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Lai QC, Zheng J, Mou J, Cui CY, Wu QC, M Musa Rizvi S, Zhang Y, Li TM, Ren YB, Liu Q, Li Q, Zhang C. Identification of hub genes in calcific aortic valve disease. Comput Biol Med 2024; 172:108214. [PMID: 38508057 DOI: 10.1016/j.compbiomed.2024.108214] [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] [Received: 11/28/2023] [Revised: 01/26/2024] [Accepted: 02/25/2024] [Indexed: 03/22/2024]
Abstract
Calcific aortic valve disease (CAVD) is a heart valve disorder characterized primarily by calcification of the aortic valve, resulting in stiffness and dysfunction of the valve. CAVD is prevalent among aging populations and is linked to factors such as hypertension, dyslipidemia, tobacco use, and genetic predisposition, and can result in becoming a growing economic and health burden. Once aortic valve calcification occurs, it will inevitably progress to aortic stenosis. At present, there are no medications available that have demonstrated effectiveness in managing or delaying the progression of the disease. In this study, we mined four publicly available microarray datasets (GSE12644 GSE51472, GSE77287, GSE233819) associated with CAVD from the GEO database with the aim of identifying hub genes associated with the occurrence of CAVD and searching for possible biological targets for the early prevention and diagnosis of CAVD. This study provides preliminary evidence for therapeutic and preventive targets for CAVD and may provide a solid foundation for subsequent biological studies.
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Affiliation(s)
- Qian-Cheng Lai
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Sichuan Provincial People's Hospital, Chengdu, 610000, Sichuan, China
| | - Jie Zheng
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jian Mou
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China; Department of Pain, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Chun-Yan Cui
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China; Department of Pain, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Qing-Chen Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Syed M Musa Rizvi
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ying Zhang
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Tian-Mei Li
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Ying-Bo Ren
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Qing Liu
- Department of Pain, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China; Hejiang Traditional Chinese Medicine Hospital, Luzhou, 646000, Sichuan, China.
| | - Qun Li
- Department of Pain, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Cheng Zhang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Sîrbulescu RF, Ilieş I, Amelung L, Zupanc GKH. Proteomic characterization of spontaneously regrowing spinal cord following injury in the teleost fish Apteronotus leptorhynchus, a regeneration-competent vertebrate. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022; 208:671-706. [PMID: 36445471 DOI: 10.1007/s00359-022-01591-w] [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] [Received: 10/03/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022]
Abstract
In adult mammals, spontaneous repair after spinal cord injury (SCI) is severely limited. By contrast, teleost fish successfully regenerate injured axons and produce new neurons from adult neural stem cells after SCI. The molecular mechanisms underlying this high regenerative capacity are largely unknown. The present study addresses this gap by examining the temporal dynamics of proteome changes in response to SCI in the brown ghost knifefish (Apteronotus leptorhynchus). Two-dimensional difference gel electrophoresis (2D DIGE) was combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and tandem mass spectrometry (MS/MS) to collect data during early (1 day), mid (10 days), and late (30 days) phases of regeneration following caudal amputation SCI. Forty-two unique proteins with significant differences in abundance between injured and intact control samples were identified. Correlation analysis uncovered six clusters of spots with similar expression patterns over time and strong conditional dependences, typically within functional families or between isoforms. Significantly regulated proteins were associated with axon development and regeneration; proliferation and morphogenesis; neuronal differentiation and re-establishment of neural connections; promotion of neuroprotection, redox homeostasis, and membrane repair; and metabolism or energy supply. Notably, at all three time points examined, significant regulation of proteins involved in inflammatory responses was absent.
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Affiliation(s)
- Ruxandra F Sîrbulescu
- School of Engineering and Science, Jacobs University Bremen, 28725, Bremen, Germany
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA
- Vaccine and Immunotherapy Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Iulian Ilieş
- School of Humanities and Social Sciences, Jacobs University Bremen, 28725, Bremen, Germany
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Lisa Amelung
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Günther K H Zupanc
- School of Engineering and Science, Jacobs University Bremen, 28725, Bremen, Germany.
