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Kralova K, Vrtelka O, Fouskova M, Smirnova TA, Michalkova L, Hribek P, Urbanek P, Kuckova S, Setnicka V. Comprehensive spectroscopic, metabolomic, and proteomic liquid biopsy in the diagnostics of hepatocellular carcinoma. Talanta 2024; 270:125527. [PMID: 38134814 DOI: 10.1016/j.talanta.2023.125527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Liquid biopsy is a very topical issue in clinical diagnostics research nowadays. In this study, we explored and compared various analytical approaches to blood plasma analysis. Finally, we proposed a comprehensive procedure, which, thanks to the utilization of multiple analytical techniques, allowed the targeting of various biomolecules in blood plasma reflecting diverse biological processes underlying disease development. The potential of such an approach, combining proteomics, metabolomics, and vibrational spectroscopy along with preceding blood plasma fractionation, was demonstrated on blood plasma samples of patients suffering from hepatocellular carcinoma in cirrhotic terrain (n = 20) and control subjects with liver cirrhosis (n = 20) as well as healthy subjects (n = 20). Most of the applied methods allowed the classification of the samples with an accuracy exceeding 80.0 % and therefore have the potential to be used as a stand-alone method in clinical diagnostics. Moreover, a final panel of 48 variables obtained by a combination of the utilized analytical methods enabled the discrimination of the hepatocellular carcinoma samples from cirrhosis with 94.3 % cross-validated accuracy. Thus, this study, although limited by the cohort size, clearly demonstrated the benefit of the multimethod approach in clinical diagnosis.
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Affiliation(s)
- Katerina Kralova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Ondrej Vrtelka
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Marketa Fouskova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Tatiana Anatolievna Smirnova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Lenka Michalkova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic; Department of Analytical Chemistry, Institute of Chemical Process Fundamentals of the CAS, Rozvojova 135, 165 02, Prague 6, Czech Republic
| | - Petr Hribek
- Military University Hospital Prague, Department of Medicine 1st Faculty of Medicine Charles University and Military University Hospital Prague, U Vojenske Nemocnice 1200, 169 02, Prague 6, Czech Republic; Department of Internal Medicine, Faculty of Military Health Sciences in Hradec Kralove, University of Defense, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic
| | - Petr Urbanek
- Military University Hospital Prague, Department of Medicine 1st Faculty of Medicine Charles University and Military University Hospital Prague, U Vojenske Nemocnice 1200, 169 02, Prague 6, Czech Republic
| | - Stepanka Kuckova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Vladimir Setnicka
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic.
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2
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Sakarin S, Rungsipipat A, Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanit S, Thaisakun S, Surachetpong SD. Proteomic analysis of the serum in dogs with pulmonary hypertension secondary to myxomatous mitral valve disease: the preliminary study. Front Vet Sci 2024; 11:1327453. [PMID: 38596466 PMCID: PMC11002142 DOI: 10.3389/fvets.2024.1327453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024] Open
Abstract
Background Pulmonary hypertension (PH) is a common complication in dogs with myxomatous mitral valve disease (MMVD), characterized by elevated blood pressure in pulmonary artery. Echocardiography is a reliable technique for PH diagnosis in veterinary medicine. However, it is limited to use as an early detection method. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has found extensive application in the discovery of serum protein biomarkers for various diseases. The objective of this study was to identify serum proteins in healthy control dogs and MMVD dogs both with and without PH using LC-MS/MS. Materials and methods In this research, a total of 81 small-breed dogs participated, and they were categorized into three groups: the control (n = 28), MMVD (n = 24) and MMVD+PH (n = 29) groups. Serum samples were collected and analyzed by LC-MS/MS. Results Differentially expressed proteins were identified, and the upregulated and downregulated proteins in MMVD+PH group including Myomesin 1 (MYOM1) and Histone deacetylase 7 (HDAC7), Pleckstrin homology domain containing M3 (PLEKHM3), Diacylglycerol lipase alpha (DAGLA) and Tubulin tyrosine ligase like 6 (TTLL6) were selected as proteins of interest in MMVD dogs with PH. Conclusion Different types of proteins have been identified in healthy dogs and MMVD dogs with and without PH. Additional studies are needed to investigate the potential of these proteins as biomarkers for PH in dogs with MMVD.
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Affiliation(s)
- Siriwan Sakarin
- Faculty of Veterinary Science, Department of Veterinary Medicine, Center of Excellence for Companion Animal Cancer, Chulalongkorn University, Bangkok, Thailand
| | - Anudep Rungsipipat
- Faculty of Veterinary Science, Department of Pathology, Chulalongkorn University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sirilak Disatian Surachetpong
- Faculty of Veterinary Science, Department of Veterinary Medicine, Center of Excellence for Companion Animal Cancer, Chulalongkorn University, Bangkok, Thailand
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Nicolás Carcelén J, Potes Rodríguez H, González-Gago A, Marchante-Gayón JM, Ballesteros A, González JM, García Alonso JI, Rodríguez-González P. Evaluation of different isotope dilution mass spectrometry strategies for the characterization of naturally abundant and isotopically labelled peptide standards. Anal Bioanal Chem 2024; 416:1717-1731. [PMID: 38363304 PMCID: PMC10899365 DOI: 10.1007/s00216-024-05176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Natural abundance and isotopically labelled tryptic peptides are routinely employed as standards in quantitative proteomics. The certification of the peptide content is usually carried out by amino acid analysis using isotope dilution mass spectrometry (IDMS) after the acid hydrolysis of the peptide. For the validation and traceability of the amino acid analysis procedure, expensive certified peptides must be employed. In this work we evaluate different IDMS alternatives which will reduce the amount of certified peptide required for validation of the amino acid analysis procedure. In this context, the characterization of both natural and isotopically labelled synthetic angiotensin I peptides was carried out. First, we applied a fast procedure for peptide hydrolysis based on microwave-assisted digestion and employed two certified peptide reference materials SRM 998 angiotensin I and CRM 6901-b C-peptide for validation of the hydrolysis procedure. The amino acids proline, leucine, isoleucine, valine, tyrosine, arginine and phenylalanine were evaluated for their suitability for peptide certification by IDMS by both liquid chromatography with tandem mass spectrometry (LC-MS/MS) and gas chromatography with mass spectrometry (GC)-MS/MS. Then, natural angiotensin I and 13C1-labelled angiotensin I were synthesized in-house and purified by preparative liquid chromatography. The concentration of the 13C1-labelled angiotensin I peptide was established by reverse IDMS in its native form using SRM 998 angiotensin I as reference. The concentration of the natural synthesized peptide was determined by IDMS both using the 13C1-labelled peptide in its native form and by amino acid analysis showing comparable results. Finally, the synthetic naturally abundant angiotensin I peptide was employed as "in-house" standard for the validation of subsequent peptide characterization procedures. Therefore, the novelty of this work relies on, first, the development of a faster hydrolysis procedure assisted by focused microwaves, providing complete hydrolysis in 150 min, and secondly, a validation strategy combining GC-MS and LC-MS/MS that allowed us to certify the purity of an in-house-synthesized peptide standard that can be employed as quality control in further experiments.
