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Son A, Kim W, Lee W, Park J, Kim H. Applicability of selected reaction monitoring for precise screening tests. Expert Rev Proteomics 2024:1-10. [PMID: 38697802 DOI: 10.1080/14789450.2024.2350975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/27/2024] [Indexed: 05/05/2024]
Abstract
INTRODUCTION The proactive identification of diseases through screening tests has long been endorsed as a means to preempt symptomatic onset. However, such screening endeavors are fraught with complications, such as diagnostic inaccuracies, procedural risks, and patient unease during examinations. These challenges are amplified when screenings for multiple diseases are administered concurrently. Selected Reaction Monitoring (SRM) offers a unique advantage, allowing for the high-throughput quantification of hundreds of analytes with minimal interferences. AREAS COVERED Our research posits that SRM-based assays, traditionally tailored for single-disease biomarker profiling, can be repurposed for multi-disease screening. This innovative approach has the potential to substantially alleviate time, labor, and cost demands on healthcare systems and patients alike. Nonetheless, there are formidable methodological hurdles to overcome. These include difficulties in detecting low-abundance proteins and the risk of model overfitting due to the multiple functionalities of single proteins across different disease spectrums - issues especially pertinent in blood-based assays where detection sensitivity is constrained. As we move forward, technological strides in sample preparation, online extraction, throughput, and automation are expected to ameliorate these limitations. EXPERT OPINION The maturation of mass spectrometry's integration into clinical laboratories appears imminent, positioning it as an invaluable asset for delivering highly sensitive, reproducible, and precise diagnostic results.
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Affiliation(s)
- Ahrum Son
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Woojin Kim
- Department of Bio-AI convergence Chungnam National University,Daejeon, South Korea
| | - Wonseok Lee
- Department of Bio-AI convergence Chungnam National University,Daejeon, South Korea
| | - Jongham Park
- Department of Bio-AI convergence Chungnam National University,Daejeon, South Korea
| | - Hyunsoo Kim
- Department of Bio-AI convergence Chungnam National University,Daejeon, South Korea
- Department of Convergent Bioscience and Informatics, Chungnam National University, Daejeon, Republic of Korea
- SCICS, Daejeon, Republic of Korea
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Lépine M, Robert MC, Sleno L. Discovery and Verification of Sjögren's Syndrome Protein Biomarkers in Tears by Targeted LC-MRM. J Proteome Res 2024. [PMID: 38682820 DOI: 10.1021/acs.jproteome.4c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Sjögren's syndrome (SS) is an autoimmune rheumatic disorder characterized by exocrine gland dysfunction, mainly from the lacrimal and salivary glands. The disease causes severe aqueous dry eye syndrome (DED) and is associated with high rates of complications, including corneal ulceration, scaring, and perforation. Systemic complications may occur as well as a higher risk of developing lymphoma. Diagnosis of SS-DED is often delayed and difficult to establish. With the aim of discovering biomarkers to help discriminate SS-DED patients, a combination of untargeted and targeted LC-MS/MS analyses were performed on tear samples collected on Schirmer strips and subjected to tryptic digestion. Following the analysis of three cohorts and the development of two targeted LC-sMRM methods for the verification of putative biomarkers found in the first cohort of samples, 64 proteins could be linked to Sjögren's syndrome, in the hopes of helping to confirm diagnoses as well as potentially stratifying the severity of disease in these patients. Proteins that were increased in SS-DED showed activation of the immune system and alterations in homeostasis. Several proteases and protease inhibitors were found to be significantly changing in SS-DED, as well as a consistent decrease in specific proteins known to be secreted by the lacrimal gland.
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Affiliation(s)
- Maggy Lépine
- University of Quebec in Montreal (UQAM), Chemistry Department, PO Box 8888, Downtown Station, Montreal, Quebec H3C 3P8, Canada
- CERMO-FC, Centre d'Excellence de Recherche sur les Maladies Orphelines-Fondation Courtois, 141 Avenue du President Kennedy, Montreal, Quebec H2X 3Y7, Canada
| | - Marie-Claude Robert
- Centre de Recherche du Centre Hospitalier Universitaire de (CR-CHUM), Ophthalmology Department, 900 Saint Denis Street, Montreal, Quebec H2X 0A9, Canada
- CERMO-FC, Centre d'Excellence de Recherche sur les Maladies Orphelines-Fondation Courtois, 141 Avenue du President Kennedy, Montreal, Quebec H2X 3Y7, Canada
| | - Lekha Sleno
- University of Quebec in Montreal (UQAM), Chemistry Department, PO Box 8888, Downtown Station, Montreal, Quebec H3C 3P8, Canada
- CERMO-FC, Centre d'Excellence de Recherche sur les Maladies Orphelines-Fondation Courtois, 141 Avenue du President Kennedy, Montreal, Quebec H2X 3Y7, Canada
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Procopio N, Bonicelli A. From flesh to bones: Multi-omics approaches in forensic science. Proteomics 2024:e2200335. [PMID: 38683823 DOI: 10.1002/pmic.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.
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Affiliation(s)
- Noemi Procopio
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
| | - Andrea Bonicelli
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
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Ohno R, Mainka M, Kirchhoff R, Hartung NM, Schebb NH. Sterol Derivatives Specifically Increase Anti-Inflammatory Oxylipin Formation in M2-like Macrophages by LXR-Mediated Induction of 15-LOX. Molecules 2024; 29:1745. [PMID: 38675565 PMCID: PMC11052137 DOI: 10.3390/molecules29081745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/29/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The understanding of the role of LXR in the regulation of macrophages during inflammation is emerging. Here, we show that LXR agonist T09 specifically increases 15-LOX abundance in primary human M2 macrophages. In time- and dose-dependent incubations with T09, an increase of 3-fold for ALOX15 and up to 15-fold for 15-LOX-derived oxylipins was observed. In addition, LXR activation has no or moderate effects on the abundance of macrophage marker proteins such as TLR2, TLR4, PPARγ, and IL-1RII, as well as surface markers (CD14, CD86, and CD163). Stimulation of M2-like macrophages with FXR and RXR agonists leads to moderate ALOX15 induction, probably due to side activity on LXR. Finally, desmosterol, 24(S),25-Ep cholesterol and 22(R)-OH cholesterol were identified as potent endogenous LXR ligands leading to an ALOX15 induction. LXR-mediated ALOX15 regulation is a new link between the two lipid mediator classes sterols, and oxylipins, possibly being an important tool in inflammatory regulation through anti-inflammatory oxylipins.
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Affiliation(s)
| | | | | | | | - Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119 Wuppertal, Germany
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Lee MJ, Cho JY, Bae S, Jung HS, Kang CM, Kim SH, Choi HJ, Lee CK, Kim H, Jo D, Paik YK. Inhibition of the Alternative Complement Pathway May Cause Secretion of Factor B, Enabling an Early Detection of Pancreatic Cancer. J Proteome Res 2024; 23:985-998. [PMID: 38306169 DOI: 10.1021/acs.jproteome.3c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
This study aims to elucidate the cellular mechanisms behind the secretion of complement factor B (CFB), known for its dual roles as an early biomarker for pancreatic ductal adenocarcinoma (PDAC) and as the initial substrate for the alternative complement pathway (ACP). Using parallel reaction monitoring analysis, we confirmed a consistent ∼2-fold increase in CFB expression in PDAC patients compared with that in both healthy donors (HD) and chronic pancreatitis (CP) patients. Elevated ACP activity was observed in CP and other benign conditions compared with that in HD and PDAC patients, suggesting a functional link between ACP and PDAC. Protein-protein interaction analyses involving key complement proteins and their regulatory factors were conducted using blood samples from PDAC patients and cultured cell lines. Our findings revealed a complex control system governing the ACP and its regulatory factors, including Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation, adrenomedullin (AM), and complement factor H (CFH). Particularly, AM emerged as a crucial player in CFB secretion, activating CFH and promoting its predominant binding to C3b over CFB. Mechanistically, our data suggest that the KRAS mutation stimulates AM expression, enhancing CFH activity in the fluid phase through binding. This heightened AM-CFH interaction conferred greater affinity for C3b over CFB, potentially suppressing the ACP cascade. This sequence of events likely culminated in the preferential release of ductal CFB into plasma during the early stages of PDAC. (Data set ID PXD047043.).
