Genome-wide transcriptome analysis upon KSHV lytic reactivation

Purpose: To characterize genome-wide mRNA expression profiles in the context of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation. Methods: We utilized a well-established model of KSHV reactivation, the doxycycline (Dox)-inducible KSHV producer cell line iSLK.219, which contains a latent KSHV genome and a Dox-inducible KSHV lytic switch protein RTA (replication and transcription activator) to mediate efficient reactivation and entry into the lytic cycle upon Dox treatment. We performed mRNA-sequencing (mRNA-seq) of RNA isolated from latent KSHV-infected iSLK.219 cells at 0 h or lytic iSLK.219 cells at 72 h post Dox-induced KSHV lytic reactivation using Illumina. The mappable reads were aligned to the human genome or the KSHV genome using Bowtie. Results: We analyzed global transcriptome changes in iSLK.219 cells during the latency to lytic transition and found that reactivated lytic iSLK.219 cells exhibited an increased abundance of cellular genes involved in cell cycle, DNA replication, and nuclear division, consistent with lytic infection activating mitogenic signaling to support viral DNA replication. In addition, expression of key viral lytic genes with strong mitogenic activities, including vIL-6 (K2), K1, and the KSHV-encoded chemokines, vCCL1 (K6), vCCL2 (K4) and vCCL3 (K4.1), were markedly induced during lytic KSHV replication. Conclusions: These results confirm that the gene expression profile of reactivated lytic iSLK.219 cells exhibit some key hallmark features of KSHV lytic reactivation. Overall design: We utilized a well-established model of KSHV reactivation, the doxycycline (Dox)-inducible KSHV producer cell line iSLK.219, which contains a latent KSHV genome and a Dox-inducible KSHV lytic switch protein RTA (replication and transcription activator) to mediate efficient reactivation and entry into the lytic cycle upon Dox treatment. We performed mRNA-sequencing (mRNA-seq) of RNA isolated from latent KSHV-infected iSLK.219 cells at 0 h or lytic iSLK.219 cells at 72 h post Dox-induced KSHV lytic reactivation using Illumina. The mappable reads were aligned to the human genome or the KSHV genome using Bowtie.