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Affiliation(s)
- Jesús Nicolás Carcelén
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Helí Potes Rodríguez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Adriana González-Gago
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | | | - Alfredo Ballesteros
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - José Manuel González
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - José Ignacio García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
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Yang H, Hu J, Tan BK, Wong KH, Huang JJ, Cheung PC, Lin S. Lesson learned from COVID-19 pandemic for the future of food industry. Heliyon 2023; 9:e22479. [PMID: 38045130 PMCID: PMC10689951 DOI: 10.1016/j.heliyon.2023.e22479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023] Open
Abstract
With WHO announcing COVID-19 no longer as a public health emergency of international concern (PHEIC) on May 5, 2023, coupled with the fact that the majority of the countries of the world have dropped strict city lockdown or border closure, this perhaps signals the end of the COVID-19 crisis caused by the SARS-CoV-2 virus. However, the COVID-19 pandemic has resulted in far-reaching effects affecting nearly every aspect of our lives and society. Notably, the food industry including agriculture, food manufacturers, food logistics, distributors and retailers have all felt the profound impact and had experienced significant stress during the pandemic. Therefore, it is essential to retrospect the lessons that can be learned from this pandemic for the food industry. This short review aims to address the food safety issues related to the COVID-19 pandemic by focusing on its foodborne transmission potential, innovations of virus detection strategies suitable for food industry; development of phathogenicaidal methods and devices to inactivate SARS-CoV-2 virus (particularly in industrial scale); and the set-up of related food regulations and guidelines as preventive and control measures for preventing the spread of SARS-CoV-2 virus through the food supply chain during the pandemic. This article may provide useful references for the food industry to minimize the food safety impact of COVID-19 (as well as other respiratory virus) and allows them to better prepare for similar future challenges.
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Affiliation(s)
- Haoqing Yang
- Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, Fujian 350002, China
| | - Jiamiao Hu
- Diabetes Research Centre, Leicester General Hospital, Leicester LE5 4PW, United Kingdom
| | - Bee K. Tan
- Diabetes Research Centre, Leicester General Hospital, Leicester LE5 4PW, United Kingdom
| | - Ka-hing Wong
- Department of Applied Biology and Chemical Technology, The Hongkong Polytechnic University, Hongkong SAR, China
| | - Jim Junhui Huang
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Republic of Singapore
| | - Peter C.K. Cheung
- Food Research Centre, School of Life Sciences, The Chinese University of Hongkong, Hongkong SAR, China
| | - Shaoling Lin
- Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, Fujian 350002, China
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Ahsan N, Fornelli L, Najar FZ, Gamagedara S, Hossan MR, Rao RSP, Punyamurtula U, Bauer A, Yang Z, Foster SB, Kane MA. Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum. Proteomics 2023; 23:e2300150. [PMID: 37199141 PMCID: PMC11166006 DOI: 10.1002/pmic.202300150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%-19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.
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Affiliation(s)
- Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
| | - Luca Fornelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Fares Z. Najar
- High-Performance Computing Center (HPCC), Oklahoma State University, Stillwater, OK, USA
| | | | | | | | - Ujwal Punyamurtula
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Bauer
- Department of Neurosurgery, University of Oklahoma-Health Science Center, Oklahoma City, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Steven B. Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
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6
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Boschetti E, Righetti PG. Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique. Int J Mol Sci 2023; 24:10329. [PMID: 37373476 DOI: 10.3390/ijms241210329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present at extremely low concentrations. In the past few years pathways towards this objective have been proposed. In this review, a general landscape of the enrichment technology situation is made first with the presentation and the use of combinatorial peptide libraries. Then, a description of this peculiar technology for the identification of early-stage biomarkers for well-known pathologies with concrete examples is given. In another field of medical applications, the determination of host cell protein traces potentially present in recombinant therapeutic proteins, such as antibodies, is discussed along with their potentially deleterious effects on the health of patients on the one hand, and on the stability of these biodrugs on the other hand. Various additional applications of medical interest are disclosed for biological fluids investigations where the target proteins are present at very low concentrations (e.g., protein allergens).
