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. 2023 Dec 4;24(1):729.
doi: 10.1186/s12864-023-09827-y.

Identification of postnatal development dependent genes and proteins in porcine epididymis

Shaoming Fang #  1 , Zhechen Li #  1 , Shuo Pang  1 , Yating Gan  1 , Xiaoning Ding  1 , Hui Peng  2
Affiliations

Identification of postnatal development dependent genes and proteins in porcine epididymis

Shaoming Fang et al. BMC Genomics. .

Abstract

Background: The epididymis is a highly regionalized tubular organ possesses vectorial functions of sperm concentration, maturation, transport, and storage. The epididymis-expressed genes and proteins are characterized by regional and developmental dependent pattern. However, a systematic and comprehensive insight into the postnatal development dependent changes in gene and protein expressions of porcine epididymis is still lacking. Here, the RNA and protein of epididymis of Duroc pigs at different postnatal development stages were extracted by using commercial RNeasy Midi kit and extraction buffer (7 M Urea, 2 M thiourea, 3% CHAPS, and 1 mM PMSF) combined with sonication, respectively, which were further subjected to transcriptomic and proteomic profiling.

Results: Transcriptome analysis indicated that 198 and 163 differentially expressed genes (DEGs) were continuously up-regulated and down-regulated along with postnatal development stage changes, respectively. Most of the up-regulated DEGs linked to functions of endoplasmic reticulum and lysosome, while the down-regulated DEGs mainly related to molecular process of extracellular matrix. Moreover, the following key genes INSIG1, PGRMC1, NPC2, GBA, MMP2, MMP14, SFRP1, ELN, WNT-2, COL3A1, and SPARC were highlighted. A total of 49 differentially expressed proteins (DEPs) corresponding to postnatal development stages changes were uncovered by the proteome analysis. Several key proteins ACSL3 and ACADM, VDAC1 and VDAC2, and KNG1, SERPINB1, C3, and TF implicated in fatty acid metabolism, voltage-gated ion channel assembly, and apoptotic and immune processes were emphasized. In the integrative network, the key genes and proteins formed different clusters and showed strong interactions. Additionally, NPC2, COL3A1, C3, and VDAC1 are located at the hub position in each cluster.

Conclusions: The identified postnatal development dependent genes and proteins in the present study will pave the way for shedding light on the molecular basis of porcine epididymis functions and are useful for further studies on the specific regulation mechanisms responsible for epididymal sperm maturation.

Keywords: Differentially expressed genes (DEGs); Differentially expressed proteins (DEPs); Duroc pigs; Epididymis functions; Molecular basis.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The principal component analysis (PCA) of porcine epididymal transcriptome at different postnatal development stages
Fig. 2
Fig. 2
The functional enrichment analysis of the differentially expressed genes (DEGs)
Fig. 3
Fig. 3
The node DEGs in the predominant GOs and KEGG functional categories. A The up-regulated node DEGs in the GOs functional categories. B The up-regulated node DEGs in the KEGG functional categories. C The down-regulated node DEGs in the GOs functional categories. D The down-regulated node DEGs in the KEGG functional categories
Fig. 4
Fig. 4
The PCA of porcine epididymal proteome at different postnatal development stages
Fig. 5
Fig. 5
The functional enrichment analysis of the differentially expressed proteins (DEPs)
Fig. 6
Fig. 6
The node DEPs in the dominant GOs and KEGG functional categories. A The increased node DEPs in the GOs functional categories. B The increased node DEPs in the KEGG functional categories. C The reduced node DEPs in the GOs functional categories. D The reduced node DEPs in the KEGG functional categories
Fig. 7
Fig. 7
The interaction network of node DEGs and DEPs
Fig. 8
Fig. 8
The validation experiments of DEGs (A-B) and DEPs (C)
See this image and copyright information in PMC

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