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Jankowski MS, Griffith D, Shastry DG, Pelham JF, Ginell GM, Thomas J, Karande P, Holehouse AS, Hurley JM. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator. Nat Commun 2024; 15:3523. [PMID: 38664421 DOI: 10.1038/s41467-024-47761-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.
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Affiliation(s)
- Meaghan S Jankowski
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua Thomas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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2
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Yazaki J, Dal-Bianco M. In Situ Protein Microarray for Identifying the Geminivirus-Arabidopsis Interactome. Methods Mol Biol 2024; 2724:307-314. [PMID: 37987915 DOI: 10.1007/978-1-0716-3485-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The protein-protein interactions (PPI) by protein array technology complement other PPI assay technologies such as AP-MS and Y2H. The in situ protein array technology (NAPPA) enables low-cost, rapid, and comprehensive protein detection. It allows standardized and simultaneous assay of a wide range of proteins with a broad range of expression in cells. This technology facilitates the detection of protein-protein interactions within species and between heterologous species such as host-microbe. Here, we described the technique that identified a syntaxin-6 protein-mediated begomovirus infection using an array containing 4600 Arabidopsis genes. The protein microarray assay also identified several other viral protein-host protein interactions.
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Affiliation(s)
- Junshi Yazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan.
| | - Maximiller Dal-Bianco
- Plant Genetics and Biochemistry Laboratory, BIOAGRO, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.
- Department of Biochemistry and Molecular Biology, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.
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3
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Pileri T, Sinibaldi A, Occhicone A, Danz N, Giordani E, Allegretti M, Sonntag F, Munzert P, Giacomini P, Michelotti F. Direct competitive assay for HER2 detection in human plasma using Bloch surface wave-based biosensors. Anal Biochem 2024; 684:115374. [PMID: 37914005 DOI: 10.1016/j.ab.2023.115374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/13/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
The overexpression and/or amplification of the HER2/neu oncogene has been proposed as a prognostic marker in breast cancer. The detection of the related peptide HER2 remains a grand challenge in cancer diagnosis and for therapeutic decision-making. Here, we used a biosensing device based on Bloch Surface Waves excited on a one-dimensional photonic crystal (1DPC) as valid alternative to standard techniques. The 1DPC was optimized to operate in the visible spectrum and the biosensor optics has been designed to combine label-free and fluorescence operation modes. This feature enables a real-time monitoring of a direct competitive assay using detection mAbs conjugated with quantum dots for an accurate discrimination in fluorescence mode between HER2-positive/negative human plasma samples. Such a competitive assay was implemented using patterned alternating areas where HER2-Fc chimera and reference molecules were bio-conjugated and monitored in a multiplexed way. By combining Label-Free and fluorescence detection analysis, we were able to tune the parameters of the assay and provide an HER2 detection in human plasma in less than 20 min, allowing for a cost-effective assay and rapid turnaround time. The proposed approach offers a promising technique capable of performing combined label-free and fluorescence detection for both diagnosis and therapeutic monitoring of diseases.
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Affiliation(s)
- Tommaso Pileri
- SAPIENZA Università di Roma, Department of Basic and Applied Sciences for Engineering, Via A. Scarpa, 16, 00161, Roma, Italy
| | - Alberto Sinibaldi
- SAPIENZA Università di Roma, Department of Basic and Applied Sciences for Engineering, Via A. Scarpa, 16, 00161, Roma, Italy; Center for Life Nano and Neuro Science, Italian Institute of Technology (IIT), Viale Regina Elena 291, 00161, Rome, Italy.
| | - Agostino Occhicone
- SAPIENZA Università di Roma, Department of Basic and Applied Sciences for Engineering, Via A. Scarpa, 16, 00161, Roma, Italy; Center for Life Nano and Neuro Science, Italian Institute of Technology (IIT), Viale Regina Elena 291, 00161, Rome, Italy
| | - Norbert Danz
- Fraunhofer Institute for Applied Optics and Precision Engineering, A.-Einstein-Str. 7, 07745, Jena, Germany
| | - Elena Giordani
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Matteo Allegretti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Frank Sonntag
- Fraunhofer Institute for Material and Beam Technology IWS, Winterbergstr. 28, 01277, Dresden, Germany
| | - Peter Munzert
- Fraunhofer Institute for Applied Optics and Precision Engineering, A.-Einstein-Str. 7, 07745, Jena, Germany
| | - Patrizio Giacomini
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesco Michelotti
- SAPIENZA Università di Roma, Department of Basic and Applied Sciences for Engineering, Via A. Scarpa, 16, 00161, Roma, Italy; Center for Life Nano and Neuro Science, Italian Institute of Technology (IIT), Viale Regina Elena 291, 00161, Rome, Italy
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4
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Takeda H. Autoantibody Profiling Using Human Autoantigen Protein Array and AlphaScreen. Methods Mol Biol 2024; 2766:107-128. [PMID: 38270871 DOI: 10.1007/978-1-0716-3682-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Autoantibodies that recognize self-antigens are believed to have a close relationship with diseases such as autoimmune diseases, cancer, and lifestyle diseases. Analysis of autoantibodies is essential for investigating pathology mechanisms, diagnosis, and therapeutics of these diseases. We developed an autoantibody profiling assay using a cell-free synthesized protein array and high-throughput screening technology. Our assay system can sensitively detect interaction between recombinant antigen protein and autoantibody and efficiently analyze autoantibody profiling in patients' sera.
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Affiliation(s)
- Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan.
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5
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Tsai PS, Du PX, Keskin BB, Lee NY, Wan SW, Lin YL, Su WY, Lin PC, Lin WH, Shih HC, Ho TS, Syu GD. Antibody Profiling of Dengue Severities Using Flavivirus Protein Microarrays. Anal Chem 2023; 95:15217-15226. [PMID: 37800729 DOI: 10.1021/acs.analchem.3c02165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Dengue is a viral disease transmitted by Aedes aegypti mosquitoes. According to the World Health Organization, about half of the world's population is at risk of dengue. There are four serotypes of the dengue virus. After infection with one serotype, it will be immune to such a serotype. However, subsequent infection with other serotypes will increase the risk of severe outcomes, e.g., dengue hemorrhagic fever, dengue shock syndrome, and even death. Since severe dengue is challenging to predict and lacks molecular markers, we aim to build a multiplexed Flavivirus protein microarray (Flaviarray) that includes all of the common Flaviviruses to profile the humoral immunity and cross-reactivity in the dengue patients with different outcomes. The Flaviarrays we fabricated contained 17 Flavivirus antigens with high reproducibility (R-square = 0.96) and low detection limits (172-214 pg). We collected serums from healthy subjects (n = 36) and dengue patients within 7 days after symptom onset (mild dengue (n = 21), hospitalized nonsevere dengue (n = 29), and severe dengue (n = 36)). After profiling the serum antibodies using Flaviarrays, we found that patients with severe dengue showed higher IgG levels against multiple Flavivirus antigens. With logistic regression, we found groups of markers with high performance in distinguishing dengue patients from healthy controls as well as hospitalized from mild cases (AUC > 0.9). We further reported some single markers that were suitable to separate dengue patients from healthy controls (AUC > 0.9) and hospitalized from mild outcomes (AUC > 0.8). Together, Flaviarray is a valuable tool to profile antibody specificities, uncover novel markers for decision-making, and shed some light on early preventions and treatments.
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Affiliation(s)
- Pei-Shan Tsai
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pin-Xian Du
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Batuhan Birol Keskin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Shu-Wen Wan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Ya-Lan Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Wen-Yu Su
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pei-Chun Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Hsun Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsi-Chang Shih
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Tzong-Shiann Ho
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Department of Pediatrics, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan R.O.C
- Department of Pediatrics, National Cheng Kung University Hospital Dou-Liou Branch, College of Medicine, National Cheng Kung University, Yunlin 640, Taiwan
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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6
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Keskin BB, Liu SF, Du PX, Tsai PS, Ho TS, Su WY, Lin PC, Shih HC, Weng KP, Yang KD, Huang YH, Kuo KC, Syu GD, Kuo HC. Profiling humoral responses to COVID-19 immunization in Kawasaki disease using SARS-CoV-2 variant protein microarrays. Analyst 2023; 148:4698-4709. [PMID: 37610260 DOI: 10.1039/d3an00802a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Kawasaki disease (KD) is a form of acute systemic vasculitis syndrome that predominantly occurs in children under the age of 5 years. Its etiology has been postulated due to not only genetic factors but also the presence of foreign antigens or infectious agents. To evaluate possible associations between Kawasaki disease (KD) and COVID-19, we investigated humoral responses of KD patients against S-protein variants with SARS-CoV-2 variant protein microarrays. In this study, plasma from a cohort of KD (N = 90) and non-KD control (non-KD) (N = 69) subjects in categories of unvaccinated-uninfected (pre-pandemic), SARS-CoV-2 infected (10-100 days after infection), and 1-dose, 2-dose, and 3-dose BNT162b2 vaccinated (10-100 days after vaccination) was collected. The principal outcomes were non-KD-KD differences for each category in terms of anti-human/anti-His for binding antibodies and neutralizing percentage for surrogate neutralizing antibodies. Binding antibodies against spikes were lower in the KD subjects with 1-dose of BNT162b2, and mean differences were significant for the P.1 S-protein (non-KD-KD, 3401; 95% CI, 289.0 to 6512; P = 0.0252), B.1.617.2 S-protein (non-KD-KD, 4652; 95% CI, 215.8 to 9087; P = 0.0351) and B.1.617.3 S-protein (non-KD-KD, 4874; 95% CI, 31.41 to 9716; P = 0.0477). Neutralizing antibodies against spikes were higher in the KD subjects with 1-dose of BNT162b2, and mean percentage differences were significant for the 1-dose BNT162b2 B.1.617.3 S-protein (non-KD-KD, -22.89%; 95% CI, -45.08 to -0.6965; P = 0.0399), B.1.1.529 S-protein (non-KD-KD, -25.96%; 95% CI, -50.53 to -1.376; P = 0.0333), BA.2.12.1 S-protein (non-KD-KD, -27.83%; 95% CI, -52.55 to -3.115; P = 0.0195), BA.4 S-protein (non-KD-KD, -28.47%; 95% CI, -53.59 to -3.342; P = 0.0184), and BA.5 S-protein (non-KD-KD, -30.42%; 95% CI, -54.98 to -5.869; P = 0.0077). In conclusion, we have found that KD patients have a comparable immunization response to healthy individuals to SARS-CoV-2 infection and COVID-19 immunization.
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Affiliation(s)
- Batuhan Birol Keskin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Room 89A07, No. 1, University Road, Tainan 701, Taiwan.
| | - Shih-Feng Liu
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Pin-Xian Du
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Room 89A07, No. 1, University Road, Tainan 701, Taiwan.
| | - Pei-Shan Tsai
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Room 89A07, No. 1, University Road, Tainan 701, Taiwan.
| | - Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, Republic of China
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan, Republic of China
- Department of Pediatrics, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan, Republic of China
| | - Wen-Yu Su
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Room 89A07, No. 1, University Road, Tainan 701, Taiwan.
| | - Pei-Chun Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Room 89A07, No. 1, University Road, Tainan 701, Taiwan.
| | - Hsi-Chang Shih
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ken-Pen Weng
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | | | - Ying-Hsien Huang
- Kawasaki Disease Center and Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan.
| | - Kuang-Che Kuo
- Kawasaki Disease Center and Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan.
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Room 89A07, No. 1, University Road, Tainan 701, Taiwan.
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Ho-Chang Kuo
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Kawasaki Disease Center and Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan.
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Kosoy G, Miller BL. Two Decades of Arrayed Imaging Reflectometry for Sensitive, High-Throughput Biosensing. Biosensors (Basel) 2023; 13:870. [PMID: 37754104 PMCID: PMC10526495 DOI: 10.3390/bios13090870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
Arrayed imaging reflectometry (AIR), first introduced in 2004, is a thin-film interference sensor technique that optimizes optical properties (angle of incidence, polarization, substrate refractive index, and thickness) to create a condition of total destructive interference at the surface of a silicon substrate. The advantages of AIR are its sensitivity, dynamic range, multiplex capability, and high-throughput compatibility. AIR has been used for the detection of antibodies against coronaviruses, influenza viruses, Staphylococcus aureus, and human autoantigens. It has also shown utility in detection of cytokines, with sensitivity comparable to bead-based and ELISA assays. Not limited to antibodies or antigens, mixed aptamer and protein arrays as well as glycan arrays have been employed in AIR for differentiating influenza strains. Mixed arrays using direct and competitive inhibition assays have enabled simultaneous measurement of cytokines and small molecules. Finally, AIR has also been used to measure affinity constants, kinetic and at equilibrium. In this review, we give an overview of AIR biosensing technologies and present the latest AIR advances.
