1
|
Mittenbühler MJ, Jedrychowski MP, Van Vranken JG, Sprenger HG, Wilensky S, Dumesic PA, Sun Y, Tartaglia A, Bogoslavski D, A M, Xiao H, Blackmore KA, Reddy A, Gygi SP, Chouchani ET, Spiegelman BM. Isolation of extracellular fluids reveals novel secreted bioactive proteins from muscle and fat tissues. Cell Metab 2023; 35:535-549.e7. [PMID: 36681077 PMCID: PMC9998376 DOI: 10.1016/j.cmet.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/24/2022] [Accepted: 12/21/2022] [Indexed: 01/21/2023]
Abstract
Proteins are secreted from cells to send information to neighboring cells or distant tissues. Because of the highly integrated nature of energy balance systems, there has been particular interest in myokines and adipokines. These are challenging to study through proteomics because serum or plasma contains highly abundant proteins that limit the detection of proteins with lower abundance. We show here that extracellular fluid (EF) from muscle and fat tissues of mice shows a different protein composition than either serum or tissues. Mass spectrometry analyses of EFs from mice with physiological perturbations, like exercise or cold exposure, allowed the quantification of many potentially novel myokines and adipokines. Using this approach, we identify prosaposin as a secreted product of muscle and fat. Prosaposin expression stimulates thermogenic gene expression and induces mitochondrial respiration in primary fat cells. These studies together illustrate the utility of EF isolation as a discovery tool for adipokines and myokines.
Collapse
Affiliation(s)
- Melanie J Mittenbühler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark P Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Hans-Georg Sprenger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Wilensky
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Phillip A Dumesic
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yizhi Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Tartaglia
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dina Bogoslavski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mu A
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Blackmore
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anita Reddy
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
2
|
Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically fluorescence two-dimensional difference gel electrophoresis (2D-DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, ProteoMiner, is the focus of this chapter. The ProteoMiner technology utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppresses the concentration of high-abundance proteins in subsequent analysis.
Collapse
Affiliation(s)
- Sandra Murphy
- Charles River Laboratories, Saffron Walden, Essex, United Kingdom
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
3
|
He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
Collapse
Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
4
|
King CD, Kapp KL, Arul AB, Choi MJ, Robinson RAS. Advancements in automation for plasma proteomics sample preparation. Mol Omics 2022; 18:828-839. [PMID: 36048090 PMCID: PMC9879274 DOI: 10.1039/d2mo00122e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Automation is necessary to increase sample processing throughput for large-scale clinical analyses. Replacement of manual pipettes with robotic liquid handler systems is especially helpful in processing blood-based samples, such as plasma and serum. These samples are very heterogenous, and protein expression can vary greatly from sample-to-sample, even for healthy controls. Detection of true biological changes requires that variation from sample preparation steps and downstream analytical detection methods, such as mass spectrometry, remains low. In this mini-review, we discuss plasma proteomics protocols and the benefits of automation towards enabling detection of low abundant proteins and providing low sample error and increased sample throughput. This discussion includes considerations for automation of major sample depletion and/or enrichment strategies for plasma toward mass spectrometry detection.
Collapse
Affiliation(s)
- Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
| |
Collapse
|
5
|
Almeida N, Rodriguez J, Pla Parada I, Perez-Riverol Y, Woldmar N, Kim Y, Oskolas H, Betancourt L, Valdés JG, Sahlin KB, Pizzatti L, Szasz AM, Kárpáti S, Appelqvist R, Malm J, B. Domont G, C. S. Nogueira F, Marko-Varga G, Sanchez A. Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database. Cancers (Basel) 2021; 13:6224. [PMID: 34944842 PMCID: PMC8699267 DOI: 10.3390/cancers13246224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022] Open
Abstract
Plasma analysis by mass spectrometry-based proteomics remains a challenge due to its large dynamic range of 10 orders in magnitude. We created a methodology for protein identification known as Wise MS Transfer (WiMT). Melanoma plasma samples from biobank archives were directly analyzed using simple sample preparation. WiMT is based on MS1 features between several MS runs together with custom protein databases for ID generation. This entails a multi-level dynamic protein database with different immunodepletion strategies by applying single-shot proteomics. The highest number of melanoma plasma proteins from undepleted and unfractionated plasma was reported, mapping >1200 proteins from >10,000 protein sequences with confirmed significance scoring. Of these, more than 660 proteins were annotated by WiMT from the resulting ~5800 protein sequences. We could verify 4000 proteins by MS1t analysis from HeLA extracts. The WiMT platform provided an output in which 12 previously well-known candidate markers were identified. We also identified low-abundant proteins with functions related to (i) cell signaling, (ii) immune system regulators, and (iii) proteins regulating folding, sorting, and degradation, as well as (iv) vesicular transport proteins. WiMT holds the potential for use in large-scale screening studies with simple sample preparation, and can lead to the discovery of novel proteins with key melanoma disease functions.