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Arya SS, Dias SB, Jelinek HF, Hadjileontiadis LJ, Pappa AM. The convergence of traditional and digital biomarkers through AI-assisted biosensing: A new era in translational diagnostics? Biosens Bioelectron 2023; 235:115387. [PMID: 37229842 DOI: 10.1016/j.bios.2023.115387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/11/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Advances in consumer electronics, alongside the fields of microfluidics and nanotechnology have brought to the fore low-cost wearable/portable smart devices. Although numerous smart devices that track digital biomarkers have been successfully translated from bench-to-bedside, only a few follow the same fate when it comes to track traditional biomarkers. Current practices still involve laboratory-based tests, followed by blood collection, conducted in a clinical setting as they require trained personnel and specialized equipment. In fact, real-time, passive/active and robust sensing of physiological and behavioural data from patients that can feed artificial intelligence (AI)-based models can significantly improve decision-making, diagnosis and treatment at the point-of-procedure, by circumventing conventional methods of sampling, and in person investigation by expert pathologists, who are scarce in developing countries. This review brings together conventional and digital biomarker sensing through portable and autonomous miniaturized devices. We first summarise the technological advances in each field vs the current clinical practices and we conclude by merging the two worlds of traditional and digital biomarkers through AI/ML technologies to improve patient diagnosis and treatment. The fundamental role, limitations and prospects of AI in realizing this potential and enhancing the existing technologies to facilitate the development and clinical translation of "point-of-care" (POC) diagnostics is finally showcased.
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Affiliation(s)
- Sagar S Arya
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Sofia B Dias
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates; Interdisciplinary Center for Human Performance, Faculdade de Motricidade Humana, Universidade de Lisboa, Portugal.
| | - Herbert F Jelinek
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates; Healthcare Engineering Innovation Center (HEIC), Khalifa University of Science and Technology, P O Box 127788, Abu Dhabi, United Arab Emirates
| | - Leontios J Hadjileontiadis
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates; Healthcare Engineering Innovation Center (HEIC), Khalifa University of Science and Technology, P O Box 127788, Abu Dhabi, United Arab Emirates; Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, GR, 54124, Thessaloniki, Greece
| | - Anna-Maria Pappa
- Department of Biomedical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates; Healthcare Engineering Innovation Center (HEIC), Khalifa University of Science and Technology, P O Box 127788, Abu Dhabi, United Arab Emirates; Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge, UK.
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8
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Gong T, Das CM, Yin MJ, Lv TR, Singh NM, Soehartono AM, Singh G, An QF, Yong KT. Development of SERS tags for human diseases screening and detection. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Ghimire ML, Cox BD, Winn CA, Rockett TW, Schifano NP, Slagle HM, Gonzalez F, Bertino MF, Caputo GA, Reiner JE. Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing. ACS NANO 2022; 16:17229-17241. [PMID: 36214366 DOI: 10.1021/acsnano.2c07842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
It was recently demonstrated that one can monitor ligand-induced structure fluctuations of individual thiolate-capped gold nanoclusters using resistive-pulse nanopore sensing. The magnitude of the fluctuations scales with the size of the capping ligand, and it was later shown one can observe ligand exchange in this nanopore setup. We expand on these results by exploring the different types of current fluctuations associated with peptide ligands attaching to tiopronin-capped gold nanoclusters. We show here that the fluctuations can be used to identify the attaching peptide through either the magnitude of the peptide-induced current jumps or the onset of high-frequency current fluctuations. Importantly, the peptide attachment process requires that the peptide contains a cysteine residue. This suggests that nanopore-based monitoring of peptide attachments with thiolate-capped clusters could provide a means for selective detection of cysteine-containing peptides. Finally, we demonstrate the cluster-based protocol with various peptide mixtures to show that one can identify more than one cysteine-containing peptide in a mixture.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Cole A Winn
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Thomas W Rockett
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nicholas P Schifano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Hannah M Slagle
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Frank Gonzalez
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Massimo F Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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10
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Mass Spectrometry Approaches for SARS-CoV-2 Detection: Harnessing for Application in Food and Environmental Samples. Viruses 2022; 14:v14050872. [PMID: 35632614 PMCID: PMC9144875 DOI: 10.3390/v14050872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
The public health crisis caused by the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 has drastically changed our lifestyle in virtually all contexts around the world. SARS-CoV-2 is mainly airborne, transmitted by the salivary droplets produced when infected people cough or sneeze. In addition, diarrhea symptoms and the detection of SARS-CoV-2 in feces suggest a fecal–oral route of contagion. Currently, the high demand for SARS-CoV-2 diagnosis has surpassed the availability of PCR and immunodetection probes and has prompted the development of other diagnostic alternatives. In this context, mass spectrometry (MS) represents a mature, robust alternative platform for detection of SARS-CoV-2 and other human viruses. This possibility has raised great interest worldwide. Therefore, it is time for the global application of MS as a feasible option for detecting SARS-CoV-2, not only in human fluids, but also in other matrices such as foods and wastewater. This review covers the most relevant established methods for MS-based SARS-CoV-2 detection and discusses the future application of these tools in different matrices. Significance: The Coronavirus Disease 2019 (COVID-19) pandemic highlighted the pros and cons of currently available PCR and immunodetection tools. The great concern over the infective potential of SARS-CoV-2 viral particles that can persist for several hours on different surfaces under various conditions further evidenced the need for reliable alternatives and high-throughput methods to meet the needs for mass detection of SARS-CoV-2. In this context, MS-based proteomics emerging from fundamental studies in life science can offer a robust option for SARS-CoV-2 detection in human fluids and other matrices. In addition, the substantial efforts towards detecting SARS-CoV-2 in clinal samples, position MS to support the detection of this virus in different matrices such as the surfaces of the packing food process, frozen foods, and wastewaters. Proteomics and mass spectrometry are, therefore, well positioned to play a role in the epidemiological control of COVID-19 and other future diseases. We are currently witnessing the opportunity to generate technologies to overcome prolonged pandemics for the first time in human history.
