Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jul 5;28(13):5224.
doi: 10.3390/molecules28135224.

Transcriptome Analysis Reveals the Immunoregulatory Activity of Rice Seed-Derived Peptide PEP1 on Dendritic Cells

Tingmin Qu  1 , Shuwen He  1 , Ying Wu  1 , Yingying Wang  1 , Ce Ni  1 , Shiyu Wen  1 , Bo Cui  2 , Yunhui Cheng  1   2 , Li Wen  1
Affiliations

Transcriptome Analysis Reveals the Immunoregulatory Activity of Rice Seed-Derived Peptide PEP1 on Dendritic Cells

Tingmin Qu et al. Molecules. .

Abstract

Some food-derived bioactive peptides exhibit prominent immunoregulatory activity. We previously demonstrated that the rice-derived PEP1 peptide, GIAASPFLQSAAFQLR, has strong immunological activity. However, the mechanism of this action is still unclear. In the present study, full-length transcripts of mouse dendritic cells (DC2.4) treated with PEP1 were sequenced using the PacBio sequencing platform, and the transcriptomes were compared via RNA sequencing (RNA-Seq). The characteristic markers of mature DCs, the cluster of differentiation CD86, and the major histocompatibility complex (MHC-II), were significantly upregulated after the PEP1 treatment. The molecular docking suggested that hydrogen bonding and electrostatic interactions played important roles in the binding between PEP1, MHC-II, and the T-cell receptor (TCR). In addition, the PEP1 peptide increased the release of anti-inflammatory factors (interleukin-4 and interleukin-10) and decreased the release of pro-inflammatory factors (interleukin-6 and tumor necrosis factor-α). Furthermore, the RNA-seq results showed the expression of genes involved in several signaling pathways, such as the NF-κB, MAPK, JAK-STAT, and TGF-β pathways, were regulated by the PEP1 treatment, and the changes confirmed the immunomodulatory effect of PEP1 on DC2.4 cells. This findings revealed that the PEP1 peptide, derived from the byproduct of rice processing, is a potential natural immunoregulatory alternative for the treatment of inflammation.

Keywords: dc2.4 cells; immunopeptide; immunoregulatory mechanism; rice-derived peptide; transcriptome.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
The effects of PEP1 on DC2.4 cells. (A) Cytotoxicity of different concentrations of PEP1 incubated with DC2.4 cells for 24 h and analyzed via the MTT assay. (B) CD86 and MHC-II expression was observed in DC2.4 cells treated with the PEP1 peptide. Q1: CD86 positive; Q2: double-positive of CD86 and MHC-II; Q3: MHC-II positive; Q4: double-negative of CD86 and MHC-II. ** p < 0.01 compared with the control group.
Figure 2
Figure 2
DC2.4 cell morphology. FV3000 Olympus laser confocal microscope was used to visualize the morphology (100× and 400×). (A) Control; (B) Pep1; (C) Pep10; (D) Pep100.
Figure 3
Figure 3
RNA-Seq analysis of gene expression in mice DC2.4 cells. (A) Length distribution of the full-length transcripts. (B) Summary of annotation in the five databases. (C) Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of the assembled full-length transcripts. (D) The transcript FPKM box plot. (E) Principal component analysis (PCA) diagram of the samples. (F) Volcano map of the differentially expressed genes compared to the control group. (G) Venn diagram of the differentially expressed genes compared to the control group.
Figure 4
Figure 4
Identification of differentially expressed mRNAs after PEP1 treatment. (A) Heat map of gene differential expression of control, pep10 and pep100 groups. (B) Gene ontology (GO) classification of differentially expressed genes. (C) Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of differentially expressed genes.
Figure 5
Figure 5
Protein−protein interaction network of all the DEGs (A) and immune-related genes. (B) PPI enrichment p−value: < 1.0 × 10−16. (A) In the PPI map, each small circles with 3D molecules filled represents different proteins in the network. The different colors of the attachment mean different interactions, including gene neighborhood, gene fusions, gene co-occurrence, and gene co-expression, supported by experimental determination or database mining. (B) A total of 19 nodes and 54 edges were included, with an average node degree of 5.68 and an average local clustering coefficient of 0.634 (p < 1.0 × 10−16). The PPI network shows that TNF (tumor necrosis factor) was the most prominent (primary) hub with 13 related proteins, and Egr1 and Fosl1 are the secondary hubs with 11 associated proteins each (details are provided in Table S9).
Figure 6
Figure 6
The validations of immune response induced by PEP1 peptide. (A) Gene expression of 9 DEGs via RT-qPCR. (B) The contents of pro-inflammatory and anti-inflammatory factors determined via ELISA. * p < 0.05 and ** p < 0.01 *** p < 0.001 and **** p < 0.0001 compared with the control group.
Figure 7
Figure 7
In silico docking of the PEP1 peptide with the targets. (A,B) The combined spatial simulation of the PEP1–MHC-II complex. (C) The contact details of the interface between the PEP1 and MHC-II molecule. (D,E) The combined spatial simulation of the PEP1–MHC-II–TCR triplet complex. (F) The contact details of the interface between the PEP1 and MHC-II–TCR complex.
Figure 8
Figure 8
The hypothetical signaling network stimulated by the PEP1 peptide in mouse DC2.4 cells.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Chen H.J., Dai F.J., Chen C.Y., Fan S.L., Zheng J.H., Huang Y.C., Chau C.F., Lin Y.S., Chen C.S. Evaluating the Antioxidants, Whitening and Antiaging Properties of Rice Protein Hydrolysates. Molecules. 2021;26:3605. doi: 10.3390/molecules26123605. - DOI - PMC - PubMed
    1. Gong X., An Q., Le L., Geng F., Jiang L., Yan J., Xiang D., Peng L., Zou L., Zhao G., et al. Prospects of cereal protein-derived bioactive peptides: Sources, bioactivities diversity, and production. Crit. Rev. Food Sci. Nutr. 2022;62:2855–2871. doi: 10.1080/10408398.2020.1860897. - DOI - PubMed
    1. Chai K.F., Voo A.Y.H., Chen W.N. Bioactive peptides from food fermentation: A comprehensive review of their sources, bioactivities, applications, and future development. Compr. Rev. Food Sci. Food Saf. 2020;19:3825–3885. doi: 10.1111/1541-4337.12651. - DOI - PubMed
    1. Elbarbary H.A., Ejima A., Sato K. Generation of antibacterial peptides from crude cheese whey using pepsin and rennet enzymes at various pH conditions. J. Sci. Food Agric. 2019;99:555–563. doi: 10.1002/jsfa.9214. - DOI - PubMed
    1. Kolliopoulos C., Chatzopoulos A., Skandalis S.S., Heldin C.H., Heldin P. TRAF4/6 is needed for CD44 cleavage and migration via RAC1 activation. Cancers. 2021;13:1021. doi: 10.3390/cancers13051021. - DOI - PMC - PubMed