Collapse
Affiliation(s)
- Natália Almeida
- Laboratory of Proteomics/LADETEC, Universidade Federal Do Rio de Janeiro, Rio de Janeiro 21941-598, Brazil;
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC D13, 22184 Lund, Sweden; (N.W.); (K.B.S.); (G.M.-V.)
| | - Jimmy Rodriguez
- Division of Chemistry I, Department of Biochemistry and Biophysics, Karolinska Institute, 17165 Stockholm, Sweden;
| | - Indira Pla Parada
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 20502 Malmö, Sweden; (I.P.P.); (J.M.)
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;
| | - Nicole Woldmar
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC D13, 22184 Lund, Sweden; (N.W.); (K.B.S.); (G.M.-V.)
- Laboratory of Molecular Biology and Blood Proteomics—LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-598, Brazil;
| | - Yonghyo Kim
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea;
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 22185 Lund, Sweden; (H.O.); (L.B.); (J.G.V.); (R.A.)
| | - Henriett Oskolas
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 22185 Lund, Sweden; (H.O.); (L.B.); (J.G.V.); (R.A.)
| | - Lazaro Betancourt
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 22185 Lund, Sweden; (H.O.); (L.B.); (J.G.V.); (R.A.)
| | - Jeovanis Gil Valdés
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 22185 Lund, Sweden; (H.O.); (L.B.); (J.G.V.); (R.A.)
| | - K. Barbara Sahlin
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC D13, 22184 Lund, Sweden; (N.W.); (K.B.S.); (G.M.-V.)
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 20502 Malmö, Sweden; (I.P.P.); (J.M.)
| | - Luciana Pizzatti
- Laboratory of Molecular Biology and Blood Proteomics—LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-598, Brazil;
| | | | - Sarolta Kárpáti
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary;
| | - Roger Appelqvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 22185 Lund, Sweden; (H.O.); (L.B.); (J.G.V.); (R.A.)
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 20502 Malmö, Sweden; (I.P.P.); (J.M.)
| | - Gilberto B. Domont
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Fábio C. S. Nogueira
- Laboratory of Proteomics/LADETEC, Universidade Federal Do Rio de Janeiro, Rio de Janeiro 21941-598, Brazil;
- Proteomics Unit, Institute of Chemistry, Universidade Federal Do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC D13, 22184 Lund, Sweden; (N.W.); (K.B.S.); (G.M.-V.)
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo 160-0023, Japan
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 20502 Malmö, Sweden; (I.P.P.); (J.M.)
| |
Collapse
|
6
|
Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
Collapse
Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| |
Collapse
|
7
|
Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery. Bioanalysis 2019; 11:1799-1812. [PMID: 31617391 DOI: 10.4155/bio-2019-0145] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
Collapse
|
8
|
Enriching for Low-Abundance Serum Proteins Using ProteoMiner™ and Protein-Level HPLC. Methods Mol Biol 2019. [PMID: 31364045 DOI: 10.1007/978-1-4939-9597-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The mammalian immune system acts to protect the body from harmful diseases ranging from cancer to infection. Differentially expressed proteins as a result of such an immune response can shed light on the mechanism of disease or serve as biomarkers. These biomarkers can be used in a diagnostic capacity or as correlates of protection following vaccination. Protein levels in the circulatory system are considered representative of the system as a whole, making serum an ideal matrix for surveilling immune responses. However, serum proteomics using mass spectrometry is extremely challenging due to the complexity of the matrix and the dynamic range of protein concentration. This chapter will describe two orthogonal enrichment strategies that can be used sequentially or in isolation to improve the identification of low-abundance serum proteins by mass spectrometry.
Collapse
|
9
|
Jankovska E, Svitek M, Holada K, Petrak J. Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin Proteomics 2019; 16:9. [PMID: 30890900 PMCID: PMC6390343 DOI: 10.1186/s12014-019-9229-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the central nervous system. This makes human CSF an attractive source of potential biomarkers for neurologic diseases. Similarly to blood plasma, proteomic analysis of CSF is complicated by a high dynamic range of individual protein concentrations and by the presence of several highly abundant proteins. To deal with the abundant human CSF proteins, methods developed for blood plasma/serum are routinely used. Multiple affinity removal systems and protein enrichment of less abundant proteins using a combinatorial peptide ligand library are among the most frequent approaches. However, their relative impact on CSF proteome coverage has never been evaluated side-by-side in a single study. Therefore, we explored the effect of CSF depletion using MARS 14 cartridge and ProteoMiner ligand library on the number of CSF proteins identified in subsequent LC–MS/MS analysis. LC–MS/MS analysis of crude (non-treated) CSF provided roughly 500 identified proteins. Depletion of CSF by MARS 14 cartridge increased the number of identifications to nearly 800, while treatment of CSF using ProteoMiner enabled identification of 600 proteins. To explore the potential losses of CSF proteins during the depletion process, we also analyzed the “waste” fractions generated by both methods, i.e., proteins retained by the MARS 14 cartridge, and the molecules present in the flow-through fraction from ProteoMiner. More than 250 proteins were bound to MARS 14 cartridge, 100 of those were not identified in the corresponding depleted CSF. Similarly, analysis of the waste fraction in ProteoMiner workflow provided almost 70 unique proteins not found in the CSF depleted by the ligand library. Both depletion strategies significantly increased the number of identified CSF proteins compared to crude CSF. However, MARS 14 depletion provided a markedly higher number of identified proteins (773) compared to ProteoMiner (611). Further, we showed that CSF proteins are lost due to co-depletion (MARS 14) or exclusion (ProteoMiner) during the depletion process. This suggests that the routinely discarded “waste” fractions contain proteins of potential interest and should be included in CSF biomarker studies.
