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Ahmed YB, Ababneh OE, Al-Khalili AA, Serhan A, Hatamleh Z, Ghammaz O, Alkhaldi M, Alomari S. Identification of Hypoxia Prognostic Signature in Glioblastoma Multiforme Based on Bulk and Single-Cell RNA-Seq. Cancers (Basel) 2024; 16:633. [PMID: 38339384 PMCID: PMC10854729 DOI: 10.3390/cancers16030633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Glioblastoma (GBM) represents a profoundly aggressive and heterogeneous brain neoplasm linked to a bleak prognosis. Hypoxia, a common feature in GBM, has been linked to tumor progression and therapy resistance. In this study, we aimed to identify hypoxia-related differentially expressed genes (DEGs) and construct a prognostic signature for GBM patients using multi-omics analysis. Patient cohorts were collected from publicly available databases, including the Gene Expression Omnibus (GEO), the Chinese Glioma Genome Atlas (CGGA), and The Cancer Genome Atlas-Glioblastoma Multiforme (TCGA-GBM), to facilitate a comprehensive analysis. Hypoxia-related genes (HRGs) were obtained from the Molecular Signatures Database (MSigDB). Differential expression analysis revealed 41 hypoxia-related DEGs in GBM patients. A consensus clustering approach, utilizing these DEGs' expression patterns, identified four distinct clusters, with cluster 1 showing significantly better overall survival. Machine learning techniques, including univariate Cox regression and LASSO regression, delineated a prognostic signature comprising six genes (ANXA1, CALD1, CP, IGFBP2, IGFBP5, and LOX). Multivariate Cox regression analysis substantiated the prognostic significance of a set of three optimal signature genes (CP, IGFBP2, and LOX). Using the hypoxia-related prognostic signature, patients were classified into high- and low-risk categories. Survival analysis demonstrated that the high-risk group exhibited inferior overall survival rates in comparison to the low-risk group. The prognostic signature showed good predictive performance, as indicated by the area under the curve (AUC) values for one-, three-, and five-year overall survival. Furthermore, functional enrichment analysis of the DEGs identified biological processes and pathways associated with hypoxia, providing insights into the underlying mechanisms of GBM. Delving into the tumor immune microenvironment, our analysis revealed correlations relating the hypoxia-related prognostic signature to the infiltration of immune cells in GBM. Overall, our study highlights the potential of a hypoxia-related prognostic signature as a valuable resource for forecasting the survival outcome of GBM patients. The multi-omics approach integrating bulk sequencing, single-cell analysis, and immune microenvironment assessment enhances our understanding of the intricate biology characterizing GBM, thereby potentially informing the tailored design of therapeutic interventions.
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Affiliation(s)
- Yaman B. Ahmed
- School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA;
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Obada E. Ababneh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Anas A. Al-Khalili
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Abdullah Serhan
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Zaid Hatamleh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Owais Ghammaz
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Mohammad Alkhaldi
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (O.E.A.); (A.A.A.-K.); (A.S.); (Z.H.); (O.G.); (M.A.)
| | - Safwan Alomari
- Department of Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
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Dunphy K, Dowling P. DIGE-Based Biomarker Discovery in Blood Cancers. Methods Mol Biol 2023; 2596:105-112. [PMID: 36378434 DOI: 10.1007/978-1-0716-2831-7_8] [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: 06/16/2023]
Abstract
Cancer of blood or bone marrow-derived cells dysregulates normal hematopoiesis and accounts for over 6% of all cancer cases annually. Proteomic analyses of blood cancers have improved our understanding of disease mechanisms and identified numerous proteins of clinical relevance. For many years, gel-based proteomic studies have aided in the discovery of novel diagnostic, prognostic, and predictive biomarkers, as well as therapeutic targets, in various diseases, including blood cancer. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) facilitates comparative proteomic research to identify differential protein expression in a simple and reproducible manner. The versatility of 2D-DIGE as a quantitative proteomic technique has provided insight into various aspects of blood cancer pathology, including disease development, prognostic subtypes, and drug resistance. The ability to couple 2D-DIGE with additional downstream mass spectrometry-based techniques yields comprehensive workflows capable of identifying proteins of biological and clinical significance. The application of 2D-DIGE in blood cancer research has significantly contributed to the increasingly important initiative of precision medicine. This chapter will focus on the influential role of 2D-DIGE as a tool in blood cancer research.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Quantitative Plasma Proteomics to Identify Candidate Biomarkers of Relapse in Pediatric/Adolescent Hodgkin Lymphoma. Int J Mol Sci 2022; 23:ijms23179911. [PMID: 36077307 PMCID: PMC9456176 DOI: 10.3390/ijms23179911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022] Open
Abstract
