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Gao K, Lian H, Xue C, Zhou J, Yan X. High-Throughput Counting and Sizing of Therapeutic Protein Aggregates in the Nanometer Size Range by Nano-Flow Cytometry. Anal Chem 2022; 94:17634-17644. [PMID: 36474427 DOI: 10.1021/acs.analchem.2c04382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein aggregation is one of the greatest challenges in biopharmaceuticals as it could decrease therapeutic efficacy, induce immunogenicity, and reduce shelf life of protein drugs. However, there lacks high-throughput methods than can count and size protein aggregates in the nanometer size range, especially for those smaller than 100 nm. Employing a laboratory-built nano-flow cytometer (nFCM) that enables light scattering detection of single silica nanoparticles as small as 24 nm with sizing resolution and accuracy comparable to those of electron microscopy, here, we report a new benchmark to analyze single protein aggregates as small as 40 nm. With an analysis rate of up to 10,000 particles/min, the size distribution and particle concentration of nanometer protein aggregates can be acquired in 2-3 min. Employing heat-induced aggregation of bovine serum albumin (BSA) at high concentrations as the model system, effects of different categories of excipients, including sugars, polyols, salts, and amino acids on the inhibition of protein aggregation were investigated. Strikingly enough, as high as 1010 to 1012 particles/mL of protein aggregates were observed in the size range of 40 to 200 nm for therapeutic proteins of human serum albumin injection, reconstituted recombinant human interieukin-2 solution, and human immunoglobulin injection. nFCM opens a new avenue to count and size nanometer protein aggregates, suggesting its future usability in the quality assessment and formulation promotion of therapeutic proteins.
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Affiliation(s)
- Kaimin Gao
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Hong Lian
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Chengfeng Xue
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Jing Zhou
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Xiaomei Yan
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
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Clement CC, Osan J, Buque A, Nanaware PP, Chang YC, Perino G, Shetty M, Yamazaki T, Tsai WL, Urbanska AM, Calvo-Calle JM, Ramsamooj S, Ramsamooj S, Vergani D, Mieli-Vergani G, Terziroli Beretta-Piccoli B, Gadina M, Montagna C, Goncalves MD, Sallusto F, Galluzzi L, Soni RK, Stern LJ, Santambrogio L. PDIA3 epitope-driven immune autoreactivity contributes to hepatic damage in type 2 diabetes. Sci Immunol 2022; 7:eabl3795. [PMID: 35984892 DOI: 10.1126/sciimmunol.abl3795] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A diet rich in saturated fat and carbohydrates causes low-grade chronic inflammation in several organs, including the liver, ultimately driving nonalcoholic steatohepatitis. In this setting, environment-driven lipotoxicity and glucotoxicity induce liver damage, which promotes dendritic cell activation and generates a major histocompatibility complex class II (MHC-II) immunopeptidome enriched with peptides derived from proteins involved in cellular metabolism, oxidative phosphorylation, and the stress responses. Here, we demonstrated that lipotoxicity and glucotoxicity, as driven by a high-fat and high-fructose (HFHF) diet, promoted MHC-II presentation of nested T and B cell epitopes from protein disulfide isomerase family A member 3 (PDIA3), which is involved in immunogenic cell death. Increased MHC-II presentation of PDIA3 peptides was associated with antigen-specific proliferation of hepatic CD4+ immune infiltrates and isotype switch of anti-PDIA3 antibodies from IgM to IgG3, indicative of cellular and humoral PDIA3 autoreactivity. Passive transfer of PDIA3-specific T cells or PDIA3-specific antibodies also exacerbated hepatocyte death, as determined by increased hepatic transaminases detected in the sera of mice subjected to an HFHF but not control diet. Increased humoral responses to PDIA3 were also observed in patients with chronic inflammatory liver conditions, including autoimmune hepatitis, primary biliary cholangitis, and type 2 diabetes. Together, our data indicated that metabolic insults caused by an HFHF diet elicited liver damage and promoted pathogenic immune autoreactivity driven by T and B cell PDIA3 epitopes.