Collapse
Affiliation(s)
- Eliska Jankovska
- 1BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marek Svitek
- 2Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University, Prague, Czech Republic.,3General University Hospital, Prague, Czech Republic
| | - Karel Holada
- 4Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jiri Petrak
- 1BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
| |
Collapse
|
10
|
Repetto O, Mussolin L, Elia C, Martina L, Bianchi M, Buffardi S, Sala A, Burnelli R, Mascarin M, De Re V. Proteomic Identification of Plasma Biomarkers in Children and Adolescents with Recurrent Hodgkin Lymphoma. J Cancer 2018; 9:4650-4658. [PMID: 30588249 PMCID: PMC6299395 DOI: 10.7150/jca.27560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/26/2018] [Indexed: 12/13/2022] Open
Abstract
The treatment of paediatric Hodgkin lymphoma (HL) has steadily improved over the years, so that 10- years survival exceed 80%. The purpose of this study was to identify prognostic markers for relapsed HL that might contribute to optimize therapeutic approaches. To this aim we retrospectively analysed differential protein expression profiles obtained from plasma of children/adolescents with HL (age ranging from 10 to 18 years) collected at diagnosis. We examined the protein profiles of 15 HL relapsed (R) patients compared with 14 HL not relapsed (NR) patients treated with the same LH-2004 protocol. Two dimensional difference in gel electrophoresis (2D-DIGE) revealed significant differences (fold change > 1.5; Student's T-test p<0.01) between R and NR patients in 10 proteins: α-1-antitrypsin chain a, apolipoprotein A-IV precursor; inter-α-trypsin inhibitor heavy chain; antithrombin-III; vitronectin; fibrinogen α, β and γ chains, complement C3, and ceruloplasmin. An up-regulation of fibrinogen α (spots 78, 196, 230, 234, 239) and β (spots 98, 291, 296, 300) chains together with a lower level of α-1-antitrypsin (spots 255, 264, 266, 272, 273) were found in R patients, and this difference was validated by immunoblotting. The functional role(s) of these proteins in the coagulation and inflammation associated with paediatric/adolescent HL progression and relapse deserves further investigations.
Collapse
Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Lara Mussolin
- Clinic of Pediatric Haemato-Oncology, Department of Women's and Children's Health, University of Padua, Padua, Institute of Paediatric Research - Fondazione Città della Speranza, Padua, Italy
| | - Caterina Elia
- Pediatric Radioterapy Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Lia Martina
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Maurizio Bianchi
- Pediatric Onco-Hematology and Stem Cell Transplant Division, City of Health and Science, Regina Margherita Children's Hospital, Turin, Italy
| | - Salvatore Buffardi
- Paediatric Haemato-Oncology department, Santobono-Pausilipon Children's Hospital, Napoli, Italy
| | - Alessandra Sala
- Department of Paediatrics, Ospedale San Gerardo, University of Milano-Bicocca, Fondazione MBBM, Monza, Italy
| | - Roberta Burnelli
- Pediatric Oncology University Hospital, Sant'Anna Hospital, Ferrara, Italy
| | - Maurizio Mascarin
- Pediatric Radioterapy Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| |
Collapse
|
11
|
Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically difference gel electrophoresis (DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, Proteominer, will be the focus of this chapter. The Proteominer technology a utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppressing the concentration of high-abundance proteins in subsequent analysis.
Collapse
|
12
|
Chutipongtanate S, Chatchen S, Svasti J. Plasma prefractionation methods for proteomic analysis and perspectives in clinical applications. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/24/2017] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital; Mahidol University; Salaya Thailand
| | - Supawat Chatchen
- Department of Tropical Pediatrics, Faculty of Tropical Medicine; Mahidol University; Salaya Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry; Chulabhorn Research Institute, Krung Thep Maha Nakhon; Thailand
- Applied Biological Sciences Program; Chulabhorn Graduate Institute; Thailand
| |
Collapse
|