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Affiliation(s)
- Min Jung Lee
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
| | - Sumi Bae
- JW BioScience Corp., 38 Gwacheon-daero, Gwacheon-si, Gyeonggi-do 13840, South Korea
| | - Hye Soo Jung
- JW BioScience Corp., 38 Gwacheon-daero, Gwacheon-si, Gyeonggi-do 13840, South Korea
| | - Chang Moo Kang
- Department of Surgery, Division of HBP Surgery, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sung Hyun Kim
- Department of Surgery, Division of HBP Surgery, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hye Jin Choi
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Daewoong Jo
- Cellivery R&D Institute, Cellivery Therapeutics, Inc., Seoul 03929, Korea
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
- Cellivery R&D Institute, Cellivery Therapeutics, Inc., Seoul 03929, Korea
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Shahjahan, Dey JK, Dey SK. Translational bioinformatics approach to combat cardiovascular disease and cancers. Adv Protein Chem Struct Biol 2024; 139:221-261. [PMID: 38448136 DOI: 10.1016/bs.apcsb.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bioinformatics is an interconnected subject of science dealing with diverse fields including biology, chemistry, physics, statistics, mathematics, and computer science as the key fields to answer complicated physiological problems. Key intention of bioinformatics is to store, analyze, organize, and retrieve essential information about genome, proteome, transcriptome, metabolome, as well as organisms to investigate the biological system along with its dynamics, if any. The outcome of bioinformatics depends on the type, quantity, and quality of the raw data provided and the algorithm employed to analyze the same. Despite several approved medicines available, cardiovascular disorders (CVDs) and cancers comprises of the two leading causes of human deaths. Understanding the unknown facts of both these non-communicable disorders is inevitable to discover new pathways, find new drug targets, and eventually newer drugs to combat them successfully. Since, all these goals involve complex investigation and handling of various types of macro- and small- molecules of the human body, bioinformatics plays a key role in such processes. Results from such investigation has direct human application and thus we call this filed as translational bioinformatics. Current book chapter thus deals with diverse scope and applications of this translational bioinformatics to find cure, diagnosis, and understanding the mechanisms of CVDs and cancers. Developing complex yet small or long algorithms to address such problems is very common in translational bioinformatics. Structure-based drug discovery or AI-guided invention of novel antibodies that too with super-high accuracy, speed, and involvement of considerably low amount of investment are some of the astonishing features of the translational bioinformatics and its applications in the fields of CVDs and cancers.
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Affiliation(s)
- Shahjahan
- Laboratory for Structural Biology of Membrane Proteins, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Joy Kumar Dey
- Central Council for Research in Homoeopathy, Ministry of Ayush, Govt. of India, New Delhi, Delhi, India
| | - Sanjay Kumar Dey
- Laboratory for Structural Biology of Membrane Proteins, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
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Fu L, Guldiken N, Remih K, Karl AS, Preisinger C, Strnad P. Serum/Plasma Proteome in Non-Malignant Liver Disease. Int J Mol Sci 2024; 25:2008. [PMID: 38396688 PMCID: PMC10889128 DOI: 10.3390/ijms25042008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The liver is the central metabolic organ and produces 85-90% of the proteins found in plasma. Accordingly, the plasma proteome is an attractive source of liver disease biomarkers that reflects the different cell types present in this organ, as well as the processes such as responses to acute and chronic injury or the formation of an extracellular matrix. In the first part, we summarize the biomarkers routinely used in clinical evaluations and their biological relevance in the different stages of non-malignant liver disease. Later, we describe the current proteomic approaches, including mass spectrometry and affinity-based techniques, that allow a more comprehensive assessment of the liver function but also require complex data processing. The many approaches of analysis and interpretation and their potential caveats are delineated. While these advances hold the promise to transform our understanding of liver diseases and support the development and validation of new liver-related drugs, an interdisciplinary collaboration is needed.
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Affiliation(s)
- Lei Fu
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Nurdan Guldiken
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Katharina Remih
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Anna Sophie Karl
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany;
| | - Pavel Strnad
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
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8
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Tu KJ, Roy SK, Keepers Z, Gartia MR, Shukla HD, Biswal NC. Docetaxel radiosensitizes castration-resistant prostate cancer by downregulating CAV-1. Int J Radiat Biol 2024; 100:256-267. [PMID: 37747697 DOI: 10.1080/09553002.2023.2263553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PURPOSE Docetaxel (DXL), a noted radiosensitizer, is one of the few chemotherapy drugs approved for castration-resistant prostate cancer (CRPC), though only a fraction of CRPCs respond to it. CAV-1, a critical regulator of radioresistance, has been known to modulate DXL and radiation effects. Combining DXL with radiotherapy may create a synergistic anticancer effect through CAV-1 and improve CRPC patients' response to therapy. Here, we investigate the effectiveness and molecular characteristics of DXL and radiation combination therapy in vitro. MATERIALS AND METHODS We used live/dead assays to determine the IC50 of DXL for PC3, DU-145, and TRAMP-C1 cells. Colony formation assay was used to determine the radioresponse of the same cells treated with radiation with/without IC50 DXL (4, 8, and 12 Gy). We performed gene expression analysis on public transcriptomic data collected from human-derived prostate cancer cell lines (C4-2, PC3, DU-145, and LNCaP) treated with DXL for 8, 16, and 72 hours. Cell cycle arrest and protein expression were assessed using flow cytometry and western blot, respectively. RESULTS Compared to radiation alone, combination therapy with DXL significantly increased CRPC death in PC3 (1.48-fold, p < .0001), DU-145 (1.64-fold, p < .05), and TRAMP-C1 (1.13-fold, p < .05) at 4 Gy of radiation. Gene expression of CRPC treated with DXL revealed downregulated genes related to cell cycle regulation and upregulated genes related to immune activation and oxidative stress. Confirming the results, G2/M cell cycle arrest was significantly increased after treatment with DXL and radiation. CAV-1 protein expression was decreased after DXL treatment in a dose-dependent manner; furthermore, CAV-1 copy number was strongly associated with poor response to therapy in CRPC patients. CONCLUSIONS Our results suggest that DXL sensitizes CRPC cells to radiation by downregulating CAV-1. DXL + radiation combination therapy may be effective at treating CRPC, especially subtypes associated with high CAV-1 expression, and should be studied further.
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Affiliation(s)
- Kevin J Tu
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Sanjit K Roy
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zachery Keepers
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Manas R Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Hem D Shukla
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nrusingh C Biswal
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
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Morretta E, Capuano A, D’Urso G, Voli A, Mozzicafreddo M, Di Gaetano S, Capasso D, Sala M, Scala MC, Campiglia P, Piccialli V, Casapullo A. Identification of Mortalin as the Main Interactor of Mycalin A, a Poly-Brominated C-15 Acetogenin Sponge Metabolite, by MS-Based Proteomics. Mar Drugs 2024; 22:52. [PMID: 38393023 PMCID: PMC10890321 DOI: 10.3390/md22020052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Mycalin A (MA) is a polybrominated C-15 acetogenin isolated from the marine sponge Mycale rotalis. Since this substance displays a strong antiproliferative bioactivity towards some tumour cells, we have now directed our studies towards the elucidation of the MA interactome through functional proteomic approaches, (DARTS and t-LIP-MS). DARTS experiments were performed on Hela cell lysates with the purpose of identifying MA main target protein(s); t-LiP-MS was then applied for an in-depth investigation of the MA-target protein interaction. Both these techniques exploit limited proteolysis coupled with MS analysis. To corroborate LiP data, molecular docking studies were performed on the complexes. Finally, biological and SPR analysis were conducted to explore the effect of the binding. Mortalin (GRP75) was identified as the MA's main interactor. This protein belongs to the Hsp70 family and has garnered significant attention due to its involvement in certain forms of cancer. Specifically, its overexpression in cancer cells appears to hinder the pro-apoptotic function of p53, one of its client proteins, because it becomes sequestered in the cytoplasm. Our research, therefore, has been focused on the possibility that MA might prevent this sequestration, promoting the re-localization of p53 to the nucleus and facilitating the apoptosis of tumor cells.
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Affiliation(s)
- Elva Morretta
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Alessandra Capuano
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Italy
| | - Gilda D’Urso
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Antonia Voli
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Italy
| | - Matteo Mozzicafreddo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy;
| | - Domenica Capasso
- Department of Physics, Ettore Pancini, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy;
| | - Marina Sala
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Maria Carmina Scala
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Vincenzo Piccialli
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Agostino Casapullo
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
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Sakson R, Beedgen L, Bernhard P, Alp KM, Lübbehusen N, Röth R, Niesler B, Luzarowski M, Shevchuk O, Mayer MP, Thiel C, Ruppert T. Targeted Proteomics Reveals Quantitative Differences in Low-Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation. Int J Mol Sci 2024; 25:1191. [PMID: 38256263 PMCID: PMC10816918 DOI: 10.3390/ijms25021191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Protein glycosylation is an essential post-translational modification in all domains of life. Its impairment in humans can result in severe diseases named congenital disorders of glycosylation (CDGs). Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging targets in proteomics. We established a multiple reaction monitoring (MRM) assay to comprehensively quantify GTs involved in the processes of N-glycosylation and O- and C-mannosylation in the endoplasmic reticulum. High robustness was achieved by using an enriched membrane protein fraction of isotopically labeled HEK 293T cells as an internal protein standard. The analysis of primary skin fibroblasts from eight CDG type I patients with impaired ALG1, ALG2, and ALG11 genes, respectively, revealed a substantial reduction in the corresponding protein levels. The abundance of the other GTs, however, remained unchanged at the transcript and protein levels, indicating that there is no fail-safe mechanism for the early steps of glycosylation in the endoplasmic reticulum. The established MRM assay was shared with the scientific community via the commonly used open source Skyline software environment, including Skyline Batch for automated data analysis. We demonstrate that another research group could easily reproduce all analysis steps, even while using different LC-MS hardware.