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Affiliation(s)
- Gabrielle Kosoy
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14526, USA;
| | - Benjamin L. Miller
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14526, USA;
- Department of Dermatology, University of Rochester, Rochester, NY 14526, USA
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8
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McKeon A, Lesnick C, Vorasoot N, Buckley MW, Dasari S, Flanagan EP, Gilligan M, Lafrance-Corey R, Miske R, Pittock SJ, Scharf M, Yang B, Zekeridou A, Dubey D, Mills J. Utility of Protein Microarrays for Detection of Classified and Novel Antibodies in Autoimmune Neurologic Disease. Neurol Neuroimmunol Neuroinflamm 2023; 10:e200145. [PMID: 37550073 PMCID: PMC10406426 DOI: 10.1212/nxi.0000000000200145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND OBJECTIVES Neural antibodies are detected by tissue-based indirect immunofluorescence assay (IFA) in Mayo Clinic's Neuroimmunology Laboratory practice, but the process of characterizing and validating novel antibodies is lengthy. We report our assessment of human protein arrays. METHODS Assessment of arrays (81% human proteome coverage) was undertaken using diverse known positive samples (17 serum and 14 CSF). Samples from patients with novel neural antibodies were reflexed from IFA to arrays. Confirmatory assays were cell-based (CBA) or line blot. Epitope mapping was undertaken using phage display immunoprecipitation sequencing (PhiPSeq). RESULTS Control positive samples known to be reactive with linear epitopes of intracellular antigens (e.g., ANNA-1 [anti-Hu]) were readily identified by arrays in 20 of 21 samples. By contrast, 10 positive controls known to be enriched with antibodies against cell surface protein conformational epitopes (e.g., GluN1 subunit of NMDA-R) were indistinguishable from background signal. Three antibodies, previously characterized by other investigators (but unclassified in our laboratory), were unmasked in 4 patients using arrays (July-December 2022): Neurexin-3α, 1 patient; regulator of gene protein signaling (RGS)8, 1 patient; and seizure-related homolog like 2 (SEZ6L2), 2 patients. All were accompanied by previously reported phenotypes (encephalitis, 1; cerebellar ataxia, 3). Patient 1 had subacute onset of seizures and encephalopathy. Neurexin-3α ranked high in CSF (second ranked neural protein) but low in serum (660th overall). Neurexin-3α CBA was positive in both samples. Patient 2 presented with rapidly progressive cerebellar ataxia. RGS8 ranked the highest neural protein in available CSF sample by array (third overall). RGS8-specific line blot was positive. Patients 3 and 4 had rapidly progressive cerebellar ataxia. SEZ6L2 was the highest ranked neural antigen by arrays in all samples (CSF, 1, serum, 2; Patient 3, ranked 9th overall in CSF, 11th in serum; Patient 4, 6th overall in serum]). By PhIPSeq, diverse neurexin-3α epitopes (including cell surface) were detected in CSF from patient 1, but no SEZ6L2 peptides were detected for serum or CSF samples from Patient 3. DISCUSSION Individualized autoimmune neurologic diagnoses may be accelerated using protein arrays. They are optimal for detection of intracellular antigen-reactive antibodies, though certain cell surface-directed antibodies (neurexin-3α and SEZ6L2) may also be detected.
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Affiliation(s)
- Andrew McKeon
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany.
| | - Connie Lesnick
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Nisa Vorasoot
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Monica W Buckley
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Surendra Dasari
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Eoin P Flanagan
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Michael Gilligan
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Reghann Lafrance-Corey
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Ramona Miske
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Sean J Pittock
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Madeleine Scharf
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Binxia Yang
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Anastasia Zekeridou
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - Divyanshu Dubey
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
| | - John Mills
- From the Departments of Laboratory Medicine and Pathology and Neurology (A.M., E.P.F., S.J.P., B.Y., A.Z., D.D.); Department of Laboratory Medicine and Pathology (C.L., N.V., M.G., R.L.-C., J.M.); Khon Kaen University (N.V.), Thailand; University of Virginia (M.W.B.); Division of Biomedical Statistics and Informatics (S.D.), Mayo Clinic, Rochester, MN; The Institute for Experimental Immunology (R.M., M.S.), affiliated to Euroimmun AG, Lubeck, Germany
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9
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Boni R, Blackburn EA, Kleinjan DJ, Jonaitis M, Hewitt-Harris F, Murdoch M, Rosser S, Hay DC, Regan L. Chemically cross-linked hydrogels from repetitive protein arrays. J Struct Biol 2023; 215:107981. [PMID: 37245604 DOI: 10.1016/j.jsb.2023.107981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Biomaterials for tissue regeneration must mimic the biophysical properties of the native physiological environment. A protein engineering approach allows the generation of protein hydrogels with specific and customised biophysical properties designed to suit a particular physiological environment. Herein, repetitive engineered proteins were successfully designed to form covalent molecular networks with defined physical characteristics able to sustain cell phenotype. Our hydrogel design was made possible by the incorporation of the SpyTag (ST) peptide and multiple repetitive units of the SpyCatcher (SC) protein that spontaneously formed covalent crosslinks upon mixing. Changing the ratios of the protein building blocks (ST:SC), allowed the viscoelastic properties and gelation speeds of the hydrogels to be altered and controlled. The physical properties of the hydrogels could readily be altered further to suit different environments by tuning the key features in the repetitive protein sequence. The resulting hydrogels were designed with a view to allow cell attachment and encapsulation of liver derived cells. Biocompatibility of the hydrogels was assayed using a HepG2 cell line constitutively expressing GFP. The cells remained viable and continued to express GFP whilst attached or encapsulated within the hydrogel. Our results demonstrate how this genetically encoded approach using repetitive proteins could be applied to bridge engineering biology with nanotechnology creating a level of biomaterial customisation previously inaccessible.
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Affiliation(s)
- Rossana Boni
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth A Blackburn
- Edinburgh Protein Production Facility (EPPF), University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk-Jan Kleinjan
- UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mantas Jonaitis
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Flora Hewitt-Harris
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Megan Murdoch
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan Rosser
- UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David C Hay
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Lynne Regan
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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10
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Kuzumi A, Norimatsu Y, Matsuda KM, Ono C, Okumura T, Kogo E, Goshima N, Fukasawa T, Fushida N, Horii M, Yamashita T, Yoshizaki-Ogawa A, Yamaguchi K, Matsushita T, Sato S, Yoshizaki A. Comprehensive autoantibody profiling in systemic autoimmunity by a highly-sensitive multiplex protein array. Front Immunol 2023; 14:1255540. [PMID: 37701440 PMCID: PMC10493387 DOI: 10.3389/fimmu.2023.1255540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023] Open
Abstract
Comprehensive autoantibody evaluation is essential for the management of autoimmune disorders. However, conventional methods suffer from poor sensitivity, low throughput, or limited availability. Here, using a proteome-wide human cDNA library, we developed a novel multiplex protein assay (autoantibody array assay; A-Cube) covering 65 antigens of 43 autoantibodies that are associated with systemic sclerosis (SSc) and polymyositis/dermatomyositis (PM/DM). The performance of A-Cube was validated against immunoprecipitation and established enzyme-linked immunosorbent assay. Further, through an evaluation of serum samples from 357 SSc and 172 PM/DM patients, A-Cube meticulously illustrated a diverse autoantibody landscape in these diseases. The wide coverage and high sensitivity of A-Cube also allowed the overlap and correlation analysis between multiple autoantibodies. Lastly, reviewing the cases with distinct autoantibody profiles by A-Cube underscored the importance of thorough autoantibody detection. Together, these data highlighted the utility of A-Cube as well as the clinical relevance of autoantibody profiles in SSc and PM/DM.
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Affiliation(s)
- Ai Kuzumi
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yuta Norimatsu
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazuki M. Matsuda
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | | | | | - Emi Kogo
- ProteoBridge Corporation, Tokyo, Japan
| | - Naoki Goshima
- ProteoBridge Corporation, Tokyo, Japan
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takemichi Fukasawa
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Clinical Cannabinoid Research, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Natsumi Fushida
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Motoki Horii
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Takashi Yamashita
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Asako Yoshizaki-Ogawa
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kei Yamaguchi
- ProteoBridge Corporation, Tokyo, Japan
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takashi Matsushita
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Shinichi Sato
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Clinical Cannabinoid Research, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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11
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García-Sanz R, García-Álvarez M, Medina A, Askari E, González-Calle V, Casanova M, de la Torre-Loizaga I, Escalante-Barrigón F, Bastos-Boente M, Bárez A, Vidaña-Bedera N, Alonso JM, Sarasquete ME, González M, Chillón MC, Alcoceba M, Jiménez C. Clonal architecture and evolutionary history of Waldenström's macroglobulinemia at the single-cell level. Dis Model Mech 2023; 16:dmm050227. [PMID: 37493341 PMCID: PMC10461465 DOI: 10.1242/dmm.050227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
To provide insight into the subclonal architecture and co-dependency patterns of the alterations in Waldenström's macroglobulinemia (WM), we performed single-cell mutational and protein profiling of eight patients. A custom panel was designed to screen for mutations and copy number alterations at the single-cell level in samples taken from patients at diagnosis (n=5) or at disease progression (n=3). Results showed that in asymptomatic WM at diagnosis, MYD88L265P was the predominant clonal alteration; other events, if present, were secondary and subclonal to MYD88L265P. In symptomatic WM, clonal diversity was more evident, uncovering combinations of alterations that synergized to promote clonal expansion and dominance. At disease progression, a dominant clone was observed, sometimes accompanied by other less complex minor clones, which could be consistent with a clonal selection process. Clonal diversity was also reduced, probably due to the effect of treatment. Finally, we combined protein expression with mutational analysis to map somatic genotype with the immunophenotype. Our findings provide a comprehensive view of the clonality of tumor populations in WM and how clonal complexity can evolve and impact disease progression.
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Affiliation(s)
- Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María García-Álvarez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Alejandro Medina
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Elham Askari
- Hematology Department, Fundación Jiménez Díaz, Centro de Investigación Biomédica en Red-Cáncer, Madrid 28040, Spain
| | - Verónica González-Calle
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María Casanova
- Hematology Department, Hospital Costa del Sol, Marbella 29603, Spain
| | - Igor de la Torre-Loizaga
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | | | - Miguel Bastos-Boente
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Abelardo Bárez
- Hematology Department, Complejo Asistencial de Ávila, Ávila 05071, Spain
| | - Nerea Vidaña-Bedera
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - José María Alonso
- Hematology Department, Complejo Asistencial Universitario de Palencia, Palencia 34005, Spain
| | - María Eugenia Sarasquete
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Marcos González
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María Carmen Chillón
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Miguel Alcoceba
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
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12
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Juanes-Velasco P, Arias-Hidalgo C, Landeira-Viñuela A, Nuño-Soriano A, Fuentes-Vacas M, Góngora R, Hernández ÁP, Fuentes M. Functional proteomics based on protein microarray technology for biomedical research. Adv Protein Chem Struct Biol 2023; 138:49-65. [PMID: 38220432 DOI: 10.1016/bs.apcsb.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This chapter traces a route through Proteomics from its origins to the present day. The different proteomics applications are discussed with a focus on microarray technology. Analytical microarrays, functional microarrays and reverse phase microarrays and their different applications are discussed. Several studies are mentioned where the great versatility of this approach is shown. Finally, the advantages and future challenges of microarray technology are outlined.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ana Nuño-Soriano
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina Fuentes-Vacas
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafa Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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13
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Bérubé S, Kobayashi T, Wesolowski A, Norris DE, Ruczinski I, Moss WJ, Louis TA. A Bayesian hierarchical model for signal extraction from protein microarrays. Stat Med 2023; 42:1445-1460. [PMID: 36872556 DOI: 10.1002/sim.9680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 11/09/2022] [Accepted: 01/30/2023] [Indexed: 03/07/2023]
Abstract
Protein microarrays are a promising technology that measure protein levels in serum or plasma samples. Due to their high technical variability and high variation in protein levels across serum samples in any population, directly answering biological questions of interest using protein microarray measurements is challenging. Analyzing preprocessed data and within-sample ranks of protein levels can mitigate the impact of between-sample variation. As for any analysis, ranks are sensitive to preprocessing, but loss function based ranks that accommodate major structural relations and components of uncertainty are very effective. Bayesian modeling with full posterior distributions for quantities of interest produce the most effective ranks. Such Bayesian models have been developed for other assays, for example, DNA microarrays, but modeling assumptions for these assays are not appropriate for protein microarrays. Consequently, we develop and evaluate a Bayesian model to extract the full posterior distribution of normalized protein levels and associated ranks for protein microarrays, and show that it fits well to data from two studies that use protein microarrays produced by different manufacturing processes. We validate the model via simulation and demonstrate the downstream impact of using estimates from this model to obtain optimal ranks.
