Profiling the full-length transcriptome of plasma cell mastitis via nanopore sequencing

Abstract

Introduction

In this study, we aimed to determine the transcriptomic profile of plasma cell mastitis (PCM) and elucidate its underlying mechanisms using nanopore sequencing technology (ONT).

Methods and results

Through comparisons and analyses of redundantly removed transcripts with known reference genome annotations, we identified 39,408 novel transcripts and 20,980 genes. By exploring full-length transcriptome data, we characterized selective splicing, selective polyadenylation events, and simple sequence repeat (SSR) site information, which enhanced our understanding of genome annotation and gene structure in plasma cell mastitis. Additionally, we investigated predicted transcription factors and LncRNAs, screening those with differences for further investigations. The GO and KEGG enrichment analysis of differentially expressed genes (DEGs) and differentially expressed transcripts (DETs) revealed subtle distinctions between them, with primary enrichments being in immune response and intercellular interactions. Our protein–protein interaction (PPI) analysis of hub proteins from DETs indicated up-regulated genes' involvement in immune response and down-regulated genes' role in cell adhesion. Furthermore, we assessed immune cell infiltration in plasma cell mastitis, observing various immune cells, such as B cells, T cells, and DC cells.

Conclusion

These preliminary findings offer novel insights into the pathogenesis of plasma cell mastitis and present promising ideas for optimizing personalized treatment approaches, warranting further exploration and follow-up studies.