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Affiliation(s)
- Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University, 69120 Heidelberg, Germany
| | - Lars Beedgen
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Patrick Bernhard
- Institute for Surgical Pathology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - K. Merve Alp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nicole Lübbehusen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Ralph Röth
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Beate Niesler
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Marcin Luzarowski
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Olga Shevchuk
- Department of Immunodynamics, Institute of Experimental Immunology and Imaging, University Hospital Essen, 45147 Essen, Germany
| | - Matthias P. Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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11
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Capuano A, D’Urso G, Aliberti M, Ruggiero D, Terracciano S, Festa C, Tosco A, Chini MG, Lauro G, Bifulco G, Casapullo A. Chemoproteomics Reveals USP5 (Ubiquitin Carboxyl-Terminal Hydrolase 5) as Promising Target of the Marine Polyketide Gracilioether A. Mar Drugs 2024; 22:41. [PMID: 38248666 PMCID: PMC10817451 DOI: 10.3390/md22010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Mass spectrometry-based chemical proteomic approaches using limited proteolysis have become a powerful tool for the identification and analysis of the interactions between a small molecule (SM) and its protein target(s). Gracilioether A (GeA) is a polyketide isolated from a marine sponge, for which we aimed to trace the interactome using this strategy. DARTS (Drug Affinity Responsive Target Stability) and t-LiP-MS (targeted-Limited Proteolysis-Mass Spectrometry) represented the main techniques used in this study. DARTS was applied on HeLa cell lysate for the identification of the GeA target proteins, and t-LiP-MS was employed to investigate the protein's regions involved in the binding with GeA. The results were complemented through the use of binding studies using Surface Plasmon Resonance (SPR) and in silico molecular docking experiments. Ubiquitin carboxyl-terminal hydrolase 5 (USP5) was identified as a promising target of GeA, and the interaction profile of the USP5-GeA complex was explained. USP5 is an enzyme involved in the pathway of protein metabolism through the disassembly of the polyubiquitin chains on degraded proteins into ubiquitin monomers. This activity is connected to different cellular functions concerning the maintenance of chromatin structure and receptors and the degradation of abnormal proteins and cancerogenic progression. On this basis, this structural information opens the way to following studies focused on the definition of the biological potential of Gracilioether A and the rational development of novel USP5 inhibitors based on a new structural skeleton.
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Affiliation(s)
- Alessandra Capuano
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | - Gilda D’Urso
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
| | - Michela Aliberti
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | - Dafne Ruggiero
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
| | - Stefania Terracciano
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
| | - Carmen Festa
- Dipartimento di Farmacia, University of Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy;
| | - Alessandra Tosco
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
| | - Maria Giovanna Chini
- Dipartimento di Bioscienze e Territorio, University of Molise, Contrada Fonte Lappone, 86090 Isernia, Italy;
| | - Gianluigi Lauro
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
| | - Agostino Casapullo
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (A.C.); (G.D.); (M.A.); (D.R.); (S.T.); (A.T.); (G.L.); (G.B.)
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12
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Fricker LD. Quantitative Peptidomics: General Considerations. Methods Mol Biol 2024; 2758:89-108. [PMID: 38549010 DOI: 10.1007/978-1-0716-3646-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomics is the detection and identification of the peptides present in a sample, and quantitative peptidomics provides additional information about the amounts of these peptides. It is possible to perform absolute quantitation of peptide levels in which the biological sample is compared to synthetic standards of each peptide. More commonly, relative quantitation is performed to compare peptide levels between two or more samples. Relative quantitation can measure differences between all peptides that are detectable, which can exceed 1000 peptides in a complex sample. In this chapter, various techniques used for quantitative peptidomics are described along with discussion of the advantages and disadvantages of each approach. A guide to selecting the optimal quantitative approach is provided, based on the goals of the experiment and the resources that are available.
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Affiliation(s)
- Lloyd D Fricker
- Departments of Molecular Pharmacology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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13
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Kusebauch U, Lorenzetti APR, Campbell DS, Pan M, Shteynberg D, Kapil C, Midha MK, López García de Lomana A, Baliga NS, Moritz RL. A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS. Sci Data 2023; 10:697. [PMID: 37833331 PMCID: PMC10575869 DOI: 10.1038/s41597-023-02590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).
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Affiliation(s)
- Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | | | - David S Campbell
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Min Pan
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - David Shteynberg
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Charu Kapil
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Mukul K Midha
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Adrián López García de Lomana
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Nitin S Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
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14
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Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB, Zhang B, Labrie M. The Breast Cancer Proteome and Precision Oncology. Cold Spring Harb Perspect Med 2023; 13:a041323. [PMID: 37137501 PMCID: PMC10547392 DOI: 10.1101/cshperspect.a041323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The goal of precision oncology is to translate the molecular features of cancer into predictive and prognostic tests that can be used to individualize treatment leading to improved outcomes and decreased toxicity. Success for this strategy in breast cancer is exemplified by efficacy of trastuzumab in tumors overexpressing ERBB2 and endocrine therapy for tumors that are estrogen receptor positive. However, other effective treatments, including chemotherapy, immune checkpoint inhibitors, and CDK4/6 inhibitors are not associated with strong predictive biomarkers. Proteomics promises another tier of information that, when added to genomic and transcriptomic features (proteogenomics), may create new opportunities to improve both treatment precision and therapeutic hypotheses. Here, we review both mass spectrometry-based and antibody-dependent proteomics as complementary approaches. We highlight how these methods have contributed toward a more complete understanding of breast cancer and describe the potential to guide diagnosis and treatment more accurately.
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Affiliation(s)
- Jonathan T Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hannah Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Matthew V Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xi Li
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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15
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Mendez Q, Driscoll HA, Mirando GR, Acca F, Chapados CD, Jones KS, Weiner M, Li X, Ferguson MR. MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation. J Immunol Methods 2023; 521:113540. [PMID: 37597727 PMCID: PMC10568614 DOI: 10.1016/j.jim.2023.113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.
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Affiliation(s)
- Qiana Mendez
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Holland A Driscoll
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Gregory R Mirando
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Felicity Acca
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Cassandra D Chapados
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Kezzia S Jones
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Michael Weiner
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Xiaofeng Li
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Mary R Ferguson
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
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16
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Miyazaki T, Aoki W, Koike N, Sato T, Ueda M. Application of peptide barcoding to obtain high-affinity anti-PD-1 nanobodies. J Biosci Bioeng 2023; 136:173-181. [PMID: 37487915 DOI: 10.1016/j.jbiosc.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Cancer treatment has been revolutionized by immune checkpoint inhibitors, which regulate immune cell function by blocking the interactions between immune checkpoint molecules and their ligands. The interaction between programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) is a target for immune checkpoint inhibitors. Nanobodies, which are recombinant variable domains of heavy-chain-only antibodies, can replace existing immune checkpoint inhibitors, such as anti-PD-1 or anti-PD-L1 conventional antibodies. However, the screening process for high-affinity nanobodies is laborious and time-consuming. Here, we identified high-affinity anti-PD-1 nanobodies using peptide barcoding, which enabled reliable and efficient screening by distinguishing each nanobody with a peptide barcode that was genetically appended to each nanobody. We prepared a peptide-barcoded nanobody (PBNb) library with thousands of variants. Three high-affinity PBNbs were identified from the PBNb library by quantifying the peptide barcodes derived from high-affinity PBNbs. Furthermore, these three PBNbs neutralized the interaction between PD-1 and PD-L1. Our results demonstrate the utility of peptide barcoding and the resulting nanobodies can be used as experimental tools and antitumor agents.
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Affiliation(s)
- Takumi Miyazaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto 600-8813, Japan.
| | - Naoki Koike
- TechnoPro, Inc. TechnoPro R&D, Company, Tokyo 106-6135, Japan
| | - Toshiko Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto 600-8813, Japan
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17
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Lépine M, Zambito O, Sleno L. Targeted Workflow Investigating Variations in the Tear Proteome by Liquid Chromatography Tandem Mass Spectrometry. ACS Omega 2023; 8:31168-31177. [PMID: 37663498 PMCID: PMC10468840 DOI: 10.1021/acsomega.3c03186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023]
Abstract
Proteins in tears have an important role in eye health and have been shown as a promising source of disease biomarkers. The goal of this study was to develop a robust, sensitive, and targeted method for profiling tear proteins to examine the variability within a group of healthy volunteers over three days. Inter-individual and inter-day variabilities were examined to contribute to understanding the normal variations in the tear proteome, as well as to establish which proteins may be better candidates as eventual biomarkers of specific diseases. Tear samples collected on Schirmer strips were subjected to bottom-up proteomics, and resulting peptides were analyzed using an optimized targeted method measuring 226 proteins by liquid chromatography-scheduled multiple reaction monitoring. This method was developed using an in-house database of identified proteins from tears compiled from high-resolution data-dependent liquid chromatography tandem mass spectrometry data. The measurement of unique peptide signals can help better understand the dynamics of each of these proteins in tears. Some interesting trends were seen in specific pathways or protein classes, including higher variabilities for those involved in glycolysis, glutathione metabolism, and cytoskeleton proteins and lower variation for those involving the degradation of the extracellular matrix. The overall aim of this study was to contribute to the field of tear proteomics with the development of a novel and targeted method that is highly amenable to the clinical laboratory using high flow LC and commonly used triple quadrupole mass spectrometry while ensuring that protein quantitation was reported based on unique peptides for each protein and robust peak areas with data normalization. These results report on variabilities on over 200 proteins that are robustly detected in tear samples from healthy volunteers with a simple sample preparation procedure.
