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Li Y, Ma Y, Zhu H, Liu Y, Pan S, Chen X, Wu T. Identifying distinct markers in two Sorghum varieties for baijiu fermentation using untargeted metabolomics and molecular network approaches. Food Chem X 2024; 23:101646. [PMID: 39139485 PMCID: PMC11321435 DOI: 10.1016/j.fochx.2024.101646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
The quality of strong-flavor Baijiu, a prominent Chinese liquor, is intricately tied to the choice of sorghum variety used in fermentation. However, a significant gap remains in our understanding of how glutinous and non-glutinous sorghum varieties comprehensively impact Baijiu flavor formation through fermentation metabolites. This study employed untargeted metabolomics combined with feature-based molecular networking (FBMN) to explore the unique metabolic characteristics of these two sorghum varieties during fermentation. FBMN analysis revealed 267 metabolites within both types of fermented sorghum (Zaopei) in the cellar. Further multidimensional statistical analyses highlighted sphingolipids, 2,5-diketopiperazines, and methionine derivatives as critical markers for quality control. These findings represent a significant advancement in our understanding and provide valuable insights for regulating the quality of Baijiu flavors.
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Affiliation(s)
- Yulan Li
- School of Food and Biotechnology, Xihua University, No.9999 Guangchang Road, Chengdu 610039, China
| | - Yi Ma
- Sichuan Province Engineering Technology Research Center of Liquor-Making Grains, Sichuan University of Science and Engineering, Zigong 643000, China
| | - Hui Zhu
- Sichuan Province Engineering Technology Research Center of Liquor-Making Grains, Sichuan University of Science and Engineering, Zigong 643000, China
| | - Yin Liu
- Sichuan Yibin Hengshengfu Liquor Industry Group Co., Ltd., Yibin 644100, China
| | - Shijiang Pan
- Sichuan Yibin Agriculture and Rural Affairs Bureau, Yibin 644100, China
| | - Xi Chen
- SCIEX Analytical Instrument Trading Co., Shanghai, 200335, China
| | - Tao Wu
- School of Food and Biotechnology, Xihua University, No.9999 Guangchang Road, Chengdu 610039, China
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Yeon Jung D, Jung Lee H, Kim M, Min Na K, Yup Lee D, Jo C. Metabolomic changes in culture media with varying passage numbers of pig muscle stem cell culture for cultured meat production. Food Res Int 2024; 182:114138. [PMID: 38519170 DOI: 10.1016/j.foodres.2024.114138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
Selecting the primary cells in an optimal state for cultured meat production is a crucial challenge in commercializing cultured meat. We investigated the metabolomic changes in culture media according to passage numbers for indirectly assessing the state of primary cells. Pig skeletal muscle stem cells (PSCs) harvested from the biceps femoris muscles of 7-d-old crossbred pigs (Landrace × Yorkshire × Duroc, LYD) were used for cell characterization. Fresh media (FM) and spent media (SM) of PSCs during passages 1 to 3 in vitro culture were prepared for metabolomics analysis. SM was collected on the third day of proliferation for each passage of PSCs. Cell characterization analysis revealed that the proliferation rate was highest at passage 2; however, a significant loss of expression of myogenic marker genes was observed at passage 3. Based on metabolomic profiles of culture media, FM and SM groups (SM1, SM2, and SM3) were clearly separated by partial least squares-discriminant analysis. A total of seven differentially abundant metabolites (DAMs) were identified from FM and SM for each passage, based on the following criteria: P < 0.05, fold change > 1.5 or < 0.66, and a variable importance in projection score > 1.5. All seven DAMs and their interconnected metabolites might be primarily used as substrates for energy production and most of them were relatively abundant in SM3. Among the seven DAMs, the three potential biomarkers (γ-glutamyl-L-leucine, cytosine, and ketoleucine), which showed significant changes exclusively in SM3, each had an area under the curve value of 1. Therefore, monitoring the levels of these key metabolites in culture media could serve as a quality control measure for cultured meat production by enabling the indirect detection of suboptimal PSCs based on their proliferation ability.
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Affiliation(s)
- Doo Yeon Jung
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun Jung Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Minsu Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong Min Na
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Do Yup Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea; Department of Animal Product Technology, Faculty of Animal Husbandry, Universitas Padjadjaran, West Java 45363, Indonesia.
