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Caldeira V, Fonseca TAH, N'Dembo L, Araújo R, Von Rekowski CP, Sampaio PNS, Calado CRC. A new methodology for a rapid and high-throughput comparison of molecular profiles and biological activity of phytoextracts. Biotechnol Bioeng 2024. [PMID: 38760962 DOI: 10.1002/bit.28739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/24/2023] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
To robustly discover and explore phytocompounds, it is necessary to evaluate the interrelationships between the plant species, plant tissue, and the extraction process on the extract composition and to predict its cytotoxicity. The present work evaluated how Fourier Transform InfraRed spectroscopy can acquire the molecular profile of aqueous and ethanol-based extracts obtained from leaves, seeds, and flowers of Cynara Cardunculus, and ethanol-based extracts from Matricaria chamomilla flowers, as well the impact of these extracts on the viability of mammalian cells. The extract molecular profile enabled to predict the extraction yield, and how the plant species, plant tissue, and extraction process affected the extract's relative composition. The molecular profile obtained from the culture media of cells exposed to extracts enabled to capture its impact on cells metabolism, at a higher sensitivity than the conventional assay used to determine the cell viability. Furthermore, it was possible to detect specific impacts on the cell's metabolism according to plant species, plant tissue, and extraction process. Since spectra were acquired on small volumes of samples (25 µL), after a simple dehydration step, and based on a plate with 96 wells, the method can be applied in a rapid, simple, high-throughput, and economic mode, consequently promoting the discovery of phytocompounds.
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Affiliation(s)
- Viviana Caldeira
- ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Tiago A H Fonseca
- ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Luana N'Dembo
- COPELABS-Computação e Cognição Centrada nas Pessoas, Faculty of Engineering, Lusófona University, Lisbon, Portugal
| | - Rúben Araújo
- ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Cristiana P Von Rekowski
- ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Pedro N S Sampaio
- COPELABS-Computação e Cognição Centrada nas Pessoas, Faculty of Engineering, Lusófona University, Lisbon, Portugal
| | - Cecília R C Calado
- ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
- i4HB - The Associate Laboratory Institute for Health and Bioeconomy, iBB - Institute for Bioengineering and Biosciences, IST - Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Sampaio PS, Calado CRC. Potential of FTIR-Spectroscopy for Drugs Screening against Helicobacter pylori. Antibiotics (Basel) 2020; 9:antibiotics9120897. [PMID: 33322665 PMCID: PMC7763841 DOI: 10.3390/antibiotics9120897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori colonizes the human stomach of half of the world's population. The infection if not treated, persists through life, leading to chronic gastric inflammation, that may progress to severe diseases as peptic ulcer, gastric adenocarcinoma, and mucosa-associated lymphoid tissue lymphoma. The first line of treatment, based on 7 to 21 days of two antibiotics associated with a proton pump inhibitor, is, however, already failing most due to patient non-compliance that leads to antibiotic resistance. It is, therefore, urgent to screen for new and more efficient antimicrobials against this bacterium. In this work, Fourier Transform Infrared (FTIR) spectroscopy was evaluated to screen new drugs against H. pylori, in rapid (between 1 to 6 h), and high-throughput mode and based on a microliter volume processes in relation to the agar dilution method. The reference H. pylori strains 26,695 and J99, were evaluated against a peptide-based antimicrobial and the clinical antibiotic clarithromycin, respectively. After optimization of the assay conditions, as the composition of the incubation mixture, the time of incubation, and spectral pre-processing, it was possible to reproducibly observe the effect of the drug on the bacterial molecular fingerprint as pointed by the spectra principal component analysis. The spectra, obtained from both reference strains, after its incubation with drugs concentrations lower than the MIC, presented peak ratios statistically different (p < 0.05) in relation to the bacteria incubated with drugs concentrations equal or higher to the MIC. It was possible to develop a partial least square regression model, enabling to predict from spectra of both bacteria strains, the drug concentration on the assay, with a high correlation coefficient between predicted and experimental data (0.91) and root square error of 40% of the minimum inhibitory concentration. All this points to the high potential of the technique for drug screening against this fastidious growth bacterium.
