Transcriptomic Changes in Mouse Bone Marrow-Derived Macrophages Exposed to Neuropeptide FF
Yulong Sun1,2, Yuanyuan Kuang1,2, Zhuo Zuo1,2
1School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Abstract:
Neuropeptide FF (NPFF) is a neuropeptide that regulates various biological activities. Currently, the regulation of NPFF on the immune system is an emerging field. However, the influence of NPFF on the transcriptome of primary macrophages has not been fully elucidated. In this study, the effect of NPFF on the transcriptome of mouse bone marrow-derived macrophages (BMDMs) was explored by RNA sequencing, bioinformatics, and molecular simulation. BMDMs were treated with 1 nM NPFF for 18 h, followed by RNA sequencing. Differentially expressed genes (DEGs) were obtained, followed by GO, KEGG, and PPI analysis. A total of eight qPCR-validated DEGs were selected as hub genes. Subsequently, the three-dimensional (3-D) structures of the eight hub proteins were constructed by Modeller and Rosetta. Next, the molecular dynamics (MD)-optimized 3-D structure of hub protein was acquired with Gromacs. Finally, the binding modes between NPFF and hub proteins were studied by Rosetta. A total of 2655 DEGs were obtained (up-regulated 1442 vs. down-regulated 1213), and enrichment analysis showed that NPFF extensively regulates multiple functional pathways mediated by BMDMs. Moreover, the 3-D structure of the hub protein was obtained after MD-optimization. Finally, the docking modes of NPFF-hub proteins were predicted. Besides, NPFFR2 was expressed on the cell membrane of BMDMs, and NPFF 1 nM significantly activated NPFFR2 protein expression. In summary, instead of significantly inhibiting the expression of the immune-related gene transcriptome of RAW 264.7 cells, NPFF simultaneously up-regulated and down-regulated the gene expression profile of a large number of BMDMs, hinting that NPFF may profoundly affect a variety of cellular processes dominated by BMDMs. Our work provides transcriptomics clues for exploring the influence of NPFF on the physiological functions of BMDMs.
Insights
Neuropeptide FF (NPFF) significantly alters the gene expression profile of mouse bone marrow-derived macrophages (BMDMs), revealing its broad impact on immune cell function. This study provides key transcriptomic insights into NPFF
Area of Science:
- Immunology
- Neuroendocrinology
- Transcriptomics
Background:
- Neuropeptide FF (NPFF) is recognized for diverse biological roles.
- Its specific regulatory influence on the immune system, particularly macrophages, remains incompletely understood.
- Elucidating NPFF's impact on macrophage gene expression is crucial for understanding immune modulation.
Purpose of the Study:
- To investigate the comprehensive effects of NPFF on the transcriptome of primary mouse bone marrow-derived macrophages (BMDMs).
- To identify key genes and pathways regulated by NPFF in BMDMs.
- To explore the structural and binding interactions between NPFF and its target proteins.
Main Methods:
- RNA sequencing was employed to analyze gene expression changes in NPFF-treated BMDMs.
- Bioinformatic analyses, including Gene Ontology (GO), KEGG pathway, and Protein-Protein Interaction (PPI) analyses, were performed on differentially expressed genes (DEGs).
- Molecular simulation techniques (Modeller, Rosetta, Gromacs) were used to determine the 3-D structures and binding modes of NPFF with identified hub proteins.
Main Results:
- A total of 2655 differentially expressed genes (DEGs) were identified, with 1442 upregulated and 1213 downregulated.
- Enrichment analyses indicated that NPFF extensively modulates multiple functional pathways in BMDMs.
- NPFF treatment significantly activated NPFF receptor 2 (NPFFR2) expression on the macrophage cell membrane.
Conclusions:
- NPFF profoundly influences a wide array of cellular processes in BMDMs by simultaneously upregulating and downregulating a large number of genes.
- The study identified eight hub genes and elucidated their structural interactions with NPFF.
- These findings provide essential transcriptomic data for further research into NPFF's physiological functions in macrophages and the immune system.
