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Integrative Multi-omics Analysis to Characterize Human Brain Ischemia. Mol Neurobiol 2021; 58:4107-4121. [PMID: 33939164 DOI: 10.1007/s12035-021-02401-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/21/2021] [Indexed: 01/14/2023]
Abstract
Stroke is a major cause of death and disability. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome. The use of high-throughput unbiased omics approaches and the integration of these data might deepen the knowledge of stroke at the molecular level, depicting the interaction between different molecular units. We aimed to identify protein and gene expression changes in the human brain after ischemia through an integrative approach to join the information of both omics analyses. The translational potential of our results was explored in a pilot study with blood samples from ischemic stroke patients. Proteomics and transcriptomics discovery studies were performed in human brain samples from six deceased stroke patients, comparing the infarct core with the corresponding contralateral brain region, unveiling 128 proteins and 2716 genes significantly dysregulated after stroke. Integrative bioinformatics analyses joining both datasets exposed canonical pathways altered in the ischemic area, highlighting the most influential molecules. Among the molecules with the highest fold-change, 28 genes and 9 proteins were selected to be validated in five independent human brain samples using orthogonal techniques. Our results were confirmed for NCDN, RAB3C, ST4A1, DNM1L, A1AG1, A1AT, JAM3, VTDB, ANXA1, ANXA2, and IL8. Finally, circulating levels of the validated proteins were explored in ischemic stroke patients. Fluctuations of A1AG1 and A1AT, both up-regulated in the ischemic brain, were detected in blood along the first week after onset. In summary, our results expand the knowledge of ischemic stroke pathology, revealing key molecules to be further explored as biomarkers and/or therapeutic targets.
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McNulty MJ, Silberstein DZ, Kuhn BT, Padgett HS, Nandi S, McDonald KA, Cross CE. Alpha-1 antitrypsin deficiency and recombinant protein sources with focus on plant sources: Updates, challenges and perspectives. Free Radic Biol Med 2021; 163:10-30. [PMID: 33279618 DOI: 10.1016/j.freeradbiomed.2020.11.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022]
Abstract
Alpha-1 antitrypsin deficiency (A1ATD) is an autosomal recessive disease characterized by low plasma levels of A1AT, a serine protease inhibitor representing the most abundant circulating antiprotease normally present at plasma levels of 1-2 g/L. The dominant clinical manifestations include predispositions to early onset emphysema due to protease/antiprotease imbalance in distal lung parenchyma and liver disease largely due to unsecreted polymerized accumulations of misfolded mutant A1AT within the endoplasmic reticulum of hepatocytes. Since 1987, the only FDA licensed specific therapy for the emphysema component has been infusions of A1AT purified from pooled human plasma at the 2020 cost of up to US $200,000/year with the risk of intermittent shortages. In the past three decades various, potentially less expensive, recombinant forms of human A1AT have reached early stages of development, one of which is just reaching the stage of human clinical trials. The focus of this review is to update strategies for the treatment of the pulmonary component of A1ATD with some focus on perspectives for therapeutic production and regulatory approval of a recombinant product from plants. We review other competitive technologies for treating the lung disease manifestations of A1ATD, highlight strategies for the generation of data potentially helpful for securing FDA Investigational New Drug (IND) approval and present challenges in the selection of clinical trial strategies required for FDA licensing of a New Drug Approval (NDA) for this disease.
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Affiliation(s)
- Matthew J McNulty
- Department of Chemical Engineering, University of California, Davis, CA, USA
| | - David Z Silberstein
- Department of Chemical Engineering, University of California, Davis, CA, USA
| | - Brooks T Kuhn
- Department of Internal Medicine, University of California, Davis, CA, USA; University of California, Davis, Alpha-1 Deficiency Clinic, Sacramento, CA, USA
| | | | - Somen Nandi
- Department of Chemical Engineering, University of California, Davis, CA, USA; Global HealthShare Initiative®, University of California, Davis, CA, USA
| | - Karen A McDonald
- Department of Chemical Engineering, University of California, Davis, CA, USA; Global HealthShare Initiative®, University of California, Davis, CA, USA
| | - Carroll E Cross
- Department of Internal Medicine, University of California, Davis, CA, USA; University of California, Davis, Alpha-1 Deficiency Clinic, Sacramento, CA, USA; Department of Physiology and Membrane Biology, University of California, Davis, CA, USA.