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Affiliation(s)
- Sophie Bérubé
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Douglas E Norris
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William J Moss
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Thomas A Louis
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
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14
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Hoff FW, Griffen TL, Brown BD, Horton TM, Burger J, Wierda W, Hubner SE, Qiu Y, Kornblau SM. Reverse Phase Protein Array Profiling Identifies Recurrent Protein Expression Patterns of DNA Damage-Related Proteins across Acute and Chronic Leukemia: Samples from Adults and the Children's Oncology Group. Int J Mol Sci 2023; 24:5460. [PMID: 36982537 PMCID: PMC10056740 DOI: 10.3390/ijms24065460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023] Open
Abstract
DNA damage response (DNADR) recognition and repair (DDR) pathways affect carcinogenesis and therapy responsiveness in cancers, including leukemia. We measured protein expression levels of 16 DNADR and DDR proteins using the Reverse Phase Protein Array methodology in acute myeloid (AML) (n = 1310), T-cell acute lymphoblastic leukemia (T-ALL) (n = 361) and chronic lymphocytic leukemia (CLL) (n = 795) cases. Clustering analysis identified five protein expression clusters; three were unique compared to normal CD34+ cells. Individual protein expression differed by disease for 14/16 proteins, with five highest in CLL and nine in T-ALL, and by age in T-ALL and AML (six and eleven proteins, respectively), but not CLL (n = 0). Most (96%) of the CLL cases clustered in one cluster; the other 4% were characterized by higher frequencies of deletion 13q and 17p, and fared poorly (p < 0.001). T-ALL predominated in C1 and AML in C5, but both occurred in all four acute-dominated clusters. Protein clusters showed similar implications for survival and remission duration in pediatric and adult T-ALL and AML populations, with C5 doing best in all. In summary, DNADR and DDR protein expression was abnormal in leukemia and formed recurrent clusters that were shared across the leukemias with shared prognostic implications across diseases, and individual proteins showed age- and disease-related differences.
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Affiliation(s)
- Fieke W. Hoff
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390-9030, USA
| | - Ti’ara L. Griffen
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, GA 30310-1458, USA
| | - Brandon D. Brown
- Division of Pediatrics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Terzah M. Horton
- Department of Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX 77030-3498, USA
| | - Jan Burger
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - William Wierda
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Stefan E. Hubner
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA
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15
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Celikgil A, Massimi AB, Nakouzi A, Herrera NG, Morano NC, Lee JH, Yoon HA, Garforth SJ, Almo SC. SARS-CoV-2 multi-antigen protein microarray for detailed characterization of antibody responses in COVID-19 patients. PLoS One 2023; 18:e0276829. [PMID: 36757919 PMCID: PMC9910743 DOI: 10.1371/journal.pone.0276829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target multiple epitopes on different domains of the spike protein, and other SARS-CoV-2 proteins. We developed a SARS-CoV-2 multi-antigen protein microarray with the nucleocapsid, spike and its domains (S1, S2), and variants with single (D614G, E484K, N501Y) or double substitutions (N501Y/Deletion69/70), allowing a more detailed high-throughput analysis of the antibody repertoire following infection. The assay was demonstrated to be reliable and comparable to ELISA. We analyzed antibodies from 18 COVID-19 patients and 12 recovered convalescent donors. The S IgG level was higher than N IgG in most of the COVID-19 patients, and the receptor-binding domain of S1 showed high reactivity, but no antibodies were detected against the heptad repeat domain 2 of S2. Furthermore, antibodies were detected against S variants with single and double substitutions in COVID-19 patients who were infected with SARS-CoV-2 early in the pandemic. Here we demonstrated that the SARS-CoV-2 multi-antigen protein microarray is a powerful tool for detailed characterization of antibody responses, with potential utility in understanding the disease progress and assessing current vaccines and therapies against evolving SARS-CoV-2.
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Affiliation(s)
- Alev Celikgil
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Aldo B. Massimi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Antonio Nakouzi
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Natalia G. Herrera
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nicholas C. Morano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - James H. Lee
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Hyun ah Yoon
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
| | - Scott J. Garforth
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
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16
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Grötzinger C. Applications of Peptide Microarrays in Autoantibody, Infection, and Cancer Detection. Methods Mol Biol 2023; 2578:1-15. [PMID: 36152276 DOI: 10.1007/978-1-0716-2732-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The diversity of the antigen-specific humoral immune response reflects the interaction of the immune system with pathogens and autoantigens. Peptide microarray analysis opens up new perspectives for the use of antibodies as diagnostic biomarkers and provides unique access to a more differentiated view on humoral responses to disease. This review focuses on the latest applications of peptide microarrays for the serologic medical diagnosis of autoimmunity, infectious diseases (including COVID-19), and cancer.
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Affiliation(s)
- Carsten Grötzinger
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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17
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Shome M, Labaer J. Protein Microarrays and their Fabrication. Methods Mol Biol 2023; 2597:131-142. [PMID: 36374419 DOI: 10.1007/978-1-0716-2835-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein microarrays are an important tool when analyzing multiple analytes simultaneously. As the human genome contains approximately 20,000 genes, examining the interactions of even just one representative protein for each gene requires a high-throughput technique. For instance, the interaction between glycosaminoglycans (GAGs), a form of polysaccharide, and chemokines, small chemoattractant proteins, is critical for local inflammation. GAGs present in the glycocalyx on the surface of the cell bind to chemokines, which are released in response to injury. These chemokines can then form concentration gradients that direct the migration and recruitment of leucocytes via leukocyte receptors which in turn leads to immune cell responses, inflammation, or innate immunity and cell or antibody-mediated immune responses. Discovering the novel interactions between the GAGs and chemokines can help in designing drugs which can alter cellular binding to organ tissues, thereby potentially reducing damaging innate immune (inflammation) or acquired immune (antibody-mediated) responses.
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Affiliation(s)
- Mahasish Shome
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua Labaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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18
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Xiu G, Li X, Chen J, Li J, Chen K, Liu P, Ling B, Yang Y. Role of Serum Inflammatory Cytokines in Sepsis Rats Following BMSCs Transplantation: Protein Microarray Analysis. Cell Transplant 2023; 32:9636897231198175. [PMID: 37706441 PMCID: PMC10503277 DOI: 10.1177/09636897231198175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023] Open
Abstract
Bone marrow stromal cells (BMSCs) have emerged as a potential therapy for sepsis, yet the underlying mechanisms remain unclear. In this study, we investigated the effects of BMSCs on serum inflammatory cytokines in a rat model of lipopolysaccharide (LPS)-induced sepsis. Sepsis was induced by intravenous injection of LPS, followed by transplantation of BMSCs. We monitored survival rates for 72 h and evaluated organ functions, histopathological changes, and cytokines expression. Sepsis rats showed decreased levels of white blood cells, platelets, lymphocyte ratio, and oxygen partial pressure, along with increased levels of neutrophil ratio, carbon dioxide partial pressure, lactic acid, alanine aminotransferase, and aspartate aminotransferase. Histologically, lung, intestine, and liver tissues exhibited congestion, edema, and infiltration of inflammatory cells. However, after BMSCs treatment, there was improvement in organ functions, histopathological injuries, and survival rates. Protein microarray analysis revealed significant changes in the expression of 12 out of 34 inflammatory cytokines. These findings were confirmed by enzyme-linked immunosorbent assay. Pro-inflammatory factors, such as interleukin-1β (IL-1β), IL-1α, tumor necrosis factor-α (TNF-α), tissue inhibitor of metal protease 1 (TIMP-1), matrix metalloproteinase 8 (MMP-8), Leptin, and L-selectin were upregulated in sepsis, whereas anti-inflammatory and growth factors, including IL-4, β-nerve growth factor (β-NGF), ciliary neurotrophic factor (CNTF), interferon γ (IFN-γ), and Activin A were downregulated. BMSCs transplantation led to a decrease in pro-inflammatory cytokines and an increase in anti-inflammatory and growth factors. We summarized relevant molecular signaling pathways that resulted from cytokines in BMSCs for treating sepsis. Our results illustrated that BMSCs could promote tissue repair and improve organ functions and survival rates in sepsis through modulating cytokine networks.
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Affiliation(s)
- Guanghui Xiu
- Affiliated Hospital of Yunnan University (The Second People’s Hospital of Yunnan Province), School of Medicine, Yunnan University, Kunming, China
| | - Xiuling Li
- Department of Obstetrics, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Juan Chen
- Department of Infectious Diseases, The First People’s Hospital of Fuzhou, Fuzhou, China
| | - Jintao Li
- Institute of Neuroscience, Kunming Medicine University, Kunming, China
| | - Kun Chen
- The Third Clinical School of Medicine, Jinzhou Medical University, Jinzhou, China
| | - Ping Liu
- Affiliated Hospital of Yunnan University (The Second People’s Hospital of Yunnan Province), School of Medicine, Yunnan University, Kunming, China
| | - Bin Ling
- Affiliated Hospital of Yunnan University (The Second People’s Hospital of Yunnan Province), School of Medicine, Yunnan University, Kunming, China
| | - Ying Yang
- Affiliated Hospital of Yunnan University (The Second People’s Hospital of Yunnan Province), School of Medicine, Yunnan University, Kunming, China
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19
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Hoornstra D, Stukolova OA, Karan LS, Sarksyan DS, Kolyasnikova NM, Markelov ML, Cherkashina AS, Dolgova AS, Sudina AE, Sokolova MI, Platonov AE, Hovius JW. Development and Validation of a Protein Array for Detection of Antibodies against the Tick-Borne Pathogen Borrelia miyamotoi. Microbiol Spectr 2022; 10:e0203622. [PMID: 36314925 PMCID: PMC9769530 DOI: 10.1128/spectrum.02036-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022] Open
Abstract
Current serological tests for the emerging tick-borne pathogen Borrelia miyamotoi lack diagnostic accuracy. To improve serodiagnosis, we investigated a protein array simultaneously screening for IgM and IgG reactivity against multiple recombinant B. miyamotoi antigens. The array included six B. miyamotoi antigens: glycerophosphodiester phosphodiesterase (GlpQ), multiple variable major proteins (Vmps), and flagellin. Sera included samples from cases of PCR-proven Borrelia miyamotoi disease (BMD), multiple potentially cross-reactive control groups (including patients with culture-proven Lyme borreliosis, confirmed Epstein-Barr virus, cytomegalovirus, or other spirochetal infections), and several healthy control groups from regions where Ixodes is endemic and regions where it is nonendemic. Based on receiver operating characteristic (ROC) analyses, the cutoff for reactivity per antigen was set at 5 μg/mL for IgM and IgG. The individual antigens demonstrated high sensitivity but relatively low specificity for both IgM and IgG. The best-performing single antigen (GlpQ) showed a sensitivity of 88.0% (95% confidence interval [CI], 78.9 to 93.5) and a specificity of 94.2% (95% CI, 92.7 to 95.6) for IgM/IgG. Applying the previous published diagnostic algorithm-defining seroreactivity as reactivity against GlpQ and any Vmp-revealed a significantly higher specificity of 98.5% (95% CI, 97.6 to 99.2) but a significantly lower sensitivity of 79.5% (95% CI, 69.3 to 87.0) for IgM/IgG compared to GlpQ alone. Therefore, we propose to define seroreactivity as reactivity against GlpQ and any Vmp or flagellin which resulted in a comparable sensitivity of 84.3% (95% CI, 74.7 to 90.8) and a significantly higher specificity of 97.9% (95% CI, 96.9 to 98.7) for IgM/IgG compared to GlpQ alone. In conclusion, we have developed and validated a novel serological tool to diagnose BMD that could be implemented in clinical practice and epidemiological studies. IMPORTANCE This paper describes the protein array as a novel serological test for the diagnosis of Borrelia miyamotoi disease (BMD), by reporting the methodology, the development of a diagnostic algorithm, and its extensive validation. With rising numbers of ticks and tick bites, tick-borne diseases, such as BMD, urgently deserve further societal and medical attention. B. miyamotoi is prevalent in Ixodes ticks across the northern hemisphere. Humans are exposed to, and infected by, B. miyamotoi and develop BMD in Asia, in North America, and to a lesser extent in Europe. However, the burden of infection and disease remains largely unknown, due to the noncharacteristic clinical presentation, together with the lack of awareness and availability of diagnostic tools. With this paper, we offer a novel diagnostic tool which will assist in assessing the burden of disease and could be implemented in clinical care.
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Affiliation(s)
- Dieuwertje Hoornstra
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Nadezhda M. Kolyasnikova
- Central Research Institute of Epidemiology, Moscow, Russia
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Anna S. Dolgova
- St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Saint Petersburg, Russia
| | - Anna E. Sudina
- Central Research Institute of Epidemiology, Moscow, Russia
| | | | | | - Joppe W. Hovius
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
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20
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Al-Amin RA, Johansson L, Abdurakhmanov E, Landegren N, Löf L, Arngården L, Blokzijl A, Svensson R, Hammond M, Lönn P, Haybaeck J, Kamali-Moghaddam M, Jensen A, Danielson U, Artursson P, Lundbäck T, Landegren U. Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ. Nucleic Acids Res 2022; 50:e129. [PMID: 36189884 PMCID: PMC9825164 DOI: 10.1093/nar/gkac842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/29/2023] Open
Abstract
Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by the dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to fixed adherent cells agreed with expectations from expression profiles of the cells. We also introduce a proximity ligation variant of TEMA to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and in tissues.
