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Sato H, Nakajima D, Ishikawa M, Konno R, Nakamura R, Ohara O, Kawashima Y. Evaluation of the Suitability of Dried Saliva Spots for In-Depth Proteome Analyses for Clinical Applications. J Proteome Res 2022; 21:1340-1348. [PMID: 35446574 DOI: 10.1021/acs.jproteome.2c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previously, we performed nontargeted proteome analysis using dried blood spots (DBSs) that are widely used in newborn screening for the clinical diagnosis of congenital genetic diseases and immunodeficiency. We have developed an efficient and simple pretreatment method for DBSs that can detect more than 1000 proteins. To complement proteins that are difficult to detect via DBS analysis with less invasive alternative body fluids, we conducted this study to investigate the proteins detected from dried saliva spots (DSSs) using single-shot LC-MS/MS, which is practical in clinical settings. We also clarified whether DSSs have the same advantages as DBSs, and we investigated the influence of saliva collection conditions and the storage environment on their protein profile. As a result, we detected approximately 5000 proteins in DSSs and whole saliva, and we concluded that they were sufficient to complement the proteins lacking in the blood analysis. DSSs could be used as an alternative tool to DBSs for detecting the presence of causative proteins.
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Affiliation(s)
- Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.,Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8677, Japan
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Ren Nakamura
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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Pollard S, Anderson JC, Bah F, Mateus M, Sidhu M, Simmons D. Non-Lethal Blood Sampling of Fish in the lab and Field With Methods for Dried Blood Plasma Spot Omic Analyses. Front Genet 2022; 13:795348. [PMID: 35401689 PMCID: PMC8988233 DOI: 10.3389/fgene.2022.795348] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
There is global acknowledgment that humane methods in animal research are a priority, but few environmental effects monitoring programs use nonlethal methods for fish. The goal of the present study was to determine the impacts of sampling small volumes of blood in larger-bodied fish on survival and healing. In addition to evaluating survival following blood sampling, we evaluated the utility of dried blood spots as an alternative for sample processing and storage in the field. In our approach, we housed 80 rainbow trout (Oncorhynchus mykiss) in our flow-through aquatic facility. We then anaesthetized using MS-222 and sampled 1 μl/g bw of blood via puncture of the caudal vasculature. We tested four different post-blood sampling treatments on the puncture wound: 1. application of liquid bandage; 2. a swab of betadine; 3. a swab of fish mucous; and 4. compared survival outcomes to a group where no post-treatment was performed (negative control). Overall, we observed 90% survival among all treatments, with the most effective approach being the negative control (100% survival). Based upon these results, we repeated the blood sampling with no-post treatment by housing 20 rainbow trout (not previously tested upon) in cages at a nearby creek and monitored survival for 2 weeks post sampling. The survival rate was 95% with full healing of the puncture site in all subjects. In addition to this, we tested the efficacy of dry blood spotting on proteomic, lipidomic and amino acid analysis as an alternative method for blood sample processing and storage. It was found that dried plasma spotting using parafilm in conjunction with a modified Bligh-Dyer extraction offered the best balance for good recovery of protein, lipid and amino acids relative to wet plasma and Noviplex dried plasma spot cards. In this article, we will present the detailed results of these combined studies and describe what we have determined to be the safest non-lethal blood sampling protocol.
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Affiliation(s)
- S Pollard
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - J C Anderson
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - F Bah
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - M Mateus
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - M Sidhu
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - Dbd Simmons
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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Molloy MP, Hill C, O'Rourke MB, Chandra J, Steffen P, McKay MJ, Pascovici D, Herbert BR. Proteomic Analysis of Whole Blood Using Volumetric Absorptive Microsampling for Precision Medicine Biomarker Studies. J Proteome Res 2022; 21:1196-1203. [PMID: 35166117 DOI: 10.1021/acs.jproteome.1c00971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microsampling of patient blood promises several benefits over conventional phlebotomy practices to facilitate precision medicine studies. These include at-home patient blood collection, supporting telehealth monitoring, minimal postcollection processing, and compatibility with nonrefrigerated transport and storage. However, for proteomic biomarker studies, mass spectrometry of whole blood has generally been avoided in favor of using plasma or serum obtained from venepuncture. We evaluated the use of a volumetric absorptive microsampling (VAMS) device as a sample preparation matrix to enable LC-MS proteomic analyses of dried whole blood. We demonstrated the detection and robust quantitation of up to 1600 proteins from single-shot shotgun-LC-MS analysis of dried whole blood, greatly enhancing proteome depth compared with conventional single-shot LC-MS analyses of undepleted plasma. Some proteins not previously reported in blood were detected using this approach. Various washing reagents were used to demonstrate that proteins can be preferentially removed from VAMS devices prior to downstream analyses. We provide a demonstration that archival frozen blood cell pellets housed under long-term storage (exceeding 5 years) are compatible with VAMS to enable quantitation of potential biomarker proteins from biobank repositories. These demonstrations are important steps in establishing viable analysis workflows to underpin large-scale precision medicine studies. Data are available via ProteomeXchange with the identifier PXD028605.