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Affiliation(s)
- Maggy Lépine
- Chemistry Department, Université du Québec à Montréal, PO Box 8888 Downtown Station, Montreal, Quebec H3C 3P8, Canada
| | - Oriana Zambito
- Chemistry Department, Université du Québec à Montréal, PO Box 8888 Downtown Station, Montreal, Quebec H3C 3P8, Canada
| | - Lekha Sleno
- Chemistry Department, Université du Québec à Montréal, PO Box 8888 Downtown Station, Montreal, Quebec H3C 3P8, Canada
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18
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Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. Mass Spectrom Rev 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
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19
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Mehta S, Bernt M, Chambers M, Fahrner M, Föll MC, Gruening B, Horro C, Johnson JE, Loux V, Rajczewski AT, Schilling O, Vandenbrouck Y, Gustafsson OJR, Thang WCM, Hyde C, Price G, Jagtap PD, Griffin TJ. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics 2023; 20:251-266. [PMID: 37787106 DOI: 10.1080/14789450.2023.2265062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 10/04/2023]
Abstract
INTRODUCTION Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting the analysis requirements of increasingly complex MS-based proteomic data and associated multi-omic data are critically needed. These requirements included availability of software that would span diverse types of analyses, scalability for large-scale, compute-intensive applications, and mechanisms to ease adoption of the software. AREAS COVERED The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses. EXPERT OPINION The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.
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Affiliation(s)
- Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Matthias Bernt
- Helmholtz Centre for Environmental Research - UFZ, Department Computational Biology, Leipzig, Germany
| | | | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Christine Föll
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Bjoern Gruening
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Carlos Horro
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Andrew T Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - W C Mike Thang
- Queensland Cyber Infrastructure Foundation (QCIF), Australia
- Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Cameron Hyde
- Queensland Cyber Infrastructure Foundation (QCIF), Australia
- Sippy Downs, University of the Sunshine Coast, Australia
| | - Gareth Price
- Queensland Cyber Infrastructure Foundation (QCIF), Australia
- Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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20
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Yildiz P, Ozcan S. A single protein to multiple peptides: Investigation of protein-peptide correlations using targeted alpha-2-macroglobulin analysis. Talanta 2023; 265:124878. [PMID: 37392709 DOI: 10.1016/j.talanta.2023.124878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/30/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023]
Abstract
Recent advances in proteomics technologies have enabled the analysis of thousands of proteins in a high-throughput manner. Mass spectrometry (MS) based proteomics uses a peptide-centric approach where biological samples undergo specific proteolytic digestion and then only unique peptides are used for protein identification and quantification. Considering the fact that a single protein may have multiple unique peptides and a number of different forms, it becomes essential to understand dynamic protein-peptide relationships to ensure robust and reliable peptide-centric protein analysis. In this study, we investigated the correlation between protein concentration and corresponding unique peptide responses under a conventional proteolytic digestion condition. Protein-peptide correlation, digestion efficiency, matrix-effect, and concentration-effect were evaluated. Twelve unique peptides of alpha-2-macroglobulin (A2MG) were monitored using a targeted MS approach to acquire insights into protein-peptide dynamics. Although the peptide responses were reproducible between replicates, protein-peptide correlation was moderate in protein standards and low in complex matrices. The results suggest that reproducible peptide signal could be misleading in clinical studies and a peptide selection could dramatically change the outcome at protein level. This is the first study investigating quantitative protein-peptide correlations in biological samples using all unique peptides representing the same protein and opens a discussion on peptide-based proteomics.
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Affiliation(s)
- Pelin Yildiz
- Department of Chemistry, Middle East Technical University (METU), 06800, Ankara, Turkiye; Nanografi Nanotechnology Co, Middle East Technical University (METU) Technopolis, 06531, Ankara, Turkiye
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University (METU), 06800, Ankara, Turkiye; Cancer Systems Biology Laboratory (CanSyL), Middle East Technical University (METU), 06800, Ankara, Turkiye.
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21
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Bai JPF, Yu LR. Modeling Clinical Phenotype Variability: Consideration of Genomic Variations, Computational Methods, and Quantitative Proteomics. J Pharm Sci 2023; 112:904-908. [PMID: 36279954 DOI: 10.1016/j.xphs.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
Advances in biomedical and computer technologies have presented the modeling community the opportunity for mechanistically modeling and simulating the variability in a disease phenotype or in a drug response. The capability to quantify response variability can inform a drug development program. Quantitative systems pharmacology scientists have published various computational approaches for creating virtual patient populations (VPops) to model and simulate drug response variability. Genomic variations can impact disease characteristics and drug exposure and response. Quantitative proteomics technologies are increasingly used to facilitate drug discovery and development and inform patient care. Incorporating variations in genomics and quantitative proteomics may potentially inform creation of VPops to model and simulate virtual patient trials, and may help account for, in a predictive manner, phenotypic variations observed clinically.
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Affiliation(s)
- Jane P F Bai
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA.
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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22
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Abstract
In targeted proteomics experiments, selecting the appropriate proteotypic peptides as surrogate for the target protein is a crucial pre-acquisition step. This step is largely a bioinformatics exercise that involves integrating information on the peptides and proteins and using various software tools and knowledgebases. We present here a few resources that automate and simplify the selection process to a great degree. These tools and knowledgebases were developed primarily to streamline targeted proteomics assay development and include PeptidePicker, PeptidePickerDB, MRMAssayDB, MouseQuaPro, and PeptideTracker. We have used these tools to develop and document thousands of targeted proteomics assays, many of them for plasma proteins with focus on human and mouse. An important aspect in all these resources is the integrative approach on which they are based. Using these tools in the first steps of designing a singleplexed or multiplexed targeted proteomic experiment can reduce the necessary experimental steps tremendously. All the tools and knowledgebases we describe here are Web-based and freely accessible so scientists can query the information conveniently from the browser. This chapter provides an overview of these software tools and knowledgebases, their content, and how to use them for targeted plasma proteomics. We further demonstrate how to use them with the results of the HUPO Human Plasma Proteome Project to produce a new database of 3.8 k targeted assays for known human plasma proteins. Upon experimental validation, these assays should help in the further quantitative characterizing of the plasma proteome.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, ZA, Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada. .,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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23
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Pauletti BA, Granato DC, M Carnielli C, Câmara GA, Normando AGC, Telles GP, Leme AFP. Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics. J Proteome Res 2023; 22:539-545. [PMID: 36480281 DOI: 10.1021/acs.jproteome.2c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The selection of a suitable proteotypic peptide remains a challenge for designing a targeted quantitative proteomics assay. Although the criteria are well-established in the literature, the selection of these peptides is often performed in a subjective and time-consuming manner. Here, we have developed a practical and semiautomated workflow implemented in an open-source program named Typic. Typic is designed to run in a command line and a graphical interface to help selecting a list of proteotypic peptides for targeted quantitation. The tool combines the input data and downloads additional data from public repositories to produce a file per protein as output. Each output file includes relevant information to the selection of proteotypic peptides organized in a table, a colored ranking of peptides according to their potential value as targets for quantitation and auxiliary plots to assist users in the task of proteotypic peptides selection. Taken together, Typic leads to a practical and straightforward data extraction from multiple data sets, allowing the identification of most suitable proteotypic peptides based on established criteria, in an unbiased and standardized manner, ultimately leading to a more robust targeted proteomics assay.
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Affiliation(s)
- Bianca A Pauletti
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Daniela C Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Carolina M Carnielli
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Guilherme A Câmara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Ana Gabriela C Normando
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Guilherme P Telles
- Instituto de Computação, Universidade Estadual de Campinas (UNICAMP), Campinas, 13083-852 São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
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24
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Brown AJP. Fungal resilience and host-pathogen interactions: Future perspectives and opportunities. Parasite Immunol 2023; 45:e12946. [PMID: 35962618 PMCID: PMC10078341 DOI: 10.1111/pim.12946] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
We are constantly exposed to the threat of fungal infection. The outcome-clearance, commensalism or infection-depends largely on the ability of our innate immune defences to clear infecting fungal cells versus the success of the fungus in mounting compensatory adaptive responses. As each seeks to gain advantage during these skirmishes, the interactions between host and fungal pathogen are complex and dynamic. Nevertheless, simply compromising the physiological robustness of fungal pathogens reduces their ability to evade antifungal immunity, their virulence, and their tolerance against antifungal therapy. In this article I argue that this physiological robustness is based on a 'Resilience Network' which mechanistically links and controls fungal growth, metabolism, stress resistance and drug tolerance. The elasticity of this network probably underlies the phenotypic variability of fungal isolates and the heterogeneity of individual cells within clonal populations. Consequently, I suggest that the definition of the fungal Resilience Network represents an important goal for the future which offers the clear potential to reveal drug targets that compromise drug tolerance and synergise with current antifungal therapies.
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Affiliation(s)
- Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK
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25
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Hu A, Zhang L, Wang Z, Yuan C, Lin L, Zhang J, Gao X, Chen X, Guo W, Yang P, Shen H. Cancer Serum Atlas-Supported Precise Pan-Targeted Proteomics Enable Multicancer Detection. Anal Chem 2023; 95:862-871. [PMID: 36584310 DOI: 10.1021/acs.analchem.2c03299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The wide dynamic range of serum proteome restrained discovery of clinically interested proteins in large cohort studies. Herein, we presented a high-sensitivity, high-throughput, and precise pan-targeted serum proteomic strategy for highly efficient cancer serum proteomic research and biomarker discovery. We constructed a resource of over 2000 cancer-secreted proteins, and the standard MS assays and spectra of at least one synthetic unique peptide per protein were acquired and documented (Cancer Serum Atlas, www.cancerserumatlas.com). Then, the standard peptide-anchored parallel reaction monitoring (SPA-PRM) method was developed with support of the Cancer Serum Atlas, achieving precise quantification of cancer-secreted proteins with high throughput and sensitivity. We directly quantified 325 cancer-related serum proteins in 288 serums of four cancer types (liver, stomach, lung, breast) and controls with the pan-targeted strategy and discovered considerable potential biomarker benefits for early detection of cancer. Finally, a proteomic-based multicancer detection model was built, demonstrating high sensitivity (87.2%) and specificity (100%), with 73.8% localization accuracy for an independent test set. In conclusion, the Cancer Serum Atlas provides a wide range of potential biomarkers that serve as targets and standard assays for systematic and highly efficient serological studies of cancer. The Cancer Serum Atlas-supported pan-targeted proteomic strategy enables highly efficient biomarker discovery and multicancer detection and thus can be a powerful tool for liquid biopsy.