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Narayanan P, Mistry PK. Update on Alpha-1 Antitrypsin Deficiency in Liver Disease. Clin Liver Dis (Hoboken) 2020; 15:228-235. [PMID: 32617155 PMCID: PMC7326637 DOI: 10.1002/cld.896] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/23/2019] [Indexed: 02/04/2023] Open
Affiliation(s)
| | - Pramod K. Mistry
- Department of Digestive DiseasesYale–New Haven HospitalNew HavenCT
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Silberstein DZ, Karuppanan K, Aung HH, Chen CH, Cross CE, McDonald KA. An oxidation-resistant, recombinant alpha-1 antitrypsin produced in Nicotiana benthamiana. Free Radic Biol Med 2018; 120:303-310. [PMID: 29551638 PMCID: PMC6093210 DOI: 10.1016/j.freeradbiomed.2018.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/11/2018] [Indexed: 02/08/2023]
Abstract
Proteases and reactive oxygen species (ROS) have long been implicated in playing key roles in host tissue injury at sites of inflammation dominated by macrophage activations and/or neutrophil infiltrations. Imbalances between proteases/antiproteases and ROS/antioxidants are recognized to contribute to amplification of inflammatory-based host tissue injury. This has been especially well-documented in such respiratory tract diseases as chronic obstructive pulmonary disease, cystic fibrosis, and acute respiratory distress syndrome. Inflammation-related protease/ROS disequilibria are further confounded by recognition that proteases can increase ROS by several different mechanisms and that ROS can inactivate proteases. The major human antiprotease, alpha-1 antitrypsin (AAT), is dramatically inactivated by ROS. AAT deficiency is the most prevalent genetic predisposing factor leading to emphysema, a condition treated by replacement infusions of plasma-derived AAT (hAAT) at a cost of up to $200,000 per year per patient. An updated method for production of a plant-made recombinant AAT (prAAT) engineered for enhanced oxidation resistance compared to hAAT is presented. Plant-made recombinant AAT shows comparable antiprotease activity to hAAT, and retains full activity under oxidative conditions that would deactivate hAAT. Additionally, we show that prAAT has similar effectiveness in preventing neutrophil elastase-induced cell death in an in vitro human bronchial epithelial cell culture model. We conclude that prAAT is potentially a "biobetter" AAT product that could be made available to individuals with a wide spectrum of inflammatory disorders characterized by overly aggressive neutrophilic infiltrations.
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Affiliation(s)
- David Z Silberstein
- University of California, Davis, Department of Chemical Engineering, 1 Shields Ave, Davis, CA 95616, USA
| | - Kalimuthu Karuppanan
- University of California, Davis, Department of Chemical Engineering, 1 Shields Ave, Davis, CA 95616, USA
| | - Hnin Hnin Aung
- University of California, Davis, Department of Medicine, 1 Shields Ave, Davis, CA 95616, USA
| | - Ching-Hsien Chen
- University of California, Davis, Department of Medicine, 1 Shields Ave, Davis, CA 95616, USA
| | - Carroll E Cross
- University of California, Davis, Department of Medicine, 1 Shields Ave, Davis, CA 95616, USA; University of California, Davis, Department of Physiology and Membrane Biology, 1 Shields Ave, Davis, CA 95616, USA.
| | - Karen A McDonald
- University of California, Davis, Department of Chemical Engineering, 1 Shields Ave, Davis, CA 95616, USA
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Nanotechnology-based delivery systems to release growth factors and other endogenous molecules for chronic wound healing. J Drug Deliv Sci Technol 2017. [DOI: 10.1016/j.jddst.2017.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Xu J, Haupt K, Tse Sum Bui B. Core-Shell Molecularly Imprinted Polymer Nanoparticles as Synthetic Antibodies in a Sandwich Fluoroimmunoassay for Trypsin Determination in Human Serum. ACS APPLIED MATERIALS & INTERFACES 2017; 9:24476-24483. [PMID: 28678476 DOI: 10.1021/acsami.7b05844] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We describe the application of a fluorescently labeled water-soluble core-shell molecularly imprinted polymer (MIP) for fluorescence immunoassay (FIA) to detect trypsin. p-Aminobenzamidine (PAB), a competitive inhibitor of trypsin, was immobilized in the wells of a microtiter plate enabling the capture of trypsin in an oriented position, thus maintaining its native conformation. Fluorescent MIP nanoparticles, which bound selectively to trypsin, were used for quantification. The MIP was prepared by a multistep solid-phase synthesis approach on glass beads functionalized with PAB, orientating all trypsin molecules in the same way. The core-MIP was first synthesized, using a thermoresponsive polymer based on N-isopropylacrylamide, so as to enable its facile liberation from the immobilized template by a simple temperature change. The shell, mainly composed of allylamine to introduce primary amino groups for postconjugation of fluorescein isothiocyanate (FITC), was grafted in situ on the core-MIP, whose binding cavities were still bound and protected by the immobilized trypsin. The resulting core-shell MIP was endowed with a homogeneous population of high-affinity binding sites, all having the same orientation. The MIP has no or little cross-reactivity with other serine proteases and unrelated proteins. Our MIP-based FIA system was successfully applied to detect low trypsin concentrations spiked into nondiluted human serum with a low limit of quantification of 50 pM, which indicates the significant potential of this assay for analytical and biomedical diagnosis applications.
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Affiliation(s)
- Jingjing Xu
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Karsten Haupt
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Bernadette Tse Sum Bui
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
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Hansen HG, Kildegaard HF, Lee GM, Kol S. Case study on human α1-antitrypsin: Recombinant protein titers obtained by commercial ELISA kits are inaccurate. Biotechnol J 2016; 11:1648-1656. [DOI: 10.1002/biot.201600409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Henning Gram Hansen
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kgs. Lyngby Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kgs. Lyngby Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kgs. Lyngby Denmark
- Department of Biological Sciences; KAIST; Daejeon Daejeon, Republic of Korea
| | - Stefan Kol
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kgs. Lyngby Denmark
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