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Petroušková P, Hudáková N, Maloveská M, Humeník F, Cizkova D. Non-Exosomal and Exosome-Derived miRNAs as Promising Biomarkers in Canine Mammary Cancer. Life (Basel) 2022; 12:life12040524. [PMID: 35455015 PMCID: PMC9032658 DOI: 10.3390/life12040524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
Canine mammary cancer (CMC), similar to human breast cancer (HBC) in many aspects, is the most common neoplasm associated with significant mortality in female dogs. Due to the limited therapy options, biomarkers are highly desirable for early clinical diagnosis or cancer progression monitoring. Since the discovery of microRNAs (miRNAs or miRs) as post-transcriptional gene regulators, they have become attractive biomarkers in oncological research. Except for intracellular miRNAs and cell-free miRNAs, exosome-derived miRNAs (exomiRs) have drawn much attention in recent years as biomarkers for cancer detection. Analysis of exosomes represents a non-invasive, pain-free, time- and money-saving alternative to conventional tissue biopsy. The purpose of this review is to provide a summary of miRNAs that come from non-exosomal sources (canine mammary tumor, mammary tumor cell lines or canine blood serum) and from exosomes as promising biomarkers of CMC based on the current literature. As is discussed, some of the miRNAs postulated as diagnostic or prognostic biomarkers in CMC were also altered in HBC (such as miR-21, miR-29b, miR-141, miR-429, miR-200c, miR-497, miR-210, miR-96, miR-18a, miR19b, miR-20b, miR-93, miR-101, miR-105a, miR-130a, miR-200c, miR-340, miR-486), which may be considered as potential disease-specific biomarkers in both CMC and HBC.
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Affiliation(s)
- Patrícia Petroušková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Nikola Hudáková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Marcela Maloveská
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Filip Humeník
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Dasa Cizkova
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 10 Bratislava, Slovakia
- Correspondence: ; Tel.: +421-918-752-157
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12
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Momenbeitollahi N, van der Zalm J, Chen A, Li H. Methods for Enhanced Fluorescence Detection of Proteins by using Entrapped Gold Nanoparticles in Membranes. Curr Protoc 2022; 2:e404. [PMID: 35333454 DOI: 10.1002/cpz1.404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Measuring protein levels from biofluids can provide important insight into human health and disease during various physiological and pathological conditions. In many situations, sensitive methods are required for protein quantification because at the early stages of many diseases, proteins in biofluids are present at very low concentrations. Here, a new and simple method is presented in the form of Basic and Alternative Protocols for an immunoassay performed on a nitrocellulose membrane, followed by the addition of gold nanoparticles prior to measuring fluorescence with a microscope. The assay protocol was optimized to achieve 3D metal-enhanced fluorescence (MEF) with increased antibody-binding capacity and enhanced fluorescence signals, improving assay sensitivity. Using different concentrations of spiked fluorescently labeled IgGs in pooled normal human plasma, a lower detection limit of 29 ng/ml was achieved. This limit of detection was found to be a thousand-fold lower than the conventional 2D assay and one order of magnitude lower than when the assay was performed on a 3D membrane without MEF. This method provides an easy way to improve immunoassay sensitivity, and it can be simply transferred to other labs. It also can extend to fluorescence detection of other analytes beyond proteins. © 2022 Wiley Periodicals LLC. Basic Protocol: Assay in nitrocellulose membrane with entrapped AuNPs using commercially available AuNPs Alternative Protocol: Assay in nitrocellulose membrane with entrapped AuNPs using lab-made AuNPs.
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Affiliation(s)
| | | | - Aicheng Chen
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada
| | - Huiyan Li
- School of Engineering, University of Guelph, Guelph, Ontario, Canada
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13
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Entrapping gold nanoparticles in membranes for simple-to-use enhanced fluorescence detection of proteins. Anal Chim Acta 2022; 1195:339443. [DOI: 10.1016/j.aca.2022.339443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/02/2022] [Accepted: 01/03/2022] [Indexed: 11/23/2022]
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14
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Bacon K, Menegatti S, Rao BM. Isolation of Single-Domain Antibodies to Transmembrane Proteins Using Magnetized Yeast Cell Targets. Methods Mol Biol 2022; 2446:95-119. [PMID: 35157270 DOI: 10.1007/978-1-0716-2075-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The isolation of binding ligands from yeast-displayed combinatorial libraries has typically relied on the use of a soluble, recombinantly expressed form of the target protein when performing magnetic selections or fluorescence-activated cell sorting. When identifying binding ligands, appropriate target protein expression and subsequent purification represents a significant bottleneck. As an alternative, we describe the use of target proteins expressed on the surface of magnetized yeast cells in the selection of yeast-displayed nanobody libraries. In this approach, yeast cells displaying the target protein also co-express an iron oxide-binding protein; incubation with iron oxide nanopowder results in magnetization of target-displaying cells. Alternatively, target-displaying cells are magnetized by nonspecific adsorption of iron oxide nanopowder. Subsequently, any library cells that interact with the magnetized target cells can be isolated using a magnet. Here, we detail protocols for the isolation of binders to membrane protein targets from a yeast display nanobody library using magnetized yeast cell targets. We provide guidance on how to generate magnetic yeast cell targets as well as library selection conditions to bias the isolation of high affinity binders. We also discuss how to assess the affinity and specificity of the isolated nanobodies using flow cytometry.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, USA.