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Affiliation(s)
- Anqi Hu
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
| | - Zhenxin Wang
- Department of Laboratory Medicine of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunyan Yuan
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
| | - Ling Lin
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiayi Zhang
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
| | - Xia Gao
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
| | - Xuguang Chen
- Informatization Office, Fudan University, Shanghai 200032, China
| | - Wei Guo
- Department of Laboratory Medicine of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
| | - Huali Shen
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai 200032, China
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26
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Dandekar T, Kunz M. Complex Systems Behave Fundamentally in a Similar Way. Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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27
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Rajoria S, Nair D, Suvarna K, Pai MGJ, Salkar A, Palanivel V, Verma A, Barpanda A, Awasthi G, Doshi H, Dhara V, Burli A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai. Adv Exp Med Biol 2023; 1412:175-195. [PMID: 37378767 DOI: 10.1007/978-3-031-28012-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gaurav Awasthi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Hastyn Doshi
- Department of Computer Science, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vivek Dhara
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ananya Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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28
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Kasahara K, Narumi R, Nagayama S, Masuda K, Esaki T, Obama K, Tomonaga T, Sakai Y, Shimizu Y, Adachi J. A large-scale targeted proteomics of plasma extracellular vesicles shows utility for prognosis prediction subtyping in colorectal cancer. Cancer Med 2022; 12:7616-7626. [PMID: 36394150 PMCID: PMC10067095 DOI: 10.1002/cam4.5442] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/03/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The pathogenesis of cancers depends on the molecular background of each individual patient. Therefore, verifying as many biomarkers as possible and clarifying their relationships with each disease status would be very valuable. We performed a large-scale targeted proteomics analysis of plasma extracellular vesicles (EVs) that may affect tumor progression and/or therapeutic resistance. EXPERIMENTAL DESIGN Plasma EVs from 59 were collected patients with colorectal cancer (CRC) and 59 healthy controls (HC) in cohort 1, and 150 patients with CRC in cohort 2 for the large-scale targeted proteomics analysis of 457 proteins as candidate CRC markers. The Mann-Whitney-Wilcoxon test and random forest model were applied in cohort 1 to select promising markers. Consensus clustering was applied to classify patients with CRC in cohort 2. The Kaplan-Meier method and Cox regression analysis were performed to identify potential molecular factors contributing to the overall survival (OS) of patients. RESULTS In the analysis of cohort 1, 99 proteins were associated with CRC. The analysis of cohort 2 revealed two clusters showing significant differences in OS (p = 0.017). Twelve proteins, including alpha-1-acid glycoprotein 1 (ORM1), were suggested to be associated with the identified CRC subtypes, and ORM1 was shown to significantly contribute to OS, suggesting that ORM1 might be one of the factors closely related to the OS. CONCLUSIONS The study identified two novel subtypes of CRC, which exhibit differences in OS, as well as important biomarker proteins that are closely related to the identified subtypes. Liquid biopsy assessment with targeted proteomics analysis was proposed to be crucial for predicting the CRC prognosis.
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Affiliation(s)
- Keiko Kasahara
- Department of SurgeryKyoto University Graduate School of MedicineKyotoJapan
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Ryohei Narumi
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Clinical and Analytical ChemistryCollaborative Research Center for Health and Medicine, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Satoshi Nagayama
- Department of Gastroenterological SurgeryGastroenterological Center, Cancer Institute Hospital, Japanese Foundation for Cancer ResearchTokyoJapan
- Department of SurgeryUji‐Tokusyukai Medical CenterKyotoJapan
| | - Keiko Masuda
- Laboratory for Cell‐Free Protein SynthesisRIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Tsuyoshi Esaki
- The Center for Data Science Education and ResearchShiga UniversityShigaJapan
| | - Kazutaka Obama
- Department of SurgeryKyoto University Graduate School of MedicineKyotoJapan
| | - Takeshi Tomonaga
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | | | - Yoshihiro Shimizu
- Laboratory for Cell‐Free Protein SynthesisRIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Jun Adachi
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Clinical and Analytical ChemistryCollaborative Research Center for Health and Medicine, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
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29
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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: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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30
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Cifani P, Kentsis A. Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. J Proteome Res 2022; 21:2535-2544. [PMID: 36154077 PMCID: PMC10494574 DOI: 10.1021/acs.jproteome.2c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In spite of extensive studies of cellular signaling, many fundamental processes such as pathway integration, cross-talk, and feedback remain poorly understood. To enable integrated and quantitative measurements of cellular biochemical activities, we have developed the Quantitative Cell Proteomics Atlas (QCPA). QCPA consists of panels of targeted mass spectrometry assays to determine the abundance and stoichiometry of regulatory post-translational modifications of sentinel proteins from most known physiologic and pathogenic signaling pathways in human cells. QCPA currently profiles 1 913 peptides from 469 effectors of cell surface signaling, apoptosis, stress response, gene expression, quiescence, and proliferation. For each protein, QCPA includes triplets of isotopically labeled peptides covering known post-translational regulatory sites to determine their stoichiometries and unmodified protein regions to measure total protein abundance. The QCPA framework incorporates analytes to control for technical variability of sample preparation and mass spectrometric analysis, including TrypQuant, a synthetic substrate for accurate quantification of proteolysis efficiency for proteins containing chemically modified residues. The ability to precisely and accurately quantify most known signaling pathways should enable improved chemoproteomic approaches for the comprehensive analysis of cell signaling and clinical proteomics of diagnostic specimens. QCPA is openly available at https://qcpa.mskcc.org.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, 10065 USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, NY, 10065 USA
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31
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Kennedy J, Whiteaker JR, Ivey RG, Burian A, Chowdhury S, Tsai CF, Liu T, Lin C, Murillo OD, Lundeen RA, Jones LA, Gafken PR, Longton G, Rodland KD, Skates SJ, Landua J, Wang P, Lewis MT, Paulovich AG. Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma. Anal Chem 2022; 94:9540-9547. [PMID: 35767427 PMCID: PMC9280723 DOI: 10.1021/acs.analchem.1c04382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R2 > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.
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Affiliation(s)
- Jacob
J. Kennedy
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Jeffrey R. Whiteaker
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Richard G. Ivey
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Aura Burian
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Shrabanti Chowdhury
- Department
of Genetics and Genomic Sciences and Icahn Institute for Data Science
and Genomic Technology, Icahn School of
Medicine at Mount Sinai, New York, New York 10029, United States
| | - Chia-Feng Tsai
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - ChenWei Lin
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Oscar D. Murillo
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Rachel A. Lundeen
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States
| | - Lisa A. Jones
- Proteomics
and Metabolomics Shared Resources, Fred
Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Philip R. Gafken
- Proteomics
and Metabolomics Shared Resources, Fred
Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Gary Longton
- Public
Health Sciences Division, Fred Hutchinson
Cancer Research Center, Seattle, Washington 98109, United States
| | - Karin D. Rodland
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Steven J. Skates
- MGH
Biostatistics Center, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - John Landua
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Pei Wang
- Department
of Genetics and Genomic Sciences, Mount
Sinai Hospital, New York, New York 10065, United States
| | - Michael T. Lewis
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Amanda G. Paulovich
- Clinical
Research Division, Fred Hutchinson Cancer
Research Center, Seattle, Washington 98109, United States,Phone: 206-667-1912. . Fax: 206-667-2277
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32
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Edfors F, Iglesias MJ, Butler LM, Odeberg J. Proteomics in thrombosis research. Res Pract Thromb Haemost 2022; 6:e12706. [PMID: 35494505 PMCID: PMC9039028 DOI: 10.1002/rth2.12706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
A State of the Art lecture titled “Proteomics in Thrombosis Research” was presented at the ISTH Congress in 2021. In clinical practice, there is a need for improved plasma biomarker‐based tools for diagnosis and risk prediction of venous thromboembolism (VTE). Analysis of blood, to identify plasma proteins with potential utility for such tools, could enable an individualized approach to treatment and prevention. Technological advances to study the plasma proteome on a large scale allows broad screening for the identification of novel plasma biomarkers, both by targeted and nontargeted proteomics methods. However, assay limitations need to be considered when interpreting results, with orthogonal validation required before conclusions are drawn. Here, we review and provide perspectives on the application of affinity‐ and mass spectrometry‐based methods for the identification and analysis of plasma protein biomarkers, with potential application in the field of VTE. We also provide a future perspective on discovery strategies and emerging technologies for targeted proteomics in thrombosis research. Finally, we summarize relevant new data on this topic, presented during the 2021 ISTH Congress.