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Affiliation(s)
- Rasel A Al-Amin
- To whom correspondence should be addressed. Tel: +46 70 0535324;
| | - Lars Johansson
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Eldar Abdurakhmanov
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nils Landegren
- Center for Molecular Medicine, Department of Medicine (Solna), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Liza Löf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linda Arngården
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andries Blokzijl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling (UDOPP), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Hammond
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Annika Jenmalm Jensen
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - U Helena Danielson
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling (UDOPP), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Lundbäck
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Ulf Landegren
- Correspondence may also be addressed to Ulf Landegren. Tel: +46 18 4714910; Fax: +46 18 4714808;
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21
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Oulton T, Obiero J, Rodriguez I, Ssewanyana I, Dabbs RA, Bachman CM, Greenhouse B, Drakeley C, Felgner PL, Stone W, Tetteh KKA. Plasmodium falciparum serology: A comparison of two protein production methods for analysis of antibody responses by protein microarray. PLoS One 2022; 17:e0273106. [PMID: 36037183 PMCID: PMC9423672 DOI: 10.1371/journal.pone.0273106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
The evaluation of protein antigens as putative serologic biomarkers of infection has increasingly shifted to high-throughput, multiplex approaches such as the protein microarray. In vitro transcription/translation (IVTT) systems-a similarly high-throughput protein expression method-are already widely utilised in the production of protein microarrays, though purified recombinant proteins derived from more traditional whole cell based expression systems also play an important role in biomarker characterisation. Here we have performed a side-by-side comparison of antigen-matched protein targets from an IVTT and purified recombinant system, on the same protein microarray. The magnitude and range of antibody responses to purified recombinants was found to be greater than that of IVTT proteins, and responses between targets from different expression systems did not clearly correlate. However, responses between amino acid sequence-matched targets from each expression system were more closely correlated. Despite the lack of a clear correlation between antigen-matched targets produced in each expression system, our data indicate that protein microarrays produced using either method can be used confidently, in a context dependent manner, though care should be taken when comparing data derived from contrasting approaches.
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Affiliation(s)
- Tate Oulton
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Joshua Obiero
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, United States of America
| | - Isabel Rodriguez
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Isaac Ssewanyana
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Makerere University College of Health Sciences, Kampala, Uganda
| | - Rebecca A. Dabbs
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Chris Drakeley
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Phil L. Felgner
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, United States of America
| | - Will Stone
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kevin K. A. Tetteh
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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22
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Uchida M, Brunk NE, Hewagama ND, Lee B, Prevelige PE, Jadhao V, Douglas T. Multilayered Ordered Protein Arrays Self-Assembled from a Mixed Population of Virus-like Particles. ACS Nano 2022; 16:7662-7673. [PMID: 35549153 DOI: 10.1021/acsnano.1c11272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biology shows many examples of spatially controlled assembly of cells and biomacromolecules into hierarchically organized structures, to which many of the complex biological functions are attributed. While such biological structures have inspired the design of synthetic materials, it is still a great challenge to control the spatial arrangement of individual building blocks when assembling multiple types of components into bulk materials. Here, we report self-assembly of multilayered, ordered protein arrays from mixed populations of virus-like particles (VLPs). We systematically tuned the magnitude of the surface charge of the VLPs via mutagenesis to prepare four different types of VLPs for mixing. A mixture of up to four types of VLPs selectively assembled into higher-order structures in the presence of oppositely charged dendrimers during a gradual lowering of the ionic strength of the solution. The assembly resulted in the formation of three-dimensional ordered VLP arrays with up to four distinct layers including a central core, with each layer comprising a single type of VLP. A coarse-grained computational model was developed and simulated using molecular dynamics to probe the formation of the multilayered, core-shell structure. Our findings establish a simple and versatile bottom-up strategy to synthesize multilayered, ordered materials by controlling the spatial arrangement of multiple types of nanoscale building blocks in a one-pot fabrication.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Avenue, Fresno, California 93740, United States
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicholas E Brunk
- Intelligent Systems Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, Indiana 47408, United States
- Wolfram Research, 100 Trade Center Drive, Champaign, Illinois 61820, United States
- VeriSIM Life Inc., 1 Sansome Street, Suite 3500, San Francisco, California 94104, United States
| | - Nathasha D Hewagama
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Vikram Jadhao
- Intelligent Systems Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, Indiana 47408, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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23
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Su WY, Du PX, Santos HM, Ho TS, Keskin BB, Pau CH, Yang AM, Chou YY, Shih HC, Syu GD. Antibody Profiling in COVID-19 Patients with Different Severities by Using Spike Variant Protein Microarrays. Anal Chem 2022; 94:6529-6539. [PMID: 35442638 PMCID: PMC9045038 DOI: 10.1021/acs.analchem.1c05567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/11/2022] [Indexed: 12/21/2022]
Abstract
The disease progression of COVID-19 varies from mild to severe, even death. However, the link between COVID-19 severities and humoral immune specificities is not clear. Here, we developed a multiplexed spike variant protein microarray (SVPM) and utilized it for quantifying neutralizing activity, drug screening, and profiling humoral immunity. First, we demonstrated the competition between antispike antibody and ACE2 on SVPM for measuring the neutralizing activity against multiple spike variants. Next, we collected the serums from healthy subjects and COVID-19 patients with different severities and profile the neutralizing activity as well as antibody isotypes. We identified the inhibition of ACE2 binding was stronger against multiple variants in severe compared to mild/moderate or critical patients. Moreover, the serum IgG against nonstructural protein 3 was elevated in severe but not in mild/moderate and critical cases. Finally, we evaluated two ACE2 inhibitors, Ramipril and Perindopril, and found the dose-dependent inhibition of ACE2 binding to all the spike variants except for B.1.617.3. Together, the SVPM and the assay procedures provide a tool for profiling neutralizing antibodies, antibody isotypes, and reagent specificities.
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Affiliation(s)
- Wen-Yu Su
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pin-Xian Du
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Harvey M. Santos
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- School
of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, Intramuros, Manila 1002, Philippines
| | - Tzong-Shiann Ho
- Department
of Pediatrics, National Cheng Kung University
Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center
of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
- Department
of Pediatrics, Tainan Hospital, Ministry
of Health and Welfare, Tainan 700, Taiwan
| | - Batuhan Birol Keskin
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi Ho Pau
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - An-Ming Yang
- Department
of Internal Medicine, En Chu Kong Hospital, New Taipei City 237, Taiwan
- Department
of Nursing, Yuanpei University of Medical
Technology, Hsinchu 300, Taiwan
| | - Yi-Yu Chou
- Department
of Nursing, Kaohsiung Armed Forces General
Hospital, Kaohsiung 802, Taiwan
| | - Hsi-Chang Shih
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Guan-Da Syu
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Research
Center of Excellence in Regenerative Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Medical
Device Innovation Center, National Cheng
Kung University, Tainan 701, Taiwan
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24
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Jiang H, Chiang CY, Chen Z, Nathan S, D'Agostino G, Paulo JA, Song G, Zhu H, Gabelli SB, Cole PA. Enzymatic analysis of WWP2 E3 ubiquitin ligase using protein microarrays identifies autophagy-related substrates. J Biol Chem 2022; 298:101854. [PMID: 35331737 PMCID: PMC9034101 DOI: 10.1016/j.jbc.2022.101854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022] Open
Abstract
WWP2 is a HECT E3 ligase that targets protein Lys residues for ubiquitination and is comprised of an N-terminal C2 domain, four central WW domains, and a C-terminal catalytic HECT domain. The peptide segment between the middle WW domains, the 2,3-linker, is known to autoinhibit the catalytic domain, and this autoinhibition can be relieved by phosphorylation at Tyr369. Several protein substrates of WWP2 have been identified, including the tumor suppressor lipid phosphatase PTEN, but the full substrate landscape and biological functions of WWP2 remain to be elucidated. Here, we used protein microarray technology and the activated enzyme phosphomimetic mutant WWP2Y369E to identify potential WWP2 substrates. We identified 31 substrate hits for WWP2Y369E using protein microarrays, of which three were known autophagy receptors (NDP52, OPTN, and SQSTM1). These three hits were validated with in vitro and cell-based transfection assays and the Lys ubiquitination sites on these proteins were mapped by mass spectrometry. Among the mapped ubiquitin sites on these autophagy receptors, many had been previously identified in the endogenous proteins. Finally, we observed that WWP2 KO SH-SH5Y neuroblastoma cells using CRISPR-Cas9 showed a defect in mitophagy, which could be rescued by WWP2Y369E transfection. These studies suggest that WWP2-mediated ubiquitination of the autophagy receptors NDP52, OPTN, and SQSTM1 may positively contribute to the regulation of autophagy.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Claire Y Chiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Zan Chen
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA; Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sara Nathan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Gabriel D'Agostino
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
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25
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Ho TS, Du PX, Su WY, Santos HM, Lin YL, Chou YY, Keskin BB, Pau CH, Syu GD. Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. Biosens Bioelectron 2022; 204:114067. [PMID: 35168024 PMCID: PMC8821029 DOI: 10.1016/j.bios.2022.114067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 is quickly evolving from wild-type to many variants and spreading around the globe. Since many people have been vaccinated with various types of vaccines, it is crucial to develop a high throughput platform for measuring the antibody responses and surrogate neutralizing activities against multiple SARS-CoV-2 variants. To meet this need, the present study developed a SARS-CoV-2 variant (CoVariant) array which consists of the extracellular domain of spike variants, e.g., wild-type, D614G, B.1.1.7, B.1.351, P.1, B.1.617, B.1.617.1, B.1.617.2, and B.1.617.3. A surrogate virus neutralization on the CoVariant array was established to quantify the bindings of antibody and host receptor ACE2 simultaneously to spike variants. By using a chimeric anti-spike antibody, we demonstrated a broad binding spectrum of antibodies while inhibiting the bindings of ACE2 to spike variants. To monitor the humoral immunities after vaccination, we collected serums from unvaccinated, partial, or fully vaccinated individuals with either mRNA-1273 or AZD1222 (ChAdOx1). The results showed partial vaccination increased the surrogate neutralization against all the mutants while full vaccination boosted the most. Although IgG, IgA, and IgM isotypes correlated with surrogate neutralizing activities, they behave differently throughout the vaccination processes. Overall, this study developed CoVariant arrays and assays for profiling the humoral responses which are useful for immune assessment, vaccine research, and drug development.
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Affiliation(s)
- Tzong-Shiann Ho
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, 701, Taiwan, ROC; Department of Pediatrics, Tainan Hospital, Ministry of Health and Welfare, Tainan, 700, Taiwan, ROC
| | - Pin-Xian Du
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Wen-Yu Su
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Harvey M Santos
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC; School of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, Intramuros, Manila, 1002, Philippines
| | - Ya-Lan Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Yi-Yu Chou
- Department of Nursing, Kaohsiung Armed Forces General Hospital, Kaohsiung, 802, Taiwan, ROC
| | - Batuhan Birol Keskin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Chi Ho Pau
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, 701, Taiwan, ROC; Research Center of Excellence in Regenerative Medicine, National Cheng Kung University, Tainan, 701, Taiwan, ROC.
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Milchram L, Fischer A, Huber J, Soldo R, Sieghart D, Vierlinger K, Blüml S, Steiner G, Weinhäusel A. Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis. Molecules 2022; 27:molecules27041452. [PMID: 35209238 PMCID: PMC8876797 DOI: 10.3390/molecules27041452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022]
Abstract
For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced arthritis (PIA) rat model (n = 24 total) were probed on AIT’s 16k protein microarray. To investigate the analogy of underlying disease pathways, differential reactivity analysis was conducted. A total of n = 602 differentially reactive antigens (DIRAGs) at a significance cutoff of p < 0.05 were identified between seropositive and seronegative RA for the human samples. Correlation with the clinical disease activity index revealed an inverse correlation of antibodies against self-proteins found in pathways relevant for antigen presentation and immune regulation. The PIA model showed n = 1291 significant DIRAGs within acute disease. Significant DIRAGs for (I) seropositive, (II) seronegative and (III) PIA were subjected to the Reactome pathway browser which also revealed pathways relevant for antigen presentation and immune regulation; of these, seven overlapping pathways had high significance. We therefore conclude that the PIA model reflects the biological similarities of the disease pathogenesis. Our data show that protein array analysis can elucidate biological differences and pathways relevant in disease as well be a useful additional layer of omics information.