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Affiliation(s)
- Mark P Molloy
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | | | - Matthew B O'Rourke
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Jason Chandra
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Pascal Steffen
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Matthew J McKay
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
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Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:39-52. [PMID: 34905164 DOI: 10.1007/978-1-0716-1936-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Dried blood spots (DBS) are widely used for screening molecular profiles, including enzymatic activity. However, hydrophilic proteins present in large amounts in blood inhibit detection of other proteins in DBS by liquid chromatography-mass spectrometry (LC-MS/MS) without preenrichment. Sodium carbonate precipitation (SCP) can concentrate hydrophobic proteins from DBS and effectively remove soluble hydrophilic proteins. Furthermore, SCP combination with data-independent acquisition (DIA) for quantitative LC-MS/MS enhanced the proteome analysis sensitivity and quantification limits. In this protocol, we have described in detail a simple preenrichment method using SCP and a deep proteome analysis method for LC-MS/MS data using DIA.
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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] [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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Watanabe E, Kawashima Y, Suda W, Kakihara T, Takazawa S, Nakajima D, Nakamura R, Nishi A, Suzuki K, Ohara O, Fujishiro J. Discovery of Candidate Stool Biomarker Proteins for Biliary Atresia Using Proteome Analysis by Data-Independent Acquisition Mass Spectrometry. Proteomes 2020; 8:proteomes8040036. [PMID: 33260872 PMCID: PMC7709124 DOI: 10.3390/proteomes8040036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022] Open
Abstract
Biliary atresia (BA) is a destructive inflammatory obliterative cholangiopathy of the neonate that affects various parts of the bile duct. If early diagnosis followed by Kasai portoenterostomy is not performed, progressive liver cirrhosis frequently leads to liver transplantation in the early stage of life. Therefore, prompt diagnosis is necessary for the rescue of BA patients. However, the prompt diagnosis of BA remains challenging because specific and reliable biomarkers for BA are currently unavailable. In this study, we discovered potential biomarkers for BA using deep proteome analysis by data-independent acquisition mass spectrometry (DIA–MS). Four patients with BA and three patients with neonatal cholestasis of other etiologies (non-BA) were recruited for stool proteome analysis. Among the 2110 host-derived proteins detected in their stools, 49 proteins were significantly higher in patients with BA and 54 proteins were significantly lower. These varying stool protein levels in infants with BA can provide potential biomarkers for BA. As demonstrated in this study, the deep proteome analysis of stools has great potential not only in detecting new stool biomarkers for BA but also in elucidating the pathophysiology of BA and other pediatric diseases, especially in the field of pediatric gastroenterology.
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Affiliation(s)
- Eiichiro Watanabe
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; (E.W.); (T.K.); (K.S.)
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan; (Y.K.); (D.N.); (R.N.); (O.O.)
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan;
| | - Tomo Kakihara
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; (E.W.); (T.K.); (K.S.)
| | - Shinya Takazawa
- Department of Surgery, Gunma Children’s Medical Center, Shibukawa 277-8577, Japan; (S.T.); (A.N.)
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan; (Y.K.); (D.N.); (R.N.); (O.O.)
| | - Ren Nakamura
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan; (Y.K.); (D.N.); (R.N.); (O.O.)
| | - Akira Nishi
- Department of Surgery, Gunma Children’s Medical Center, Shibukawa 277-8577, Japan; (S.T.); (A.N.)
| | - Kan Suzuki
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; (E.W.); (T.K.); (K.S.)
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan; (Y.K.); (D.N.); (R.N.); (O.O.)
| | - Jun Fujishiro
- Department of Pediatric Surgery, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; (E.W.); (T.K.); (K.S.)
- Correspondence: ; Tel.: +81-3-5800-8671; Fax: +81-3-5800-5104
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Hoshino A, Xi Y, Nakao T, Kato K, Fujiyama S, Koh K, Imamura T, Kanegane H. A Cry for the Development of Newborn Screening for Familial Hemophagocytic Lymphohistiocytosis. J Clin Immunol 2020; 40:1196-1198. [DOI: 10.1007/s10875-020-00863-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/04/2020] [Indexed: 11/29/2022]
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