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Singh R, Fatima E, Thakur L, Singh S, Ratan C, Kumar N. Advancements in CHO metabolomics: techniques, current state and evolving methodologies. Front Bioeng Biotechnol 2024; 12:1347138. [PMID: 38600943 PMCID: PMC11004234 DOI: 10.3389/fbioe.2024.1347138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background: Investigating the metabolic behaviour of different cellular phenotypes, i.e., good/bad grower and/or producer, in production culture is important to identify the key metabolite(s)/pathway(s) that regulate cell growth and/or recombinant protein production to improve the overall yield. Currently, LC-MS, GC-MS and NMR are the most used and advanced technologies for investigating the metabolome. Although contributed significantly in the domain, each technique has its own biasness towards specific metabolites or class of metabolites due to various reasons including variability in the concept of working, sample preparation, metabolite-extraction methods, metabolite identification tools, and databases. As a result, the application of appropriate analytical technique(s) is very critical. Purpose and scope: This review provides a state-of-the-art technological insights and overview of metabolic mechanisms involved in regulation of cell growth and/or recombinant protein production for improving yield from CHO cultures. Summary and conclusion: In this review, the advancements in CHO metabolomics over the last 10 years are traced based on a bibliometric analysis of previous publications and discussed. With the technical advancement in the domain of LC-MS, GC-MS and NMR, metabolites of glycolytic and nucleotide biosynthesis pathway (glucose, fructose, pyruvate and phenylalanine, threonine, tryptophan, arginine, valine, asparagine, and serine, etc.) were observed to be upregulated in exponential-phase thereby potentially associated with cell growth regulation, whereas metabolites/intermediates of TCA, oxidative phosphorylation (aspartate, glutamate, succinate, malate, fumarate and citrate), intracellular NAD+/NADH ratio, and glutathione metabolic pathways were observed to be upregulated in stationary-phase and hence potentially associated with increased cell-specific productivity in CHO bioprocess. Moreover, each of technique has its own bias towards metabolite identification, indicating their complementarity, along with a number of critical gaps in the CHO metabolomics pipeline and hence first time discussed here to identify their potential remedies. This knowledge may help in future study designs to improve the metabolomic coverage facilitating identification of the metabolites/pathways which might get missed otherwise and explore the full potential of metabolomics for improving the CHO bioprocess performances.
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Affiliation(s)
- Rita Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Eram Fatima
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sevaram Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Chandra Ratan
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Niraj Kumar
- Translational Health Science and Technology Institute, Faridabad, India
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Dodia H, Sunder AV, Borkar Y, Wangikar PP. Precision fermentation with mass spectrometry-based spent media analysis. Biotechnol Bioeng 2023; 120:2809-2826. [PMID: 37272489 DOI: 10.1002/bit.28450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023]
Abstract
Optimization and monitoring of bioprocesses requires the measurement of several process parameters and quality attributes. Mass spectrometry (MS)-based techniques such as those coupled to gas chromatography (GCMS) and liquid Chromatography (LCMS) enable the simultaneous measurement of hundreds of metabolites with high sensitivity. When applied to spent media, such metabolome analysis can help determine the sequence of substrate uptake and metabolite secretion, consequently facilitating better design of initial media and feeding strategy. Furthermore, the analysis of metabolite diversity and abundance from spent media will aid the determination of metabolic phases of the culture and the identification of metabolites as surrogate markers for product titer and quality. This review covers the recent advances in metabolomics analysis applied to the development and monitoring of bioprocesses. In this regard, we recommend a stepwise workflow and guidelines that a bioprocesses engineer can adopt to develop and optimize a fermentation process using spent media analysis. Finally, we show examples of how the use of MS can revolutionize the design and monitoring of bioprocesses.
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Affiliation(s)
- Hardik Dodia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | | | - Yogen Borkar
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Clarity Bio Systems India Pvt. Ltd., Pune, India
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Casian T, Nagy B, Kovács B, Galata DL, Hirsch E, Farkas A. Challenges and Opportunities of Implementing Data Fusion in Process Analytical Technology-A Review. Molecules 2022; 27:4846. [PMID: 35956791 PMCID: PMC9369811 DOI: 10.3390/molecules27154846] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
The release of the FDA's guidance on Process Analytical Technology has motivated and supported the pharmaceutical industry to deliver consistent quality medicine by acquiring a deeper understanding of the product performance and process interplay. The technical opportunities to reach this high-level control have considerably evolved since 2004 due to the development of advanced analytical sensors and chemometric tools. However, their transfer to the highly regulated pharmaceutical sector has been limited. To this respect, data fusion strategies have been extensively applied in different sectors, such as food or chemical, to provide a more robust performance of the analytical platforms. This survey evaluates the challenges and opportunities of implementing data fusion within the PAT concept by identifying transfer opportunities from other sectors. Special attention is given to the data types available from pharmaceutical manufacturing and their compatibility with data fusion strategies. Furthermore, the integration into Pharma 4.0 is discussed.