Classical pediatric Hodgkin Lymphoma (HL) is a rare malignancy. Therapeutic regimens for its management may be optimized by establishing treatment response early on. The aim of this study was to identify plasma protein biomarkers enabling the prediction of relapse in pediatric/adolescent HL patients treated under the pediatric EuroNet-PHL-C2 trial. We used untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics at the time of diagnosis—before any therapy—as semiquantitative method to profile plasma proteins specifically associated with relapse in 42 children with nodular sclerosing HL. In both the exploratory and the validation cohorts, six proteins (apolipoprotein E, C4b-binding protein α chain, clusterin, fibrinogen γ chain, prothrombin, and vitronectin) were more abundant in the plasma of patients whose HL relapsed (|fold change| ≥ 1.2, p < 0.05, Student’s t-test). Predicting protein function with the Gene Ontology classification model, the proteins were included in four biological processes (p < 0.01). Using immunoblotting and Luminex assays, we validated two of these candidate biomarkers—C4b-binding protein α chain and clusterin—linked to innate immune response function (GO:0045087). This study identified C4b-binding protein α chain and clusterin as candidate early plasma biomarkers of HL relapse, and important for the purpose of shedding light on the molecular scenario associated with immune response in patients treated under the EuroNet-PHL-C2 trial.
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Zhuang K, Zhang Y, Mo P, Deng L, Jiang Y, Yu L, Mei F, Huang S, Chen X, Yan Y, Tang H, Li X, Xiong Y, Wu S, Ke H, Gui X, Lan K. Plasma proteomic analysis reveals altered protein abundances in HIV-infected patients with or without Non-Hodgkin Lymphoma. J Med Virol 2022; 94:3876-3889. [PMID: 35415847 DOI: 10.1002/jmv.27775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/07/2022]
Abstract
The identification of circulating proteins associated with acquired immunodeficiency syndrome-related non-Hodgkin lymphoma (AIDS-NHL) may help in the development of promising biomarkers for screening, diagnosis, treatment and prognosis. Here, we used quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify differentially expressed proteins (DEPs) in plasma collected from patients with AIDS-NHL and human immunodeficiency virus (HIV)-infected patients without NHL (HIV+ ). Proteins with a log2 (fold change) in abundance >0.26 and p value less than 0.05 (p < 0.05) were considered differentially abundant. In total, 84 DEPs were identified, among which 20 were further validated as potential biomarkers, with immunoglobulin and complement components being the most common proteins. Some of the proteins were further verified in a retrospective analysis of the medical records of patients in a larger cohort. These markedly altered proteins were found to mediate pathophysiological pathways that likely contribute to AIDS-NHL pathogenesis, such as the humoral immune response, complement activation, and complement and coagulation cascades. Our findings provide a new molecular understanding of AIDS-NHL pathogenesis and provide new evidence supporting the identification of these proteins as possible biomarkers in AIDS-NHL. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ke Zhuang
- ABSL-III Laboratory at the Center for Animal Experiment, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, China
| | - Yongxi Zhang
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Pingzheng Mo
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liping Deng
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yong Jiang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Lei Yu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Fanghua Mei
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Shaoxin Huang
- SpecAlly Life Technology Co., Ltd., Wuhan, Hubei, China
| | - Xi Chen
- SpecAlly Life Technology Co., Ltd., Wuhan, Hubei, China
| | - Yajun Yan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Hongbin Tang
- ABSL-III Laboratory at the Center for Animal Experiment, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, China
| | - Xiangdong Li
- ABSL-III Laboratory at the Center for Animal Experiment, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, China
| | - Yong Xiong
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Shuwen Wu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
| | - Hengning Ke
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xien Gui
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ke Lan
- ABSL-III Laboratory at the Center for Animal Experiment, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei, China.,State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei, P. R. China
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6
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Aibara N, Miyata Y, Araki K, Sagara Y, Mitsunari K, Matsuo T, Ohba K, Mochizuki Y, Sakai H, Ohyama K. Detection of Novel Urine Markers Using Immune Complexome Analysis in Bladder Cancer Patients: A Preliminary Study. In Vivo 2021; 35:2073-2080. [PMID: 34182482 DOI: 10.21873/invivo.12476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND/AIM Little is known on urine biomarkers that are associated with malignant behavior in patients with bladder cancer (BC). Our aim was to identify BC-related factors in urine samples using our original method "immune complexome analysis", based on detecting the immune complex (IC). PATIENTS AND METHODS Immune complexome analysis was performed using urine samples from 97 BC patients, including 67 with non-muscle invasive BC (NMIBC). RESULTS Eight IC-antigens were recognized as candidates for BC-related factors from 20,165 proteins. IC-serum albumin, -fibrinogen γ chain, -hemoglobin subunit α, -hemoglobin subunit β, -ceruloplasmin, and fibrinogen β chain were significantly associated with either pathological features and/or outcome. IC-ceruloplasmin was most widely associated with pathological features in all BC patients and lamina propria invasion and urinary tract recurrence in NMIBC. CONCLUSION Based on detection of IC-antigens it was demonstrated that six IC-antigens, especially IC-ceruloplasmin, are potential urine biomarkers in BC.
