Comparative analysis of the cell transcriptome of primary B lymphocytes infected with the Epstein-Barr virus (EBV), its EBNA2 or EBNALP KO derivatives, or activated by CD40L and IL4 at 48 hours post-infection or treatment.

Epstein-Barr virus (EBV) is a human herpesvirus that has been associated with the development of human cancers across the globe. In laboratory settings, the virus efficiently infects resting human B lymphocytes, inducing their growth transformation and leading to the establishment of lymphoblastoid cell lines (LCLs) within a few weeks. This process is accompanied by a global reprogramming of cellular gene transcription. A systematic time-resolved analysis of cellular mRNA splice variant expression during EBV infection of resting B lymphocytes has previously been performed. The results demonstrated that significant alterations in alternative splice variant expression occur as early as day 1 post-infection, indicating that splicing regulation, in addition to transcription, represents an additional mechanism of gene expression regulation at the onset of B cell activation and proliferation. The present study had two principal objectives. The first was to identify which transcriptional and splice events are specific to the EBV infection, in comparison to the activation of primary B lymphocytes by a combination of CD40 ligand (CD40L) and interleukin 4 (IL4). The second was to ascertain which events are dependent on the EBNA2 and EBNALP viral factors. In order to achieve these objectives, a comparative RNA-seq analysis of the transcriptome of the infected cells or those treated with CD40L/IL4, as well as LCLs derived from the wild-type and EBNALP KO EBV-infected cells, was conducted. Overall design: RNA-seq profiling of human primary B lymphocytes infected or not by wild-type Epstein-Barr virus (EBV) or its knockdown derivatives (EBNA2 or EBNALP KO) at day 2 post-infection, or treated by a combination of CD40 ligand (CD40L) and interleukin 4 (IL4) at day 2 post-treatment. RNA-seq profiling was also conducted on the lymphoblastoid cell lines (LCLs) derived from the wild-type EBV and EBNALP KO infections at 2 to 3 weeks post-infection.