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Affiliation(s)
- Pedro Sousa Sampaio
- DREAMS—Interdisciplinary Center for Development and Research in Environment, Applied Management and Space, Faculty of Engineering, Lusophone University of Humanities and Technologies, Campo Grande, 376, 1749‑024 Lisbon, Portugal;
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Cecília R. C. Calado
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
- Correspondence:
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Ribeiro da Cunha B, Fonseca LP, Calado CRC. A phenotypic screening bioassay for Escherichia coli stress and antibiotic responses based on Fourier-transform infrared (FTIR) spectroscopy and multivariate analysis. J Appl Microbiol 2019; 127:1776-1789. [PMID: 31464358 DOI: 10.1111/jam.14429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 08/21/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022]
Abstract
AIMS To develop and optimize a Fourier-transform infrared spectroscopy (FTIRS) phenotypic screening bioassay for stress responses, regarding the effect of nutrient content, bacterial growth phase and stress agent exposure time. METHODS AND RESULTS A high-throughput FTIRS bioassay was developed to distinguish the stress responses of Escherichia coli to sodium hydroxide, hydrochloric acid, sodium chloride, sodium hypochlorite and ethanol. Principal component analysis and hierarchical clustering were used to quantify the effect of each parameter on bioassay performance, namely its reproducibility and metabolic resolution. Bioassay performance varied greatly, ranging from poor to very good. Spectra were partitioned into biologically relevant regions to evaluate their contributions to bioassay performance, but further improvements were not observed. Bioassay optimization was validated against empirical parameters, which confirmed a closer representation of known mechanisms on the antibiotic-induced stress responses. CONCLUSIONS The optimized bioassay used standard nutrient content, cells in the late-stationary growth phase and a one-shift exposure duration. Only the optimized bioassay adequately and reproducibly distinguished the E. coli stress and antibiotic responses. The absence of performance improvements using partitioned spectra indicated that stress responses are imprinted on the whole-spectra metabolic signature. SIGNIFICANCE AND IMPACT OF THE STUDY Highly optimized FTIRS bioassay parameters are vital in capturing whole-spectra metabolic signatures that can be used for satisfactory and reproducible phenotypic screening of stress and antibiotic responses.
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Affiliation(s)
- B Ribeiro da Cunha
- iBB - Institute of Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal.,ISEL - Instituto Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa (IPL), Lisboa, Portugal
| | - L P Fonseca
- iBB - Institute of Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisboa, Portugal
| | - C R C Calado
- ISEL - Instituto Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa (IPL), Lisboa, Portugal
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Metabolic and proliferation evaluation of human adipose-derived mesenchymal stromal cells (ASC) in different culture medium volumes: standardization of static culture. Biologicals 2019; 62:93-101. [PMID: 31495708 DOI: 10.1016/j.biologicals.2019.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 07/01/2019] [Accepted: 08/20/2019] [Indexed: 01/22/2023] Open
Abstract
Adipose-derived mesenchymal stromal/stem cells (ASC) have acquired a prominent role in tissue engineering and regenerative medicine. However, the standardization of basic culture procedures in this cellular type is still not well established according to the main qualitative cellular attributes. We evaluate the cell growth profile of human ASC in a different culture medium volumes and their nutritional composition utilizing static cultivation. Culture medium volumes (5, 10 and 15 mL/25 cm2) in T-flasks were evaluated by kinetic parameters and the metabolic composition was determined by biochemical analysis and Fourier transform infrared (FT-IR) absorption spectroscopy. 50% renewal of culture medium volume every 48 h was adopted. Immunophenotypic characterization and cell differentiation were performed. There was no difference (p > 0.05) in the kinetic parameters of cell proliferation between the culture medium volumes or in FT-IR composition. However, the concentrations of glucose, glutamine, lactate, and glutamate varied significantly during the cultivation process as a function of the medium volume. ASC presented specific antigens and differentiation potential of mesenchymal stromal/stem cells. It was concluded that the minimal culture medium volume (5 mL/25 cm2 in static culture) was sufficient to maintain the stability, potency, and growth of ASC, representing an economic and safe standardization for this cell culture process.
