Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers

Salehabadi, Ehsan; Motamedian, Ehsan; Shojaosadati, Seyed Abbas

doi:10.1371/journal.pone.0254270

Cited by 5 publications

(5 citation statements)

References 72 publications

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“…In 2022, the first G. gallus GEM, iES1300, was developed and used to investigate how metabolic requirements changes with cell types. Salehabadi et al (2022) found that fat and cancerous chicken liver cells are metabolically similar. They explained that this was due to their similarities of flux through certain pathways, namely, fatty acid synthesis, glycerophospholipid, and sphingolipid metabolisms.…”

Section: Chicken (Gallus Gallus)mentioning

confidence: 99%

“…Salehabadi et al. (2022) found that fat and cancerous chicken liver cells are metabolically similar. They explained that this was due to their similarities of flux through certain pathways, namely, fatty acid synthesis, glycerophospholipid, and sphingolipid metabolisms.…”

Section: Animals Of Interest To the Cultivated Meat Industrymentioning

confidence: 99%

“…Additionally, the lean cell model had higher starch, sucrose, and lipid metabolism as compared to the other cells in the study. Importantly, the authors found that chicken biomass production can be optimized by upregulating the production of palmitoyl‐COA (Salehabadi et al., 2022). Chickens, like most avian species, are not able to adequately synthesize glycine or proline relative to their nutritional requirements (W. He et al., 2021).…”

Section: Animals Of Interest To the Cultivated Meat Industrymentioning

confidence: 99%

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Systems biology and metabolic modeling for cultivated meat: A promising approach for cell culture media optimization and cost reduction

Gomez Romero,

Boyle

2023

Comp Rev Food Sci Food Safe

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The cultivated meat industry, also known as cell-based meat, cultured meat, lab-grown meat, or meat alternatives, is a growing field that aims to generate animal tissues ex-vivo in a cost-effective manner that achieves price parity with traditional agricultural products. However, cell culture media costs account for 55%-90% of production costs. To address this issue, efforts are aimed at optimizing media composition. Systems biology-driven approaches have been successfully used to improve the biomass and productivity of multiple bioproduction platforms, like Chinese hamster ovary cells, by accelerating the development of cell line-specific media and reducing research and development and production costs related to cell media and its optimization. In this review, we summarize systems biology modeling approaches, methods for cell culture media and bioprocess optimization, and metabolic studies done in animals of interest to the cultivated meat industry. More importantly, we identify current gaps in knowledge that prevent the identification of metabolic bottlenecks. These include the lack of genome-scale metabolic models for some species (pigs and ducks), a lack of accurate biomass composition studies for different growth conditions, and 13 C-metabolic flux analysis (MFA) studies for many of the species of interest for the cultivated meat industry (only shrimp and duck cells have been subjected to 13 C-MFA). We also highlight the importance of characterizing the metabolic requirements of cells at the organism, breed, and cell line-specific levels, and we outline future steps that this nascent field needs to take to achieve price parity and production efficiency similar to those of other bioproduction platforms. Practical Application: Our article summarizes systems biology techniques for cell culture media design and bioprocess optimization, which may be used to significantly reduce cell-based meat production costs. We also present the results of experimental studies done on some of the species of interest to the cultivated meat industry and highlight why modeling approaches are required for multiple species, cell-types, and cell lines.

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Section: Chicken (Gallus Gallus)mentioning

confidence: 99%

Section: Animals Of Interest To the Cultivated Meat Industrymentioning

confidence: 99%

Section: Animals Of Interest To the Cultivated Meat Industrymentioning

confidence: 99%

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Systems biology and metabolic modeling for cultivated meat: A promising approach for cell culture media optimization and cost reduction

Gomez Romero,

Boyle

2023

Comp Rev Food Sci Food Safe

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“…Chicken ( G. gallus ) is the most domesticated species in the poultry industry, and it is also the first sequenced avian creature. The first comprehensive GEM for the chicken was published in 2022, which consists of 2427 reactions, 2569 metabolites, and 1300 genes and was reconstructed manually based on databases including KEGG, BiGG, CHEBI, UNIPROT, REACTOME, and MetaNetX using the bottom–up approach [49].…”

Section: Gem Reconstructionmentioning

confidence: 99%

Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

Li,

Chen,

Gustafsson

et al. 2023

Quant. Biol.

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Over the last 15 years, genome‐scale metabolic models (GEMs) have been reconstructed for human and model animals, such as mouse and rat, to systematically understand metabolism, simulate multicellular or multi‐tissue interplay, understand human diseases, and guide cell factory design for biopharmaceutical protein production. Here, we describe how metabolic networks can be represented using stoichiometric matrices and well‐defined constraints for flux simulation. Then, we review the history of GEM development for quantitative understanding of Homo sapiens and other relevant animals, together with their applications. We describe how model develops from H. sapiens to other animals and from generic purpose to precise context‐specific simulation. The progress of GEMs for animals greatly expand our systematic understanding of metabolism in human and related animals. We discuss the difficulties and present perspectives on the GEM development and the quest to integrate more biological processes and omics data for future research and translation. We truly hope that this review can inspire new models developed for other mammalian organisms and generate new algorithms for integrating big data to conduct more in‐depth analysis to further make progress on human health and biopharmaceutical engineering.

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“…Statistical significance of differential expression of TSS and CTSS peaks was calculated using the DeSeq2 tool. Genome-scale metabolic model reconstruction: We utilized the recently published generic genome-scale metabolic model for chicken [1]. Then we fine-tuned the model for chicken whole embryo knowledge and data based on the original transcriptomics data and BioUML platform [2].…”

mentioning

confidence: 99%

Reconstruction of a genome-scale metabolic model for chicken whole embryo considering transcriptomics data

2022

The Thirteenth International Multiconference

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Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers

Cited by 5 publications

References 72 publications

Systems biology and metabolic modeling for cultivated meat: A promising approach for cell culture media optimization and cost reduction

Systems biology and metabolic modeling for cultivated meat: A promising approach for cell culture media optimization and cost reduction

Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

Reconstruction of a genome-scale metabolic model for chicken whole embryo considering transcriptomics data

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