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Affiliation(s)
- Nozomi Aibara
- Department of Pharmacy Practice, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yasuyoshi Miyata
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kyohei Araki
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuji Sagara
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kensuke Mitsunari
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomohiro Matsuo
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kojiro Ohba
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yasushi Mochizuki
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideki Sakai
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kaname Ohyama
- Department of Pharmacy Practice, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Proteomic Exploration of Plasma Exosomes and Other Small Extracellular Vesicles in Pediatric Hodgkin Lymphoma: A Potential Source of Biomarkers for Relapse Occurrence. Diagnostics (Basel) 2021; 11:diagnostics11060917. [PMID: 34063765 PMCID: PMC8223799 DOI: 10.3390/diagnostics11060917] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
Exosomes and other small extracellular vesicles (EVs) are potential sources of cancer biomarkers. Plasma-derived EVs have not yet been studied in pediatric Hodgkin lymphoma (HL), for which predictive biomarkers of relapse are greatly needed. In this two-part proteomic study, we used two-dimensional difference gel electrophoresis (2D-DIGE) followed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) to analyze EV proteins of plasma collected at diagnosis from children with nodular sclerosis HL, relapsed or not. EVs isolated using membrane affinity had radii ranging from 20 to 130 nm and contained the programmed cell death 6-interacting (ALIX) and the tumor susceptibility gene 101 (TSG101) proteins, whereas calnexin (CANX) was not detected. 2D-DIGE identified 16 spots as differentially abundant between non-relapsed and relapsed HL (|fold change| ≥ 1.5, p < 0.05). LC–MS/MS identified these spots as 11 unique proteins, including five more abundant in non-relapsed HL (e.g., complement C4b, C4B; fibrinogen γ chain, FGG) and six more abundant in relapsed HL (e.g., transthyretin, TTR). Shotgun LC–MS/MS on pooled EV proteins from non-relapsed HL identified 161 proteins, including 127 already identified in human exosomes (ExoCarta data). This EV cargo included 89 proteins not yet identified in exosomes from healthy plasma. Functional interrogation by the Database for Annotation, Visualization and Integrated Discovery (DAVID) revealed that the EV proteins participate in platelet degranulation and serine-type endopeptidase activity as the most significant Gene Ontology (GO) biological process and molecular function (p < 0.01).
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8
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Marsilio S, Dröes FC, Dangott L, Chow B, Hill S, Ackermann M, Estep JS, Lidbury JA, Suchodolski JS, Steiner JM. Characterization of the intestinal mucosal proteome in cats with inflammatory bowel disease and alimentary small cell lymphoma. J Vet Intern Med 2021; 35:179-189. [PMID: 33471936 PMCID: PMC7848303 DOI: 10.1111/jvim.16003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Current tests for diagnosis and differentiation of lymphoplasmacytic enteritis (LPE) and small cell lymphoma (SCL) in cats are expensive, invasive, and lack specificity. The identification of less invasive, more reliable biomarkers would facilitate diagnosis. OBJECTIVES To characterize the mucosal proteome in endoscopically obtained, small intestinal tissue biopsy specimens. We hypothesized that differentially expressed proteins could be identified and serve as biomarker candidates for the differentiation of LPE and SCL in cats. ANIMALS Six healthy control cats, 6 cats with LPE, and 8 cats with SCL. METHODS The mucosal proteome was analyzed using 2-dimensional fluorescence difference gel electrophoresis (2D DIGE) and nanoflow liquid chromatography tandem mass spectrometry. For 5 proteins, results were verified by Western blot analysis. RESULTS A total of 2349 spots were identified, of which 9 were differentially expressed with a ≥2-fold change between healthy cats and cats with LPE and SCL (.01 < P < .001). Eight of these 9 spots were also differentially expressed between cats with LPE and cats with SCL (P .001 < P < .04). However, Western blot analysis for malate dehydrogenase-1, malate dehydrogenase-2, apolipoprotein, annexin IV, and annexin V did not confirm significant differential protein expression for any of the 5 proteins assessed. CONCLUSIONS AND CLINICAL IMPORTANCE Two-D DIGE did not identify potential biomarker candidates in the intestinal mucosa of cats with LPE and SCL. Future studies should focus on different techniques to identify biomarker candidates for cats with chronic enteropathies (CE).