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15
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Smirnova TA, Viskin A, Hoskova M, Habartova L, Setnicka V, Cejnar P, Kuckova S. Comparison of proteomic approaches used for the detection of potential biomarkers of Alzheimer's disease in blood plasma. J Sep Sci 2021; 44:4132-4140. [PMID: 34545700 DOI: 10.1002/jssc.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/03/2021] [Accepted: 09/12/2021] [Indexed: 11/10/2022]
Abstract
At present, Alzheimer's disease is detected mainly using psychological tests, which can only confirm the disease in its more advanced phases. Therefore, bioanalytical possibilities for detecting this disease earlier are being investigated. To date, the results of analyses, which focus mainly on the study of lipids and proteins either in cerebrospinal fluid or much less often in blood plasma, do not provide satisfactory results. In addition, cerebrospinal fluid sampling is uncomfortable for the patients and involves many health risks. In this work, we deal with proteomic analysis using Matrix-Assisted Laser Desorption/Ionisation-Time of Flight and Liquid Chromatography coupled to tandem Mass Spectrometry of blood plasma with a focus on various ways of preanalytical sample treatments. This should lead to results improvement and facilitate the subsequent evaluation using principal component analysis and partial least squares discriminant analysis. The obtained results indicate the direction of further research, namely the study of interactions between proteins and lipids contained in blood plasma. These substances may be regarded as potential biomarkers allowing for the diagnosis of Alzheimer´s disease even in its early stages.
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Affiliation(s)
- Tatiana Anatolievna Smirnova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Anton Viskin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Martina Hoskova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Lucie Habartova
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Vladimir Setnicka
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Pavel Cejnar
- Department of Computing and Control Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Stepanka Kuckova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
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16
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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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17
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Silva MLS. Microfluidic devices for glycobiomarker detection in cancer. Clin Chim Acta 2021; 521:229-243. [PMID: 34273337 DOI: 10.1016/j.cca.2021.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022]
Abstract
During oncogenesis, several alterations occur within cells, one of them being the abnormal glycosylation of proteins, resulting in the formation of glycoproteins with aberrant glycan structures, which can be secreted into the blood stream. Their specific association to tumour cells makes them useful indicators (biomarkers) of the oncogenic process and their detection in blood can be employed in different stages of tumour development for early detection, prognosis and therapeutic drug monitoring. Due to the importance of detecting cancer-associated glycoproteins with aberrant glycosylation in blood or serum, analytical methodologies with improved performance are required to ameliorate the laboratorial tests currently used for the detection of these analytes. Microfluidics was created to facilitate the implementation of simple and point-of-care analysis, away from a centralized laboratory. The massive use of microfluidic systems in clinical settings can be seen in pregnancy tests and diabetes control, for example. But what about other clinical domains, such as the detection of glycoproteins with aberrant glycans secreted by tumour cells? Are microfluidic systems helpful in this case? This review analyses the requirements of a microfluidic assay for the detection of low-abundant blood/serum cancer-associated glycoproteins with abnormal glycans and the progresses that have been made in the last years to develop integrated microfluidic devices for this particular application. The diverse microfluidic systems found in literature present, in general, the same analytical performance as the conventional assays but have additional advantages, namely a reduction in assay times, a decrease of sample and reagent consumption and lower costs. The review will also focus on the improvements that are still needed for better biosensing of this type of cancer biomarkers using microfluidic devices.
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Affiliation(s)
- M Luísa S Silva
- Centre of Chemical Research, Autonomous University of Hidalgo State, Carr. Pachuca-Tulancingo km 4.5, Pachuca, Hidalgo 42076, Mexico.
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18
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Tans R, van Rijswijck DMH, Davidson A, Hannam R, Ricketts B, Tack CJ, Wessels HJCT, Gloerich J, van Gool AJ. Affimers as an alternative to antibodies for protein biomarker enrichment. Protein Expr Purif 2020; 174:105677. [PMID: 32461183 DOI: 10.1016/j.pep.2020.105677] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Assessing the specificity of protein binders is an essential first step in protein biomarker assay development. Affimers are novel protein binders and can potentially replace antibodies in multiple protein capture-based assays. Affimers are selected for their high specificity against the target protein and have benefits over antibodies like batch-to-batch reproducibility and are stable across a wide range of chemical conditions. Here we mimicked a typical initial screening of affimers and commercially available monoclonal antibodies against two non-related proteins, IL-37b and proinsulin, to assess the potential of affimers as alternative to antibodies. METHODS Binding specificity of anti-IL-37b and anti-proinsulin affimers and antibodies was investigated via magnetic bead-based capture of their recombinant protein targets in human plasma. Captured proteins were analyzed using SDS-PAGE, Coomassie blue staining, Western blotting and LC-MS/MS-based proteomics. RESULTS All affimers and antibodies were able to bind their target protein in human plasma. Gel and LC-MS/MS analysis showed that both affimer and antibody-based captures resulted in co-purified background proteins. However, affimer-based captures showed the highest relative enrichment of IL-37b and proinsulin. CONCLUSIONS For both proteins tested, affimers show higher specificity in purifying their target proteins from human plasma compared to monoclonal antibodies. These results indicate that affimers are promising antibody-replacement tools for protein biomarker assay development.