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Affiliation(s)
- Lisa Milchram
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Anita Fischer
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Jasmin Huber
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Regina Soldo
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Daniela Sieghart
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Stephan Blüml
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Günter Steiner
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
- Correspondence:
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27
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Owens AE, Iannotti MJ, Sanchez TW, Voss T, Kapoor A, Hall MD, Marugan JJ, Michael S, Southall N, Henderson MJ. High-Throughput Cellular Thermal Shift Assay Using Acoustic Transfer of Protein Lysates. ACS Chem Biol 2022; 17:322-330. [PMID: 35119255 PMCID: PMC10026039 DOI: 10.1021/acschembio.1c00760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cellular thermal shift assay (CETSA) is a valuable method to confirm target engagement within a complex cellular environment, by detecting changes in a protein's thermal stability upon ligand binding. The classical CETSA method measures changes in the thermal stability of endogenous proteins using immunoblotting, which is low-throughput and laborious. Reverse-phase protein arrays (RPPAs) have been demonstrated as a detection modality for CETSA; however, the reported procedure requires manual processing steps that limit throughput and preclude screening applications. We developed a high-throughput CETSA using an acoustic RPPA (HT-CETSA-aRPPA) protocol that is compatible with 96- and 384-well microplates from start-to-finish, using low speed centrifugation to remove thermally destabilized proteins. The utility of HT-CETSA-aRPPA for guiding structure-activity relationship studies was demonstrated for inhibitors of lactate dehydrogenase A. Additionally, a collection of kinase inhibitors was screened to identify compounds that engage MEK1, a clinically relevant kinase target.
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Affiliation(s)
- Ashley E. Owens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Michael J. Iannotti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Tino W. Sanchez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Ty Voss
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Abhijeet Kapoor
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Juan J. Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
- Corresponding Author: Mark Henderson;
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28
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Meanor JN, Keung AJ, Rao BM. Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity. Int J Mol Sci 2022; 23:ijms23031691. [PMID: 35163614 PMCID: PMC8836101 DOI: 10.3390/ijms23031691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
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Affiliation(s)
- Jenna N. Meanor
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
| | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Correspondence: (A.J.K.); (B.M.R.)
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Golden LEAF Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: (A.J.K.); (B.M.R.)
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29
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Obata F, Ozuru R, Tsuji T, Matsuba T, Fujii J. Stx2 Induces Differential Gene Expression and Disturbs Circadian Rhythm Genes in the Proximal Tubule. Toxins (Basel) 2022; 14:toxins14020069. [PMID: 35202097 PMCID: PMC8874938 DOI: 10.3390/toxins14020069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/04/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes proximal tubular defects in the kidney. However, factors altered by Shiga toxin (Stx) within the proximal tubules are yet to be shown. We determined Stx receptor Gb3 in murine and human kidneys and confirmed the receptor expression in the proximal tubules. Stx2-injected mouse kidney tissues and Stx2-treated human primary renal proximal tubular epithelial cell (RPTEC) were collected and microarray analysis was performed. We compared murine kidney and RPTEC arrays and selected common 58 genes that are differentially expressed vs. control (0 h, no toxin-treated). We found that the most highly expressed gene was GDF15, which may be involved in Stx2-induced weight loss. Genes associated with previously reported Stx2 activities such as src kinase Yes phosphorylation pathway activation, unfolded protein response (UPR) and ribotoxic stress response (RSR) showed differential expressions. Moreover, circadian clock genes were differentially expressed, suggesting Stx2-induced renal circadian rhythm disturbance. Circadian rhythm-regulated proximal tubular Na+-glucose transporter SGLT1 (SLC5A1) was down-regulated, indicating proximal tubular functional deterioration, and mice developed glucosuria confirming proximal tubular dysfunction. Stx2 alters gene expression in murine and human proximal tubules through known activities and newly investigated circadian rhythm disturbance, which may result in proximal tubular dysfunctions.
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Affiliation(s)
- Fumiko Obata
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago 683-8503, Japan; (T.T.); (J.F.)
- Correspondence:
| | - Ryo Ozuru
- Department of Microbiology and Immunology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan;
| | - Takahiro Tsuji
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago 683-8503, Japan; (T.T.); (J.F.)
| | - Takashi Matsuba
- Division of Infectious Disease Control and Prevention, Department of Animal Pharmaceutical Science, School of Pharmaceutical Science, Kyusyu University of Health and Welfare, 1714-1 Yoshino-machi, Nobeoka 882-8508, Japan;
| | - Jun Fujii
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, 86 Nishicho, Yonago 683-8503, Japan; (T.T.); (J.F.)
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Wang Y, Ye H, Yang Y, Li J, Cen A, Zhao L. microRNA-181a promotes the oncogene S100A2 and enhances papillary thyroid carcinoma growth by mediating the expression of histone demethylase KDM5C. J Endocrinol Invest 2022; 45:17-28. [PMID: 34143366 DOI: 10.1007/s40618-021-01606-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND PURPOSE Papillary thyroid carcinoma (PTC) is an endocrine malignancy. Increasing evidence highlights microRNAs (miRNAs) as important participants in PTC. Here, we investigated the role of miR-181a in PTC. METHODS A microarray-based analysis was performed to identify the differential expression of miR-181a in PTC, which was validated with RT-qPCR. Protein expression of the proliferation-related factor Ki-67 and apoptosis- and migration-related factors in PTC was assessed with immunoblot analysis. A dual-luciferase reporter gene assay was adopted to verify the relationship between miR-181a and lysine demethylase 5C (KDM5C). Chromatin immunoprecipitation (ChIP) was used to detect the level of the H3K4me3 modification on S100 calcium-binding protein A2 (S100A2). Cell viability, apoptosis, and invasion and migration abilities were evaluated by Cell Counting Kit-8 (CCK-8), flow cytometry, and transwell assays, respectively. The in vitro results were verified in in vivo nude mouse models. RESULTS miR-181a was highly expressed in PTC tissues and cell lines. Silencing miR-181a repressed the proliferation and migration of PTC cells. KDM5C was identified as the target gene of miR-181a and represses S100A2 expression through histone demethylation to diminish the migration and proliferation of PTC cells. miR-181a depletion suppressed tumor growth. CONCLUSION Collectively, these results suggest that highly expressed miR-181a promotes the proliferation of PTC cells by increasing the expression of the oncogene S100A2. This study contributes to the advancement of miR-181a-targeted therapeutics.
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Affiliation(s)
- Y Wang
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, No. 613, West Huangpu Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, People's Republic of China.
| | - H Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Hepatopancreatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Y Yang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - J Li
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, No. 613, West Huangpu Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, People's Republic of China
| | - A Cen
- Department of Endocrinology, the First Affiliated Hospital of Jinan University, No. 613, West Huangpu Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, People's Republic of China
| | - L Zhao
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
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31
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Zhou AE, Jain A, Nakajima R, Shrestha B, Stucke EM, Joshi S, Strauss KA, Hedde PN, Berry AA, Felgner PL, Travassos MA. Protein Microarrays as a Tool to Analyze Antibody Responses to Variant Surface Antigens Expressed on the Surface of Plasmodium falciparum-Infected Erythrocytes. Methods Mol Biol 2022. [PMID: 35881357 DOI: 10.1007/978-1-0716-2189-9_25/cover] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Enzyme-linked immunosorbent assays (ELISAs) remain the gold standard for measuring antibodies, but are time-consuming and use significant amounts of precious sample and reagents. Protein microarrays represent an appealing alternative, particularly for studies focused on large gene families such as those encoding variant surface antigens in the malaria parasite Plasmodium falciparum. Such microarrays represent an ideal high-throughput platform to study antibody responses to hundreds of malaria parasite variant surface antigens at once, providing critical insights into the development of natural immunity to malaria. We describe the essential background and approach to run an assay using a P. falciparum microarray populated with variant surface antigens. This allows the user to define serologic profiles and identify serodominant antigens that represent promising targets for vaccine or therapeutic development.
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Affiliation(s)
- Albert E Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aarti Jain
- Vaccine R&D Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Rie Nakajima
- Vaccine R&D Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Biraj Shrestha
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emily M Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sudhaunshu Joshi
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kathy A Strauss
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Per N Hedde
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Andrea A Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Philip L Felgner
- Vaccine R&D Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Mark A Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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32
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Zhou AE, Jain A, Nakajima R, Shrestha B, Stucke EM, Joshi S, Strauss KA, Hedde PN, Berry AA, Felgner PL, Travassos MA. Protein Microarrays as a Tool to Analyze Antibody Responses to Variant Surface Antigens Expressed on the Surface of Plasmodium falciparum-Infected Erythrocytes. Methods Mol Biol 2022; 2470:343-358. [PMID: 35881357 DOI: 10.1007/978-1-0716-2189-9_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Enzyme-linked immunosorbent assays (ELISAs) remain the gold standard for measuring antibodies, but are time-consuming and use significant amounts of precious sample and reagents. Protein microarrays represent an appealing alternative, particularly for studies focused on large gene families such as those encoding variant surface antigens in the malaria parasite Plasmodium falciparum. Such microarrays represent an ideal high-throughput platform to study antibody responses to hundreds of malaria parasite variant surface antigens at once, providing critical insights into the development of natural immunity to malaria. We describe the essential background and approach to run an assay using a P. falciparum microarray populated with variant surface antigens. This allows the user to define serologic profiles and identify serodominant antigens that represent promising targets for vaccine or therapeutic development.
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Affiliation(s)
- Albert E Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aarti Jain
- Vaccine R&D Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Rie Nakajima
- Vaccine R&D Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Biraj Shrestha
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emily M Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sudhaunshu Joshi
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kathy A Strauss
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Per N Hedde
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Andrea A Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Philip L Felgner
- Vaccine R&D Center, Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Mark A Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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Kishore A, Fetter A, Zeilinger C. Microarray-Based Screening of Putative HSP90 Inhibitors Predicted and Isolated from Microorganisms. Methods Mol Biol 2022; 2489:435-448. [PMID: 35524063 DOI: 10.1007/978-1-0716-2273-5_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein microarrays are useful tools for detecting the presence of a target where different prey and bait combinations exist. Here we describe the extended application for a functional target-oriented screening assay with full length Heat shock proteins (HSPs ) for the identification of novel compounds.
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Affiliation(s)
- Anusha Kishore
- Gottfried-Wilhelm-Leibniz University of Hannover, BMWZ (Zentrum für Biomolekulare Wirkstoffe), Hannover, Germany
| | - Artem Fetter
- Gottfried-Wilhelm-Leibniz University of Hannover, BMWZ (Zentrum für Biomolekulare Wirkstoffe), Hannover, Germany
| | - Carsten Zeilinger
- Gottfried-Wilhelm-Leibniz University of Hannover, BMWZ (Zentrum für Biomolekulare Wirkstoffe), Hannover, Germany.
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34
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Zheng Z, Wang J. Bone marrow mesenchymal stem cells combined with Atractylodes macrocephala polysaccharide attenuate ulcerative colitis. Bioengineered 2022; 13:824-833. [PMID: 34898358 PMCID: PMC8805825 DOI: 10.1080/21655979.2021.2012954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/27/2021] [Indexed: 11/01/2022] Open
Abstract
The aim of the present study was to explore the effects of bone marrow mesenchymal stem cells (BMSCs), combined with Atractylodes macrocephala polysaccharide (AMP), in an experimental model of ulcerative colitis. BMSCs were first isolated, cultured, and identified by flow cytometry. A rat model of colitis was established by trinitrobenzene sulfonic acid (TNBS) injection. Rats were treated with BMSCs with or without AMP for 1 or 2 weeks. H&E staining was performed to assess the extent of histological injury. IEC-6 and BMSCs were co-cultured and treated with AMP. Cell migration was measured using the Transwell assay, whilst the levels of cytokines in the rat blood samples were detected using ELISA. In addition, cytokine levels in the cell supernatant were measured by microarray. The results showed that BMSCs were successfully isolated. BMSCs treatment could markedly alleviate injury according to histological analysis and regulate inflammatory cytokine production in this rat model of TNBS-induced colitis, where a higher number of BMSCs was found in the intestinal tract, compared to the model. AMP not only potentiated the effects of BMSCs on preventing TNBS-induced colitis but also promoted BMSC homing to the injured tissue and regulated cytokines. Furthermore, BMSCs and AMP promoted the migration of IEC in vitro and influenced multiple genes. In conclusion, AMP treatment improved the therapeutic effects of BMSCs on ulcerative colitis, potentially providing a novel clinical treatment strategy for colitis.