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Affiliation(s)
- Tibor Casian
- Department of Pharmaceutical Technology and Biopharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Brigitta Nagy
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary; (D.L.G.); (E.H.); (A.F.)
| | - Béla Kovács
- Department of Biochemistry and Environmental Chemistry, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540139 Târgu Mureș, Romania;
| | - Dorián László Galata
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary; (D.L.G.); (E.H.); (A.F.)
| | - Edit Hirsch
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary; (D.L.G.); (E.H.); (A.F.)
| | - Attila Farkas
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary; (D.L.G.); (E.H.); (A.F.)
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Walter TH, Alden BA, Berthelette K, Field JA, Lawrence NL, McLaughlin J, Patel AV. Characterization of a highly stable zwitterionic hydrophilic interaction chromatography stationary phase based on hybrid organic/inorganic particles. J Sep Sci 2021; 45:1389-1399. [PMID: 34937126 PMCID: PMC9487986 DOI: 10.1002/jssc.202100859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/08/2022]
Abstract
We have characterized a sulfobetaine stationary phase based on 1.7 μm ethylene-bridged hybrid organic/inorganic particles, which is intended for use in hydrophilic interaction chromatography. The efficiency of columns packed with this material were determined as a function of flow rate, demonstrating a minimum reduced plate height of 2.4. The batch-to-batch reproducibility was assessed using the separation of a mixture of acids, bases and neutrals. We compared the retention and selectivity of the hybrid sulfobetaine stationary phase to that of several benchmark materials. The hybrid sulfobetaine material gave strong retention for polar neutrals and high selectivity for methyl groups, hydroxy groups and configurational isomers. Large differences in cation and anion retention were observed among the columns. We characterized the acid and base stability of the hybrid sulfobetaine stationary phase, using accelerated tests at pH 1.3 and 11.0, both at 70°C. The results support a recommended pH range of 2 to 10. We also investigated the performance of columns packed with this material for metal-sensitive analytes, comparing conventional stainless steel column hardware to hardware that incorporates hybrid surface technology to mitigate interactions with metal surfaces. Compared to the conventional columns, the hybrid surface technology columns showed greatly improved peak shape. This article is protected by copyright. All rights reserved.
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Pinto IF, Soares RRG, Mäkinen MEL, Chotteau V, Russom A. Multiplexed Microfluidic Cartridge for At-Line Protein Monitoring in Mammalian Cell Culture Processes for Biopharmaceutical Production. ACS Sens 2021; 6:842-851. [PMID: 33724791 PMCID: PMC8034812 DOI: 10.1021/acssensors.0c01884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The biopharmaceutical
market has been rapidly growing in recent
years, creating a highly competitive arena where R&D is critical
to strike a balance between clinical safety and profitability. Toward
process optimization, the recent development and adoption of new process
analytical technologies (PAT) highlight the dynamic complexity of
mammalian/human cell culture processes, as well as the importance
of fine-tuning and modeling key metabolites and proteins. In this
context, simple, rapid, and cost-effective devices allowing routine
at-line monitoring of specific proteins during process development
and production are currently lacking. Here, we report the development
of a versatile microfluidic protein analysis cartridge allowing the
multiplexed bead-based immunodetection of specific proteins directly
from complex mixtures with minimal hands-on time. Colorimetric quantification
of Chinese hamster ovary (CHO) host cell proteins as key impurities,
monoclonal antibodies as target biopharmaceuticals, and lactate dehydrogenase
as a marker of cell viability was achieved with limits of detection
in the 1–10 ng/mL range and analysis times as short as 30 min.
The device was further demonstrated for the monitoring of a Rituximab-producing
CHO cell bioreactor over the course of 8 days, providing comparable
recoveries to standard enzyme-linked immunosorbent assay (ELISA) kits.
The high sensitivity combined with robustness to matrix interference
highlights the potential of the device to perform at-line measurements
spanning from the bioreactor to the downstream processing.
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Affiliation(s)
- Inês F. Pinto
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, 171 21 Solna, Sweden
| | - Ruben R. G. Soares
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, 171 21 Solna, Sweden
| | - Meeri E.-L. Mäkinen
- KTH Royal Institute of Technology, Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, 106 91 Stockholm, Sweden
- AdBIOPRO, Competence Centre for Advanced BioProduction by Continuous Processing, KTH, 100 44 Stockholm, Sweden
| | - Veronique Chotteau
- KTH Royal Institute of Technology, Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, 106 91 Stockholm, Sweden
- AdBIOPRO, Competence Centre for Advanced BioProduction by Continuous Processing, KTH, 100 44 Stockholm, Sweden
| | - Aman Russom
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, 171 21 Solna, Sweden
- AIMES, Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
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