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Affiliation(s)
- Cristina C Clement
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jaspreet Osan
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Aitziber Buque
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Padma P Nanaware
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yoke-Chen Chang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Giorgio Perino
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Madhur Shetty
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Takahiro Yamazaki
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wanxia Li Tsai
- Translational Immunology Section, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 10916, USA
| | | | | | - Shakti Ramsamooj
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shakti Ramsamooj
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Diego Vergani
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana and Epatocentro Ticino, Lugano 6900, Switzerland.,King's College London Faculty of Life Sciences and Medicine, King's College Hospital, London WC2R 2LS, UK
| | - Giorgina Mieli-Vergani
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana and Epatocentro Ticino, Lugano 6900, Switzerland.,King's College London Faculty of Life Sciences and Medicine, King's College Hospital, London WC2R 2LS, UK
| | - Benedetta Terziroli Beretta-Piccoli
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana and Epatocentro Ticino, Lugano 6900, Switzerland.,King's College London Faculty of Life Sciences and Medicine, King's College Hospital, London WC2R 2LS, UK
| | - Massimo Gadina
- Translational Immunology Section, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 10916, USA
| | - Cristina Montagna
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana and Epatocentro Ticino, Lugano 6900, Switzerland
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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Marassi V, De Marchis F, Roda B, Bellucci M, Capecchi A, Reschiglian P, Pompa A, Zattoni A. Perspectives on protein biopolymers: miniaturized flow field-flow fractionation-assisted characterization of a single-cysteine mutated phaseolin expressed in transplastomic tobacco plants. J Chromatogr A 2021; 1637:461806. [PMID: 33360435 DOI: 10.1016/j.chroma.2020.461806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/17/2023]
Abstract
The development of plant-based protein polymers to employ in biofilm production represents the promising intersection between material science and sustainability, and allows to obtain biodegradable materials that also possess excellent physicochemical properties. A possible candidate for protein biopolymer production is phaseolin, a storage protein highly abundant in P Vulgaris beans. We previously showed that transformed tobacco chloroplasts could be employed to express a mutated phaseolin carrying a signal peptide (directing it into the thylakoids) also enriched of a cysteine residue added to its C-terminal region. This modification allows for the formation of inter-chain disulfide bonds, as we previously demonstrated, and should promote polymerization. To verify the effect of the peptide modification and to quantify polymer formation, we employed hollow-fiber flow field-flow fractionation coupled to UV and multi-angle laser scattering detection (HF5-UV-MALS): HF5 allows for the selective size-based separation of phaseolin species, whereas MALS calculates molar mass and conformation state of each population. With the use of two different HF5 separation methods we first observed the native state of P.Vulgaris phaseolin, mainly assembled into trimers, and compared it to mutated phaseolin (P*) which instead resulted highly aggregated. Then we further characterized P* using a second separation method, discriminating between two and distinct high-molecular weight (HMW) species, one averaging 0.8 × 106 Da and the second reaching the tens of million Da. Insight on the conformation of these HMW species was offered from their conformation plots, which confirmed the positive impact of the Cys modification on polymerization.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry G. Ciamician, University of Bologna, Bologna, Italy; byFlow srl, via dell'Arcoveggio 74, 40128 Bologna (BO), Italy
| | - Francesca De Marchis
- Institute of Biosciences and Bioresources-Research Division of Perugia, National Research Council of Italy, via della Madonna Alta 130, 06128, Perugia (PG), Italy
| | - Barbara Roda
- Department of Chemistry G. Ciamician, University of Bologna, Bologna, Italy; byFlow srl, via dell'Arcoveggio 74, 40128 Bologna (BO), Italy
| | - Michele Bellucci
- Institute of Biosciences and Bioresources-Research Division of Perugia, National Research Council of Italy, via della Madonna Alta 130, 06128, Perugia (PG), Italy
| | - Alice Capecchi
- Institute of Biosciences and Bioresources-Research Division of Perugia, National Research Council of Italy, via della Madonna Alta 130, 06128, Perugia (PG), Italy
| | - Pierluigi Reschiglian
- Department of Chemistry G. Ciamician, University of Bologna, Bologna, Italy; byFlow srl, via dell'Arcoveggio 74, 40128 Bologna (BO), Italy
| | - Andrea Pompa
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", via Donato Bramante 28, 61029 Urbino (PU), Italy
| | - Andrea Zattoni
- Department of Chemistry G. Ciamician, University of Bologna, Bologna, Italy; byFlow srl, via dell'Arcoveggio 74, 40128 Bologna (BO), Italy.