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Affiliation(s)
- Zhijuan Zheng
- Experimental Center, Key Laboratory of Traditional Chinese Medicine Classical Theory, Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Junqing Wang
- College of Health Science, Shandong University of Traditional Chinese Medicine, Jinan, China
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DePasquale EAK, Alganem K, Bentea E, Nawreen N, McGuire JL, Tomar T, Naji F, Hilhorst R, Meller J, McCullumsmith RE. KRSA: An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data. PLoS One 2021; 16:e0260440. [PMID: 34919543 PMCID: PMC8682895 DOI: 10.1371/journal.pone.0260440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/09/2021] [Indexed: 12/22/2022] Open
Abstract
Phosphorylation by serine-threonine and tyrosine kinases is critical for determining protein function. Array-based platforms for measuring reporter peptide signal levels allow for differential phosphorylation analysis between conditions for distinct active kinases. Peptide array technologies like the PamStation12 from PamGene allow for generating high-throughput, multi-dimensional, and complex functional proteomics data. As the adoption rate of such technologies increases, there is an imperative need for software tools that streamline the process of analyzing such data. We present Kinome Random Sampling Analyzer (KRSA), an R package and R Shiny web-application for analyzing kinome array data to help users better understand the patterns of functional proteomics in complex biological systems. KRSA is an All-In-One tool that reads, formats, fits models, analyzes, and visualizes PamStation12 kinome data. While the underlying algorithm has been experimentally validated in previous publications, we demonstrate KRSA workflow on dorsolateral prefrontal cortex (DLPFC) in male (n = 3) and female (n = 3) subjects to identify differential phosphorylation signatures and upstream kinase activity. Kinase activity differences between males and females were compared to a previously published kinome dataset (11 female and 7 male subjects) which showed similar global phosphorylation signals patterns.
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Affiliation(s)
- Erica A. K. DePasquale
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Boston, Massachusetts, United States of America
| | - Khaled Alganem
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, Ohio, United States of America
- * E-mail:
| | - Eduard Bentea
- Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nawshaba Nawreen
- Department of Neuroscience, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Jennifer L. McGuire
- Department of Neurosurgery, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Tushar Tomar
- PamGene International B.V., s’-Hertogenbosch, The Netherlands
| | - Faris Naji
- Tercen Data Analytics Ltd, Co Waterford, Ireland
| | - Riet Hilhorst
- PamGene International B.V., s’-Hertogenbosch, The Netherlands
| | - Jaroslaw Meller
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computing Systems, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Informatics, Nicolaus Copernicus University, Torun, Poland
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, Ohio, United States of America
- Neurosciences institute, ProMedica, Toledo, Ohio, United States of America
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Landeira-Viñuela A, Díez P, Juanes-Velasco P, Lécrevisse Q, Orfao A, De Las Rivas J, Fuentes M. Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. Biomolecules 2021; 11:1776. [PMID: 34944421 PMCID: PMC8699084 DOI: 10.3390/biom11121776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Human Proteome Project (HPP) presents a systematic characterization of the protein landscape under different conditions using several complementary-omic techniques (LC-MS/MS proteomics, affinity proteomics, transcriptomics, etc.). In the present study, using a B-cell lymphoma cell line as a model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics (combined with size-exclusion chromatography) (SEC-MAP) were performed to uncover correlations that could provide insights into protein dynamics at the intracellular level. Here, 5672 unique proteins were systematically identified by MS/MS analysis and subcellular protein extraction strategies (neXtProt release 2020-21, MS/MS data are available via ProteomeXchange with identifier PXD003939). Moreover, RNA deep sequencing analysis of this lymphoma B-cell line identified 19,518 expressed genes and 5707 protein coding genes (mapped to neXtProt). Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization. Finally, a bioinformatic pipeline has been designed and developed for orthogonal integration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehensive and global characterization of intracellular protein profiles.
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Affiliation(s)
- Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Quentin Lécrevisse
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain;
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, USAL/IBSAL, 37000 Salamanca, Spain; (A.L.-V.); (P.D.); (P.J.-V.); (Q.L.); (A.O.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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Bizjak DA, Zügel M, Treff G, Winkert K, Jerg A, Hudemann J, Mooren FC, Krüger K, Nieß A, Steinacker JM. Effects of Training Status and Exercise Mode on Global Gene Expression in Skeletal Muscle. Int J Mol Sci 2021; 22:ijms222212578. [PMID: 34830458 PMCID: PMC8674764 DOI: 10.3390/ijms222212578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/29/2022] Open
Abstract
The aim of this study was to investigate differences in skeletal muscle gene expression of highly trained endurance and strength athletes in comparison to untrained individuals at rest and in response to either an acute bout of endurance or strength exercise. Endurance (ET, n = 8, VO2max 67 ± 9 mL/kg/min) and strength athletes (ST, n = 8, 5.8 ± 3.0 training years) as well as untrained controls (E-UT and S-UT, each n = 8) performed an acute endurance or strength exercise test. One day before testing (Pre), 30 min (30'Post) and 3 h (180'Post) afterwards, a skeletal muscle biopsy was obtained from the m. vastus lateralis. Skeletal muscle mRNA was isolated and analyzed by Affymetrix-microarray technology. Pathway analyses were performed to evaluate the effects of training status (trained vs. untrained) and exercise mode-specific (ET vs. ST) transcriptional responses. Differences in global skeletal muscle gene expression between trained and untrained were smaller compared to differences in exercise mode. Maximum differences between ET and ST were found between Pre and 180'Post. Pathway analyses showed increased expression of exercise-related genes, such as nuclear transcription factors (NR4A family), metabolism and vascularization (PGC1-α and VEGF-A), and muscle growth/structure (myostatin, IRS1/2 and HIF1-α. The most upregulated genes in response to acute endurance or strength exercise were the NR4A genes (NR4A1, NR4A2, NR4A3). The mode of acute exercise had a significant effect on transcriptional regulation Pre vs. 180'Post. In contrast, the effect of training status on human skeletal muscle gene expression profiles was negligible compared to strength or endurance specialization. The highest variability in gene expression, especially for the NR4A-family, was observed in trained individuals at 180'Post. Assessment of these receptors might be suitable to obtain a deeper understanding of skeletal muscle adaptive processes to develop optimized training strategies.
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Affiliation(s)
- Daniel A. Bizjak
- Division of Sports and Rehabilitation Medicine, Department of Internal Medicine II, University of Ulm, 89075 Ulm, Germany; (M.Z.); (G.T.); (K.W.); (A.J.); (J.M.S.)
- Correspondence: ; Tel.: +49-73150045368; Fax: +49-73150045301
| | - Martina Zügel
- Division of Sports and Rehabilitation Medicine, Department of Internal Medicine II, University of Ulm, 89075 Ulm, Germany; (M.Z.); (G.T.); (K.W.); (A.J.); (J.M.S.)
| | - Gunnar Treff
- Division of Sports and Rehabilitation Medicine, Department of Internal Medicine II, University of Ulm, 89075 Ulm, Germany; (M.Z.); (G.T.); (K.W.); (A.J.); (J.M.S.)
| | - Kay Winkert
- Division of Sports and Rehabilitation Medicine, Department of Internal Medicine II, University of Ulm, 89075 Ulm, Germany; (M.Z.); (G.T.); (K.W.); (A.J.); (J.M.S.)
| | - Achim Jerg
- Division of Sports and Rehabilitation Medicine, Department of Internal Medicine II, University of Ulm, 89075 Ulm, Germany; (M.Z.); (G.T.); (K.W.); (A.J.); (J.M.S.)
| | - Jens Hudemann
- Department of Sports Medicine, University Hospital Tübingen, 72074 Tübingen, Germany; (J.H.); (A.N.)
| | - Frank C. Mooren
- Department of Medicine, Faculty of Health, University of Witten/Herdecke, 58455 Witten, Germany;
| | - Karsten Krüger
- Department of Exercise Physiology and Sports Therapy, University of Gießen, 35394 Gießen, Germany;
| | - Andreas Nieß
- Department of Sports Medicine, University Hospital Tübingen, 72074 Tübingen, Germany; (J.H.); (A.N.)
| | - Jürgen M. Steinacker
- Division of Sports and Rehabilitation Medicine, Department of Internal Medicine II, University of Ulm, 89075 Ulm, Germany; (M.Z.); (G.T.); (K.W.); (A.J.); (J.M.S.)
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Jia X, Zhai T, Zhang JA. Circulating Exosome Involves in the Pathogenesis of Autoimmune Thyroid Diseases Through Immunomodulatory Proteins. Front Immunol 2021; 12:730089. [PMID: 34867951 PMCID: PMC8636008 DOI: 10.3389/fimmu.2021.730089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/25/2021] [Indexed: 01/07/2023] Open
Abstract
Autoimmune thyroid diseases (AITDs) are chronic organ-specific autoimmune diseases, mainly including Graves' disease (GD) and Hashimoto's thyroiditis (HT). Exosomes, as extracellular vesicles, contain a variety of biologically active substances that play a role in information exchange, thereby affecting the occurrence and progression of diseases. However, it is unclear whether exosomes are involved in the pathogenesis of AITDs. In this study, the role of exosomes in AITDs was explored from a proteomics perspective. Plasma exosomes were isolated from 12 patients with GD, 10 patients with HT, and seven normal controls (NC). Protein profiles were detected using the data-independent acquisition (DIA) method and analyzed to investigate changes in plasma exosome proteins. In the setting of GD, 11 proteins were upregulated while 197 proteins were downregulated compared with healthy people. Among them, MAP1S (log2 FC = 4.669, p = 0.009) and VAMP8 (log2 FC = 3.216, p = 0.003) were the most significantly upregulated, and RSU1 (log2 FC = -6.797, p = 0.001), ACTB (log2 FC = -4.795, p < 0.001), and CXCL7 (log2 FC = -4.674, p < 0.001) were the most significantly downregulated. In the cases of HT, HGFL (log2 FC = 2.766, p = 0.001), FAK1 (log2 FC = 2.213, p < 0.001), and PTN12 (log2 FC = 1.624, p < 0.001) were significantly upregulated, while PSMF1 (log2 FC = -3.591, p < 0.001), PXL2B (log2 FC = -2.622, p = 0.001), and CYTM (log2 FC = -1.609, p < 0.001) were the most downregulated. These differential proteins were mainly enriched in the immune system and metabolic system, indicating that plasma exosomes may play an important role in systemic immune imbalance in AITDs.
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Affiliation(s)
- Xi Jia
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Tianyu Zhai
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Department of Endocrinology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin-an Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
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Wolfe M, Webb S, Chushak Y, Krabacher R, Liu Y, Swami N, Harbaugh S, Chávez J. A high-throughput pipeline for design and selection of peptides targeting the SARS-Cov-2 Spike protein. Sci Rep 2021; 11:21768. [PMID: 34741099 PMCID: PMC8571316 DOI: 10.1038/s41598-021-01225-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/22/2021] [Indexed: 12/23/2022] Open
Abstract
Rapid design, screening, and characterization of biorecognition elements (BREs) is essential for the development of diagnostic tests and antiviral therapeutics needed to combat the spread of viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address this need, we developed a high-throughput pipeline combining in silico design of a peptide library specific for SARS-CoV-2 spike (S) protein and microarray screening to identify binding sequences. Our optimized microarray platform allowed the simultaneous screening of ~ 2.5 k peptides and rapid identification of binding sequences resulting in selection of four peptides with nanomolar affinity to the SARS-CoV-2 S protein. Finally, we demonstrated the successful integration of one of the top peptides into an electrochemical sensor with a clinically relevant limit of detection for S protein in spiked saliva. Our results demonstrate the utility of this novel pipeline for the selection of peptide BREs in response to the SARS-CoV-2 pandemic, and the broader application of such a platform in response to future viral threats.
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Affiliation(s)
- Monica Wolfe
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- UES, Inc., Dayton, OH, 45432, USA
| | - Sean Webb
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- UES, Inc., Dayton, OH, 45432, USA
| | - Yaroslav Chushak
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- Henry M. Jackson Foundation, Dayton, OH, 45433, USA
| | - Rachel Krabacher
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
- Materials & Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Yi Liu
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904, USA
| | - Nathan Swami
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, 22904, USA
| | - Svetlana Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Jorge Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA.
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Pras A, Houben B, Aprile FA, Seinstra R, Gallardo R, Janssen L, Hogewerf W, Gallrein C, De Vleeschouwer M, Mata‐Cabana A, Koopman M, Stroo E, de Vries M, Louise Edwards S, Kirstein J, Vendruscolo M, Falsone SF, Rousseau F, Schymkowitz J, Nollen EAA. The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation. EMBO J 2021; 40:e107568. [PMID: 34617299 PMCID: PMC8561633 DOI: 10.15252/embj.2020107568] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 11/09/2022] Open
Abstract
While aggregation-prone proteins are known to accelerate aging and cause age-related diseases, the cellular mechanisms that drive their cytotoxicity remain unresolved. The orthologous proteins MOAG-4, SERF1A, and SERF2 have recently been identified as cellular modifiers of such proteotoxicity. Using a peptide array screening approach on human amyloidogenic proteins, we found that SERF2 interacted with protein segments enriched in negatively charged and hydrophobic, aromatic amino acids. The absence of such segments, or the neutralization of the positive charge in SERF2, prevented these interactions and abolished the amyloid-promoting activity of SERF2. In protein aggregation models in the nematode worm Caenorhabditis elegans, protein aggregation and toxicity were suppressed by mutating the endogenous locus of MOAG-4 to neutralize charge. Our data indicate that MOAG-4 and SERF2 drive protein aggregation and toxicity by interactions with negatively charged segments in aggregation-prone proteins. Such charge interactions might accelerate primary nucleation of amyloid by initiating structural changes and by decreasing colloidal stability. Our study points at charge interactions between cellular modifiers and amyloidogenic proteins as potential targets for interventions to reduce age-related protein toxicity.
