Identification of postnatal development dependent genes and proteins in porcine epididymis

• Published in: BMC genomics Vol. 24; no. 1; pp. 1 - 729
• Main Authors: Fang, Shaoming, Li, Zhechen, Pang, Shuo, Gan, Yating, Ding, Xiaoning, peng, Hui
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 04.12.2023; BioMed Central; BMC
• Subjects: Analysis; Annotations; Apoptosis; Cell cycle; Channel gating; Developmental stages; Differentially expressed genes (DEGs); Differentially expressed proteins (DEPs); Duroc pigs; Endoplasmic reticulum; Enzymes; Epididymis; Epididymis functions; Extracellular matrix; Fatty acids; Fetus; Frizzled-related protein 1; Gelatinase A; Gene expression; Genes; Genetic aspects; Genetic research; Genomics; Growth; Health aspects; Information processing; Ion channels; Localization; Maturation; Metabolism; Molecular basis; Osteonectin; Physiological aspects; Proteins; Proteomes; Proteomics; Regional development; RNA; Sonication; Sperm; Swine; Testis; Transcription factors; Transcriptomes; Transcriptomics; Urea; Wnt protein; Japan; China
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09827-y

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. 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. 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.