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Marassi V, Beretti F, Roda B, Alessandrini A, Facci P, Maraldi T, Zattoni A, Reschiglian P, Portolani M. A new approach for the separation, characterization and testing of potential prionoid protein aggregates through hollow-fiber flow field-flow fractionation and multi-angle light scattering. Anal Chim Acta 2019; 1087:121-130. [PMID: 31585560 DOI: 10.1016/j.aca.2019.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022]
Abstract
Protein misfolding and aggregation are the common mechanisms in a variety of aggregation-dependent diseases. The compromised proteins often assemble into toxic, accumulating amyloid-like structures of various lengths and their toxicity can also be transferred both in vivo and in vitro a prion-like behavior. The characterization of protein interactions, degradation and conformational dynamics in biological systems still represents an analytical challenge in the prion-like protein comprehension. In our work, we investigated the nature of a transferable cytotoxic agent, presumably a misfolded protein, through the coupling of a multi-detector, non-destructive separation platform based on hollow-fiber flow field-flow fractionation with imaging and downstream in vitro tests. After purification with ion exchange chromatography, the transferable cytotoxic agentwas analyzed with Atomic Force Microscopy and statistical analysis, showing that the concentration of protein dimers and low n-oligomer forms was higher in the cytotoxic sample than in the control preparation. To assess whether the presence of these species was the actual toxic and/or self-propagating factor, we employed HF5 fractionation, with UV and Multi-Angle Light Scattering detection, to define proteins molar mass distribution and abundance, and fractionate the sample into size-homogeneous fractions. These fractions were then tested individually in vitro to investigate the direct correlation with cytotoxicity. Only the later-eluted fraction, which contains high-molar mass aggregates, proved to be toxic onto cell cultures. Moreover, it was observed that the selective transfer of toxicity also occurs for one lower-mass fraction, suggesting that two different mechanisms, acute and later induced toxicity, are in place. These results strongly encourage the efficacy of this platform to enable the identification of protein toxicants.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy
| | - Francesca Beretti
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124, Modena, Italy
| | - Barbara Roda
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy.
| | - Andrea Alessandrini
- CNR-Istituto Nanoscienze, S3, Via Campi 213/A, 41125, Modena, Italy; Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125, Modena, Italy
| | - Paolo Facci
- CNR-Istituto Nanoscienze, S3, Via Campi 213/A, 41125, Modena, Italy; Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125, Modena, Italy
| | - Tullia Maraldi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124, Modena, Italy
| | - Andrea Zattoni
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy; ByFlow Srl, Via dell'Arcoveggio 74, 40129, Bologna, Italy
| | - Marinella Portolani
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Via del Pozzo, 71, 41124, Modena, Italy
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Gimpl K, Klement J, Keller S. Characterising protein/detergent complexes by triple-detection size-exclusion chromatography. Biol Proced Online 2016; 18:4. [PMID: 26880869 PMCID: PMC4753644 DOI: 10.1186/s12575-015-0031-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/29/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In vitro investigations of membrane proteins usually depend on detergents for protein solubilisation and stabilisation. The amount of detergent bound to a membrane protein is relevant to successful experiment design and data analysis but is often unknown. Triple-detection size-exclusion chromatography enables simultaneous separation of protein/detergent complexes and protein-free detergent micelles and determination of their molar masses in a straightforward and absolute manner. Size-exclusion chromatography is used to separate different species, while ultraviolet absorbance, static light scattering, and refractive index measurements allow molar mass determination of protein and detergent components. RESULTS We refined standard experimental and data-analysis procedures for challenging membrane-protein samples that elude routine approaches. The general procedures including preparatory steps, measurements, and data analysis for the characterisation of both routine and complex samples in difficult solvents such as concentrated denaturant solutions are demonstrated. The applicability of the protocol but also its limitations and possible solutions are discussed, and an extensive troubleshooting section is provided. CONCLUSIONS We established and validated a protocol for triple-detection size-exclusion chromatography that enables the inexperienced user to perform and analyse measurements of well-behaved protein/detergent complexes. More experienced users are provided with an example of a more sophisticated analysis procedure allowing mass determination under challenging separation conditions.
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Affiliation(s)
- Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Jessica Klement
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
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Role of Carbonyl Modifications on Aging-Associated Protein Aggregation. Sci Rep 2016; 6:19311. [PMID: 26776680 PMCID: PMC4726109 DOI: 10.1038/srep19311] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/09/2015] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation is a common biological phenomenon, observed in different physiological and pathological conditions. Decreased protein solubility and a tendency to aggregate is also observed during physiological aging but the causes are currently unknown. Herein we performed a biophysical separation of aging-related high molecular weight aggregates, isolated from the bone marrow and splenic cells of aging mice and followed by biochemical and mass spectrometric analysis. The analysis indicated that compared to younger mice an increase in protein post-translational carbonylation was observed. The causative role of these modifications in inducing protein misfolding and aggregation was determined by inducing carbonyl stress in young mice, which recapitulated the increased protein aggregation observed in old mice. Altogether our analysis indicates that oxidative stress-related post-translational modifications accumulate in the aging proteome and are responsible for increased protein aggregation and altered cell proteostasis.
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Adverse-Mode FFF: Multi-Force Ideal Retention Theory. CHROMATOGRAPHY 2015. [DOI: 10.3390/chromatography2030392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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