proteomic approach for profiling the proteomic changes associated with exosomal Tat production in human cell lines. Comparative proteomic analysis revealed that >30% peptides were differentially expressed in abundance in the Tat-expressing cell line compared with relevant controls. As expected, many of the known Tat-interactor proteins were upregulated. Tat expression also led to the upregulation of antioxidant proteins suggesting Tat-mediates an oxidative burst. Gene ontology and pathway analyses of these differentially expressed proteins showed enrichment of extracellular vesicular exosome and spliceosome localized proteins and proteins involved with transcriptional and translational mechanisms. Our work suggests that HIV-1 Tat expression leads to perturbations in cellular protein expression. In vivo administration of Tat using HIV/SIV animal models needs to be performed to assess the physiologic significance of Tat-induced proteomic changes prior to developing HIV-1 Tat as an LRA.
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Affiliation(s)
- Huafei Lu
- Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Xiaoli Tang
- Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Mitchell Sibley
- Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Jillian Coburn
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
| | - R. Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangalore 575018, India
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
- Division of Biology and Medicine, Brown University, Providence, RI 02903, USA
| | - Bharat Ramratnam
- Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
- Clinical Research Center of Lifespan, Providence, RI 02903, USA
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21
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Scrimgeour LA, Potz BA, Aboul Gheit A, Shi G, Stanley M, Zhang Z, Sodha NR, Ahsan N, Abid MR, Sellke FW. Extracellular Vesicles Promote Arteriogenesis in Chronically Ischemic Myocardium in the Setting of Metabolic Syndrome. J Am Heart Assoc 2019; 8:e012617. [PMID: 31354010 PMCID: PMC6761642 DOI: 10.1161/jaha.119.012617] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Ischemic heart disease continues to be a leading cause of mortality in patients. Extracellular vesicles (EVs) provide a potential for treatment that may induce collateral vessel growth to increase myocardial perfusion. Methods and Results Nineteen male Yorkshire pigs were given a high‐fat diet for 4 weeks, then underwent placement of an ameroid constrictor on the left circumflex artery to induce chronic myocardial ischemia. Two weeks later, the pigs received either intramyocardial vehicle (n=6), EVs (high‐fat diet with myocardial EV injection [HVM]; n=8), or HVM and calpain inhibition (n=5). Five weeks later, myocardial function, perfusion, coronary vascular density, and cell signaling were examined. Perfusion in the collateral‐dependent myocardium was increased during rapid ventricular pacing in the HVM group in both nonischemic (P=0.04) and ischemic areas of the ventricle (P=0.05). Cardiac output and stroke volume were significantly improved in the HVM group compared with the control group during ventricular pacing (P=0.006). Increased arteriolar density was seen in the HVM group in both nonischemic and ischemic myocardium (P=0.003 for both). However, no significant changes in the capillary density were observed between the control, HVM, and HVM and calpain inhibition groups (P=0.07). The group that received EVs with oral calpain inhibition had neither increased vessel density (P>0.99) nor improvement in blood flow or cardiac function (P=0.48) when compared with the control group. Conclusions These findings suggest that EVs promote angiogenesis in areas of chronic myocardial ischemia and improve cardiac function under conditions of diet‐induced metabolic syndrome.
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Affiliation(s)
- Laura A Scrimgeour
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Brittany A Potz
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Ahmad Aboul Gheit
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Guangbin Shi
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Melissa Stanley
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Zhiqi Zhang
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Neel R Sodha
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Nagib Ahsan
- Center of Biomedical Research Excellence Center for Cancer Research Development Proteomics Core Facility Rhode Island Hospital Providence RI.,Division of Biology and Medicine Brown University Providence RI
| | - M Ruhul Abid
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
| | - Frank W Sellke
- Division of Cardiothoracic Surgery Department of Surgery Cardiovascular Research Center Rhode Island Hospital Warren Alpert Medical School of Brown University Providence RI
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Al-Mohanna T, Ahsan N, Bokros NT, Dimlioglu G, Reddy KR, Shankle M, Popescu GV, Popescu SC. Proteomics and Proteogenomics Analysis of Sweetpotato (Ipomoea batatas) Leaf and Root. J Proteome Res 2019; 18:2719-2734. [DOI: 10.1021/acs.jproteome.8b00943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island, USA Hospital, Providence, Rhode Island 02903, United States
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02903, United States
| | - Norbert T. Bokros
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Gizem Dimlioglu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Kambham R. Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Mark Shankle
- Pontotoc Experimental Station, Mississippi State University, Pontotoc, Mississippi 38863, United States
| | - George V. Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39759, United States
- The National Institute for Laser, Plasma and Radiation Physics, Bucharest RO-077125, Romania
| | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
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23