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Affiliation(s)
- Sina Marsilio
- Department of Medicine and EpidemiologySchool of Veterinary Medicine, University of CaliforniaDavisCAUSA
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Floris C. Dröes
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Lawrence Dangott
- Protein Chemistry Laboratory, Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Betty Chow
- Veterinary Specialty HospitalSan DiegoCaliforniaUSA
- VCA Animal Specialty & Emergency CenterLos AngelesCaliforniaUSA
| | - Steve Hill
- Veterinary Specialty HospitalSan DiegoCaliforniaUSA
- Flagstaff Veterinary Internal Medicine ConsultingFlagstaffArizonaUSA
| | - Mark Ackermann
- Oregon Veterinary Diagnostic LaboratoryCarlson College of Veterinary Medicine, Oregon State UniversityCorvallisOregonUSA
| | | | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Jörg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
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Proteomic Profiles and Biological Processes of Relapsed vs. Non-Relapsed Pediatric Hodgkin Lymphoma. Int J Mol Sci 2020; 21:ijms21062185. [PMID: 32235718 PMCID: PMC7139997 DOI: 10.3390/ijms21062185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of circulating proteins associated with relapse in pediatric Hodgkin lymphoma (HL) may help develop predictive biomarkers. We previously identified a set of predictive biomarkers by difference gel electrophoresis. Here we used label-free quantitative liquid chromatography-mass spectrometry (LC-MS/MS) on plasma collected at diagnosis from 12 children (age 12–16 years) with nodular sclerosis HL, including six in whom the disease relapsed within 5 years of treatment in the LH2004 trial. Plasma proteins were pooled in groups of three, separately for non-relapsing and relapsing HL, and differentially abundant proteins between the two disease states were identified by LC-MS/MS in an explorative and validation design. Proteins with a fold change in abundance >1.2 or ≤0.8 were considered “differentially abundant”. LC-MS/MS identified 60 and 32 proteins that were more abundant in non-relapsing and relapsing HL plasma, respectively, in the explorative phase; these numbers were 39 and 34 in the validation phase. In both analyses, 11 proteins were more abundant in non-relapsing HL (e.g., angiotensinogen, serum paraoxonase/arylesterase 1, transthyretin), including two previously identified by difference gel electrophoresis (antithrombin III and α-1-antitrypsin); seven proteins were more abundant in relapsing HL (e.g., fibronectin and thrombospondin-1), including two previously identified proteins (fibrinogen β and γ chains). The differentially abundant proteins participated in numerous biological processes, which were manually grouped into 10 biological classes and 11 biological regulatory subclasses. The biological class Lipid metabolism, and its regulatory subclass, included angiotensinogen and serum paraoxonase/arylesterase 1 (more abundant in non-relapsing HL). The biological classes Immune system and Cell and extracellular matrix architecture included fibronectin and thrombospondin-1 (more abundant in relapsing HL). These findings deepen our understanding of the molecular scenario underlying responses to therapy and provide new evidence about these proteins as possible biomarkers of relapse in pediatric HL.
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10
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Bellei E, Rustichelli C, Bergamini S, Monari E, Baraldi C, Lo Castro F, Tomasi A, Ferrari A. Proteomic serum profile in menstrual-related and post menopause migraine. J Pharm Biomed Anal 2020; 184:113165. [PMID: 32113117 DOI: 10.1016/j.jpba.2020.113165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/06/2020] [Accepted: 02/09/2020] [Indexed: 12/22/2022]
Abstract
The aim of this pilot study was to analyze the serum proteomic profile of women suffering from menstrual-related migraine (MM group, n = 15) and migraine in post-menopause (PM group, n = 15) in comparison with non-headache control females (C group, n = 15). Serum samples were subjected to two-dimensional gel electrophoresis (2-DE) followed by mass spectrometry (MS) analysis for protein identification. Based on 2D-gel maps and PDQuest 2-D software, 13 differentially expressed spots, corresponding to 12 unique proteins identified by Liquid Chromatography-Electrospray Ionization-Quadrupole-Time of Flight/tandem mass spectrometry (LC-ESI-QToF-MS/MS), were detected in the MM and PM groups vs C group. Five inflammatory and regulatory of vascular integrity proteins (prothrombin, serum amyloid P-component, Ig kappa chain C region, apolipoprotein A-I, serum amyloid A-4 protein) were found deregulated in both MM and PM groups compared to C group; MM group showed the upregulation of other inflammatory protein fragments (inter-alpha-trypsin inhibitor heavy chain H4 and complement C4-A) compared to C group; PM group, in comparison with C group, displayed a noteworthy upregulation of transthyretin and other deregulated proteins (tetranectin, alpha-1-antitrypsin, haptoglobin, apolipoprotein A-IV) playing a role in anti-inflammatory and reparative processes. In conclusion, proteomic analysis was able to reveal differences in protein expression between migraine sufferers and non-headache women; as in other neurological diseases characterized by neuroinflammation, the serum proteome of migraine women presents an abundance of proteins indicative of cellular damage, oxidative stress and inflammation. This relevant inflammatory status, if confirmed in larger series, could represent a target for menstrual-related migraine treatment.
