Application of Genomics/Proteomics Technologies in the Research of Biocom-patibility of Biomaterials

Lü, Xiaoying; Huang, Yan; Yu, Yadong; Yang, Yamin

doi:10.3724/sp.j.1077.2013.12269

Cited by 10 publications

(4 citation statements)

References 40 publications

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“…Although transcriptomic and proteomic technology can be used to comprehensively reveal overall changes at the molecular level, there may be incongruent expression between mRNAs and proteins [23,24]. Our group also found significant differences between mRNA and protein expression levels in both quantity and type compared with the results from transcriptomic and proteomic analysis of the molecular biocompatibility of gold nanoparticles with human dermal fibroblasts [25].…”

Section: Introductionmentioning

confidence: 51%

An integrated study of natural hydroxyapatite-induced osteogenic differentiation of mesenchymal stem cells using transcriptomics, proteomics and microRNA analyses

Zhang¹,

Wang²,

Lü³

2014

Biomed. Mater.

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This work combined transcriptomics, proteomics, and microRNA (miRNA) analyses to elucidate the mechanism of natural hydroxyapatite (NHA)-induced osteogenic differentiation of mesenchymal stem cells (MSCs). First, NHA powder was obtained from pig bones and fabricated into disc-shaped samples. Subsequently, the proliferation and osteogenic differentiation of MSCs cultured on NHA were investigated. Then, proteomics was employed to detect the protein expression profiles of MSCs cultured on NHA, and the effect of NHA on MSCs was analyzed through an integrated pathway analysis (including proteomics and previous transcriptomics data) in which specific NHA-induced differentiation pathways were analyzed. The pathway nodes with expression data at both the mRNA and protein levels (mRNA-protein pairs) were filtered in differentiation-related pathways. miRNAs corresponding to these target mRNA-protein pairs were predicted, screened and tested, and the regulatory effects of miRNAs on mRNA-protein pairs were analyzed. Finally, the NHA-induced osteogenic pathways were verified. The results of an MTT assay and alkaline phosphatase (ALP) staining showed that the cell proliferation rate decreased and the osteogenic performance improved in the presence of NHA. By integrating transcriptomics and proteomics, the genes and proteins involved in 89 pathways were shown to be differentially expressed. Among them, 5 differentiation-associated pathways, in which 9 miRNAs and 8 regulated-target mRNA-protein zby inhibiting the target mRNA-protein pair HSPA8 in the MAPK signaling pathway, and miR-26a and miR-26b might inhibit adipogenic differentiation by repressing the target mRNA-protein pair HMGA1 in the adipogenesis pathway. A verification experiment for the osteogenic pathway indicated that the ERK1/2 or JNK MAPK pathways might play an important role in NHA-induced osteogenic differentiation. In conclusion, NHA affected MSCs at both the transcriptional and translational levels, and MSC osteogenic differentiation eventually occurred through the MAPK and adipogenesis pathways, in which miRNAs and target mRNAs/proteins participated cooperatively.

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Section: Introductionmentioning

confidence: 51%

An integrated study of natural hydroxyapatite-induced osteogenic differentiation of mesenchymal stem cells using transcriptomics, proteomics and microRNA analyses

Zhang¹,

Wang²,

Lü³

2014

Biomed. Mater.

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“…cDNA microarray has become an important method in the field of biocompatibility research [ 12 ] to analyze the influence on gene expression of cell–biomaterial interaction in vitro . It identifies differentially expressed genes, provides the essential gene information affecting biomaterial biocompatibility [ 13 ] and reveals the mechanism of cell–biomaterial interaction at the molecular level.…”

Section: Introductionmentioning

confidence: 99%

Integrated transcriptomic and proteomic study on the different molecular mechanisms of PC12 cell growth on chitosan and collagen/chitosan films