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James NE, Cantillo E, Yano N, Chichester CO, DiSilvestro PA, Hovanesian V, Rao RSP, Kim KK, Moore RG, Ahsan N, Ribeiro JR. Septin-2 is overexpressed in epithelial ovarian cancer and mediates proliferation via regulation of cellular metabolic proteins. Oncotarget 2019; 10:2959-2972. [PMID: 31105878 PMCID: PMC6508204 DOI: 10.18632/oncotarget.26836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/23/2019] [Indexed: 02/06/2023] Open
Abstract
Epithelial Ovarian Cancer (EOC) is associated with dismal survival rates due to the fact that patients are frequently diagnosed at an advanced stage and eventually become resistant to traditional chemotherapeutics. Hence, there is a crucial need for new and innovative therapies. Septin-2, a member of the septin family of GTP binding proteins, has been characterized in EOC for the first time and represents a potential future target. Septin-2 was found to be overexpressed in serous and clear cell human patient tissue compared to benign disease. Stable septin-2 knockdown clones developed in an ovarian cancer cell line exhibited a significant decrease in proliferation rates. Comparative label-free proteomic analysis of septin-2 knockdown cells revealed differential protein expression of pathways associated with the TCA cycle, acetyl CoA, proteasome and spliceosome. Further validation of target proteins indicated that septin-2 plays a predominant role in post-transcriptional and translational modifications as well as cellular metabolism, and suggested the potential novel role of septin-2 in promoting EOC tumorigenesis through these mechanisms.
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Affiliation(s)
- Nicole E. James
- Division of Gynecologic Oncology, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants Hospital, Providence, RI, USA
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Evelyn Cantillo
- Division of Gynecologic Oncology, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants Hospital, Providence, RI, USA
| | - Naohiro Yano
- Department of Surgery, Roger Williams Medical Center, Boston University Medical School, Providence, RI, USA
| | - Clinton O. Chichester
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Paul A. DiSilvestro
- Division of Gynecologic Oncology, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants Hospital, Providence, RI, USA
- Division of Biology and Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | | | - R. Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangalore, India
| | - Kyukwang K. Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Richard G. Moore
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Nagib Ahsan
- Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI, USA
- Division of Biology and Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jennifer R. Ribeiro
- Division of Gynecologic Oncology, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants Hospital, Providence, RI, USA
- Division of Biology and Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
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Bone marrow-specific loss of ABI1 induces myeloproliferative neoplasm with features resembling human myelofibrosis. Blood 2018; 132:2053-2066. [PMID: 30213875 DOI: 10.1182/blood-2018-05-848408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/01/2018] [Indexed: 12/23/2022] Open
Abstract
Although the pathogenesis of primary myelofibrosis (PMF) and other myeloproliferative neoplasms (MPNs) is linked to constitutive activation of the JAK-STAT pathway, JAK inhibitors have neither curative nor MPN-stem cell-eradicating potential, indicating that other targetable mechanisms are contributing to the pathophysiology of MPNs. We previously demonstrated that Abelson interactor 1 (Abi-1), a negative regulator of Abelson kinase 1, functions as a tumor suppressor. Here we present data showing that bone marrow-specific deletion of Abi1 in a novel mouse model leads to development of an MPN-like phenotype resembling human PMF. Abi1 loss resulted in a significant increase in the activity of the Src family kinases (SFKs), STAT3, and NF-κB signaling. We also observed impairment of hematopoietic stem cell self-renewal and fitness, as evidenced in noncompetitive and competitive bone marrow transplant experiments. CD34+ hematopoietic progenitors and granulocytes from patients with PMF showed decreased levels of ABI1 transcript as well as increased activity of SFKs, STAT3, and NF-κB. In aggregate, our data link the loss of Abi-1 function to hyperactive SFKs/STAT3/NF-κB signaling and suggest that this signaling axis may represent a regulatory module involved in the molecular pathophysiology of PMF.
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25
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Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT. Nat Immunol 2018; 19:733-741. [PMID: 29915297 PMCID: PMC6202249 DOI: 10.1038/s41590-018-0131-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/18/2018] [Indexed: 12/23/2022]
Abstract
T cell-antigen receptor (TCR) signaling requires the sequential activities of the kinases Lck and Zap70. Upon TCR stimulation, Lck phosphorylates the TCR, thus leading to the recruitment, phosphorylation, and activation of Zap70. Lck binds and stabilizes phosho-Zap70 by using its SH2 domain, and Zap70 phosphorylates the critical adaptors LAT and SLP76, which coordinate downstream signaling. It is unclear whether phosphorylation of these adaptors occurs through passive diffusion or active recruitment. We report the discovery of a conserved proline-rich motif in LAT that mediates efficient LAT phosphorylation. Lck associates with this motif via its SH3 domain, and with phospho-Zap70 via its SH2 domain, thereby acting as a molecular bridge that facilitates the colocalization of Zap70 and LAT. Elimination of this proline-rich motif compromises TCR signaling and T cell development. These results demonstrate the remarkable multifunctionality of Lck, wherein each of its domains has evolved to orchestrate a distinct step in TCR signaling.