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Affiliation(s)
- Elisa Bellei
- Department of Surgery, Medicine, Dentistry and Morphological Sciences with Transplant Surgery, Oncology and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, via del Pozzo, 71, 41124 Modena, Italy
| | - Cecilia Rustichelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi, 103, 41125 Modena, Italy.
| | - Stefania Bergamini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences with Transplant Surgery, Oncology and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, via del Pozzo, 71, 41124 Modena, Italy
| | - Emanuela Monari
- Department of Surgery, Medicine, Dentistry and Morphological Sciences with Transplant Surgery, Oncology and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, via del Pozzo, 71, 41124 Modena, Italy
| | - Carlo Baraldi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124 Modena, Italy
| | - Flavia Lo Castro
- School of Pharmacology and Clinical Toxicology, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124 Modena, Italy
| | - Aldo Tomasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences with Transplant Surgery, Oncology and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, via del Pozzo, 71, 41124 Modena, Italy
| | - Anna Ferrari
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124 Modena, Italy
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11
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kisluk J, Michalska-Falkowska A, Reszec J, Sierko E, Nikliński J. Identification of protein changes in the blood plasma of lung cancer patients subjected to chemotherapy using a 2D-DIGE approach. PLoS One 2019; 14:e0223840. [PMID: 31622403 PMCID: PMC6797170 DOI: 10.1371/journal.pone.0223840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
A comparative analysis of blood samples (depleted of albumin and IgG) obtained from lung cancer patients before chemotherapy versus after a second cycle of chemotherapy was performed using two-dimensional difference gel electrophoresis (2D-DIGE). The control group consisted of eight patients with non-cancerous lung diseases, and the experimental group consisted of four adenocarcinoma (ADC) and four squamous cell carcinoma (SCC) patients. Analyses of gels revealed significant changes in proteins and/or their proteoforms between control patients and lung cancer patients, both before and after a second cycle of chemotherapy. Most of these proteins were related to inflammation, including acute phase proteins (APPs) such as forms of haptoglobin and transferrin, complement component C3, and clusterin. The variable expression of APPs can potentially be used for profiling lung cancer. The greatest changes observed after chemotherapy were in transferrin and serotransferrin, which likely reflect disturbances in iron turnover after chemotherapy-induced anaemia. Significant changes in plasma proteins between ADC and SCC patients were also revealed, suggesting use of plasma vitronectin as a potential marker of SCC.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | | | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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12
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Classical Hodgkin's Lymphoma in the Era of Immune Checkpoint Inhibition. J Clin Med 2019; 8:jcm8101596. [PMID: 31581738 PMCID: PMC6832444 DOI: 10.3390/jcm8101596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/12/2019] [Accepted: 09/23/2019] [Indexed: 12/16/2022] Open
Abstract
The ligation of programmed cell death 1 (PD-1) with programmed cell death ligand PD-L activates the immune checkpoint leading to T-cell dysfunction, exhaustion, and tolerance, especially in Hodgkin lymphoma (HL) where the PD-L/ Janus kinase (Jak) signaling was frequently found altered. Anti-PD-1 or anti-PD-L1 monoclonal antibodies can reverse this immune checkpoint, releasing the brake on T-cell responses. The characterization of the mechanisms regulating both the expression of PD-1 and PD-L and their function(s) in HL is ongoing. We provide in this review the recent findings focused on this aim with special attention on the major research topics, such as adverse events and resistance to PD-1–PD-L1 inhibitor treatment, together with a part about angiogenesis, extracellular vesicles, and microbiome in HL pathogenesis.
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