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Affiliation(s)
- Roel Tans
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Danique M H van Rijswijck
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Alex Davidson
- Avacta Life Sciences, Unit 20, Ash Way, Thorp Arch Estate & Retail Park, Wetherby, LS23 7FA, United Kingdom
| | - Ryan Hannam
- Avacta Life Sciences, Unit 20, Ash Way, Thorp Arch Estate & Retail Park, Wetherby, LS23 7FA, United Kingdom
| | - Bryon Ricketts
- Avacta Life Sciences, Unit 20, Ash Way, Thorp Arch Estate & Retail Park, Wetherby, LS23 7FA, United Kingdom
| | - Cees J Tack
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Jolein Gloerich
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
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19
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Axelrod T, Eltzov E, Marks RS. Capture-Layer Lateral Flow Immunoassay: A New Platform Validated in the Detection and Quantification of Dengue NS1. ACS OMEGA 2020; 5:10433-10440. [PMID: 32426600 PMCID: PMC7226885 DOI: 10.1021/acsomega.0c00367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 03/31/2020] [Indexed: 05/07/2023]
Abstract
The lateral flow immunoassay (LFIA) is the most successful point-of-care testing (POCT) method to date. In the case of clinical biomarkers that require quantification, it remains a challenge to quantitate those biomarkers using the lateral flow immunoassay remains a challenge due to the cost of the reader and possibly the type of marker used. In the present work, a new concept of a platform LFIA device configuration is proposed in which different, aligned membrane components, some already existing in the classical lateral flow immunoassay, and the others created with special new functions in the present device. As the sample containing the target analyte passes through the aforementioned membranes, the target analyte will initially interact with a target-specific antibody-conjugated to horseradish peroxidase (HRP). Thereafter, the newly formed immunocomplex will diffuse through a proprietary capture membrane (that ensures that the nontarget-bound antibodies do not continue further and thus remain "captured" to that specific area). This is done by having the target molecules (or components thereof) immobilized onto the said capture layer. The target-bound immunocomplexes will then be allowed by the system configuration to continue further to the last layer, where the signal will be generated and quantified. Thus, in the absence of the target analyte in the sample, the free antibodies will be filtered at the capture layer by preimmobilized analyte molecules, thus preventing a false positive signal to occur. We validated the concept in the detection of dengue NS1 protein in view of making a triage test. The sample containing NS1 will first meet HRP-conjugated NS1-specific antibodies and become attached, thus producing an NS1-specific antibody-HRP immunocomplex. The sample then flows through the blocking layer, where the immunocomplex is unchallenged and thus allowed to reach the last "absorbent" pad, incorporating the substrate for the HRP marker. In the case of a positive test, a signal is generated, that is proportional to the amount of immunocomplexes (and therefore the NS1 concentration), and then analyzed and measured at the absorbent pad. Any unbound anti-NS1 antibody will be stopped at the blocking matrix by preimmobilized NS1, so there will be no false positive. As this study is the initial study of a novel configuration, much of the work comprised of optimization steps, such as determining the required NS1 membrane-immobilization concentration and the required target-specific capture antibody concentration. Our immunoassay was tested with spiked buffer and serum samples to mimic the clinical conditions, with a range of NS1 concentrations, and was found, at this time, to be fivefold more sensitive than a gold standard enzyme-linked immunosorbent assay (ELISA) test (5 ng mL-1) performed in our laboratory. This method shows another form of LFIA that has the potential to be quantitative (at least semiquantitative), albeit not solving the reader cost; however, unlike the regular LFIA, we do not use nanobeads but instead enzymes, allowing, in theory, greater sensitivity, while retaining the one-step procedure. The test is accurate and has low production costs.
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Affiliation(s)
- Tim Axelrod
- Department
of Biotechnology Engineering, Faculty of Engineering Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Evgeni Eltzov
- Department
of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Robert S. Marks
- Department
of Biotechnology Engineering, Faculty of Engineering Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- National
Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The
Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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20
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Nassar FJ, Chamandi G, Tfaily MA, Zgheib NK, Nasr R. Peripheral Blood-Based Biopsy for Breast Cancer Risk Prediction and Early Detection. Front Med (Lausanne) 2020; 7:28. [PMID: 32118013 PMCID: PMC7026666 DOI: 10.3389/fmed.2020.00028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Among women, breast cancer (BC) is not only the most common cancer worldwide but also the leading cause of cancer death. Only 5–10% of breast cancer cases are attributed to inherited mutations (BRCA1, BRCA2, and other breast cancer susceptibility genes). Breast cancer incidence has been rising particularly in young women who are not eligible for mammography, and it has been acting as a burden especially in developing countries that lack screening and awareness programs. For this reason, research has shifted to use minimally invasive liquid biopsies especially blood-based biomarkers with potential value for breast cancer risk prediction and early detection. This mini-review will tackle the different blood-based biomarkers focusing mainly on circulating miRNA, circulating proteins, cell-free nucleic acids, methylation patterns, and exosomes. It also introduces the potential opportunities for the clinical use of these blood-based biomarkers for breast cancer risk prediction.
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Affiliation(s)
- Farah J Nassar
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghada Chamandi
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Mohamad Ali Tfaily
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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21
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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22
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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23
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Bacon K, Burroughs M, Blain A, Menegatti S, Rao BM. Screening Yeast Display Libraries against Magnetized Yeast Cell Targets Enables Efficient Isolation of Membrane Protein Binders. ACS COMBINATORIAL SCIENCE 2019; 21:817-832. [PMID: 31693340 DOI: 10.1021/acscombsci.9b00147] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
When isolating binders from yeast displayed combinatorial libraries, a soluble, recombinantly expressed form of the target protein is typically utilized. As an alternative, we describe the use of target proteins displayed as surface fusions on magnetized yeast cells. In our strategy, the target protein is coexpressed on the yeast surface with an iron oxide binding protein; incubation of these yeast cells with iron oxide nanoparticles results in their magnetization. Subsequently, binder cells that interact with the magnetized target cells can be isolated using a magnet. Using a known binder-target pair with modest binding affinity (KD ≈ 400 nM), we showed that a binder present at low frequency (1 in 105) could be enriched more than 100-fold, in a single round of screening, suggesting feasibility of screening combinatorial libraries. Subsequently, we screened yeast display libraries of Sso7d and nanobody variants against yeast displayed targets to isolate binders specific to the cytosolic domain of the mitochondrial membrane protein TOM22 (KD ≈ 272-1934 nM) and the extracellular domain of the c-Kit receptor (KD ≈ 93 to KD > 2000 nM). Additional studies showed that the TOM22 binders identified using this approach could be used for the enrichment of mitochondria from cell lysates, thereby confirming binding to the native mitochondrial protein. The ease of expressing a membrane protein or a domain thereof as a yeast cell surface fusion-in contrast to recombinant soluble expression-makes the use of yeast-displayed targets particularly attractive. Therefore, we expect the use of magnetized yeast cell targets will enable efficient isolation of binders to membrane proteins.