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Potz BA, Scrimgeour LA, Pavlov VI, Sodha NR, Abid MR, Sellke FW. Extracellular Vesicle Injection Improves Myocardial Function and Increases Angiogenesis in a Swine Model of Chronic Ischemia. J Am Heart Assoc 2018; 7:e008344. [PMID: 29895586 PMCID: PMC6220556 DOI: 10.1161/jaha.117.008344] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/04/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mesenchymal stem cell-derived extracellular vesicles (EVs) are believed to be cardioprotective in myocardial infarct. The objective of this study was to examine the effects of human mesenchymal cell-derived EV injection on cardiac function, myocardial blood flow, and vessel density in the setting of chronic myocardial ischemia. METHODS AND RESULTS Twenty-three Yorkshire swine underwent placement of an ameroid constrictor on their left circumflex artery. Two weeks later, the animals were split into 2 groups: the control group (CON; n=7) and the EV myocardial injection group (MVM; n=10). The MVM group underwent myocardial injection of 50 μg of EVs in 2 mL 0.9% saline into the ischemic myocardium. Five weeks later, the pigs underwent a harvest procedure, and the left ventricular myocardium was analyzed. Absolute blood flow and the ischemic/nonischemic myocardial perfusion ratio were increased in the ischemic myocardium in the MVM group compared with the CON group. Pigs in the MVM group had increased capillary and arteriolar density in the ischemic myocardial tissue compared with CON pigs. There was an increase in expression of the phospho-mitogen-activated protein kinase/mitogen-activated protein kinase ratio, the phospho-endothelial nitric oxide synthase/endothelial nitric oxide synthase ratio, and total protein kinase B in the MVM group compared with CON. There was an increase in cardiac output and stroke volume in the MVM group compared with CON. CONCLUSIONS In the setting of chronic myocardial ischemia, myocardial injection of human mesenchymal cell-derived EVs increases blood flow to ischemic myocardial tissue by induction of capillary and arteriolar growth via activation of the protein kinase B/endothelial nitric oxide synthase and mitogen-activated protein kinase signaling pathways resulting in increased cardiac output and stroke volume.
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Affiliation(s)
- Brittany A Potz
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI
| | - Laura A Scrimgeour
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI
| | - Vasile I Pavlov
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI
| | - Neel R Sodha
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI
| | - M Ruhul Abid
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI
| | - Frank W Sellke
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI
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Chorzalska A, Ahsan N, Rao RSP, Roder K, Yu X, Morgan J, Tepper A, Hines S, Zhang P, Treaba DO, Zhao TC, Olszewski AJ, Reagan JL, Liang O, Gruppuso PA, Dubielecka PM. Overexpression of Tpl2 is linked to imatinib resistance and activation of MEK-ERK and NF-κB pathways in a model of chronic myeloid leukemia. Mol Oncol 2018; 12:630-647. [PMID: 29485707 PMCID: PMC5928369 DOI: 10.1002/1878-0261.12186] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 12/12/2022] Open
Abstract
The introduction of tyrosine kinase inhibitors (TKI) has transformed chronic myeloid leukemia (CML) into a chronic disease with long-term survival exceeding 85%. However, resistance of CML stem cells to TKI may contribute to the 50% relapse rate observed after TKI discontinuation in molecular remission. We previously described a model of resistance to imatinib mesylate (IM), in which K562 cells cultured in high concentrations of imatinib mesylate showed reduced Bcr-Abl1 protein and activity levels while maintaining proliferative potential. Using quantitative phosphoproteomic analysis of these IM-resistant cells, we have now identified significant upregulation of tumor progression locus (Tpl2), also known as cancer Osaka thyroid (COT1) kinase or Map3k8. Overexpression of Tpl2 in IM-resistant cells was accompanied by elevated activities of Src family kinases (SFKs) and NF-κB, MEK-ERK signaling. CD34+ cells isolated from the bone marrow of patients with CML and exposed to IMin vitro showed increased MAP3K8 transcript levels. Dasatinib (SFK inhibitor), U0126 (MEK inhibitor), and PS-1145 (IκB kinase (IKK) inhibitor) used in combination resulted in elimination of 65% of IM-resistant cells and reduction in the colony-forming capacity of CML CD34+ cells in methylcellulose assays by 80%. In addition, CML CD34+ cells cultured with the combination of inhibitors showed reduced MAP3K8 transcript levels. Overall, our data indicate that elevated Tpl2 protein and transcript levels are associated with resistance to IM and that combined inhibition of SFK, MEK, and NF-κB signaling attenuates the survival of IM-resistant CML cells and CML CD34+ cells. Therefore, combination of SFK, MEK, and NF-κB inhibitors may offer a new therapeutic approach to overcome TKI resistance in CML patients.
