| Literature DB >> 36103219 |
Lu Xiao1, Juan Zhu1,2,3, Zheng Liu4, Bangyong Wu2,3, Xiaohua Zhou1, Yanxing Wei1, Fei Sun1, Zhijian Wang1, Song Quan1, Qi Li2,3, Jun Wang5, Liping Huang1, Yanlin Ma1,2,3.
Abstract
Feeder cells provide an optimal microenvironment for the propagation of human embryonic stem cells (hESCs) by supplying currently known or unknown factors. However, the hESCs grown on feeder cells are not suitable for the purpose of clinical application because of the risk of contamination. In recent years, the feeder-free culture method has been developed to eliminate contamination, but some studies show that hESCs exhibit poor growth patterns in a feeder-free culture system. Regarding this phenomenon, we speculate that some genes related to hESC propagation were differently expressed in hESCs grown on feeder cells. To test this hypothesis, 3 hESC lines (NF4, NF5 and P096) were efficiently expanded in a feeder-free culture system or on human foreskin fibroblast (HFF) cells. The different gene expression patterns of hESCs in these 2 conditions were analyzed through microarrays. The results revealed that the hESCs cultured in both conditions maintained the expression of stemness markers and the ability to spontaneously differentiate into the 3 germ layers. The analysis of gene expression profiles revealed that 23 lncRNA and 15 genes were significantly differentially expressed in these two culture conditions. Furthermore, GO analyses showed that these genes were involved in such biological processes as growth factor stimuli, cell growth, and stem cell maintenance. To summarize, our study demonstrated that the hESCs grown on the HFF showed different gene expression patterns compared to those grown in a feeder-free culture system, suggesting that these differently expressed lncRNAs and genes played important roles in maintaining hESC propagation.Entities:
Keywords: feeder-free culture system; human embryonic stem cell; human foreskin fibroblast cells; microarray; transcriptional profiles
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Year: 2022 PMID: 36103219 PMCID: PMC9550256 DOI: 10.18632/aging.204282
Source DB: PubMed Journal: Aging (Albany NY) ISSN: 1945-4589 Impact factor: 5.955
Figure 1hESCs (NF4, NF5 and P096) grown on human foreskin fibroblast. (A) hESCs are positive for alkaline phosphatase staining. The scale bar was 200 μm. (B) Karyotype analysis revealed that these hESCs had a normal karyotype.
Figure 2Immunofluorescence staining. The expressions of OCT4, Nanog, TRA-1-60 and TRA-1-181 in hESCs were detected through immunofluorescence staining. The scale bar was 100 μm.
Figure 3Teratomas containing derivatives of all the 3 germ layers. Histological evidence of germ layer differentiation in NF4, NF5 and P096 in the feeder-free culture system or on HFF feeder layers. A typical teratoma containing endoderm (respiratory epithelium), mesoderm (cartilage tissue) and ectoderm (neuroepithelium). Magnification was 400× in total.
Summary of differentially expressed genes and lncRNAs in feeder-free culture system and on human foreskin fibroblast feeder layers.
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| mRNA | 8 | 7 | 15 |
| LncRNA | 6 | 17 | 23 |
Significant differential expression was defined as probes with P≤0.05 and absolute fold change ≥2.
Figure 4The profiles of the differentially-expressed genes in hESCs. (A) Hierarchical clustered heat maps show the Log2-transformed expression values of differentially-expressed genes in the feeder-free culture system and on human foreskin fibroblast feeder layers. Scatter plots (B) and volcano plots (C) of genes are of significantly different expressions.
Figure 5The profiles of the differentially-expressed lncRNA in hESCs. (A) Hierarchical clustered heat maps show the Log2-transformed expression values of differentially-expressed lncRNA in the feeder-free culture system and on human foreskin fibroblast feeder layers. Scatter plots (B) and volcano plots (C) of lncRNA are of significantly different expressions.
Figure 6The gene ontology enrichment analysis. The results of gene ontology enrichment analysis revealed that these differentially-expressed genes were involved in several biological processes including growth factor stimulus, organ morphogenesis, negative regulation of chemokine (C-X-C motif) ligand 2 production, inter-male aggressive behavior, cell growth, transforming growth factor beta and stem cell maintenance.
KEGG pathway analysis.
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| ko04350 TGF-beta signaling pathway | LEFTY2; LEFTY1 | 0.00244515308437387 |
| ko00512 Mucin type O-Glycan biosynthesis | GCNT4 | 0.0203768610313273 |
| ko04744 Phototransduction | CABP7 | 0.0415987534109394 |
| ko04745 Phototransduction - fly | CABP7 | 0.0487835224034567 |
Figure 7Correlated expression networks of differentially-expressed lncRNA and genes. Co-expression networks were constructed with differentially-expressed lncRNA and genes from 3 paired hESC lines in a feeder-free culture system vs on human foreskin fibroblast feeder layers. Pearson’s correlation > 0.99 or < -0.99, and P < 0.05.
Figure 8Validation of gene-relative changes through real-time RT-PCR. Fold changes of the gene expression in 3-line hESCs (NF4, NF5, P096) were calculated in a feeder-free culture system vs on human foreskin fibroblast feeder layers. Data was presented as mean values ± SD (n=3). The significant level was determined as P<0.05 using unpaired students’ test. **, P < 0.01.
The primers used in this study.
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| Forward | GGTTACCTCTTCCTCCCACTCC |
| Reverse | CCCTCCCATTTCCCTCGTTT | |
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| Forward | ACCTATGCCTGTGATTTGTGG |
| Reverse | AGTGGGTTGTTTGCCTTTGG | |
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| Forward | GGCCTGCATGAGGGTTTCT |
| Reverse | CCCCTGAGAAAGGAGACCCA | |
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| Forward | CTCGCCCTTCTTCACCGATG |
| Reverse | GTAGGACTCGTAGGCGTTGTA | |
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| Forward | TGGACCTCAGGGACTATGGAG |
| Reverse | CCGAGGCGATACACTGTCG | |
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| Forward | CGGACATCAACGACGTGAG |
| Reverse | GACGCCTTCAGCACGAACT | |
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| Forward | TGAATGATCCCGCTACAGATGA |
| Reverse | TCCTTACAGACAAGACGAGAGC | |
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| Forward | TGATGCCCGACATCCTGTTG |
| Reverse | ATGTTAGCTCCGTAGGCGAAG | |
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| Forward | TCCCTAAGTACCTCGCCTTTT |
| Reverse | GCTCCTGTTCATAGATACCCGAA | |
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| Forward | CATGTTCGTCATGGGTGTGAACCA |
| Reverse | AGTGATGGCATGGACTGTGGTCAT |