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Affiliation(s)
- Anita Pras
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Bert Houben
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Francesco A Aprile
- Department of ChemistryCentre for Misfolding DiseasesUniversity of CambridgeCambridgeUK
- Present address:
Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonUK
| | - Renée Seinstra
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Rodrigo Gallardo
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Present address:
Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Leen Janssen
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Wytse Hogewerf
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Christian Gallrein
- Department of Molecular Physiology and Cell BiologyLeibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V. (FMP)BerlinGermany
| | - Matthias De Vleeschouwer
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Alejandro Mata‐Cabana
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Mandy Koopman
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Esther Stroo
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Minke de Vries
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Samantha Louise Edwards
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Janine Kirstein
- Department of Molecular Physiology and Cell BiologyLeibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V. (FMP)BerlinGermany
- Faculty of Biology & ChemistryUniversity of BremenBremenGermany
| | - Michele Vendruscolo
- Department of ChemistryCentre for Misfolding DiseasesUniversity of CambridgeCambridgeUK
| | | | - Frederic Rousseau
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Joost Schymkowitz
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Ellen A A Nollen
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
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Niu J, Huo J, Sun J, Huang J, Wang L, Liu A, Chen D, Li T, Yin J, Liu T. [Optimization of platform conditions for simultaneous detection of multiple nutritional marker proteins by liquid protein microarray]. Wei Sheng Yan Jiu 2021; 50:986-992. [PMID: 34949328 DOI: 10.19813/j.cnki.weishengyanjiu.2021.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To optimize the technical conditions for simultaneous detection of serum ferritin(SF), soluble transferrin receptor(sTfR), C-reactive protein(CRP)and retinol-binding protein four(RBP4)by liquid protein microarray. METHODS The trapping antibodies of the four proteins were coupled to magnetic beads with different codes, and the samples were added to the 96-well plate. The antibodies were detected by double antibody sandwich method. The serum of 5 patients were diluted with commercial diluent, 1% albumin from bovine serum(BSA) and phosphate buffer saline(PBS) to detect 4 target proteins, and the results were compared. The antibody specific binding ability was tested by antibody specific validation test. The interference between proteins was verified by the paired t test of the signal values of the single reaction system and the mixed reaction system. The lower limit of detection and the limit of biological detection of each protein were found by using multiple dilution method. The standard curve and regression equation were established. RESULTS 1%BSA and PBS were selected to replace commercial diluent as diluents for the detection of 4 proteins in this experiment. The cross-reaction rate of the four antigens with other capture antibodies and detection antibodies was less than 2%. There was no significant difference in the signal value of each protein in the single reaction system and the mixed reaction system. The limit of detection and the limit of biological detection of SF were 1.155 and 1.625 ng/mL, respectively. The lower limit of detection and the limit of biological detection of sTfR were 2.682 and 5.208 ng/mL, respectively. The detection limit and biological detection limit of CRP were 0.302 and 0.391 ng/mL, respectively. The lower limit of detection and the limit of biological detection for RBP4 were 1.814 and 3.540 ng/mL, respectively. The standard curve and regression equation of the four proteins within the common linear range were as follows: SF y=172.5x-39.65, R~2=0.9968;sTfR y=60.10x+77.38, R~2=0.9972;CRP y=-6.000x~2+210.3x+246.1, R~2=0.9063;RBP4 y=-0.6998x~2+64.31x+134.8, R~2=0.9748. CONCLUSION The conditions of the detection platform for four proteins such as SF, sTfR, CRP and RBP4 were optimized by using liquid protein chip technology.
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Affiliation(s)
- Jiangping Niu
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Junsheng Huo
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Jing Sun
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Jian Huang
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Lijuan Wang
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Ailing Liu
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Di Chen
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Tiantong Li
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Jiyong Yin
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Tingting Liu
- Key Laboratory of Trace Element Nutrition, National Health Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
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Chen X, Hu J. Long Noncoding RNA 3632454L22Rik Contributes to Corneal Epithelial Wound Healing by Sponging miR-181a-5p in Diabetic Mice. Invest Ophthalmol Vis Sci 2021; 62:16. [PMID: 34787641 PMCID: PMC8606839 DOI: 10.1167/iovs.62.14.16] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose This work explores the abnormal expression of long noncoding RNAs (lncRNAs), microRNAs (miRNAs) and messenger RNAs (mRNAs) in diabetic corneal epithelial cells (CECs) and constructs an associated competitive endogenous RNA (ceRNA) network. Moreover, we revealed that Rik may exert advantageous effects on diabetic corneal epithelial wound closure by sponging miR-181a-5p. Methods We obtained the profiles of differentially expressed lncRNAs (DELs) of CECs of type 1 diabetic versus control corneas by microarray and summarized the differentially expressed miRNAs (DEmiRs) and differentially expressed genes (DEGs) data by published literature. Subsequently, the ceRNA network was constructed using bioinformatics analyses. The levels of lncRNA ENSMUST00000153610/3632454L22Rik (Rik) and miR-181a-5p were verified. The localization of Rik was identified with fluorescence in situ hybridization (FISH), and dual-luciferase assays proved the targeted relationship between Rik and miR-181a-5p. Furthermore, we validated the functional impact of Rik in vitro. Results Overall, 111 upregulated and 117 downregulated DELs were detected in diabetic versus control CECs. The level of Rik located in both the cytoplasm and the nucleus was clearly downregulated, whereas miR-181a-5p was upregulated in vitro and in vivo in the diabetic group versus the control group. Rik can act as a ceRNA to bind to miR-181a-5p, thus promoting diabetic corneal epithelial wound healing in vitro. Conclusions This work investigated the expression profile of DELs and constructed ceRNA networks of diabetic CECs for the first time. Furthermore, we revealed that Rik may positively impact diabetic corneal epithelial wound healing by sponging miR-181a-5p, providing a novel potential therapeutic target of diabetic keratopathy (DK).
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Affiliation(s)
- Xiaxue Chen
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fu Zhou, China
| | - Jianzhang Hu
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fu Zhou, China
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Mu J, Gao S, Yang J, Wu F, Zhou H. Fundamental and Clinical Applications of Materials Based on Cancer-Associated Fibroblasts in Cancers. Int J Mol Sci 2021; 22:11671. [PMID: 34769102 PMCID: PMC8583912 DOI: 10.3390/ijms222111671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
Cancer stromal cells play a role in promoting tumor relapse and therapeutic resistance. Therefore, the current treatment paradigms for cancers are usually insufficient to eradicate cancer cells, and anti-cancer therapeutic strategies targeting stromal cells have been developed. Cancer-associated fibroblasts (CAFs) are perpetually activated fibroblasts in the tumor stroma. CAFs are the most abundant and highly heterogeneous stromal cells, and they are critically involved in cancer occurrence and progression. These effects are due to their various roles in the remodeling of the extracellular matrix, maintenance of cancer stemness, modulation of tumor metabolism, and promotion of therapy resistance. Recently, biomaterials and nanomaterials based on CAFs have been increasingly developed to perform gene or protein expression analysis, three-dimensional (3D) co-cultivation, and targeted drug delivery in cancer treatment. In this review, we systematically summarize the current research to fully understand the relevant materials and their functional diversity in CAFs, and we highlight the potential clinical applications of CAFs-oriented biomaterials and nanomaterials in anti-cancer therapy.
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Affiliation(s)
- Jingtian Mu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
| | - Shengtao Gao
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu 610041, China;
| | - Jin Yang
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
| | - Fanglong Wu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
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Frey SE, Stapleton JT, Ballas ZK, Rasmussen WL, Kaufman TM, Blevins TP, Jensen TL, Davies DH, Tary-Lehmann M, Chaplin P, Hill H, Goll JB. Human Antibody Responses Following Vaccinia Immunization Using Protein Microarrays and Correlation With Cell-Mediated Immunity and Antibody-Dependent Cellular Cytotoxicity Responses. J Infect Dis 2021; 224:1372-1382. [PMID: 33675226 PMCID: PMC8861366 DOI: 10.1093/infdis/jiab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND There are limited data regarding immunological correlates of protection for the modified vaccinia Ankara (MVA) smallpox vaccine. METHODS A total of 523 vaccinia-naive subjects were randomized to receive 2 vaccine doses, as lyophilized MVA given subcutaneously, liquid MVA given subcutaneously (liquid-SC group), or liquid MVA given intradermally (liquid-ID group) 28 days apart. For a subset of subjects, antibody-dependent cellular cytotoxicity (ADCC), interferon-γ release enzyme-linked immunospot (ELISPOT), and protein microarray antibody-binding assays were conducted. Protein microarray responses were assessed for correlations with plaque reduction neutralization titer (PRNT), enzyme-linked immunosorbent assay, ADCC, and ELISPOT results. RESULTS MVA elicited significant microarray antibody responses to 15 of 224 antigens, mostly virion membrane proteins, at day 28 or 42, particularly WR113/D8L and WR101H3L. In the liquid-SC group, responses to 9 antigens, including WR113/D8L and WR101/H3L, correlated with PRNT results. Three were correlated in the liquid-ID group. No significant correlations were observed with ELISPOT responses. In the liquid-ID group, WR052/F13L, a membrane glycoprotein, correlated with ADCC responses. CONCLUSIONS MVA elicited antibodies to 15 vaccinia strain antigens representing virion membrane. Antibody responses to 2 proteins strongly increased and significantly correlated with increases in PRNT. Responses to these proteins are potential correlates of protection and may serve as immunogens for future vaccine development. CLINICAL TRIALS REGISTRATION NCT00914732.
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Affiliation(s)
- Sharon E Frey
- Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - Jack T Stapleton
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Zuhair K Ballas
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Wendy L Rasmussen
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Thomas M Kaufman
- Department of Internal Medicine, University of Iowa and Iowa City VA Medical Center, Iowa City, Iowa, USA
| | - Tammy P Blevins
- Department of Internal Medicine, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | | | - D Huw Davies
- Vaccine Research & Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California, USA
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Byrd-Leotis L, Lasanajak Y, Bowen T, Baker K, Song X, Suthar MS, Cummings RD, Steinhauer DA. SARS-CoV-2 and other coronaviruses bind to phosphorylated glycans from the human lung. Virology 2021; 562:142-148. [PMID: 34325286 PMCID: PMC8299723 DOI: 10.1016/j.virol.2021.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 10/25/2022]
Abstract
SARS-CoV, MERS-CoV, and potentially SARS-CoV-2 emerged as novel human coronaviruses following cross-species transmission from animal hosts. Although the receptor binding characteristics of human coronaviruses are well documented, the role of carbohydrate binding in addition to recognition of proteinaceous receptors has not been fully explored. Using natural glycan microarray technology, we identified N-glycans in the human lung that are recognized by various human and animal coronaviruses. All viruses tested, including SARS-CoV-2, bound strongly to a range of phosphorylated, high mannose N-glycans and to a very specific set of sialylated structures. Examination of two linked strains, human CoV OC43 and bovine CoV Mebus, reveals shared binding to the sialic acid form Neu5Gc (not found in humans), supporting the evidence for cross-species transmission of the bovine strain. Our findings, revealing robust recognition of lung glycans, suggest that these receptors could play a role in the initial stages of coronavirus attachment and entry.
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Affiliation(s)
- Lauren Byrd-Leotis
- Department of Microbiology and Immunology, Emory University School of Medicine Atlanta, GA, 30322, USA; Centers for Excellence in Influenza Research and Surveillance, Emory-UGA CEIRS, Atlanta, GA, 30322, USA.
| | - Yi Lasanajak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Thomas Bowen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kelly Baker
- Beth Israel Deaconess Medical Center, Department of Surgery and Harvard Medical School Center for Glycoscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Richard D Cummings
- Beth Israel Deaconess Medical Center, Department of Surgery and Harvard Medical School Center for Glycoscience, Harvard Medical School, Boston, MA, 02115, USA; Centers for Excellence in Influenza Research and Surveillance, Emory-UGA CEIRS, Atlanta, GA, 30322, USA
| | - David A Steinhauer
- Department of Microbiology and Immunology, Emory University School of Medicine Atlanta, GA, 30322, USA; Centers for Excellence in Influenza Research and Surveillance, Emory-UGA CEIRS, Atlanta, GA, 30322, USA
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Schweiggert J, Habeck G, Hess S, Mikus F, Beloshistov R, Meese K, Hata S, Knobeloch K, Melchior F. SCF Fbxw5 targets kinesin-13 proteins to facilitate ciliogenesis. EMBO J 2021; 40:e107735. [PMID: 34368969 PMCID: PMC8441365 DOI: 10.15252/embj.2021107735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022] Open
Abstract
Microtubule depolymerases of the kinesin-13 family play important roles in various cellular processes and are frequently overexpressed in different cancer types. Despite the importance of their correct abundance, remarkably little is known about how their levels are regulated in cells. Using comprehensive screening on protein microarrays, we identified 161 candidate substrates of the multi-subunit ubiquitin E3 ligase SCFFbxw5 , including the kinesin-13 member Kif2c/MCAK. In vitro reconstitution assays demonstrate that MCAK and its closely related orthologs Kif2a and Kif2b become efficiently polyubiquitylated by neddylated SCFFbxw5 and Cdc34, without requiring preceding modifications. In cells, SCFFbxw5 targets MCAK for proteasomal degradation predominantly during G2 . While this seems largely dispensable for mitotic progression, loss of Fbxw5 leads to increased MCAK levels at basal bodies and impairs ciliogenesis in the following G1 /G0 , which can be rescued by concomitant knockdown of MCAK, Kif2a or Kif2b. We thus propose a novel regulatory event of ciliogenesis that begins already within the G2 phase of the preceding cell cycle.