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Affiliation(s)
- Anna Chorzalska
- Signal Transduction Lab, Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Nagib Ahsan
- Division of Biology and Medicine, COBRE CCRD Proteomics Core Facility, Rhode Island Hospital, Brown University, Providence, RI, USA
| | - R Shyama Prasad Rao
- Division of Biostatistics and Bioinformatics, Yenepoya Research Center, Yenepoya University, Mangalore, India
| | - Karim Roder
- Cardiovascular Research Center, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Xiaoqing Yu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - John Morgan
- Flow Cytometry and Cell Sorting Core Facility, Roger Williams Medical Center, Providence, RI, USA
| | - Alexander Tepper
- Signal Transduction Lab, Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Steven Hines
- Signal Transduction Lab, Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Peng Zhang
- Cardiovascular Research Center, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Diana O Treaba
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Ting C Zhao
- Cardiovascular Lab, Department of Surgery, Roger Williams Medical Center, Boston University School of Medicine, Providence, RI, USA
| | - Adam J Olszewski
- Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - John L Reagan
- Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Olin Liang
- Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Philip A Gruppuso
- Department of Pediatrics, Rhode Island Hospital, Brown University, Providence, RI, USA
| | - Patrycja M Dubielecka
- Signal Transduction Lab, Division of Hematology/Oncology, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, USA
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Post S, Karashchuk G, Wade JD, Sajid W, De Meyts P, Tatar M. Drosophila Insulin-Like Peptides DILP2 and DILP5 Differentially Stimulate Cell Signaling and Glycogen Phosphorylase to Regulate Longevity. Front Endocrinol (Lausanne) 2018; 9:245. [PMID: 29892262 PMCID: PMC5985746 DOI: 10.3389/fendo.2018.00245] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/02/2018] [Indexed: 01/08/2023] Open
Abstract
Insulin and IGF signaling (IIS) is a complex system that controls diverse processes including growth, development, metabolism, stress responses, and aging. Drosophila melanogaster IIS is propagated by eight Drosophila insulin-like peptides (DILPs), homologs of both mammalian insulin and IGFs, with various spatiotemporal expression patterns and functions. DILPs 1-7 are thought to act through a single Drosophila insulin/IGF receptor, InR, but it is unclear how the DILPs thereby mediate a range of physiological phenotypes. We determined the distinct cell signaling effects of DILP2 and DILP5 stimulation upon Drosophila S2 cells. DILP2 and DILP5 induced similar transcriptional patterns but differed in signal transduction kinetics. DILP5 induced sustained phosphorylation of Akt, while DILP2 produced acute, transient Akt phosphorylation. Accordingly, we used phosphoproteomic analysis to identify distinct patterns of non-genomic signaling induced by DILP2 and DILP5. Across all treatments and replicates, 5,250 unique phosphopeptides were identified, representing 1,575 proteins. Among these peptides, DILP2, but not DILP5, dephosphorylated Ser15 on glycogen phosphorylase (GlyP), and DILP2, but not DILP5, was subsequently shown to repress enzymatic GlyP activity in S2 cells. The functional consequences of this difference were evaluated in adult Drosophila dilp mutants: dilp2 null adults have elevated GlyP enzymatic activity relative to wild type, while dilp5 mutants have reduced GlyP activity. In flies with intact insulin genes, GlyP overexpression extended lifespan in a Ser15 phosphorylation-dependent manner. In dilp2 mutants, that are otherwise long-lived, longevity was repressed by expression of phosphonull GlyP that is enzymatically inactive. Overall, DILP2, unlike DILP5, signals to affect longevity in part through its control of phosphorylation to deactivate glycogen phosphorylase, a central modulator of glycogen storage and gluconeogenesis.
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Affiliation(s)
- Stephanie Post
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
- *Correspondence: Stephanie Post, ; Marc Tatar,
| | - Galina Karashchuk
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - John D. Wade
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
- School of Chemistry, University of Melbourne, Melbourne, VIC, Australia
| | | | - Pierre De Meyts
- Department of Cell Signalling, de Duve Institute, Brussels, Belgium
- Department of Stem Cell Research Novo Nordisk A/S, Måløv, Denmark
| | - Marc Tatar
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
- *Correspondence: Stephanie Post, ; Marc Tatar,
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