RNA-seq analysis in equine papillomavirus type 2-positive carcinomas identifies affected pathways and potential cancer markers as well as viral gene expression and splicing events.

The study identifies potential cancer markers, impacted pathways, and viral gene expression and splicing events in carcinomas connected with the recently discovered Equine papillomavirus type 2 (EcPV2). The researchers analyzed the host and viral transcriptome in EcPV2-affected horses and determined that there were differentially expressed host genes linked with DNA replication, cell cycle, receptor interaction, and focal adhesion, among others.

Methodology

• The researchers collected genital tissue samples from horses with EcPV2-positive lesions and healthy EcPV2-negative horses for analysis.
• RNA-seq analysis was then performed on these samples to ascertain the genes impacted by the presence of EcPV2. This process enabled a comparison of gene expression between diseased and healthy samples, revealing differences in the expressed genes.
• Reads from viral DNA were also analyzed to get insights into the active genes of EcPV2.
• In one instance, the integration of EcPV2 DNA into the host genome was detected by DNA-seq and confirmed by PCR.

Findings

• The analysis identified 1957 differentially expressed (DE) host genes between the carcinoma and control samples.
• The most frequently indicated genes related to DNA replication, cell cycle, extracellular matrix-receptor interaction, and focal adhesion.
• By comparing the findings with other cancer studies, it was deduced that the genes MMP1 and IL8 could serve as potential marker genes for the development of squamous cell carcinomas (SCCs).
• On analyzing viral transcript reads, it was observed that the transcriptional activity of EcPV2 was evident in all SCC samples.
• Within these reads, a distinct pattern of splicing events essential for the expression of different genes in PV infections was recognized.
• The majority of the reads were mapped to the non-structural early (E) genes. These were particularly noted for E6, E7, and E2/E4.

Conclusion

• The study concludes that while host MMP1 and IL8 expression and the presence of EcPV2 may be useful markers in genital SCCs, further research on EcPV2-related pathomechanisms may focus on cell cycle-related genes, the viral genes E6, E7, and E2/E4, and integration events.
• The findings could contribute considerably to the expansion of knowledge on the potential disease agent, EcPV2, thus supporting the development of treatments for equine papillomavirus type 2-positive carcinomas.