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24
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Yang X, Liu Q, Wen D, Gao M, Zhang D, Jin Q, Kong J, Zhang J. Ultrasensitive fluorescence detection of sequence-specific DNA via labeling hairpin DNA probes for fluorescein o-acrylate polymers. Anal Chim Acta 2019; 1088:144-149. [PMID: 31623710 DOI: 10.1016/j.aca.2019.08.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/12/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
Sensitive detection of DNA is conducive to enhance the accuracy of diseases diagnosis and risk prediction. In this work, we report the use of activators generated by electron transfer for atom transfer radical polymerization (AGET ATRP) as a novel on-chip amplification strategy for the fluorescence detection of DNA. More specifically, the target DNA was captured by the on-chip immobilized hairpin DNA probes. Upon hybridization, exposed 3'-N3 of the hairpin was used to attach AGET ATRP initiators onto the silicon surface by click chemistry. Then, numerous fluorescent labeling linked to the end of the probes via the formation of long chain polymers of fluorescein o-acrylate, which in turn amplified the fluorescence signal for DNA detection. Under optimal conditions, it showed a good linear range from 100 fM to 1 μM in DNA detection, with the limit of detection as low as 4.3 fM. Moreover, this strategy showed good detection performance in complex real serum samples, the fluorescence intensity of 0.1 nM tDNA in 1% fetal bovine serum samples was 97.6% of that in Tris-EDTA buffer. Based on its high sensitivity, reduced cost and simplicity, the proposed signal amplification strategy displays translational potential in clinical application.
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Affiliation(s)
- Xinxiu Yang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Qianrui Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, PR China
| | - Dongxiao Wen
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450008, PR China
| | - Meng Gao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Dongjian Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Qiaomei Jin
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, PR China.
| | - Jian Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China.
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25
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Abstract
Protein analysis of potential disease markers in blood is complicated by the fact that proteins in plasma show very different abundances. As a result, high-abundance proteins dominate the analysis, which often render the analysis of low-abundance proteins impossible. Depleting high-abundance proteins is one strategy to solve this problem. Here, we present, for the first time, a very simple approach based on selective binding of serum proteins to the surface of nanodiamonds. In our first proof-of-principle experiments, we were able to detect, on average, eight proteins that are present at a concentration of 1 ng/mL (instead of 0.5 ng/mL in the control without sample preparation). Remarkably, we detect proteins down to a concentration of 400 pg/mL after only one simple depletion step. Among the proteins we could analyze are also numerous disease biomarkers, including markers for multiple cancer forms, cardiovascular diseases, or Alzheimer's disease. Remarkably, many of the biomarkers we find also could not be detected with a state-of-the-art ultrahigh-performance liquid chromatography column (which depletes the 64 most-abundant serum proteins).
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Affiliation(s)
- Felipe Perona Martinez
- Groningen University, University Medical Center Groningen , Antonius Deusinglaan 1 , 9713 AW Groningen , The Netherlands
| | - Andreas Nagl
- Groningen University, University Medical Center Groningen , Antonius Deusinglaan 1 , 9713 AW Groningen , The Netherlands
| | - Sona Guluzade
- Groningen University, University Medical Center Groningen , Antonius Deusinglaan 1 , 9713 AW Groningen , The Netherlands
| | - Romana Schirhagl
- Groningen University, University Medical Center Groningen , Antonius Deusinglaan 1 , 9713 AW Groningen , The Netherlands
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Sun H, Xu W, Liu B, Liu Q, Wang Q, Li L, Kong J, Zhang X. Ultrasensitive Detection of DNA via SI-eRAFT and in Situ Metalization Dual-Signal Amplification. Anal Chem 2019; 91:9198-9205. [PMID: 31192582 DOI: 10.1021/acs.analchem.9b01961] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, we report a new amplification strategy based on electrochemically mediated reversible addition-fragmentation chain transfer (eRAFT) and in situ metalization for electrochemical detection of DNA. First, peptide nucleic acid (PNA) probes were immobilized on the surface of the gold electrode, and when they hybridized with the target DNA, the chain transfer agent (CTA), 4-cyano-4-(phenylcarbonothioylthio)pentanoic acid (CPAD), of RAFT was connected to the PNA/DNA heteroduplex formed by the coordination bonding of Zr4+. Then glycosyloxyethyl methacrylates (GEMA) were assembled on the surface of the electrode by electrochemically mediated surface-initiated reversible addition-fragmentation chain transfer (SI-eRAFT) to form a polymer-containing sugar glucose. Next, the o-hydroxyl groups on the polysaccharide molecular skeleton were oxidized to aldehyde groups by sodium periodate (NaIO4). The aldehyde groups generated then reduce silver ions to silver particles deposited on the electrode surface in situ, and this system was then subjected to differential pulse voltammetry (DPV). Under optimal conditions, the intensity of the stripping current and the logarithm of the target DNA (tDNA) concentration has a good linear relationship in the range of 10 aM to 1 pM (R2 = 0.996), and the detection limit can go down to 5.4 aM (S/N = 3). Moreover, the method is suitable for single-nucleotide polymorphism (SNP) analysis and has strong anti-interference ability for the analysis of target ssDNA in serum samples.