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Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
| | - Lynn M. Butler
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Clinical Chemistry and Blood Coagulation Research Department of Molecular Medicine and Surgery Karolinska Institute Stockholm Sweden
- Clinical Chemistry Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
| | - Jacob Odeberg
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
- Division of Internal Medicine University Hospital of North Norway Tromsø Norway
- Coagulation Unit Department of Hematology Karolinska University Hospital Stockholm Sweden
- Department of Medicine Solna Karolinska Institute Stockholm Sweden
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33
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Archakov A, Vavilov N, Ilgisonis E, Lisitsa A, Ponomarenko E, Farafonova T, Tikhonova O, Zgoda V. Number of Detected Proteins as the Function of the Sensitivity of Proteomic
Technology in Human Liver Cells. Curr Protein Pept Sci 2022; 23:290-298. [DOI: 10.2174/1389203723666220526092941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 11/22/2022]
Abstract
Aims:
The main goal of the Russian part of C-HPP is to detect and functionally annotate
missing proteins (PE2-PE4) encoded by human chromosome 18. To achieve this goal, it is necessary to
use the most sensitive methods of analysis.
Background:
However, identifying such proteins in a complex biological mixture using mass spectrometry
(MS)-based methods is difficult due to the insufficient sensitivity of proteomic analysis methods.
A possible solution to the problem is the pre-fractionation of a complex biological sample at the
sample preparation stage.
Objective:
This study aims to measure the detection limit of SRM SIS analysis using a standard set of
UPS1 proteins and find a way to enhance the sensitivity of the analysis and to, detect proteins encoded
by the human chromosome 18 in liver tissue samples, and compare the data with transcriptomic analysis
of the same samples.
Methods:
Mass spectrometry, data-dependent acquisition, selected reaction monitoring, highperformance
liquid chromatography, data-dependent acquisition in combination with pre-fractionation
by alkaline reversed-phase chromatography, selected reaction monitoring in combination with prefractionation
by alkaline reversed-phase chromatography methods were used in this study.
Results:
The results revealed that 100% of UPS1 proteins in a mixture could only be identified at a
concentration of at least 10-9 М. The decrease in concentration leads to protein losses associated with
technology sensitivity, and no UPS1 protein is detected at a concentration of 10-13 М. Therefore, the
two-dimensional fractionation of samples was applied to improve sensitivity. The human liver tissue
was examined by selected reaction monitoring and shotgun methods of MS analysis using onedimensional
and two-dimensional fractionation to identify the proteins encoded by human chromosome
18. A total of 134 proteins were identified. The overlap between proteomic and transcriptomic data in
human liver tissue was ~50%.
Conclusion:
The sample concentration technique is well suited for a standard UPS1 system that is not
contaminated with a complex biological sample. However, it is not suitable for use with a complex biological
protein mixture. Thus, it is necessary to develop more sophisticated fractionation systems for the
detection of all low-copy proteins. This weak convergence is due to the low sensitivity of proteomic
technology compared to transcriptomic approaches. Also, total mRNA was used to perform RNA-seq
analysis, but not all detected mRNA molecules could be translated into proteins. This introduces additional
uncertainty in the data; in the future, we plan to study only translated mRNA molecules-the translatome.
Data is available via ProteomeXchange with identifier PXD026997.
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Affiliation(s)
- Alexander Archakov
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Nikita Vavilov
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Ekaterina Ilgisonis
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Andrey Lisitsa
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
- East China University of Technology, Nanchang City, Jiangxi, China
- East-Siberian Research and Education Center, Tyumen, Russia
| | - Elena Ponomarenko
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Tatiana Farafonova
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tikhonova
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
| | - Victor Zgoda
- Department of Proteomics and Mass Spectrometry, Institute of Biomedical Chemistry, Moscow, Russia
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34
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Vavilov NE, Ilgisonis EV, Lisitsa AV, Ponomarenko EA, Farafonova TE, Tikhonova OV, Zgoda VG, Archakov AI. Deep proteomic dataset of human liver samples obtained by two-dimensional sample fractionation coupled with tandem mass spectrometry. Data Brief 2022; 42:108055. [PMID: 35345844 PMCID: PMC8956907 DOI: 10.1016/j.dib.2022.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
The data was acquired from 3 normal human liver tissues by LC-MS methods. The tissue liver samples from male subjects post mortem were obtained from ILSBio LLC (https://bioivt.com/). Liver tissue was frozen in liquid nitrogen, transported and shipped on dry ice. The proteins were extracted and purified followed up by trypsin hydrolysis. The peptide mixture was aliquoted and analyzed by different LC-MS approaches: one-dimensional shotgun LC-MS, two-dimensional LC-MS, two-dimensional SRM SIS (Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards). The Shotgun assay resulted in a qualitative in-depth human liver proteome, and a semi-quantitative iBAQ (intensity-based absolute quantification) value was calculated to show the relative protein content of the sample. Absolute quantitative concentrations of proteins encoded by human chromosome 18 using SRM SIS were obtained.
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35
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Masui K, Cavenee WK, Mischel PS, Shibata N. The metabolomic landscape plays a critical role in glioma oncogenesis. Cancer Sci 2022; 113:1555-1563. [PMID: 35271755 PMCID: PMC9128185 DOI: 10.1111/cas.15325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 12/01/2022] Open
Abstract
Cancer cells depend on metabolic reprogramming for survival, undergoing profound shifts in nutrient sensing, nutrient uptake and flux through anabolic pathways, in order to drive nucleotide, lipid, and protein synthesis and provide key intermediates needed for those pathways. Although metabolic enzymes themselves can be mutated, including to generate oncometabolites, this is a relatively rare event in cancer. Usually, gene amplification, overexpression, and/or downstream signal transduction upregulate rate‐limiting metabolic enzymes and limit feedback loops, to drive persistent tumor growth. Recent molecular‐genetic advances have revealed discrete links between oncogenotypes and the resultant metabolic phenotypes. However, more comprehensive approaches are needed to unravel the dynamic spatio‐temporal regulatory map of enzymes and metabolites that enable cancer cells to adapt to their microenvironment to maximize tumor growth. Proteomic and metabolomic analyses are powerful tools for analyzing a repertoire of metabolic enzymes as well as intermediary metabolites, and in conjunction with other omics approaches could provide critical information in this regard. Here, we provide an overview of cancer metabolism, especially from an omics perspective and with a particular focus on the genomically well characterized malignant brain tumor, glioblastoma. We further discuss how metabolomics could be leveraged to improve the management of patients, by linking cancer cell genotype, epigenotype, and phenotype through metabolic reprogramming.
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Affiliation(s)
- Kenta Masui
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Noriyuki Shibata
- Department of Pathology, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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36
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Bongrand P. Is There a Need for a More Precise Description of Biomolecule Interactions to Understand Cell Function? Curr Issues Mol Biol 2022; 44:505-525. [PMID: 35723321 PMCID: PMC8929073 DOI: 10.3390/cimb44020035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 11/16/2022] Open
Abstract
An important goal of biological research is to explain and hopefully predict cell behavior from the molecular properties of cellular components. Accordingly, much work was done to build extensive “omic” datasets and develop theoretical methods, including computer simulation and network analysis to process as quantitatively as possible the parameters contained in these resources. Furthermore, substantial effort was made to standardize data presentation and make experimental results accessible to data scientists. However, the power and complexity of current experimental and theoretical tools make it more and more difficult to assess the capacity of gathered parameters to support optimal progress in our understanding of cell function. The purpose of this review is to focus on biomolecule interactions, the interactome, as a specific and important example, and examine the limitations of the explanatory and predictive power of parameters that are considered as suitable descriptors of molecular interactions. Recent experimental studies on important cell functions, such as adhesion and processing of environmental cues for decision-making, support the suggestion that it should be rewarding to complement standard binding properties such as affinity and kinetic constants, or even force dependence, with less frequently used parameters such as conformational flexibility or size of binding molecules.
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Affiliation(s)
- Pierre Bongrand
- Lab Adhesion and Inflammation (LAI), Inserm UMR 1067, Cnrs UMR 7333, Aix-Marseille Université UM 61, Marseille 13009, France
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37
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Xiong Y, Zheng Y, Yan Y, Yao J, Liu H, Shen F, Kong S, Yang S, Yan G, Zhao H, Zhou X, Hu J, Zhou B, Jin T, Shen H, Leng B, Yang P, Liu X. Circulating proteomic panels for risk stratification of intracranial aneurysm and its rupture. EMBO Mol Med 2022; 14:e14713. [PMID: 34978375 PMCID: PMC8819334 DOI: 10.15252/emmm.202114713] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 01/02/2023] Open
Abstract
The prevalence of intracranial aneurysm (IA) is increasing, and the consequences of its rupture are severe. This study aimed to reveal specific, sensitive, and non-invasive biomarkers for diagnosis and classification of ruptured and unruptured IA, to benefit the development of novel treatment strategies and therapeutics altering the course of the disease. We first assembled an extensive candidate biomarker bank of IA, comprising up to 717 proteins, based on altered proteins discovered in the current tissue and serum proteomic analysis, as well as from previous studies. Mass spectrometry assays for hundreds of biomarkers were efficiently designed using our proposed deep learning-based method, termed DeepPRM. A total of 113 potential markers were further quantitated in serum cohort I (n = 212) & II (n = 32). Combined with a machine-learning-based pipeline, we built two sets of biomarker combinations (P6 & P8) to accurately distinguish IA from healthy controls (accuracy: 87.50%) or classify IA rupture patients (accuracy: 91.67%) upon evaluation in the external validation set (n = 32). This extensive circulating biomarker development study provides valuable knowledge about IA biomarkers.