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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Fonghem P, Pisitkun T, Rattanapinyopituk K, Sirivisoot S, Rungsipipat A. Investigation of proteomic profiles in canine lymphoma using tandem mass tag-based quantitative proteomics approach. Vet World 2022; 15:1333-1340. [PMID: 35765478 PMCID: PMC9210836 DOI: 10.14202/vetworld.2022.1333-1340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/18/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Specific tumor biomarkers are useful for the early diagnosis of cancer or can predict the recurrence of neoplastic disease in humans and animals. Lymphoma in dogs could be classified into B-, T-, and NK-cell origins. T-cell lymphoma has the worst prognosis with a shorter survival time and disease-free interval. This study aimed to identify the differential serum protein expressions of canine B- and T-cell lymphomas compared with healthy dogs using a tandem mass tag (TMT)-based quantitative proteomics. Materials and Methods: Serum samples were collected from 20 untreated canine lymphomas (14 B-cells and 6 T-cells) and four healthy control dogs. Sera peptides from each sample were processed for TMT 10-plex tagging and analyzed using liquid chromatography-mass spectrometry (MS). Differential proteome profiling was then compared between lymphoma and control. Results: We discovered 20 elevated and 14 decreased serum proteins in the lymphoma group relative to the healthy group. Six candidate increased proteins in canine lymphomas were beta-actin cytoplasmic 1 (ACTB, p=0.04), haptoglobin (p=0.002), beta-2 microglobulin (aaaaaaaa2M, p=0.007), beta-2 glycoprotein 1 (APOH, p=0.03), metalloproteinase inhibitor 1 (TIMP-1, p=0.03), and CD44 antigen (p=0.02). When compared between B- and T-cell lymphomas, B-cell phenotypes had upregulated immunoglobulin (Ig) heavy chain V region GOM (p=0.02), clusterin (p=0.01), apolipoprotein C1 (APOC1, p=0.05), and plasminogen (p=0.02). Conclusion: These findings were investigated quantitative serum proteomes between B- and T-cell lymphomas using TMT-based MS. ACTB, aaaaaaaa2M, APOH, TIMP-1, CD44 antigen, Ig heavy chain V region GOM, and APOC1 are novel candidate proteins and might serve as a lymphoma biomarker in dogs. However, evaluation with an increased sample size is needed to confirm their diagnostic and prognostic ability.
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Affiliation(s)
- Piyanoot Fonghem
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kasem Rattanapinyopituk
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sirintra Sirivisoot
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Anudep Rungsipipat
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:1341. [PMID: 35456020 PMCID: PMC9027113 DOI: 10.3390/cells11081341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Antibodies are central effectors of the adaptive immune response, widespread used therapeutics, but also potentially disease-causing biomolecules. Antibody folding catalysts in the plasma cell are incompletely defined. Idiopathic pulmonary fibrosis (IPF) is a fatal chronic lung disease with increasingly recognized autoimmune features. We found elevated expression of FK506-binding protein 11 (FKBP11) in IPF lungs where FKBP11 specifically localized to antibody-producing plasma cells. Suggesting a general role in plasma cells, plasma cell-specific FKBP11 expression was equally observed in lymphatic tissues, and in vitro B cell to plasma cell differentiation was accompanied by induction of FKBP11 expression. Recombinant human FKBP11 was able to refold IgG antibody in vitro and inhibited by FK506, strongly supporting a function as antibody peptidyl-prolyl cis-trans isomerase. Induction of ER stress in cell lines demonstrated induction of FKBP11 in the context of the unfolded protein response in an X-box-binding protein 1 (XBP1)-dependent manner. While deficiency of FKBP11 increased susceptibility to ER stress-mediated cell death in an alveolar epithelial cell line, FKBP11 knockdown in an antibody-producing hybridoma cell line neither induced cell death nor decreased expression or secretion of IgG antibody. Similarly, antibody secretion by the same hybridoma cell line was not affected by knockdown of the established antibody peptidyl-prolyl isomerase cyclophilin B. The results are consistent with FKBP11 as a novel XBP1-regulated antibody peptidyl-prolyl cis-trans isomerase and indicate significant redundancy in the ER-resident folding machinery of antibody-producing hybridoma cells.
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Affiliation(s)
- Stefan Preisendörfer
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Yoshihiro Ishikawa
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; (Y.I.); (H.P.B.)
| | - Elisabeth Hennen
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Stephan Winklmeier
- Institute of Clinical Neuroimmunology, Biomedical Center and LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; (S.W.); (E.M.)
| | - Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
- Department of Respiratory Medicine, Hannover Medical School, Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Larissa Knüppel
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Isis E. Fernandez
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Leonhard Binzenhöfer
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Brenda M. Juan-Guardela
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
| | - Clemens Ruppert
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), 35392 Giessen, Germany; (C.R.); (A.G.)
| | - Andreas Guenther
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), 35392 Giessen, Germany; (C.R.); (A.G.)
| | - Marion Frankenberger
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Rudolf A. Hatz
- Thoraxchirurgisches Zentrum, Klinik für Allgemeine-, Viszeral-, Transplantations-, Gefäß- und Thoraxchirurgie, LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany;
- Asklepios Fachkliniken München-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Jürgen Behr
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
| | - Edgar Meinl
- Institute of Clinical Neuroimmunology, Biomedical Center and LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; (S.W.); (E.M.)
| | - Hans Peter Bächinger
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; (Y.I.); (H.P.B.)
| | - Oliver Eickelberg
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Claudia A. Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
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