Multi-Omics Profiles of Small Intestine Organoids in Reaction to Breast Milk and Different Infant Formula Preparations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Breast Milk Donors
2.2. Breast Milk Collection
2.3. Infant Formulas
2.4. Induced Differentiation of Small Intestine Organoids
2.5. In Vitro Digestion Simulation of Milk
2.6. Establishment of the Absorption Metabolism Model
2.7. RNA Sequencing
2.8. Untargeted Metabolite Sequencing
2.9. Data Analysis of Transcriptome
2.10. Data Analysis of Untargeted Metabolomics
2.11. Data Processing and Statistical Analysis
2.12. RT-qPCR
3. Results
3.1. Transcriptome Profiles of Organoids Feeding by Breast Milk and Different Infant Formulas
3.2. Metabolite Profiles of Breast Milk and Different Infant Formulas Treated Cells
3.3. Pro-Development Effects of Breast Milk and Different Infant Formulae on Intestine Organoid
3.4. Effects on Cell Junction of Different Infant Formulae and Breast Milk
3.5. Extracellular Matrix Processes of Small Intestine Organoids Feeding by Different Infant Formulae and Breast Milk
4. Discussion
4.1. Application of Induced Pluripotent Stem Cell-Derived Organoid Models
4.2. Nutritional Absorption Effects Revealed by Transcriptomics and Metabolomics of Formula Feeding
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
ESC | embryo stem cell |
FA% | % of fatty acids |
DHA | Docosahexaenoic acid |
ARA | arachidonic acid |
CACO-2 | a widely used human colorectal adenocarcinoma cell line, simulating intestine epithelial cells |
BM | breast milk |
PMF1, PMF2, PMF3 (p1, p2, p3) | experimental groups in our study, representing infant formulas groups |
BM1~5 (b1~5) | experimental groups in our study, representing breast milk groups |
DEG | differential expressed genes |
GSVA | Gene Set Variation Analysis |
GSEA | Gene Set Enrichment analysis |
KEGG | kyoto encyclopedia of genes and genomes |
GO | gene ontology |
IPA | Ingenuity Pathway Analysis, a software application for analyzing omics data |
STRING | a database of functional protein association networks |
OPO | 1,3-Dioleoyl-2-palmitoyl glycerol |
ECM | extracellular matrix |
HMO | Human Milk Oligosaccharides |
SEM | standard error of the mean |
NES | normalized enrichment score |
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Wang, X.; Yang, S.; Zheng, C.; Huang, C.; Yao, H.; Guo, Z.; Wu, Y.; Wang, Z.; Wu, Z.; Ge, R.; et al. Multi-Omics Profiles of Small Intestine Organoids in Reaction to Breast Milk and Different Infant Formula Preparations. Nutrients 2024, 16, 2951. https://doi.org/10.3390/nu16172951
Wang X, Yang S, Zheng C, Huang C, Yao H, Guo Z, Wu Y, Wang Z, Wu Z, Ge R, et al. Multi-Omics Profiles of Small Intestine Organoids in Reaction to Breast Milk and Different Infant Formula Preparations. Nutrients. 2024; 16(17):2951. https://doi.org/10.3390/nu16172951
Chicago/Turabian StyleWang, Xianli, Shangzhi Yang, Chengdong Zheng, Chenxuan Huang, Haiyang Yao, Zimo Guo, Yilun Wu, Zening Wang, Zhenyang Wu, Ruihong Ge, and et al. 2024. "Multi-Omics Profiles of Small Intestine Organoids in Reaction to Breast Milk and Different Infant Formula Preparations" Nutrients 16, no. 17: 2951. https://doi.org/10.3390/nu16172951