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Affiliation(s)
- Jörg Schweiggert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Gregor Habeck
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Sandra Hess
- Institute of NeuropathologyFaculty of MedicineUniversity of FreiburgFreiburgGermany
- Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Felix Mikus
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Roman Beloshistov
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Klaus Meese
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Shoji Hata
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | | | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
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Santos NJ, Barquilha CN, Barbosa IC, Macedo RT, Lima FO, Justulin LA, Barbosa GO, Carvalho HF, Felisbino SL. Syndecan Family Gene and Protein Expression and Their Prognostic Values for Prostate Cancer. Int J Mol Sci 2021; 22:ijms22168669. [PMID: 34445387 PMCID: PMC8395474 DOI: 10.3390/ijms22168669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is the leading cause of cancer-associated mortality in men, and new biomarkers are still needed. The expression pattern and protein tissue localization of proteoglycans of the syndecan family (SDC 1-4) and syntenin-1 (SDCBP) were determined in normal and prostatic tumor tissue from two genetically engineered mouse models and human prostate tumors. Studies were validated using SDC 1-4 and SDCBP mRNA levels and patient survival data from The Cancer Genome Atlas and CamCAP databases. RNAseq showed increased expression of Sdc1 in Pb-Cre4/Ptenf/f mouse Pca and upregulation of Sdc3 expression and downregulation of Sdc2 and Sdc4 when compared to the normal prostatic tissue in Pb-Cre4/Trp53f/f-;Rb1f/f mouse tumors. These changes were confirmed by immunohistochemistry. In human PCa, SDC 1-4 and SDCBP immunostaining showed variable localization. Furthermore, Kaplan-Meier analysis showed that patients expressing SDC3 had shorter prostate-specific survival than those without SDC3 expression (log-rank test, p = 0.0047). Analysis of the MSKCC-derived expression showed that SDC1 and SDC3 overexpression is predictive of decreased biochemical recurrence-free survival (p = 0.0099 and p = 0.045, respectively), and SDC4 overexpression is predictive of increased biochemical recurrence-free survival (p = 0.035). SDC4 overexpression was associated with a better prognosis, while SDC1 and SDC3 were associated with more aggressive tumors and a worse prognosis.
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Affiliation(s)
- Nilton José Santos
- Department of Structural and Functional BIology, Institute of Bioscience of Botucatu (IBB), São Paulo State University, Botucatu 18618-689, SP, Brazil; (N.J.S.); (C.N.B.); (I.C.B.); (L.A.J.)
- Department of Structural and Functional Biology, Institute of Biology (IB), UNICAMP—State University of Campinas, Campinas 13083-970, SP, Brazil; (G.O.B.); (H.F.C.)
| | - Caroline Nascimento Barquilha
- Department of Structural and Functional BIology, Institute of Bioscience of Botucatu (IBB), São Paulo State University, Botucatu 18618-689, SP, Brazil; (N.J.S.); (C.N.B.); (I.C.B.); (L.A.J.)
- Department of Structural and Functional Biology, Institute of Biology (IB), UNICAMP—State University of Campinas, Campinas 13083-970, SP, Brazil; (G.O.B.); (H.F.C.)
| | - Isabela Correa Barbosa
- Department of Structural and Functional BIology, Institute of Bioscience of Botucatu (IBB), São Paulo State University, Botucatu 18618-689, SP, Brazil; (N.J.S.); (C.N.B.); (I.C.B.); (L.A.J.)
- Department of Structural and Functional Biology, Institute of Biology (IB), UNICAMP—State University of Campinas, Campinas 13083-970, SP, Brazil; (G.O.B.); (H.F.C.)
| | - Rodrigo Tavares Macedo
- Botucatu School of Medicine (FMB), São Paulo State University, Botucatu 01049-010, SP, Brazil; (R.T.M.); (F.O.L.)
| | - Flávio Oliveira Lima
- Botucatu School of Medicine (FMB), São Paulo State University, Botucatu 01049-010, SP, Brazil; (R.T.M.); (F.O.L.)
| | - Luis Antônio Justulin
- Department of Structural and Functional BIology, Institute of Bioscience of Botucatu (IBB), São Paulo State University, Botucatu 18618-689, SP, Brazil; (N.J.S.); (C.N.B.); (I.C.B.); (L.A.J.)
| | - Guilherme Oliveira Barbosa
- Department of Structural and Functional Biology, Institute of Biology (IB), UNICAMP—State University of Campinas, Campinas 13083-970, SP, Brazil; (G.O.B.); (H.F.C.)
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology, Institute of Biology (IB), UNICAMP—State University of Campinas, Campinas 13083-970, SP, Brazil; (G.O.B.); (H.F.C.)
| | - Sérgio Luis Felisbino
- Department of Structural and Functional BIology, Institute of Bioscience of Botucatu (IBB), São Paulo State University, Botucatu 18618-689, SP, Brazil; (N.J.S.); (C.N.B.); (I.C.B.); (L.A.J.)
- Correspondence:
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Ahn HT, Jang IS, Dang TV, Kim YH, Lee DH, Choi HS, Yu BJ, Kim MI. Effective Cryopreservation of a Bioluminescent Auxotrophic Escherichia coli-Based Amino Acid Array to Enable Long-Term Ready-to-Use Applications. Biosensors (Basel) 2021; 11:bios11080252. [PMID: 34436054 PMCID: PMC8393857 DOI: 10.3390/bios11080252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/24/2021] [Accepted: 07/25/2021] [Indexed: 11/16/2022]
Abstract
Amino acid arrays comprising bioluminescent amino acid auxotrophic Escherichia coli are effective systems to quantitatively determine multiple amino acids. However, there is a need to develop a method for convenient long-term preservation of the array to enable its practical applications. Here, we reported a potential strategy to efficiently maintain cell viability within the portable array. The method involves immobilization of cells within agarose gel supplemented with an appropriate cryoprotectant in individual wells of a 96-well plate, followed by storage under freezing conditions. Six cryoprotectants, namely dimethyl sulfoxide, glycerol, ethylene glycol, polyethylene glycol, sucrose, and trehalose, were tested in the methionine (Met) auxotroph-based array. Carbohydrate-type cryoprotectants (glycerol, sucrose, and trehalose) efficiently preserved the linearity of determination of Met concentration. In particular, the array with 5% trehalose exhibited the best performance. The Met array with 5% trehalose could determine Met concentration with high linearity (R2 value = approximately 0.99) even after storage at −20 °C for up to 3 months. The clinical utilities of the Met and Leu array, preserved at −20 °C for 3 months, were also verified by successfully quantifying Met and Leu in spiked blood serum samples for the diagnosis of the corresponding metabolic diseases. This long-term preservation protocol enables the development of a ready-to-use bioluminescent E. coli-based amino acid array to quantify multiple amino acids and can replace the currently used laborious analytical methods.
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Affiliation(s)
- Hee Tae Ahn
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
| | - In Seung Jang
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
| | - Thinh Viet Dang
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
| | - Yi Hyang Kim
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
| | - Dong Hoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
| | - Hyeun Seok Choi
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
| | - Byung Jo Yu
- Green and Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Cheonan 31056, Korea; (I.S.J.); (Y.H.K.); (H.S.C.)
- Correspondence: (B.J.Y.); (M.I.K.); Tel.: +82-41-589-8456 (B.J.Y.); +82-31-750-8563 (M.I.K.)
| | - Moon Il Kim
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam 13120, Korea; (H.T.A.); (T.V.D.); (D.H.L.)
- Correspondence: (B.J.Y.); (M.I.K.); Tel.: +82-41-589-8456 (B.J.Y.); +82-31-750-8563 (M.I.K.)
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McGregor R, Tay ML, Carlton LH, Hanson-Manful P, Raynes JM, Forsyth WO, Brewster DT, Middleditch MJ, Bennett J, Martin WJ, Wilson N, Atatoa Carr P, Baker MG, Moreland NJ. Mapping Autoantibodies in Children With Acute Rheumatic Fever. Front Immunol 2021; 12:702877. [PMID: 34335616 PMCID: PMC8320770 DOI: 10.3389/fimmu.2021.702877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/02/2021] [Indexed: 01/16/2023] Open
Abstract
Background Acute rheumatic fever (ARF) is a serious sequela of Group A Streptococcus (GAS) infection associated with significant global mortality. Pathogenesis remains poorly understood, with the current prevailing hypothesis based on molecular mimicry and the notion that antibodies generated in response to GAS infection cross-react with cardiac proteins such as myosin. Contemporary investigations of the broader autoantibody response in ARF are needed to both inform pathogenesis models and identify new biomarkers for the disease. Methods This study has utilised a multi-platform approach to profile circulating autoantibodies in ARF. Sera from patients with ARF, matched healthy controls and patients with uncomplicated GAS pharyngitis were initially analysed for autoreactivity using high content protein arrays (Protoarray, 9000 autoantigens), and further explored using a second protein array platform (HuProt Array, 16,000 autoantigens) and 2-D gel electrophoresis of heart tissue combined with mass spectrometry. Selected autoantigens were orthogonally validated using conventional immunoassays with sera from an ARF case-control study (n=79 cases and n=89 matched healthy controls) and a related study of GAS pharyngitis (n=39) conducted in New Zealand. Results Global analysis of the protein array data showed an increase in total autoantigen reactivity in ARF patients compared with controls, as well as marked heterogeneity in the autoantibody profiles between ARF patients. Autoantigens previously implicated in ARF pathogenesis, such as myosin and collagens were detected, as were novel candidates. Disease pathway analysis revealed several autoantigens within pathways linked to arthritic and myocardial disease. Orthogonal validation of three novel autoantigens (PTPN2, DMD and ANXA6) showed significant elevation of serum antibodies in ARF (p < 0.05), and further highlighted heterogeneity with patients reactive to different combinations of the three antigens. Conclusions The broad yet heterogenous elevation of autoantibodies observed suggests epitope spreading, and an expansion of the autoantibody repertoire, likely plays a key role in ARF pathogenesis and disease progression. Multiple autoantigens may be needed as diagnostic biomarkers to capture this heterogeneity.
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Affiliation(s)
- Reuben McGregor
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Mei Lin Tay
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Lauren H. Carlton
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Jeremy M. Raynes
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Wasan O. Forsyth
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - Julie Bennett
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - William John Martin
- Science for Technological Innovation Science Challenge, Callaghan Innovation, Wellington, New Zealand
| | - Nigel Wilson
- Starship Children’s Hospital, Auckland, New Zealand
| | - Polly Atatoa Carr
- Waikato District Health Board and Waikato University, Hamilton, New Zealand
| | - Michael G. Baker
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Nicole J. Moreland
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
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Abstract
The supported lipid bilayer (SLB) is a powerful tool for studying dynamic cell-environment interactions and has been widely used for biosensing applications. Using a reusable microfluidic chip, we present here a strategy to fabricate highly multiplexed SLB and protein arrays for cell signaling research. This approach allows for the rapid patterning of hundreds of highly reproducible and size-tunable SLB arrays with distinct lipid composition and mobility. Using fluorescence microscopy and fluorescence correlation spectroscopy, the lipid mobility is found to play a central role for patterning this membrane assay. Adding protein rings as diffusion barriers extends the accessible mobility range and maintains long-term stability of the hybrid array. Subsequent protein functionalizations on the SLB could be conducted using standard conjugation methods. The utility of the hybrid array for cell signaling experiments is demonstrated by studying the immune NF-κB signaling, whose activity is triggered by the binding of the membrane receptor, toll-like-receptor 4 (TLR 4), to its ligand, lipopolysaccharide (LPS), that is functionalized on the SLB. The patterned array allows cells to adhere and spread on areas without LPS before migrating to interact with membrane-bound LPS to initiate NF-κB activation. Overall, the strategy offers an efficient route to rapidly generate easily controllable and multiplexed molecular arrays that can serve as versatile platforms for biosensing and cell signaling research.
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Affiliation(s)
- Yu-Ting Ti
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan. and Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hsiao-Chi Cheng
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Ying Li
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan. and Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taiwan
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