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Affiliation(s)
- Haobo Sun
- School of Chemistry and Chemical Engineering , Liaocheng University , Liaocheng 252059 , People's Republic of China.,School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , People's Republic of China
| | - Wen Xu
- School of Chemistry and Chemical Engineering , Huangshan University , Huangshan 245041 , People's Republic of China
| | - Bang Liu
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , People's Republic of China
| | - Qianrui Liu
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , People's Republic of China
| | - Qiangwei Wang
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , People's Republic of China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering , Liaocheng University , Liaocheng 252059 , People's Republic of China
| | - Jinming Kong
- School of Environmental and Biological Engineering , Nanjing University of Science and Technology , Nanjing 210094 , People's Republic of China
| | - Xueji Zhang
- School of Biomedical Engineering , Shenzhen University Health Science Center , Shenzhen , Guangdong 518060 , People's Republic of China
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27
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Il n'y a pas d'amour heureux
pour Casanova: Chemical‐ and bio‐analysis of his
Memoirs. Electrophoresis 2019; 40:3050-3056. [DOI: 10.1002/elps.201800505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 01/30/2023]
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Boschetti E, Hernández-Castellano LE, Righetti PG. Progress in farm animal proteomics: The contribution of combinatorial peptide ligand libraries. J Proteomics 2019; 197:1-13. [DOI: 10.1016/j.jprot.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/17/2019] [Accepted: 02/07/2019] [Indexed: 02/08/2023]
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Åström M, Tajeddinn W, Karlsson MG, Linder O, Palmblad J, Lindblad P. Cytokine Measurements for Diagnosing and Characterizing Leukemoid Reactions and Immunohistochemical Validation of a Granulocyte Colony-Stimulating Factor and CXCL8-Producing Renal Cell Carcinoma. Biomark Insights 2018; 13:1177271918792246. [PMID: 30147294 PMCID: PMC6100120 DOI: 10.1177/1177271918792246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022] Open
Abstract
Background Various paraneoplastic syndromes are encountered in renal cell carcinomas. This case report illustrates that a paraneoplastic leukemoid reaction may precede the diagnosis of renal cell carcinoma and be explained by cytokine production from the cancer cells. Case presentations A 64-year-old man was referred for hematology workup due to pronounced leukocytosis. While being evaluated for a possible hematologic malignancy as the cause, he was found to have a metastasized renal cell carcinoma, and hyperleukocytosis was classified as a leukemoid reaction. A multiplex panel for measurement of 25 serum cytokines/chemokines showed highly elevated levels of granulocyte colony-stimulating factor (G-CSF) and CXCL8 (C-X-C-motif chemokine ligand 8, previously known as interleukin [IL]-8). By immunohistochemistry it was shown that the renal carcinoma cells expressed both these cytokines. Two additional, consecutive patients with renal cell carcinoma with paraneoplastic leukocytosis also showed elevated serum levels of CXCL8, but not of G-CSF. Nonparametric statistical evaluation showed significantly higher serum concentrations of CXCL8, IL-6, IL-10, monocyte chemoattractant protein 1 (MCP-1), and tumor necrosis factor, but lower interferon gamma (IFN-γ) and IL-1α, for the 3 renal cell carcinoma cases compared with healthy blood donors. Conclusions In suspected paraneoplastic leukocytosis, multiplex serum cytokine analyses may facilitate diagnosis and provide an understanding of the mechanisms for the reaction. In the index patient, combined G-CSF and CXCL8 protein expression by renal carcinoma cells was uniquely documented. A rapidly fatal course was detected in all 3 cases, congruent with the concept that autocrine/paracrine growth signaling in renal carcinoma cells may induce an aggressive tumor phenotype. Immune profiling studies could improve our understanding for possible targets when choosing therapies for patients with metastatic renal cell carcinoma.
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Affiliation(s)
- Maria Åström
- Division of Hematology, Department of Medicine, Örebro University Hospital, Örebro, Sweden.,Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Walid Tajeddinn
- iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mats G Karlsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Olle Linder
- Division of Hematology, Department of Medicine, Örebro University Hospital, Örebro, Sweden
| | - Jan Palmblad
- Division of Hematology, Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Per Lindblad
- Department of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Proteomic biomarkers in body fluids associated with pancreatic cancer. Oncotarget 2018; 9:16573-16587. [PMID: 29662668 PMCID: PMC5893263 DOI: 10.18632/oncotarget.24654] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer (PC) is a highly malignant disease that represents the fourth leading cancer-related death worldwide. There has been very little improvement in survival rates over recent years, and surgical resection remains the only reliable curative approach. Factors that contribute to this dismal prognosis for PC include its rapid progression and invasion, the absence of specific symptoms, and the little impact of available chemotherapy. Importantly, the management of this malignancy is also limited by the lack of highly specific and sensitive biomarkers for its diagnosis and follow-up, and their identification is therefore considered a promising strategy to improve outcomes in these patients. Numerous translational studies have explored the usefulness of body fluids as a non-invasive source of PC-specific biomarkers, and innovations in proteomic methods and technologies have provided a myriad of protein biomarkers for different cancers. The adoption of a proteomic approach has improved understanding of the biology of PC and contributed to the potential identification of protein biomarkers for this disease. This review considers the most recent research efforts to develop novel proteomic biomarkers in body fluids for PC.
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Gao J, Meyer K, Borucki K, Ueland PM. Multiplex Immuno-MALDI-TOF MS for Targeted Quantification of Protein Biomarkers and Their Proteoforms Related to Inflammation and Renal Dysfunction. Anal Chem 2018; 90:3366-3373. [DOI: 10.1021/acs.analchem.7b04975] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jie Gao
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Klaus Meyer
- Bevital AS, Jonas Lies veg 87, Laboratory Building, Ninth Floor, 5021 Bergen, Norway
| | - Katrin Borucki
- Institute for Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44 , 39120 Magdeburg, Germany
| | - Per Magne Ueland
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Laboratory of Clinical Biochemistry, Haukeland University Hospital, 5021 Bergen, Norway
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