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de Almeida Fuzeta M, de Matos Branco AD, Fernandes-Platzgummer A, da Silva CL, Cabral JMS. Addressing the Manufacturing Challenges of Cell-Based Therapies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 171:225-278. [PMID: 31844924 DOI: 10.1007/10_2019_118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exciting developments in the cell therapy field over the last decades have led to an increasing number of clinical trials and the first cell products receiving marketing authorization. In spite of substantial progress in the field, manufacturing of cell-based therapies presents multiple challenges that need to be addressed in order to assure the development of safe, efficacious, and cost-effective cell therapies.The manufacturing process of cell-based therapies generally requires tissue collection, cell isolation, culture and expansion (upstream processing), cell harvest, separation and purification (downstream processing), and, finally, product formulation and storage. Each one of these stages presents significant challenges that have been the focus of study over the years, leading to innovative and groundbreaking technological advances, as discussed throughout this chapter.Delivery of cell-based therapies relies on defining product targets while controlling process variable impact on cellular features. Moreover, commercial viability is a critical issue that has had damaging consequences for some therapies. Implementation of cost-effectiveness measures facilitates healthy process development, potentially being able to influence end product pricing.Although cell-based therapies represent a new level in bioprocessing complexity in every manufacturing stage, they also show unprecedented levels of therapeutic potential, already radically changing the landscape of medical care.
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Affiliation(s)
- Miguel de Almeida Fuzeta
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - André Dargen de Matos Branco
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Fernandes-Platzgummer
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Cláudia Lobato da Silva
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
| | - Joaquim M S Cabral
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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Paim Á, Tessaro IC, Cardozo NSM, Pranke P. Mesenchymal stem cell cultivation in electrospun scaffolds: mechanistic modeling for tissue engineering. J Biol Phys 2018; 44:245-271. [PMID: 29508186 PMCID: PMC6082795 DOI: 10.1007/s10867-018-9482-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/19/2018] [Indexed: 12/17/2022] Open
Abstract
Tissue engineering is a multidisciplinary field of research in which the cells, biomaterials, and processes can be optimized to develop a tissue substitute. Three-dimensional (3D) architectural features from electrospun scaffolds, such as porosity, tortuosity, fiber diameter, pore size, and interconnectivity have a great impact on cell behavior. Regarding tissue development in vitro, culture conditions such as pH, osmolality, temperature, nutrient, and metabolite concentrations dictate cell viability inside the constructs. The effect of different electrospun scaffold properties, bioreactor designs, mesenchymal stem cell culture parameters, and seeding techniques on cell behavior can be studied individually or combined with phenomenological modeling techniques. This work reviews the main culture and scaffold factors that affect tissue development in vitro regarding the culture of cells inside 3D matrices. The mathematical modeling of the relationship between these factors and cell behavior inside 3D constructs has also been critically reviewed, focusing on mesenchymal stem cell culture in electrospun scaffolds.
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Affiliation(s)
- Ágata Paim
- Department of Chemical Engineering, Universidade Federal do Rio Grande do Sul (UFRGS), R. Eng. Luis Englert, s/n, Porto Alegre, Rio Grande do Sul, 90040-040, Brazil.
| | - Isabel C Tessaro
- Department of Chemical Engineering, Universidade Federal do Rio Grande do Sul (UFRGS), R. Eng. Luis Englert, s/n, Porto Alegre, Rio Grande do Sul, 90040-040, Brazil
| | - Nilo S M Cardozo
- Department of Chemical Engineering, Universidade Federal do Rio Grande do Sul (UFRGS), R. Eng. Luis Englert, s/n, Porto Alegre, Rio Grande do Sul, 90040-040, Brazil
| | - Patricia Pranke
- Faculty of Pharmacy, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Ipiranga, 2752, Porto Alegre, Rio Grande do Sul, 90610-000, Brazil
- Stem Cell Research Institute, Porto Alegre, Rio Grande do Sul, 90020-010, Brazil
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Sampaio PNS, Calado CRC. Comparative analysis of different transformed Saccharomyces cerevisiae strains based on high-throughput Fourier transform infrared spectroscopy. J Biotechnol 2017; 260:1-10. [DOI: 10.1016/j.jbiotec.2017.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 07/31/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022]
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