Lü

Huang

et al. 2020

Regenerative Biomaterials

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The purpose of this article is to integrate the transcriptomic analysis and the proteomic profiles and to reveal and compare the different molecular mechanisms of PC12 cell growth on the surface of chitosan films and collagen/chitosan films. First, the chitosan films and the collagen/chitosan films were prepared. Subsequently, the cell viability assay was performed; the cell viability of the PC12 cells cultured on the collagen/chitosan films for 24 h was significantly higher than that on the chitosan films. Then, with cDNA microarray, the numbers of differentially expressed genes of PC12 cells on the surface of chitosan and collagen/chitosan films were 13349 and 5165, respectively. Next, the biological pathway analysis indicated that the differentially expressed genes were involved in 40 pathways directly related to cell adhesion and growth. The integrated transcriptomic and our previous proteomic analysis revealed that three biological pathways—extracellular matrix–receptor interaction, focal adhesion and regulation of actin cytoskeleton—were regulated in the processes of protein adsorption, cell adhesion and growth. The adsorbed proteins on the material surfaces further influenced the expression of important downstream genes by regulating the expression of related receptor genes in these three pathways. In comparison, chitosan films had a strong inhibitory effect on PC12 cell adhesion and growth, resulting in the significantly lower cell viability on its surface; on the contrary, collagen/chitosan films were more conducive to promoting PC12 cell adhesion and growth, resulting in higher cell viability.

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“…Though the expressions of genes and proteins in cells can be detected by different biomics technologies with high-throughput and high sensitivity, false-positive or false-negative results in the experiments might be generated [ 20 ], thus bioinformatics analyses are required for further verification. The main verification methods include molecular biology and cell biology experiments, such as RNA interference, inhibition of signaling pathway, verification experiments at the cellular level [ 5–8 , 21–23 ], etc. In order to study the mechanism of the interaction between biomaterials and cells, our group has adopted the ‘multiple biomics study + bioinformatics analysis + verification experiment’ research strategy ( Fig.…”

Section: Introductionmentioning

confidence: 99%

A high-throughput study on endothelial cell adhesion and growth mediated by adsorbed serum protein via signaling pathway PCR array

Lü

Hong

et al. 2017

Regenerative Biomaterials

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The purpose of this paper is to utilize the signaling pathway polymerase chain reaction (PCR) arrays to investigate the activation of two important biological signaling pathways in endothelial cell adhesion and growth mediated by adsorbed serum protein on the surface of bare and titanium nitride (TiN)-coated nickel titanium (NiTi) alloys. First, the endothelial cells were cultured on the bare and TiN-coated NiTi alloys and chitosan films as control for 4 h and 24 h, respectively. Then, the total RNA of the cells was collected and the PCR arrays were performed. After that, the differentially expressed genes in the transforming growth factor beta (TGF-β) signaling pathway and the regulation of actin cytoskeleton pathway were screened out; and the further bioinformatics analyses were performed. The results showed that both TGF-β signaling pathway and regulation of actin cytoskeleton pathway were activated in the cells after 4 h and 24 h culturing on the surface of bare and TiN-coated NiTi alloys compared to the chitosan group. The activated TGF-β signaling pathway promoted cell adhesion; the activated regulation of actin cytoskeleton pathway promoted cell adhesion, spreading, growth and motility. In addition, the activation of both pathways was much stronger in the cells cultured for 24 h versus 4 h, which indicated that cell adhesion and growth became more favorable with longer time on the surface of two NiTi alloy materials.

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Application of Genomics/Proteomics Technologies in the Research of Biocom-patibility of Biomaterials

Cited by 10 publications

References 40 publications

An integrated study of natural hydroxyapatite-induced osteogenic differentiation of mesenchymal stem cells using transcriptomics, proteomics and microRNA analyses

An integrated study of natural hydroxyapatite-induced osteogenic differentiation of mesenchymal stem cells using transcriptomics, proteomics and microRNA analyses

Integrated transcriptomic and proteomic study on the different molecular mechanisms of PC12 cell growth on chitosan and collagen/chitosan films

A high-throughput study on endothelial cell adhesion and growth mediated by adsorbed serum protein via signaling pathway PCR array

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