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Affiliation(s)
- Yueting Xiong
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yongtao Zheng
- Department of Neurosurgery, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yan Yan
- Huashan Hospital, Fudan University, Shanghai, China
| | - Jun Yao
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hebin Liu
- Shanghai Omicsolution Co., Ltd., Shanghai, China
| | - Fenglin Shen
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shuang Yang
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guoquan Yan
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Huanhuan Zhao
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xinwen Zhou
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Hu
- Huashan Hospital, Fudan University, Shanghai, China
| | - Bin Zhou
- Huashan Hospital, Fudan University, Shanghai, China
| | - Tao Jin
- Huashan Hospital, Fudan University, Shanghai, China
| | - Huali Shen
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Bing Leng
- Huashan Hospital, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaohui Liu
- The Fifth People's Hospital of Shanghai, Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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38
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Abstract
Molecular diversification of the cellular proteome through alternative splicing has emerged as an important biological principle. However, the lack of tools to specifically detect and quantify proteoforms (Smith et al., Nat Methods 10:186-187, 2013) is a major impediment to functional studies. Recently, biological mass spectrometry (MS) has undergone impressive advances (Mann, Nat Rev Mol Cell Biol 17:678, 2016), including the generation of a highly diverse set of biological applications (Aebersold and Mann, Nature 537:347-355, 2016), and has demonstrated to be an essential tool to address many biological questions (Savitski et al., Science 346:1255784, 2014; Rinner et al., Nat Methods 5:315-318, 2008). In particular, targeted LC-MS, with its high selectivity and specificity, is ideally suited for the precise and sensitive quantification of specific proteins and their proteoforms (Picotti and Aebersold, Nat Methods 9:555-566, 2012). We describe in detail the application of this workflow applied to dissect the molecular diversity of the synaptic adhesion proteins and their splicing-derived proteoforms (Schreiner et al., Elife 4:e07794, 2015).
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39
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Pinto G, Illiano A, Ferrucci V, Quarantelli F, Fontanarosa C, Siciliano R, Di Domenico C, Izzo B, Pucci P, Marino G, Zollo M, Amoresano A. Identification of SARS-CoV-2 Proteins from Nasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem Mass Spectrometry. ACS Omega 2021; 6:34945-34953. [PMID: 34926968 PMCID: PMC8672425 DOI: 10.1021/acsomega.1c05587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 05/12/2023]
Abstract
Numerous reverse transcription polymerase chain reaction (RT-PCR) tests have emerged over the past year as the gold standard for detecting millions of cases of SARS-CoV-2 reported daily worldwide. However, problems with critical shortages of key reagents such as PCR primers and RNA extraction kits and unpredictable test reliability related to high viral replication cycles have triggered the need for alternative methodologies to PCR to detect specific COVID-19 proteins. Several authors have developed methods based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) to confirm the potential of the technique to detect two major proteins, the spike and the nucleoprotein, of COVID-19. In the present work, an S-Trap mini spin column digestion protocol was used for sample preparation prodromal to LC-MS/MS analysis in multiple reactions monitoring ion mode (MRM) to obtain a comprehensive method capable of detecting different viral proteins. The developed method was applied to n. 81 oro/nasopharyngeal swabs submitted in parallel to quantitative reverse transcription PCR (RT-qPCR) assays to detect RdRP, the S and N genes specific for COVID-19, and the E gene for all Sarbecoviruses, including SARS-CoV-2 (with cycle negativity threshold set to 40). A total of 23 peptides representative of the six specific viral proteins were detected in the monitoring of 128 transitions found to have good ionic currents extracted in clinical samples that reacted differently to the PCR assay. The best instrumental response came from the FLPFQFGR sequence of spike [558-566] peptide used to test the analytical performance of the method that has good sensitivity with a low false-negative rate. Transition monitoring using a targeted MS approach has the great potential to detect the fragmentation reactions of any peptide molecularly defined by a specific amino acid sequence, offering the extensibility of the approach to any viral sequence including derived variants and thus providing insights into the development of new types of clinical diagnostics.
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Affiliation(s)
- Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Anna Illiano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Veronica Ferrucci
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | | | - Carolina Fontanarosa
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Roberto Siciliano
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Carmela Di Domenico
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Barbara Izzo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Piero Pucci
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Gennaro Marino
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Massimo Zollo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
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40
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Abstract
Phagocytosis is an important physiological process, which, in higher organisms, is a means of fighting infections and clearing cellular debris. During phagocytosis, detrimental foreign particles (e.g. pathogens and apoptotic cells) are engulfed by phagocytes (e.g. macrophages), enclosed in membrane-bound vesicles called phagosomes, and transported to the lysosome for eventual detoxification. During this well-choreographed process, the nascent phagosome (also called early phagosome, EP) undergoes a series of spatiotemporally regulated changes in its protein and lipid composition and matures into a late phagosome (LP), which subsequently fuses with the lysosomal membrane to form the phagolysosome. While several elegant proteomic studies have identified the role of unique proteins during phagosomal maturation, the corresponding lipidomic studies are sparse. Recently, we reported a comparative lipidomic analysis between EPs and LPs and showed that ceramides are enriched on the LPs. Further, we found that this ceramide accumulation on LPs was orchestrated by ceramide synthase 2, inhibition of which hampers phagosomal maturation. Following up on this study, here, using biochemical assays, we first show that the increased ceramidase activity on EPs also significantly contributes to the accumulation of ceramides on LPs. Next, leveraging lipidomics, we show that de novo ceramide synthesis does not significantly contribute to the ceramide accumulation on LPs, while concomitant to increased ceramides, glucosylceramides are substantially elevated on LPs. We validate this interesting finding using biochemical assays and show that LPs indeed have heightened glucosylceramide synthase activity. Taken together, our studies provide interesting insights and possible new roles of sphingolipid metabolism during phagosomal maturation.
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Affiliation(s)
- Neelay Mehendale
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Roop Mallik
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Powai, Mumbai 400076, India
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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41
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Guerrero L, Sangro B, Ambao V, Granero JI, Ramos-Fernández A, Paradela A, Corrales FJ. Monitoring one-carbon metabolism by mass spectrometry to assess liver function and disease. J Physiol Biochem 2021; 78:229-243. [PMID: 34897580 PMCID: PMC8666175 DOI: 10.1007/s13105-021-00856-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
Precision medicine promises to overcome the constraints of the traditional “one-for-all” healthcare approach through a clear understanding of the molecular features of a disease, allowing for innovative and tailored treatments. State-of-the-art proteomics has the potential to accurately explore the human proteome to identify, quantify, and characterize proteins associated with disease progression. There is a pressing need for informative biomarkers to diagnose liver disease early in its course to prevent severe disease for which no efficient treatment is yet available. Here, we propose the concept of a cellular pathway as a functional biomarker, whose monitorization may inform normal and pathological status. We have developed a standardized targeted selected-reaction monitoring assay to detect and quantify 13 enzymes of one-carbon metabolism (1CM). The assay is compliant with Clinical Proteomics Tumor Analysis Consortium (CPTAC) guidelines and has been included in the protein quantification assays that can be accessed through the assay portal at the CPTAC web page. To test the feasibility of the assay, we conducted a retrospective, proof-of-concept study on a collection of liver samples from healthy controls and from patients with cirrhosis or hepatocellular carcinoma (HCC). Our results indicate a significant reconfiguration of 1CM upon HCC development resulting from a process that can already be identified in cirrhosis. Our findings indicate that the systematic and integrated quantification of 1CM enzymes is a promising cell function-based biomarker for patient stratification, although further experiments with larger cohorts are needed to confirm these findings.
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Affiliation(s)
- Laura Guerrero
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, Darwin 3, 28049, Madrid, Spain
| | - Bruno Sangro
- Hepatology Department, University Clinic of Navarra, University of Navarra, 31008, Pamplona, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain.,IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Verónica Ambao
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET-FEI-División de Endocrinología, Hospital de Niños R. Gutiérrez, 1330, C1425EFD, Buenos Aires, Gallo, Argentina
| | - José Ignacio Granero
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, Darwin 3, 28049, Madrid, Spain
| | | | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, Darwin 3, 28049, Madrid, Spain
| | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, Darwin 3, 28049, Madrid, Spain. .,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain.
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Zhang YH, Hoopmann MR, Castaldi PJ, Simonsen KA, Midha MK, Cho MH, Criner GJ, Bueno R, Liu J, Moritz RL, Silverman EK. Lung proteomic biomarkers associated with chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2021; 321:L1119-L1130. [PMID: 34668408 PMCID: PMC8715017 DOI: 10.1152/ajplung.00198.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/27/2021] [Accepted: 10/15/2021] [Indexed: 11/22/2022] Open
Abstract
Identifying protein biomarkers for chronic obstructive pulmonary disease (COPD) has been challenging. Most previous studies have used individual proteins or preselected protein panels measured in blood samples. Mass spectrometry proteomic studies of lung tissue have been based on small sample sizes. We used mass spectrometry proteomic approaches to discover protein biomarkers from 150 lung tissue samples representing COPD cases and controls. Top COPD-associated proteins were identified based on multiple linear regression analysis with false discovery rate (FDR) < 0.05. Correlations between pairs of COPD-associated proteins were examined. Machine learning models were also evaluated to identify potential combinations of protein biomarkers related to COPD. We identified 4,407 proteins passing quality controls. Twenty-five proteins were significantly associated with COPD at FDR < 0.05, including interleukin 33, ferritin (light chain and heavy chain), and two proteins related to caveolae (CAV1 and CAVIN1). Multiple previously reported plasma protein biomarkers for COPD were not significantly associated with proteomic analysis of COPD in lung tissue, although RAGE was borderline significant. Eleven pairs of top significant proteins were highly correlated (r > 0.8), including several strongly correlated with RAGE (EHD2 and CAVIN1). Machine learning models using Random Forests with the top 5% of protein biomarkers demonstrated reasonable accuracy (0.707) and area under the curve (0.714) for COPD prediction. Mass spectrometry-based proteomic analysis of lung tissue is a promising approach for the identification of biomarkers for COPD.
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Affiliation(s)
- Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gerard J Criner
- Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jiangyuan Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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43
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Liljedahl L, Malmström J, Kristjansdottir B, Waldemarson S, Sundfeldt K. Targeted Selected Reaction Monitoring Verifies Histology Specific Peptide Signatures in Epithelial Ovarian Cancer. Cancers (Basel) 2021; 13:5713. [PMID: 34830868 DOI: 10.3390/cancers13225713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Ovarian cancer is a lethal disease due to its late phase discovery. Any steps towards improving early diagnostics will dramatically increase survival rates. To identify new ovarian cancer biomarker panels, we need to focus on early-stage disease and all histologic subtypes. In this study we have, based on prior discoveries, constructed a multiplexed targeted selected-reaction-monitoring assay to detect peptides from 177 proteins in only 20 µL of plasma. The assay was evaluated in patients with a focus on early-stages and all ovarian cancer histologies in separate groups. With multivariate analysis, we found the highest predictive value in the benign vs. low-grade serous (Q2 = 0.615) and mucinous (Q2 = 0.611) early stage compared to all malignant (Q2 = 0.226) or late stage (Q2 = 0.43) ovarian cancers. The results show that each ovarian cancer histology subgroup can be identified by a unique panel of proteins. Abstract Epithelial ovarian cancer (OC) is a disease with high mortality due to vague early clinical symptoms. Benign ovarian cysts are common and accurate diagnosis remains a challenge because of the molecular heterogeneity of OC. We set out to investigate whether the disease diversity seen in ovarian cyst fluids and tumor tissue could be detected in plasma. Using existing mass spectrometry (MS)-based proteomics data, we constructed a selected reaction monitoring (SRM) assay targeting peptides from 177 cancer-related and classical proteins associated with OC. Plasma from benign, borderline, and malignant ovarian tumors were used to verify expression (n = 74). Unsupervised and supervised multivariate analyses were used for comparisons. The peptide signatures revealed by the supervised multivariate analysis contained 55 to 77 peptides each. The predictive (Q2) values were higher for benign vs. low-grade serous Q2 = 0.615, mucinous Q2 = 0.611, endometrioid Q2 = 0.428 and high-grade serous Q2 = 0.375 (stage I–II Q2 = 0.515; stage III Q2 = 0.43) OC compared to benign vs. all malignant Q2 = 0.226. With targeted SRM MS we constructed a multiplexed assay for simultaneous detection and relative quantification of 185 peptides from 177 proteins in only 20 µL of plasma. With the approach of histology-specific peptide patterns, derived from pre-selected proteins, we may be able to detect not only high-grade serous OC but also the less common OC subtypes.
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Matsuzaki Y, Aoki W, Miyazaki T, Aburaya S, Ohtani Y, Kajiwara K, Koike N, Minakuchi H, Miura N, Kadonosono T, Ueda M. Peptide barcoding for one-pot evaluation of sequence-function relationships of nanobodies. Sci Rep 2021; 11:21516. [PMID: 34728738 PMCID: PMC8563947 DOI: 10.1038/s41598-021-01019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Optimisation of protein binders relies on laborious screening processes. Investigation of sequence–function relationships of protein binders is particularly slow, since mutants are purified and evaluated individually. Here we developed peptide barcoding, a high-throughput approach for accurate investigation of sequence–function relationships of hundreds of protein binders at once. Our approach is based on combining the generation of a mutagenised nanobody library fused with unique peptide barcodes, the formation of nanobody–antigen complexes at different ratios, their fine fractionation by size-exclusion chromatography and quantification of peptide barcodes by targeted proteomics. Applying peptide barcoding to an anti-GFP nanobody as a model, we successfully identified residues important for the binding affinity of anti-GFP nanobody at once. Peptide barcoding discriminated subtle changes in KD at the order of nM to sub-nM. Therefore, peptide barcoding is a powerful tool for engineering protein binders, enabling reliable one-pot evaluation of sequence–function relationships.
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Affiliation(s)
- Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. .,Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto, 600-8813, Japan. .,JST, CREST, Chiyoda-ku, Tokyo, 102-0076, Japan. .,JST, COI-NEXT, Chiyoda-ku, Tokyo, 102-0076, Japan. .,JST, FOREST, Chiyoda-ku, Tokyo, 102-0076, Japan.
| | - Takumi Miyazaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naoki Koike
- TechnoPro, Inc. TechnoPro R&D, Company, Tokyo, 106-6135, Japan
| | | | - Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka-ku, Sakai, 599-8531, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.,Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto, 600-8813, Japan.,JST, CREST, Chiyoda-ku, Tokyo, 102-0076, Japan.,JST, COI-NEXT, Chiyoda-ku, Tokyo, 102-0076, Japan
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45
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Abstract
Targeted proteomics via selected reaction monitoring (SRM) or parallel reaction monitoring (PRM) enables fast and sensitive detection of a preselected set of target peptides. However, the number of peptides that can be monitored in conventional targeting methods is usually rather small. Recently, a series of methods has been described that employ intelligent acquisition strategies to increase the efficiency of mass spectrometers to detect target peptides. These methods are based on one of two strategies. First, retention time adjustment-based methods enable intelligent scheduling of target peptide retention times. These include Picky, iRT, as well as spike-in free real-time adjustment methods such as MaxQuant.Live. Second, in spike-in triggered acquisition methods such as SureQuant, Pseudo-PRM, TOMAHAQ, and Scout-MRM, targeted scans are initiated by abundant labeled synthetic peptides added to samples before the run. Both strategies enable the mass spectrometer to better focus data acquisition time on target peptides. This either enables more sensitive detection or a higher number of targets per run. Here, we provide an overview of available advanced targeting methods and highlight their intrinsic strengths and weaknesses and compatibility with specific experimental setups. Our goal is to provide a basic introduction to advanced targeting methods for people starting to work in this field. Advanced acquisition methods improve focus of mass spectrometers on target peptides. This review discusses existing methods based on two strategies. Retention time adjustment-based methods enable intelligent scheduling of peptide RTs. In spike-in triggered acquisition methods targeted scans are initiated by spike-ins.
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Affiliation(s)
- Mirjam van Bentum
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
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46
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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47
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Kotol D, Hober A, Strandberg L, Svensson AS, Uhlén M, Edfors F. Targeted proteomics analysis of plasma proteins using recombinant protein standards for addition only workflows. Biotechniques 2021; 71:473-483. [PMID: 34431357 DOI: 10.2144/btn-2021-0047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Targeted proteomics is an attractive approach for the analysis of blood proteins. Here, we describe a novel analytical platform based on isotope-labeled recombinant protein standards stored in a chaotropic agent and subsequently dried down to allow storage at ambient temperature. This enables a straightforward protocol suitable for robotic workstations. Plasma samples to be analyzed are simply added to the dried pellet followed by enzymatic treatment and mass spectrometry analysis. Here, we show that this approach can be used to precisely (coefficient of variation <10%) determine the absolute concentrations in human plasma of hundred clinically relevant protein targets, spanning four orders of magnitude, using simultaneous analysis of 292 peptides. The use of this next-generation analytical platform for high-throughput clinical proteome profiling is discussed.
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Affiliation(s)
- David Kotol
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Linnéa Strandberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anne-Sophie Svensson
- Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
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48
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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49
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Nakajima D, Ohara O, Kawashima Y. Toward proteome-wide exploration of proteins in dried blood spots using liquid chromatography-coupled mass spectrometry. Proteomics 2021; 21:e2100019. [PMID: 34379369 DOI: 10.1002/pmic.202100019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022]
Abstract
Dried blood spot (DBS) sampling is a method with advantages over conventional blood sampling in relation to collection, cost, storage, and transportation. Such advantages have led to its wide use in newborn screening (NBS). Although target analysis of various biomolecules is conducted in NBS, protein quantification-based NBS is still in its infancy. Thus, it is important to clarify how many proteins could be quantitatively detected in DBS samples using advanced liquid chromatography-mass spectrometry (LC-MS/MS) technologies; a catalog of proteins detectable in DBSs by LC-MS/MS will enable us to judge which causative proteins in genetic diseases can be monitored at the protein level in NBS. In this review, we outline conventional proteome analyses of DBSs with a distinction between target and nontarget approaches. Additionally, we discuss the future perspectives for proteome analysis of DBSs in NBS of genetic diseases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
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50
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Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Cell Rep Methods 2021; 1:100015. [PMID: 34671754 PMCID: PMC8525888 DOI: 10.1016/j.crmeth.2021.100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SUMMARY A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. MOTIVATION A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kanika Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Melissa A. Hoffman
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra R. Cocco
- Gillings School of Global Public Health, Kenan-Flagler Business School, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Simona Colantonio
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - William Bocik
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew Holderfield
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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